Sample records for reducing bacterial enrichment
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Sulfate-reducing bacterial enrichments were obtained from a shallow anoxic aquifer for their ability to metabolize either
o -,m -, orp -cresol. GC/MS and simultaneous adaptation experiments suggested that the anaerobic decomposition ofp -cresol proceeds ... -
Effects of the antimicrobial sulfamethoxazole on groundwater bacterial enrichment
Underwood, Jennifer C.; Harvey, Ronald W.; Metge, David W.; Repert, Deborah A.; Baumgartner, Laura K.; Smith, Richard L.; Roane, Timberly M.; Barber, Larry B.
2011-01-01
The effects of “trace” (environmentally relevant) concentrations of the antimicrobial agent sulfamethoxazole (SMX) on the growth, nitrate reduction activity, and bacterial composition of an enrichment culture prepared with groundwater from a pristine zone of a sandy drinking-water aquifer on Cape Cod, MA, were assessed by laboratory incubations. When the enrichments were grown under heterotrophic denitrifying conditions and exposed to SMX, noticeable differences from the control (no SMX) were observed. Exposure to SMX in concentrations as low as 0.005 μM delayed the initiation of cell growth by up to 1 day and decreased nitrate reduction potential (total amount of nitrate reduced after 19 days) by 47% (p = 0.02). Exposure to 1 μM SMX, a concentration below those prescribed for clinical applications but higher than concentrations typically detected in aqueous environments, resulted in additional inhibitions: reduced growth rates (p = 5 × 10−6), lower nitrate reduction rate potentials (p = 0.01), and decreased overall representation of 16S rRNA gene sequences belonging to the genus Pseudomonas. The reduced abundance of Pseudomonas sequences in the libraries was replaced by sequences representing the genus Variovorax. Results of these growth and nitrate reduction experiments collectively suggest that subtherapeutic concentrations of SMX altered the composition of the enriched nitrate-reducing microcosms and inhibited nitrate reduction capabilities.
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Biodegradation of munitions compounds by a sulfate reducing bacterial enrichment culture
DOE Office of Scientific and Technical Information (OSTI.GOV)
Boopathy, R.; Manning, J.
1997-08-01
The degradation of several munitions compounds was studied. The compounds included 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine, 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrotoluene. All of the compounds studied were degraded by the sulfate reducing bacterial (SRB) enrichment culture. The SRB culture did not use the munitions compounds as their sole source of carbon. However, all the munitions compounds tested served as the sole source of nitrogen for the SRB culture. Degradation of munitions compounds was achieved by a co-metabolic process. The SRB culture used a variety of carbon sources including pyruvate, ethanol, formate, lactate, and H{sub 2}-CO{sub 2}. The SRB culture was an incompletemore » oxidizer, unable to carry out the terminal oxidation of organic substrates to CO{sub 2} as the sole product, and it did not use acetate or methanol as a carbon source. In addition to serving as nitrogen sources, the munitions compounds also served as electron acceptors in the absence of sulfate. A soil slurry experiment with 5% and 10% munitions compounds-contaminated soil showed that the contaminant TNT was metabolized by the SRB culture in the presence of pyruvate as electron donor. This culture may be useful in decontaminating munitions compounds-contaminated soil and water under anaerobic conditions.« less
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Soil Bacterial Community Shifts after Chitin Enrichment: An Integrative Metagenomic Approach
Jacquiod, Samuel; Franqueville, Laure; Cécillon, Sébastien; M. Vogel, Timothy; Simonet, Pascal
2013-01-01
Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome. PMID:24278158
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Kaur, Ravinder; Wischmeyer, Jareth; Morris, Matthew; Pichichero, Michael E
2017-11-01
We compared the recovery of potential respiratory bacterial pathogens and normal flora from nasopharyngeal specimens collected from children during health and at the onset of acute otitis media (AOM) by selective direct-plating and overnight broth-enrichment. Overall, 3442 nasal wash (NW) samples collected from young children were analysed from a 10-year prospective study. NWs were cultured by (1) direct-plating to TSAII/5 % sheep blood agar and chocolate agar plates and (2) overnight broth-enrichment in BacT/ALERT SA-broth followed by plating. Standard microbiology techniques were applied to identify three dominant respiratory bacterial pathogens: Streptococcus pneumoniae (Spn), Haemophilus influenzae (Hflu) and Moraxella catarrhalis (Mcat) as well as two common nasal flora, Staphylococcus aureus (SA) and alpha-haemolytic Streptococci (AHS).Results/Key findings. Direct-plating of NW resulted in isolation of Spn from 37.8 %, Hflu from 13.6 % and Mcat from 33.2 % of samples. In comparison, overnight broth-enrichment isolated fewer Spn (30.1 %), Hflu (6.2 %) and Mcat (16.2 %) (P<0.001-0.0001). Broth-enrichment resulted in significant increased isolation of SA (6.0 %) and AHS (30.1 %) (P<0.0001). Competition between bacterial species in broth when both species were detected by direct-plating was assessed, and it was found that SA and AHS out-competed other species during broth-enrichment when samples were collected from healthy children but not during AOM. In middle ear fluids (MEF) at the onset of AOM, broth-enrichment resulted in higher recovery of Spn (+10.4 %, P<0.001), Hflu (+4.4 %, P=0.39) and Mcat (+13.5 %, <0.001). Broth-enrichment significantly reduces the accurate detection of bacterial respiratory pathogens and increases identification of SA and AHS in NW. Broth-enrichment improves detection of bacterial respiratory pathogens in MEF samples.
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In-Vessel Co-Composting of Food Waste Employing Enriched Bacterial Consortium
2018-01-01
Summary The aim of the present study is to develop a good initial composting mix using a bacterial consortium and 2% lime for effective co-composting of food waste in a 60-litre in-vessel composter. In the experiment that lasted for 42 days, the food waste was first mixed with sawdust and 2% lime (by dry mass), then one of the reactors was inoculated with an enriched bacterial consortium, while the other served as control. The results show that inoculation of the enriched natural bacterial consortium effectively overcame the oil-laden co-composting mass in the composter and increased the rate of mineralization. In addition, CO2 evolution rate of (0.81±0.2) g/(kg·day), seed germination index of (105±3) %, extractable ammonium mass fraction of 305.78 mg/kg, C/N ratio of 16.18, pH=7.6 and electrical conductivity of 3.12 mS/cm clearly indicate that the compost was well matured and met the composting standard requirements. In contrast, control treatment exhibited a delayed thermophilic phase and did not mature after 42 days, as evidenced by the maturity parameters. Therefore, a good composting mix and potential bacterial inoculum to degrade the oil are essential for food waste co-composting systems. PMID:29796000
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In-Vessel Co-Composting of Food Waste Employing Enriched Bacterial Consortium.
Awasthi, Mukesh Kumar; Wang, Quan; Wang, Meijing; Chen, Hongyu; Ren, Xiuna; Zhao, Junchao; Zhang, Zengqiang
2018-03-01
The aim of the present study is to develop a good initial composting mix using a bacterial consortium and 2% lime for effective co-composting of food waste in a 60-litre in-vessel composter. In the experiment that lasted for 42 days, the food waste was first mixed with sawdust and 2% lime (by dry mass), then one of the reactors was inoculated with an enriched bacterial consortium, while the other served as control. The results show that inoculation of the enriched natural bacterial consortium effectively overcame the oil-laden co-composting mass in the composter and increased the rate of mineralization. In addition, CO 2 evolution rate of (0.81±0.2) g/(kg·day), seed germination index of (105±3) %, extractable ammonium mass fraction of 305.78 mg/kg, C/N ratio of 16.18, pH=7.6 and electrical conductivity of 3.12 mS/cm clearly indicate that the compost was well matured and met the composting standard requirements. In contrast, control treatment exhibited a delayed thermophilic phase and did not mature after 42 days, as evidenced by the maturity parameters. Therefore, a good composting mix and potential bacterial inoculum to degrade the oil are essential for food waste co-composting systems.
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Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael
2014-10-01
The organophosphate pesticide chlorpyrifos (CP) has been used extensively since the 1960s for insect control. However, its toxic effects on mammals and persistence in environment necessitate its removal from contaminated sites, biodegradation studies of CP-degrading microbes are therefore of immense importance. Samples from a Pakistani agricultural soil with an extensive history of CP application were used to prepare enrichment cultures using CP as sole carbon source for bacterial community analysis and isolation of CP metabolizing bacteria. Bacterial community analysis (denaturing gradient gel electrophoresis) revealed that the dominant genera enriched under these conditions were Pseudomonas, Acinetobacter and Stenotrophomonas, along with lower numbers of Sphingomonas, Agrobacterium and Burkholderia. Furthermore, it revealed that members of Bacteroidetes, Firmicutes, α- and γ-Proteobacteria and Actinobacteria were present at initial steps of enrichment whereas β-Proteobacteria appeared in later steps and only Proteobacteria were selected by enrichment culturing. However, when CP-degrading strains were isolated from this enrichment culture, the most active organisms were strains of Acinetobacter calcoaceticus, Pseudomonas mendocina and Pseudomonas aeruginosa. These strains degraded 6-7.4 mg L(-1) day(-1) of CP when cultivated in mineral medium, while the consortium of all four strains degraded 9.2 mg L(-1) day(-1) of CP (100 mg L(-1)). Addition of glucose as an additional C source increased the degradation capacity by 8-14 %. After inoculation of contaminated soil with CP (200 mg kg(-1)) disappearance rates were 3.83-4.30 mg kg(-1) day(-1) for individual strains and 4.76 mg kg(-1) day(-1) for the consortium. These results indicate that these organisms are involved in the degradation of CP in soil and represent valuable candidates for in situ bioremediation of contaminated soils and waters.
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Use of Nitrogen-15-Enriched Escherichia coli as a Bacterial Tracer in Karst Aquifers.
Ward, James W; Warden, John G; Bandy, Ashley M; Fryar, Alan E; Brion, Gail M; Macko, Stephen A; Romanek, Christopher S; Coyne, Mark S
2016-11-01
Karst aquifers are susceptible to contamination by microorganisms, but relatively few studies have used bacteria as tracers. We demonstrate the utility of Escherichia coli enriched in the stable isotope nitrogen-15 ( 15 N) as a novel bacterial tracer. Nonpathogenic E. coli from two springs in central Kentucky were grown on 15 N-enriched media. Survival of E. coli and persistence of the isotopic signal were assessed in two sets of laboratory experiments conducted with sterilized spring water in dark microcosms at 14 °C. First, isotopically labeled bacteria survived for 130 d at concentrations within one log unit of the average initial value, and there was no significant difference in δ 15 N values from Day 1 to Day 130. Second, water samples with E. coli were inoculated with either of two different species of protozoa (Tetrahymena pyriformis or Colpoda steinii). During 7 d, δ 15 N values increased in T. pyriformis while bacterial populations decreased. In a field test, following a 2.1-cm rainfall, 15 N-labeled E. coli, solutes (rhodamine WT dye and bromide), and latex microspheres were injected into a sinkhole approximately 530 m upgradient of a spring. Breakthrough of all tracers coincided, but microspheres were remobilized by subsequent storms, unlike other tracers. Enriched E. coli exhibited more tailing than solute tracers during the initial storm-flow recession. These results indicate that 15 N-enriched E. coli is a viable tracer of bacterial transport in karst aquifers, although predation may attenuate the isotopic signal in systems that are not rapidly flushed. © 2016, National Ground Water Association.
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Ghosh, Suchismita; Ayayee, Paul A; Valverde-Barrantes, Oscar J; Blackwood, Christopher B; Royer, Todd V; Leff, Laura G
2017-04-04
The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity and N substrate utilization by heterotrophic bacteria isolated from streams under complex and simple N-enrichment conditions. Diversity estimates differed among isolates from the enrichments, but no significant composition were detected. Substrate utilization and substrate range of bacterial assemblages differed within and among enrichments types, and not simply between simple and complex N-enrichments. N substrate use patterns differed between isolates from some complex and simple N-enrichments while others were unexpectedly similar. Taxonomic composition of isolates did not differ among enrichments and was unrelated to N use suggesting strong functional redundancy. Ultimately, our results imply that the available N pool influences physiology and selects for bacteria with various abilities that are unrelated to their taxonomic affiliation.
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Tetrachloromethane-Degrading Bacterial Enrichment Cultures and Isolates from a Contaminated Aquifer.
Penny, Christian; Gruffaz, Christelle; Nadalig, Thierry; Cauchie, Henry-Michel; Vuilleumier, Stéphane; Bringel, Françoise
2015-07-02
The prokaryotic community of a groundwater aquifer exposed to high concentrations of tetrachloromethane (CCl₄) for more than three decades was followed by terminal restriction fragment length polymorphism (T-RFLP) during pump-and-treat remediation at the contamination source. Bacterial enrichments and isolates were obtained under selective anoxic conditions, and degraded 10 mg·L(-1) CCl₄, with less than 10% transient formation of chloroform. Dichloromethane and chloromethane were not detected. Several tetrachloromethane-degrading strains were isolated from these enrichments, including bacteria from the Klebsiella and Clostridium genera closely related to previously described CCl₄ degrading bacteria, and strain TM1, assigned to the genus Pelosinus, for which this property was not yet described. Pelosinus sp. TM1, an oxygen-tolerant, Gram-positive bacterium with strictly anaerobic metabolism, excreted a thermostable metabolite into the culture medium that allowed extracellular CCl₄ transformation. As estimated by T-RFLP, phylotypes of CCl₄-degrading enrichment cultures represented less than 7%, and archaeal and Pelosinus strains less than 0.5% of the total prokaryotic groundwater community.
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Tetrachloromethane-Degrading Bacterial Enrichment Cultures and Isolates from a Contaminated Aquifer
Penny, Christian; Gruffaz, Christelle; Nadalig, Thierry; Cauchie, Henry-Michel; Vuilleumier, Stéphane; Bringel, Françoise
2015-01-01
Abstract: The prokaryotic community of a groundwater aquifer exposed to high concentrations of tetrachloromethane (CCl4) for more than three decades was followed by terminal restriction fragment length polymorphism (T-RFLP) during pump-and-treat remediation at the contamination source. Bacterial enrichments and isolates were obtained under selective anoxic conditions, and degraded 10 mg·L−1 CCl4, with less than 10% transient formation of chloroform. Dichloromethane and chloromethane were not detected. Several tetrachloromethane-degrading strains were isolated from these enrichments, including bacteria from the Klebsiella and Clostridium genera closely related to previously described CCl4 degrading bacteria, and strain TM1, assigned to the genus Pelosinus, for which this property was not yet described. Pelosinus sp. TM1, an oxygen-tolerant, Gram-positive bacterium with strictly anaerobic metabolism, excreted a thermostable metabolite into the culture medium that allowed extracellular CCl4 transformation. As estimated by T-RFLP, phylotypes of CCl4-degrading enrichment cultures represented less than 7%, and archaeal and Pelosinus strains less than 0.5% of the total prokaryotic groundwater community. PMID:27682092
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RERTR 2009 (Reduced Enrichment for Research and Test Reactors)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Totev, T.; Stevens, J.; Kim, Y. S.
2010-03-01
The U.S. Department of Energy/National Nuclear Security Administration's Office of Global Threat Reduction in cooperation with the China Atomic Energy Authority and International Atomic Energy Agency hosted the 'RERTR 2009 International Meeting on Reduced Enrichment for Research and Test Reactors.' The meeting was organized by Argonne National Laboratory, China Institute of Atomic Energy and Idaho National Laboratory and was held in Beijing, China from November 1-5, 2009. This was the 31st annual meeting in a series on the same general subject regarding the conversion of reactors within the Global Threat Reduction Initiative (GTRI). The Reduced Enrichment for Research and Testmore » Reactors (RERTR) Program develops technology necessary to enable the conversion of civilian facilities using high enriched uranium (HEU) to low enriched uranium (LEU) fuels and targets.« less
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2010-01-01
Background Bacteria possess a reservoir of metabolic functionalities ready to be exploited for multiple purposes. The use of microorganisms to clean up xenobiotics from polluted ecosystems (e.g. soil and water) represents an eco-sustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and accurate strategies for monitoring and identification of bacteria and catabolic genes involved in the degradation of xenobiotics, key processes to follow up the activities in situ. Results We report the characterization of the response of an enriched bacterial community of a 1,2-dichloroethane (1,2-DCA) contaminated aquifer to the spiking with 5 mM lactate as electron donor in microcosm studies. After 15 days of incubation, the microbial community structure was analyzed. The bacterial 16S rRNA gene clone library showed that the most represented phylogenetic group within the consortium was affiliated with the phylum Firmicutes. Among them, known degraders of chlorinated compounds were identified. A reductive dehalogenase genes clone library showed that the community held four phylogenetically-distinct catalytic enzymes, all conserving signature residues previously shown to be linked to 1,2-DCA dehalogenation. Conclusions The overall data indicate that the enriched bacterial consortium shares the metabolic functionality between different members of the microbial community and is characterized by a high functional redundancy. These are fundamental features for the maintenance of the community's functionality, especially under stress conditions and suggest the feasibility of a bioremediation treatment with a potential prompt dehalogenation and a process stability over time. PMID:20170484
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Bacterial oxidation of dibromomethane and methyl bromide in natural waters and enrichment cultures
Goodwin, K.D.; Schaefer, J.K.; Oremland, R.S.
1998-01-01
Bacterial oxidation of 14CH2Br2 and 14CH3Br was measured in freshwater, estuarine, seawater, and hypersaline-alkaline samples. In general, bacteria from the various sites oxidized similar amounts of 14CH2Br2 and comparatively less 14CH3Br. Bacterial oxidation of 14CH3Br was rapid in freshwater samples compared to bacterial oxidation of 14CH3Br in more saline waters. Freshwater was also the only site in which methyl fluoride-sensitive bacteria (e.g., methanotrophs or nitrifiers) governed brominated methane oxidation. Half-life calculations indicated that bacterial oxidation of CH2Br2 was potentially significant in all of the waters tested. In contrast, only in freshwater was bacterial oxidation of CH3Br as fast as chemical removal. The values calculated for more saline sites suggested that bacterial oxidation of CH3Br was relatively slow compared to chemical and physical loss mechanisms. However, enrichment cultures demonstrated that bacteria in seawater can rapidly oxidize brominated methanes. Two distinct cultures of nonmethanotrophic methylotrophs were recovered; one of these cultures was able to utilize CH2Br2 as a sole carbon source, and the other was able to utilize CH3Br as a sole carbon source.
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Techtmann, Stephen M; Zhuang, Mobing; Campo, Pablo; Holder, Edith; Elk, Michael; Hazen, Terry C; Conmy, Robyn; Santo Domingo, Jorge W
2017-05-15
To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio , Idiomarina , Marinobacter , Alcanivorax , and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium , Alcanivorax , and Oleispira Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus , known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira , Marinobacter , and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C. IMPORTANCE While dispersants such as Corexit 9500 can be used to treat oil spills, there is still debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on oil-degrading microbial communities. The results of this study provide some insights on the microbial dynamics of hydrocarbon-degrading bacterial populations in the presence of Corexit 9500. Operational taxonomic unit (OTU) analyses
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Zhuang, Mobing; Campo, Pablo; Holder, Edith; Elk, Michael; Conmy, Robyn
2017-01-01
ABSTRACT To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio, Idiomarina, Marinobacter, Alcanivorax, and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium, Alcanivorax, and Oleispira. Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus, known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira, Marinobacter, and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C. IMPORTANCE While dispersants such as Corexit 9500 can be used to treat oil spills, there is still debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on oil-degrading microbial communities. The results of this study provide some insights on the microbial dynamics of hydrocarbon-degrading bacterial populations in the presence of Corexit 9500. Operational taxonomic unit (OTU) analyses
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The current state of the Russian reduced enrichment research reactors program
DOE Office of Scientific and Technical Information (OSTI.GOV)
Aden, V.G.; Kartashov, E.F.; Lukichev, V.A.
1997-08-01
During the last year after the 16-th International Conference on Reducing Fuel Enrichment in Research Reactors held in October, 1993 in Oarai, Japan, the conclusive stage of the Program on reducing fuel enrichment (to 20% in U-235) in research reactors was finally made up in Russia. The Program was started late in 70th and the first stage of the Program was completed by 1986 which allowed to reduce fuel enrichment from 80-90% to 36%. The completion of the Program current stage, which is counted for 5-6 years, will exclude the use of the fuel enriched by more than 20% frommore » RF to other countries such as: Poland, Czeck Republick, Hungary, Roumania, Bulgaria, Libya, Viet-Nam, North Korea, Egypt, Latvia, Ukraine, Uzbekistan and Kazakhstan. In 1994 the Program, approved by RF Minatom authorities, has received the status of an inter-branch program since it was admitted by the RF Ministry for Science and Technical Policy. The Head of RF Minatom central administrative division N.I.Ermakov was nominated as the Head of the Russian Program, V.G.Aden, RDIPE Deputy Director, was nominated as the scientific leader. The Program was submitted to the Commission for Scientific, Technical and Economical Cooperation between USA and Russia headed by Vice-President A. Gore and Prime Minister V. Chemomyrdin and was given support also.« less
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van Dixhoorn, Ingrid D. E.; Reimert, Inonge; Middelkoop, Jenny; Bolhuis, J. Elizabeth; Wisselink, Henk J.; Groot Koerkamp, Peter W. G.; Kemp, Bas; Stockhofe-Zurwieden, Norbert
2016-01-01
Until today, anti-microbial drugs have been the therapy of choice to combat bacterial diseases. Resistance against antibiotics is of growing concern in man and animals. Stress, caused by demanding environmental conditions, can reduce immune protection in the host, influencing the onset and outcome of infectious diseases. Therefore psychoneuro-immunological intervention may prove to be a successful approach to diminish the impact of diseases and antibiotics use. This study was designed to investigate the effect of social and environmental enrichment on the impact of disease, referred to as “disease susceptibility”, in pigs using a co-infection model of PRRSV and A. pleuropneumoniae. Twenty-eight pigs were raised in four pens under barren conditions and twenty-eight other pigs were raised in four pens under enriched conditions. In the enriched pens a combination of established social and environmental enrichment factors were introduced. Two pens of the barren (BH) and two pens of the enriched housed (EH) pigs were infected with PRRSV followed by A. pleuropneumoniae, the other two pens in each housing treatment served as control groups. We tested if differences in disease susceptibility in terms of pathological and clinical outcome were related to the different housing regimes and if this was reflected in differences in behavioural and immunological states of the animals. Enriched housed pigs showed a faster clearance of viral PRRSV RNA in blood serum (p = 0.014) and histologically 2.8 fold less interstitial pneumonia signs in the lungs (p = 0.014). More barren housed than enriched housed pigs developed lesions in the lungs (OR = 19.2, p = 0.048) and the lesions in the barren housed pigs showed a higher total pathologic tissue damage score (p<0.001) than those in enriched housed pigs. EH pigs showed less stress-related behaviour and differed immunologically and clinically from BH pigs. We conclude that enriched housing management reduces disease susceptibility to
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van Dixhoorn, Ingrid D E; Reimert, Inonge; Middelkoop, Jenny; Bolhuis, J Elizabeth; Wisselink, Henk J; Groot Koerkamp, Peter W G; Kemp, Bas; Stockhofe-Zurwieden, Norbert
2016-01-01
Until today, anti-microbial drugs have been the therapy of choice to combat bacterial diseases. Resistance against antibiotics is of growing concern in man and animals. Stress, caused by demanding environmental conditions, can reduce immune protection in the host, influencing the onset and outcome of infectious diseases. Therefore psychoneuro-immunological intervention may prove to be a successful approach to diminish the impact of diseases and antibiotics use. This study was designed to investigate the effect of social and environmental enrichment on the impact of disease, referred to as "disease susceptibility", in pigs using a co-infection model of PRRSV and A. pleuropneumoniae. Twenty-eight pigs were raised in four pens under barren conditions and twenty-eight other pigs were raised in four pens under enriched conditions. In the enriched pens a combination of established social and environmental enrichment factors were introduced. Two pens of the barren (BH) and two pens of the enriched housed (EH) pigs were infected with PRRSV followed by A. pleuropneumoniae, the other two pens in each housing treatment served as control groups. We tested if differences in disease susceptibility in terms of pathological and clinical outcome were related to the different housing regimes and if this was reflected in differences in behavioural and immunological states of the animals. Enriched housed pigs showed a faster clearance of viral PRRSV RNA in blood serum (p = 0.014) and histologically 2.8 fold less interstitial pneumonia signs in the lungs (p = 0.014). More barren housed than enriched housed pigs developed lesions in the lungs (OR = 19.2, p = 0.048) and the lesions in the barren housed pigs showed a higher total pathologic tissue damage score (p<0.001) than those in enriched housed pigs. EH pigs showed less stress-related behaviour and differed immunologically and clinically from BH pigs. We conclude that enriched housing management reduces disease susceptibility to co
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Nelson, Craig E.; Carlson, Craig A.
2011-01-01
Nutrient enrichment of high-elevation freshwater ecosystems by atmospheric deposition is increasing worldwide, and bacteria are a key conduit for the metabolism of organic matter in these oligotrophic environments. We conducted two distinct in situ microcosm experiments in a high-elevation lake (Emerald Lake, Sierra Nevada, California, USA) to evaluate responses in bacterioplankton growth, carbon utilization, and community structure to short-term enrichment by nitrate and phosphate. The first experiment, conducted just following ice-off, employed dark dilution culture to directly assess the impact of nutrients on bacterioplankton growth and consumption of terrigenous dissolved organic matter during snowmelt. The second experiment, conducted in transparent microcosms during autumn overturn, examined how bacterioplankton in unmanipulated microbial communities responded to nutrients concomitant with increasing phytoplankton-derived organic matter. In both experiments, phosphate enrichment (but not nitrate) caused significant increases in bacterioplankton growth, changed particulate organic stoichiometry, and induced shifts in bacterial community composition, including consistent declines in the relative abundance of Actinobacteria. The dark dilution culture showed a significant increase in dissolved organic carbon removal in response to phosphate enrichment. In transparent microcosms nutrient enrichment had no effect on concentrations of chlorophyll, carbon, or the fluorescence characteristics of dissolved organic matter, suggesting that bacterioplankton responses were independent of phytoplankton responses. These results demonstrate that bacterioplankton communities in unproductive high-elevation habitats can rapidly alter their taxonomic composition and metabolism in response to short-term phosphate enrichment. Our results reinforce the key role that phosphorus plays in oligotrophic lake ecosystems, clarify the nature of bacterioplankton nutrient limitation, and
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Úbeda, María; Lario, Margaret; Muñoz, Leticia; Borrero, María-José; Rodríguez-Serrano, Macarena; Sánchez-Díaz, Ana-María; Del Campo, Rosa; Lledó, Lourdes; Pastor, Óscar; García-Bermejo, Laura; Díaz, David; Álvarez-Mon, Melchor; Albillos, Agustín
2016-05-01
In advanced cirrhosis, gut bacterial translocation is the consequence of intestinal barrier disruption and leads to bacterial infection. Bile acid abnormalities in cirrhosis could play a role in the integrity of the intestinal barrier and the control of microbiota, mainly through the farnesoid X receptor. We investigated the long-term effects of the farnesoid X receptor agonist, obeticholic acid, on gut bacterial translocation, intestinal microbiota composition, barrier integrity and inflammation in rats with CCl4-induced cirrhosis with ascites. Cirrhotic rats received a 2-week course of obeticholic acid or vehicle starting once ascites developed. We then determined: bacterial translocation by mesenteric lymph node culture, ileum expression of antimicrobial peptides and tight junction proteins by qPCR, fecal albumin loss, enteric bacterial load and microbiota composition by qPCR and pyrosequencing of ileum mucosa-attached contents, and intestinal inflammation by cytometry of the inflammatory infiltrate. Obeticholic acid reduced bacterial translocation from 78.3% to 33.3% (p<0.01) and upregulated the expression of the farnesoid X receptor-associated gene small heterodimer partner. Treatment improved ileum expression of antimicrobial peptides, angiogenin-1 and alpha-5-defensin, tight junction proteins zonulin-1 and occludin, and reduced fecal albumin loss and liver fibrosis. Enteric bacterial load normalized, and the distinctive mucosal microbiota of cirrhosis was reduced. Gut immune cell infiltration was reduced and inflammatory cytokine and Toll-like receptor 4 expression normalized. In ascitic cirrhotic rats, obeticholic acid reduces gut bacterial translocation via several complementary mechanisms at the intestinal level. This agent could be used as an alternative to antibiotics to prevent bacterial infection in cirrhosis. Copyright © 2016 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.
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Proceedings of the 1988 International Meeting on Reduced Enrichment for Research and Test Reactors
DOE Office of Scientific and Technical Information (OSTI.GOV)
Not Available
1993-07-01
The international effort to develop and implement new research reactor fuels utilizing low-enriched uranium, instead of highly- enriched uranium, continues to make solid progress. This effort is the cornerstone of a widely shared policy aimed at reducing, and possibly eliminating, international traffic in highly-enriched uranium and the nuclear weapon proliferation concerns associated with this traffic. To foster direct communication and exchange of ideas among the specialists in this area, the Reduced Enrichment Research and Test Reactor (RERTR) Program, at Argonne National Laboratory, sponsored this meeting as the eleventh of a series which began 1978. Individual papers presented at the meetingmore » have been cataloged separately.« less
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Wei, Yuquan; Zhao, Yue; Shi, Mingzi; Cao, Zhenyu; Lu, Qian; Yang, Tianxue; Fan, Yuying; Wei, Zimin
2018-01-01
Enriched phosphate-solubilizing bacteria (PSB) agent were acquired by domesticated cultivation, and inoculated into kitchen waste composting in different stages. The effect of different treatments on organic acids production, tricalcium phosphate (TCP) solubilization and their relationship with bacterial community were investigated during composting. Our results pointed out that inoculation affected pH, total acidity and the production of oxalic, lactic, citric, succinic, acetic and formic acids. We also found a strong advantage in the solubilization of TCP and phosphorus (P) availability for PSB inoculation especially in the cooling stage. Redundancy analysis and structural equation models demonstrated inoculation by different methods changed the correlation of the bacterial community composition with P fractions as well as organic acids, and strengthened the cooperative function related to P transformation among species during composting. Finally, we proposed a possible mechanism of P solubilization with enriched PSB inoculation, which was induced by bacterial community and organic acids production. Copyright © 2017 Elsevier Ltd. All rights reserved.
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He, Wei-Jie; Yuan, Qing-Song; Zhang, You-Bing; Guo, Mao-Wei; Gong, An-Dong; Zhang, Jing-Bo; Wu, Ai-Bo; Huang, Tao; Qu, Bo; Li, He-Ping; Liao, Yu-Cai
2016-09-24
Globally, the trichothecene mycotoxins deoxynivalenol (DON) and nivalenol (NIV) are among the most widely distributed mycotoxins that contaminate small grain cereals. In this study, a bacterial consortium, PGC-3, with de-epoxydation activity was isolated from soil by an in situ soil enrichment method. Screening of 14 soil samples that were sprayed with DON revealed that 4 samples were able to biotransform DON into de-epoxydized DON (dE-DON). Among these, the PGC-3 consortium showed the highest and most stable activity to biotransform DON into dE-DON and NIV into dE-NIV. PGC-3 exhibited de-epoxydation activity at a wide range of pH (5-10) and temperatures (20-37 °C) values under aerobic conditions. Sequential subculturing with a continued exposure to DON substantially reduced the microbial population diversity of this consortium. Analyses of the 16S rDNA sequences indicated that PGC-3 comprised 10 bacterial genera. Among these, one species, Desulfitobacterium, showed a steady increase in relative abundance, from 0.03% to 1.55% (a 52-fold increase), as higher concentrations of DON were used in the subculture media, from 0 to 500 μg/mL. This study establishes the foundation to further develop bioactive agents that can detoxify trichothecene mycotoxins in cereals and enables for the characterization of detoxifying genes and their regulation.
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He, Wei-Jie; Yuan, Qing-Song; Zhang, You-Bing; Guo, Mao-Wei; Gong, An-Dong; Zhang, Jing-Bo; Wu, Ai-Bo; Huang, Tao; Qu, Bo; Li, He-Ping; Liao, Yu-Cai
2016-01-01
Globally, the trichothecene mycotoxins deoxynivalenol (DON) and nivalenol (NIV) are among the most widely distributed mycotoxins that contaminate small grain cereals. In this study, a bacterial consortium, PGC-3, with de-epoxydation activity was isolated from soil by an in situ soil enrichment method. Screening of 14 soil samples that were sprayed with DON revealed that 4 samples were able to biotransform DON into de-epoxydized DON (dE-DON). Among these, the PGC-3 consortium showed the highest and most stable activity to biotransform DON into dE-DON and NIV into dE-NIV. PGC-3 exhibited de-epoxydation activity at a wide range of pH (5–10) and temperatures (20–37 °C) values under aerobic conditions. Sequential subculturing with a continued exposure to DON substantially reduced the microbial population diversity of this consortium. Analyses of the 16S rDNA sequences indicated that PGC-3 comprised 10 bacterial genera. Among these, one species, Desulfitobacterium, showed a steady increase in relative abundance, from 0.03% to 1.55% (a 52-fold increase), as higher concentrations of DON were used in the subculture media, from 0 to 500 μg/mL. This study establishes the foundation to further develop bioactive agents that can detoxify trichothecene mycotoxins in cereals and enables for the characterization of detoxifying genes and their regulation. PMID:27669304
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Reduced enrichment for research and test reactors: Proceedings
DOE Office of Scientific and Technical Information (OSTI.GOV)
Not Available
1993-07-01
The 15th annual Reduced Enrichment for Research and Test Reactors (RERTR) international meeting was organized by Ris{o} National Laboratory in cooperation with the International Atomic Energy Agency and Argonne National Laboratory. The topics of the meeting were the following: National Programs, Fuel Fabrication, Licensing Aspects, States of Conversion, Fuel Testing, and Fuel Cycle. Individual papers have been cataloged separately.
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Zeng, Jing; Gou, Min; Tang, Yue-Qin; Li, Guo-Ying; Sun, Zhao-Yong; Kida, Kenji
2016-10-01
In this study, a sulfur-oxidizing community was enriched from activated sludge generated in tannery wastewater treatment plants. Bioleaching of tannery sludge containing 0.9-1.2% chromium was investigated to evaluate the effectiveness of the enriched community, the effect of chromium binding forms on bioleaching efficiency, and the dominant microbes contributing to chromium bioleaching. Sludge samples inoculated with the enriched community presented 79.9-96.8% of chromium leaching efficiencies, much higher than those without the enriched community. High bioleaching efficiencies of over 95% were achieved for chromium in reducible fraction, while 60.9-97.9% were observed for chromium in oxidizable and residual fractions. Acidithiobacillus thiooxidans, the predominant bacteria in the enriched community, played an important role in bioleaching, whereas some indigenous heterotrophic species in sludge might have had a supporting role. The results indicated that A. thiooxidans-dominant enriched microbial community had high chromium bioleaching efficiency, and chromium binding forms affected the bioleaching performance. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Liu, Hongyan; Wang, Hongyu
2016-07-01
To enrich the Fe (III)-reducing bacteria, sludge from marine sediment was inoculated into the medium using Fe (OH)3 as the sole electron acceptor. Efficiency of Fe (III) reduction and composition of Fe (III)-reducing enrichment culture were analyzed. The results indicated that the Fe (III)-reducing enrichment culture with the dominant bacteria relating to Clostridium and Enterobacter sp. had high Fe (III) reduction of (2.73 ± 0.13) mmol/L-Fe (II). A new Fe (III)-reducing bacterium was isolated from the Fe (III)-reducing enrichment culture and identified as Enterobacter sp. L6 by 16S rRNA gene sequence analysis. The Fe (III)-reducing ability of strain L6 under different culture conditions was investigated. The results indicated that strain L6 had high Fe (III)-reducing activity using glucose and pyruvate as carbon sources. Strain L6 could reduce Fe (III) at the range of NaCl concentrations tested and had the highest Fe (III) reduction of (4.63 ± 0.27) mmol/L Fe (II) at the NaCl concentration of 4 g/L. This strain L6 could reduce Fe (III) with unique properties in adaptability to salt variation, which indicated that it can be used as a model organism to study Fe (III)-reducing activity isolated from marine environment. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.
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NASA Astrophysics Data System (ADS)
Liu, Hai-Tao; Wen, Zhi-Yu; Xu, Yi; Shang, Zheng-Guo; Peng, Jin-Lan; Tian, Peng
2017-09-01
In this paper, an integrated microfluidic analysis microsystems with bacterial capture enrichment and in-situ impedance detection was purposed based on microfluidic chips dielectrophoresis technique and electrochemical impedance detection principle. The microsystems include microfluidic chip, main control module, and drive and control module, and signal detection and processing modulet and result display unit. The main control module produce the work sequence of impedance detection system parts and achieve data communication functions, the drive and control circuit generate AC signal which amplitude and frequency adjustable, and it was applied on the foodborne pathogens impedance analysis microsystems to realize the capture enrichment and impedance detection. The signal detection and processing circuit translate the current signal into impendence of bacteria, and transfer to computer, the last detection result is displayed on the computer. The experiment sample was prepared by adding Escherichia coli standard sample into chicken sample solution, and the samples were tested on the dielectrophoresis chip capture enrichment and in-situ impedance detection microsystems with micro-array electrode microfluidic chips. The experiments show that the Escherichia coli detection limit of microsystems is 5 × 104 CFU/mL and the detection time is within 6 min in the optimization of voltage detection 10 V and detection frequency 500 KHz operating conditions. The integrated microfluidic analysis microsystems laid the solid foundation for rapid real-time in-situ detection of bacteria.
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Effect of different mixing methods on the bacterial microleakage of calcium-enriched mixture cement.
Shahi, Shahriar; Jeddi Khajeh, Soniya; Rahimi, Saeed; Yavari, Hamid R; Jafari, Farnaz; Samiei, Mohammad; Ghasemi, Negin; Milani, Amin S
2016-10-01
Calcium-enriched mixture (CEM) cement is used in the field of endodontics. It is similar to mineral trioxide aggregate in its main ingredients. The present study investigated the effect of different mixing methods on the bacterial microleakage of CEM cement. A total of 55 human single-rooted human permanent teeth were decoronated so that 14-mm-long samples were obtained and obturated with AH26 sealer and gutta-percha using lateral condensation technique. Three millimeters of the root end were cut off and randomly divided into 3 groups of 15 each (3 mixing methods of amalgamator, ultrasonic and conventional) and 2 negative and positive control groups (each containing 5 samples). BHI (brain-heart infusion agar) suspension containing Enterococcus faecalis was used for bacterial leakage assessment. Statistical analysis was carried out using descriptive statistics, Kaplan-Meier survival analysis with censored data and log rank test. Statistical significance was set at P<0.05. The survival means for conventional, amalgamator and ultrasonic methods were 62.13±12.44, 68.87±12.79 and 77.53±12.52 days, respectively. The log rank test showed no significant differences between the groups. Based on the results of the present study it can be concluded that different mixing methods had no significant effect on the bacterial microleakage of CEM cement.
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Fougy, Lysiane; Desmonts, Marie-Hélène; Coeuret, Gwendoline; Fassel, Christine; Hamon, Erwann; Hézard, Bernard; Champomier-Vergès, Marie-Christine
2016-01-01
ABSTRACT Raw sausages are perishable foodstuffs; reducing their salt content raises questions about a possible increased spoilage of these products. In this study, we evaluated the influence of salt reduction (from 2.0% to 1.5% [wt/wt]), in combination with two types of packaging (modified atmosphere [50% mix of CO2-N2] and vacuum packaging), on the onset of spoilage and on the diversity of spoilage-associated bacteria. After 21 days of storage at 8°C, spoilage was easily observed, characterized by noticeable graying of the products and the production of gas and off-odors defined as rancid, sulfurous, or sour. At least one of these types of spoilage occurred in each sample, and the global spoilage intensity was more pronounced in samples stored under modified atmosphere than under vacuum packaging and in samples with the lower salt content. Metagenetic 16S rRNA pyrosequencing revealed that vacuum-packaged samples contained a higher total bacterial richness (n = 69 operational taxonomic units [OTUs]) than samples under the other packaging condition (n = 46 OTUs). The core community was composed of 6 OTUs (Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Carnobacterium maltaromaticum, Serratia proteamaculans, and Brochothrix thermosphacta), whereas 13 OTUs taxonomically assigned to the Enterobacteriaceae, Enterococcaceae, and Leuconostocaceae families comprised a less-abundant subpopulation. This subdominant community was significantly more abundant when 2.0% salt and vacuum packaging were used, and this correlated with a lower degree of spoilage. Our results demonstrate that salt reduction, particularly when it is combined with CO2-enriched packaging, promotes faster spoilage of raw sausages by lowering the overall bacterial diversity (both richness and evenness). IMPORTANCE Our study takes place in the context of raw meat product manufacturing and is linked to a requirement for salt reduction. Health guidelines are calling for a reduction in
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Fougy, Lysiane; Desmonts, Marie-Hélène; Coeuret, Gwendoline; Fassel, Christine; Hamon, Erwann; Hézard, Bernard; Champomier-Vergès, Marie-Christine; Chaillou, Stéphane
2016-07-01
Raw sausages are perishable foodstuffs; reducing their salt content raises questions about a possible increased spoilage of these products. In this study, we evaluated the influence of salt reduction (from 2.0% to 1.5% [wt/wt]), in combination with two types of packaging (modified atmosphere [50% mix of CO2-N2] and vacuum packaging), on the onset of spoilage and on the diversity of spoilage-associated bacteria. After 21 days of storage at 8°C, spoilage was easily observed, characterized by noticeable graying of the products and the production of gas and off-odors defined as rancid, sulfurous, or sour. At least one of these types of spoilage occurred in each sample, and the global spoilage intensity was more pronounced in samples stored under modified atmosphere than under vacuum packaging and in samples with the lower salt content. Metagenetic 16S rRNA pyrosequencing revealed that vacuum-packaged samples contained a higher total bacterial richness (n = 69 operational taxonomic units [OTUs]) than samples under the other packaging condition (n = 46 OTUs). The core community was composed of 6 OTUs (Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Carnobacterium maltaromaticum, Serratia proteamaculans, and Brochothrix thermosphacta), whereas 13 OTUs taxonomically assigned to the Enterobacteriaceae, Enterococcaceae, and Leuconostocaceae families comprised a less-abundant subpopulation. This subdominant community was significantly more abundant when 2.0% salt and vacuum packaging were used, and this correlated with a lower degree of spoilage. Our results demonstrate that salt reduction, particularly when it is combined with CO2-enriched packaging, promotes faster spoilage of raw sausages by lowering the overall bacterial diversity (both richness and evenness). Our study takes place in the context of raw meat product manufacturing and is linked to a requirement for salt reduction. Health guidelines are calling for a reduction in dietary salt intake
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Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Zhang, Wei-Peng; Bajic, Vladimir; Qian, Pei-Yuan
2014-11-04
the community structure and functional gene composition, revealing that copper treatment had a selective effect on the functions of the bacterial community in the sponge. These findings suggest that copper pollution has an ecological impact on the sponge symbiont. The analysis showed that the untreated sponges hosted symbiotic autotrophic bacteria as dominant species, and the high-concentration copper treatment enriched for a heterotrophic bacterial community with enrichment for genes important for bacterial motility, supplementary cellular components, signaling and regulation, and virulence. Microscopic observation showed obvious bacterial aggregation and a reduction of sponge cell numbers in treated sponges, which suggested the formation of aggregates to reduce the copper concentration. The enrichment for functions of directional bacterial movement and supplementary cellular components and the formation of bacterial aggregates and phage enrichment are novel findings in sponge studies. Copyright © 2014 Tian et al.
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NASA Astrophysics Data System (ADS)
Kim, Y.; Park, B.; Seo, H.; Roh, Y.
2009-12-01
Dissimilatory metal-reducing bacteria utilize diverse metal oxides as electron acceptors and couple this microbial metal reduciton to growth. However, the microbe-metal interactions playing important roles in the metal geochemistry and organic matter degradation in the tidal flat sediments have not been uncovered enough to employ in various environmental and industrial applications. The objective of this study was to examine biomineralization and bioremediation by the facultative metal-reducing bacteria isolated from the inter-tidal flat sediments in southwestern of Korea. 16S-rRNA analysis showed bacterial consortium mainly consists of genus of Clostridium sp. The enriched bacteria were capable of reducing diverse metals such as iron oxide, maganese oxide, Cr(VI) and Se(VI) during glucose fermentation process at room temperature. The bacteria reduced highly toxic and reactive elements such as Cr(VI) and Se(VI) to Cr(III) and Se(0). The results showed that microbial processes induced transformation from toxic states of heavy metals to less toxic and mobile states in natural environments. Andthe bacteria also reduced iron oxyhydroxide such as ferrihydrite and akaganeite (β-FeOOH) and formed nanometer-sized magnetite (Fe3O4). This study indicates microbial processes not only can be used for bioremediation of inorganic contaminants existing in the marine environments, but also form the magnetite nanoparticles which are exhibit superparamagnetic properties that can be useful for relevant medical and industrial applications.
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Cooking rice in excess water reduces both arsenic and enriched vitamins in the cooked grain.
Gray, Patrick J; Conklin, Sean D; Todorov, Todor I; Kasko, Sasha M
2016-01-01
This paper reports the effects of rinsing rice and cooking it in variable amounts of water on total arsenic, inorganic arsenic, iron, cadmium, manganese, folate, thiamin and niacin in the cooked grain. We prepared multiple rice varietals both rinsed and unrinsed and with varying amounts of cooking water. Rinsing rice before cooking has a minimal effect on the arsenic (As) content of the cooked grain, but washes enriched iron, folate, thiamin and niacin from polished and parboiled rice. Cooking rice in excess water efficiently reduces the amount of As in the cooked grain. Excess water cooking reduces average inorganic As by 40% from long grain polished, 60% from parboiled and 50% from brown rice. Iron, folate, niacin and thiamin are reduced by 50-70% for enriched polished and parboiled rice, but significantly less so for brown rice, which is not enriched.
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El-Fantroussi, Said
2000-01-01
Soil treated with linuron for more than 10 years showed high biodegradation activity towards methoxy-methyl urea herbicides. Untreated control soil samples taken from the same location did not express any linuron degradation activity, even after 40 days of incubation. Hence, the occurrence in the field of a microbiota having the capacity to degrade a specific herbicide was related to the long-term treatment of the soil. The enrichment culture isolated from treated soil showed specific degradation activity towards methoxy-methyl urea herbicides, such as linuron and metobromuron, while dimethyl urea herbicides, such as diuron, chlorotoluron, and isoproturon, were not transformed. The putative metabolic intermediates of linuron and metobromuron, the aniline derivatives 3,4-dichloroaniline and 4-bromoaniline, were also degraded. The temperature of incubation drastically affected degradation of the aniline derivatives. Whereas linuron was transformed at 28 and 37°C, 3,4-dichloroaniline was transformed only at 28°C. Monitoring the enrichment process by reverse transcription-PCR and denaturing gradient gel electrophoresis (DGGE) showed that a mixture of bacterial species under adequate physiological conditions was required to completely transform linuron. This research indicates that for biodegradation of linuron, several years of adaptation have led to selection of a bacterial consortium capable of completely transforming linuron. Moreover, several of the putative species appear to be difficult to culture since they were detectable by DGGE but were not culturable on agar plates. PMID:11097876
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Intraspecific differences in bacterial responses to modelled reduced gravity
NASA Technical Reports Server (NTRS)
Baker, P. W.; Leff, L. G.
2005-01-01
AIMS: Bacteria are important residents of water systems, including those of space stations which feature specific environmental conditions, such as lowered effects of gravity. The purpose of this study was to compare responses with modelled reduced gravity of space station, water system bacterial isolates with other isolates of the same species. METHODS AND RESULTS: Bacterial isolates, Stenotrophomonas paucimobilis and Acinetobacter radioresistens, originally recovered from the water supply aboard the International Space Station (ISS) were grown in nutrient broth under modelled reduced gravity. Their growth was compared with type strains S. paucimobilis ATCC 10829 and A. radioresistens ATCC 49000. Acinetobacter radioresistens ATCC 49000 and the two ISS isolates showed similar growth profiles under modelled reduced gravity compared with normal gravity, whereas S. paucimobilis ATCC 10829 was negatively affected by modelled reduced gravity. CONCLUSIONS: These results suggest that microgravity might have selected for bacteria that were able to thrive under this unusual condition. These responses, coupled with impacts of other features (such as radiation resistance and ability to persist under very oligotrophic conditions), may contribute to the success of these water system bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: Water quality is a significant factor in many environments including the ISS. Efforts to remove microbial contaminants are likely to be complicated by the features of these bacteria which allow them to persist under the extreme conditions of the systems.
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Glyburide reduces bacterial dissemination in a mouse model of melioidosis.
Koh, Gavin C K W; Weehuizen, Tassili A; Breitbach, Katrin; Krause, Kathrin; de Jong, Hanna K; Kager, Liesbeth M; Hoogendijk, Arjan J; Bast, Antje; Peacock, Sharon J; van der Poll, Tom; Steinmetz, Ivo; Wiersinga, W Joost
2013-01-01
Burkholderia pseudomallei infection (melioidosis) is an important cause of community-acquired Gram-negative sepsis in Northeast Thailand, where it is associated with a ~40% mortality rate despite antimicrobial chemotherapy. We showed in a previous cohort study that patients taking glyburide ( = glibenclamide) prior to admission have lower mortality and attenuated inflammatory responses compared to patients not taking glyburide. We sought to define the mechanism underlying this observation in a murine model of melioidosis. Mice (C57BL/6) with streptozocin-induced diabetes were inoculated with ~6 × 10(2) cfu B. pseudomallei intranasally, then treated with therapeutic ceftazidime (600 mg/kg intraperitoneally twice daily starting 24 h after inoculation) in order to mimic the clinical scenario. Glyburide (50 mg/kg) or vehicle was started 7 d before inoculation and continued until sacrifice. The minimum inhibitory concentration of glyburide for B. pseudomallei was determined by broth microdilution. We also examined the effect of glyburide on interleukin (IL) 1β by bone-marrow-derived macrophages (BMDM). Diabetic mice had increased susceptibility to melioidosis, with increased bacterial dissemination but no effect was seen of diabetes on inflammation compared to non-diabetic controls. Glyburide treatment did not affect glucose levels but was associated with reduced pulmonary cellular influx, reduced bacterial dissemination to both liver and spleen and reduced IL1β production when compared to untreated controls. Other cytokines were not different in glyburide-treated animals. There was no direct effect of glyburide on B. pseudomallei growth in vitro or in vivo. Glyburide directly reduced the secretion of IL1β by BMDMs in a dose-dependent fashion. Diabetes increases the susceptibility to melioidosis. We further show, for the first time in any model of sepsis, that glyburide acts as an anti-inflammatory agent by reducing IL1β secretion accompanied by diminished cellular
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Glyburide Reduces Bacterial Dissemination in a Mouse Model of Melioidosis
Koh, Gavin C. K. W.; Weehuizen, Tassili A.; Breitbach, Katrin; Krause, Kathrin; de Jong, Hanna K.; Kager, Liesbeth M.; Hoogendijk, Arjan J.; Bast, Antje; Peacock, Sharon J.; van der Poll, Tom; Steinmetz, Ivo; Wiersinga, W. Joost
2013-01-01
Background Burkholderia pseudomallei infection (melioidosis) is an important cause of community-acquired Gram-negative sepsis in Northeast Thailand, where it is associated with a ∼40% mortality rate despite antimicrobial chemotherapy. We showed in a previous cohort study that patients taking glyburide ( = glibenclamide) prior to admission have lower mortality and attenuated inflammatory responses compared to patients not taking glyburide. We sought to define the mechanism underlying this observation in a murine model of melioidosis. Methods Mice (C57BL/6) with streptozocin-induced diabetes were inoculated with ∼6×102 cfu B. pseudomallei intranasally, then treated with therapeutic ceftazidime (600 mg/kg intraperitoneally twice daily starting 24 h after inoculation) in order to mimic the clinical scenario. Glyburide (50 mg/kg) or vehicle was started 7 d before inoculation and continued until sacrifice. The minimum inhibitory concentration of glyburide for B. pseudomallei was determined by broth microdilution. We also examined the effect of glyburide on interleukin (IL) 1β by bone-marrow-derived macrophages (BMDM). Results Diabetic mice had increased susceptibility to melioidosis, with increased bacterial dissemination but no effect was seen of diabetes on inflammation compared to non-diabetic controls. Glyburide treatment did not affect glucose levels but was associated with reduced pulmonary cellular influx, reduced bacterial dissemination to both liver and spleen and reduced IL1β production when compared to untreated controls. Other cytokines were not different in glyburide-treated animals. There was no direct effect of glyburide on B. pseudomallei growth in vitro or in vivo. Glyburide directly reduced the secretion of IL1β by BMDMs in a dose-dependent fashion. Conclusions Diabetes increases the susceptibility to melioidosis. We further show, for the first time in any model of sepsis, that glyburide acts as an anti-inflammatory agent by reducing IL1
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Kuppardt, Anke; Kleinsteuber, Sabine; Vogt, Carsten; Lüders, Tillmann; Harms, Hauke; Chatzinotas, Antonis
2014-08-01
Three toluene-degrading microbial consortia were enriched under sulphate-reducing conditions from different zones of a benzene, toluene, ethylbenzene and xylenes (BTEX) plume of two connected contaminated aquifers. Two cultures were obtained from a weakly contaminated zone of the lower aquifer, while one culture originated from the highly contaminated upper aquifer. We hypothesised that the different habitat characteristics are reflected by distinct degrader populations. Degradation of toluene with concomitant production of sulphide was demonstrated in laboratory microcosms and the enrichment cultures were phylogenetically characterised. The benzylsuccinate synthase alpha-subunit (bssA) marker gene, encoding the enzyme initiating anaerobic toluene degradation, was targeted to characterise the catabolic diversity within the enrichment cultures. It was shown that the hydrogeochemical parameters in the different zones of the plume determined the microbial composition of the enrichment cultures. Both enrichment cultures from the weakly contaminated zone were of a very similar composition, dominated by Deltaproteobacteria with the Desulfobulbaceae (a Desulfopila-related phylotype) as key players. Two different bssA sequence types were found, which were both affiliated to genes from sulphate-reducing Deltaproteobacteria. In contrast, the enrichment culture from the highly contaminated zone was dominated by Clostridia with a Desulfosporosinus-related phylotype as presumed key player. A distinct bssA sequence type with high similarity to other recently detected sequences from clostridial toluene degraders was dominant in this culture. This work contributes to our understanding of the niche partitioning between degrader populations in distinct compartments of BTEX-contaminated aquifers.
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Yang, Zhiman; Guo, Rongbo; Xu, Xiaohui; Wang, Lin; Dai, Meng
2016-09-01
Using batch and repeated batch cultivations, this study investigated the effects of bioaugmentation with enriched microbial consortia (named as EMC) on methane production from effluents of hydrogen-producing stage of potato slurry, as well as on the indigenous bacterial community. The results demonstrated that the improved methane production and shift of the indigenous bacterial community structure were dependent on the EMC/sludge ratio and bioaugmentation patterns. The methane yield and production rate in repeated batch bioaugmentation pattern of EMC were, respectively, average 15% and 10% higher than in one-time bioaugmentation pattern of EMC. DNA-sequencing approach showed that the enhanced methane production in the repeated batch bioaugmentation pattern of EMC mainly resulted from the enriched iron-reducing bacteria and the persistence of the introduced Syntrophomonas, which led to a rapid degradation of individual VFAs to methane. The findings contributed to understanding the correlation between the bioaugmentation of microbial consortia, community shift, and methane production. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Limitation of Bacterial Growth by Dissolved Organic Matter and Iron in the Southern Ocean†
Church, Matthew J.; Hutchins, David A.; Ducklow, Hugh W.
2000-01-01
The importance of resource limitation in controlling bacterial growth in the high-nutrient, low-chlorophyll (HNLC) region of the Southern Ocean was experimentally determined during February and March 1998. Organic- and inorganic-nutrient enrichment experiments were performed between 42°S and 55°S along 141°E. Bacterial abundance, mean cell volume, and [3H]thymidine and [3H]leucine incorporation were measured during 4- to 5-day incubations. Bacterial biomass, production, and rates of growth all responded to organic enrichments in three of the four experiments. These results indicate that bacterial growth was constrained primarily by the availability of dissolved organic matter. Bacterial growth in the subtropical front, subantarctic zone, and subantarctic front responded most favorably to additions of dissolved free amino acids or glucose plus ammonium. Bacterial growth in these regions may be limited by input of both organic matter and reduced nitrogen. Unlike similar experimental results in other HNLC regions (subarctic and equatorial Pacific), growth stimulation of bacteria in the Southern Ocean resulted in significant biomass accumulation, apparently by stimulating bacterial growth in excess of removal processes. Bacterial growth was relatively unchanged by additions of iron alone; however, additions of glucose plus iron resulted in substantial increases in rates of bacterial growth and biomass accumulation. These results imply that bacterial growth efficiency and nitrogen utilization may be partly constrained by iron availability in the HNLC Southern Ocean. PMID:10653704
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Enrichment and characterization of sulfate reducing, naphthalene degrading microorganisms
NASA Astrophysics Data System (ADS)
Steffen, Kümmel; Florian-Alexander, Herbst; Márcia, Duarte; Dietmar, Pieper; Jana, Seifert; Bergen Martin, von; Hans-Hermann, Richnow; Carsten, Vogt
2014-05-01
Polycyclic aromatic hydrocarbons (PAH) are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. PAH are widely distributed in the environment by accidental discharges during the transport, use and disposal of petroleum products, and during forest and grass fires. Caused by their hydrophobic nature, PAH basically accumulate in sediments from where they are slowly released into the groundwater. Although generally limited by the low water solubility of PAH, microbial degradation is one of the major mechanisms leading to the complete clean-up of PAH-contaminated sites. Whereas organisms and biochemical pathways responsible for the aerobic breakdown of PAH are well known, anaerobic PAH biodegradation is less understood; only a few anaerobic PAH degrading cultures have been described. We studied the anaerobic PAH degradation in a microcosm approach to enrich anaerobic PAH degraders. Anoxic groundwater and sediment samples were used as inoculum. Groundwater samples were purchased from the erstwhile gas works facility and a former wood impregnation site. In contrast, sources of sediment samples were a former coal refining area and an old fuel depot. Samples were incubated in anoxic mineral salt medium with naphthalene as sole carbon source and sulfate as terminal electron acceptor. Grown cultures were characterized by feeding with 13C-labeled naphthalene, 16S rRNA gene sequencing using an Illumina® approach, and functional proteome analyses. Finally, six enrichment cultures able to degrade naphthalene under anoxic conditions were established. First results point to a dominance of identified sequences affiliated to the freshwater sulfate-reducing strain N47, which is a known anaerobic naphthalene degrader, in four out of the six enrichments. In those enrichments, peptides related to the pathway of anoxic naphthalene degradation in N47 were abundant. Overall the data underlines the importance of Desulfobacteria for natural
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Jurickova, I; Collins, M H; Chalk, C; Seese, A; Bezold, R; Lake, K; Allmen, D; Frischer, J S; Falcone, R A; Trapnell, B C; Denson, L A
2013-01-01
Granulocyte–macrophage colony-stimulating factor (GM-CSF) autoantibodies are associated with stricturing behaviour in Crohn disease (CD). We hypothesized that CD ileal lamina propria mononuclear cells (LPMC) would produce GM-CSF autoantibodies and peripheral blood (PB) samples would contain GM-CSF neutralizing capacity (NC). Paediatric CD and control PBMC and ileal biopsies or LPMC were isolated and cultured and GM-CSF, immunoglobulin (Ig)G and GM-CSF autoantibodies production were measured by enzyme-linked immunosorbent assay (ELISA). Basal and GM-CSF-primed neutrophil bacterial killing and signal transducer and activator of transcription 5 (STAT5) tyrosine phosphorylation (pSTAT5) were measured by flow cytometry. GM-CSF autoantibodies were enriched within total IgG for LPMC isolated from CD ileal strictures and proximal margins compared to control ileum. Neutrophil bacterial killing was reduced in CD patients compared to controls. Within CD, neutrophil GM-CSF-dependent STAT5 activation and bacterial killing were reduced as GM-CSF autoantibodies increased. GM-CSF stimulation of pSTAT5 did not vary between controls and CD patients in washed PB granulocytes in which serum was removed. However, GM-CSF stimulation of pSTAT5 was reduced in whole PB samples from CD patients. These data were used to calculate the GM-CSF NC. CD patients with GM-CSF NC greater than 25% exhibited a fourfold higher rate of stricturing behaviour and surgery. The likelihood ratio (95% confidence interval) for stricturing behaviour for patients with elevation in both GM-CSF autoantibodies and GM-CSF NC was equal to 5 (2, 11). GM-CSF autoantibodies are produced by LPMC isolated from CD ileal resection specimens and are associated with reduced neutrophil bacterial killing. CD peripheral blood contains GM-CSF NC, which is associated with increased rates of stricturing behaviour. PMID:23600834
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Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum▿
Ettwig, Katharina F.; van Alen, Theo; van de Pas-Schoonen, Katinka T.; Jetten, Mike S. M.; Strous, Marc
2009-01-01
Anaerobic methane oxidation coupled to denitrification was recently assigned to bacteria belonging to the uncultured phylum NC10. In this study, we incubated sediment from a eutrophic ditch harboring a diverse community of NC10 bacteria in a bioreactor with a constant supply of methane and nitrite. After 6 months, fluorescence in situ hybridization showed that NC10 bacteria dominated the resulting population. The enrichment culture oxidized methane and reduced nitrite to dinitrogen gas. We assessed NC10 phylum diversity in the inoculum and the enrichment culture, compiled the sequences currently available for this bacterial phylum, and showed that of the initial diversity, only members of one subgroup had been enriched. The growth of this subgroup was monitored by quantitative PCR and correlated to nitrite-reducing activity and the total biomass of the culture. Together, the results indicate that the enriched subgroup of NC10 bacteria is responsible for anaerobic methane oxidation coupled to nitrite reduction. Due to methodological limitations (a strong bias against NC10 bacteria in 16S rRNA gene clone libraries and inhibition by commonly used stopper material) the environmental distribution and importance of these bacteria could be largely underestimated at present. PMID:19329658
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Two decades of warming increases diversity of a potentially lignolytic bacterial community
Pold, Grace; Melillo, Jerry M.; DeAngelis, Kristen M.
2015-01-01
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming. PMID:26042112
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Poulin, Brett A.; Ryan, Joseph N.; Nagy, Kathryn L.; Stubbins, Aron; Dittmar, Thorsten; Orem, William H.; Krabbenhoft, David P.; Aiken, George R.
2017-01-01
Sulfate inputs to the Florida Everglades stimulate sulfidic conditions in freshwater wetland sediments that affect ecological and biogeochemical processes. An unexplored implication of sulfate enrichment is alteration of the content and speciation of sulfur in dissolved organic matter (DOM), which influences the reactivity of DOM with trace metals. Here, we describe the vertical and lateral spatial dependence of sulfur chemistry in the hydrophobic organic acid fraction of DOM from unimpacted and sulfate-impacted Everglades wetlands using X-ray absorption spectroscopy and ultrahigh-resolution mass spectrometry. Spatial variation in DOM sulfur content and speciation reflects the degree of sulfate enrichment and resulting sulfide concentrations in sediment pore waters. Sulfur is incorporated into DOM predominantly as highly reduced species in sulfidic pore waters. Sulfur-enriched DOM in sediment pore waters exchanges with overlying surface waters and the sulfur likely undergoes oxidative transformations in the water column. Across all wetland sites and depths, the total sulfur content of DOM correlated with the relative abundance of highly reduced sulfur functionality. The results identify sulfate input as a primary determinant on DOM sulfur chemistry to be considered in the context of wetland restoration and sulfur and trace metal cycling.
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Strong, Amy L; Wolfe, Emily T; Shank, Nina; Chaffin, Abigail E; Jansen, David A
2018-06-01
Surgical site infection after breast reconstruction is associated with increased length of hospital stay, readmission rates, cost, morbidity, and mortality. Identifying methods to reduce surgical site infection without the use of antibiotics may be beneficial at reducing antimicrobial resistance, reserving the use of antibiotics for more severe cases. Quaternary ammonium salts have previously been shown to be a safe and effective antimicrobial agent in the setting of in vitro and in vivo animal experiments. A retrospective study was conducted to investigate the antimicrobial properties of a quaternary ammonium salt, 3-trimethoxysilyl propyldimethyloctadecyl ammonium chloride (QAS-3PAC; Bio-spear), at reducing surgical drain site colonization and infection after breast reconstruction (deep inferior epigastric perforator flap reconstruction or tissue expander placement). Twenty patients were enrolled, with 14 surgical drains covered with nonimpregnated gauze and 17 surgical drains covered with QAS-3PAC impregnated gauze, for the purposes of investigating bacterial colonization. Antibiotic sensitivity analysis was also conducted when bacterial cultures were positive. The overall incidence of bacterial colonization of surgical drains was lower in the treatment group compared with the control group (17.6% vs 64.3%, respectively; P = 0.008). QAS-3PAC impregnated gauze reduced the incidence of bacterial colonization of surgical drains during the first (0.0% vs 33.3%) and second (33.3% vs 87.5%; P = 0.04) postoperative week. Furthermore, no enhanced antibiotic resistance was noted on drains treated with QAS-3PAC impregnated gauze. The results of this study suggest that QAS-3PAC impregnated gauze applied over surgical drains may be an effective method for reducing the incidence of bacterial colonization.
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Development of antifouling surfaces to reduce bacterial attachment
NASA Astrophysics Data System (ADS)
Graham, Mary Viola
Bacteria are exceptionally good at adhering to surfaces and forming complex structures known as biofilms. This process, known as biofouling, can cause problems for infrastructure (eg, clogging and damaging pipes), for the food industry (eg, contamination of processing surfaces and equipment, and for the medical industry (eg, contamination of indwelling medical devices). Accordingly, multiple strategies have been explored to combat biofouling, including chemical modification of surfaces, development of antibiotic coatings, and more recently, the use of engineered surface topography. When designed properly, engineered surface topographies can significantly reduce bacterial surface attachment, ultimately limiting surface colonization. In this work, we hypothesized that the morphology, size, spacing, and surface pre-treatment of topographical features should directly correlate with the size and shape of target organisms, in order to reduce biofouling. Topographical features with size and spacing from 0.25 to 2 mum were fabricated in silicone elastomer and tested against rod shaped bacteria with an average size of 0.5 x 2 mum and spherical bacteria (cocci) ranging from 0.5 - 1 μm in diameter. Antifouling properties of the different topographical features were tested in both static and flow-based assays, and under oxygen plasma-treated (hydrophilic) and untreated (hydrophobic) surface conditions. We found that surface pre-treatment universally affects the ability bacteria to attach to surfaces, while surface topography limits attachment in a manner dependent on the bacterial size/shape and the size/spacing of the topography.
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Surface imaging techniques were combined to determine appropriate manipulation of technologically important surfaces for commercial applications. Stainless steel surfaces were engineered to reduce bacterial contamination, biofilm formation, and corrosion during product processing...
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Evaluation of free-stall mattress bedding treatments to reduce mastitis bacterial growth.
Kristula, M A; Dou, Z; Toth, J D; Smith, B I; Harvey, N; Sabo, M
2008-05-01
Bacterial counts were compared in free-stall mattresses and teat ends exposed to 5 treatments in a factorial study design on 1 dairy farm. Mattresses in five 30-cow groups were subjected to 1 of 5 bedding treatments every other day: 0.5 kg of hydrated limestone, 120 mL of commercial acidic conditioner, 1 kg of coal fly ash, 1 kg of kiln-dried wood shavings, and control (no bedding). Counts of coliforms, Klebsiella spp., Escherichia coli, and Streptococcus spp. were lowest on mattresses bedded with lime. Mattresses bedded with the commercial acidic conditioner had the next lowest counts for coliforms, Klebsiella spp., and Streptococcus spp. Wood shavings and the no-bedding control had the highest counts for coliform and Klebsiella spp. Compared with wood shavings or control, fly ash reduced the counts of coliforms, whereas for the other 3 bacterial groups, the reduction was not always significant. Streptococcus spp. counts were greatest in the control group and did not differ among the shavings and fly ash groups. Teat swab results indicated that hydrated lime was the only bedding treatment that significantly decreased the counts of both coliforms and Klebsiella spp. There were no differences in Streptococcus spp. numbers on the teats between any of the bedding treatments. Bacterial populations grew steadily on mattresses and were generally higher at 36 to 48 h than at 12 to 24 h, whereas bacterial populations on teats grew rapidly by 12 h and then remained constant. Hydrated lime was the only treatment that significantly reduced bacterial counts on both mattresses and teat ends, but it caused some skin irritation.
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Evaluation of free-stall mattress bedding treatments to reduce mastitis bacterial growth
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kristula, M.A.; Dou, Z.; Toth, J.D.
2008-05-15
Bacterial counts were compared in free-stall mattresses and teat ends exposed to 5 treatments in a factorial study design on 1 dairy farm. Mattresses in five 30-cow groups were subjected to 1 of 5 bedding treatments every other day: 0.5 kg of hydrated limestone, 120 mL of commercial acidic conditioner, 1 kg of coal fly ash, 1 kg of kiln-dried wood shavings, and control (no bedding). Counts of coliforms, Klebsiella spp., Escherichia coli, and Streptococcus spp. were lowest on mattresses bedded with lime. Mattresses bedded with the commercial acidic conditioner had the next lowest counts for coliforms, Klebsiella spp., andmore » Streptococcus spp. Wood shavings and the no-bedding control had the highest counts for coliform and Klebsiella spp. Compared with wood shavings or control, fly ash reduced the counts of coliforms, whereas for the other 3 bacterial groups, the reduction was not always significant. Streptococcus spp. counts were greatest in the control group and did not differ among the shavings and fly ash groups. Teat swab results indicated that hydrated lime was the only bedding treatment that significantly decreased the counts of both coliforms and Klebsiella spp. There were no differences in Streptococcus spp. numbers on the teats between any of the bedding treatments. Bacterial populations grew steadily on mattresses and were generally higher at 36 to 48 h than at 12 to 24 h, whereas bacterial populations on teats grew rapidly by 12 h and then remained constant. Hydrated lime was the only treatment that significantly reduced bacterial counts on both mattresses and teat ends, but it caused some skin irritation.« less
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Vavricka, S R; Tutuian, R; Imhof, A; Wildi, S; Gubler, C; Fruehauf, H; Ruef, C; Schoepfer, A M; Fried, M
2010-09-01
Bacterial contamination of endoscopy suites is of concern; however studies evaluating bacterial aerosols are lacking. We aimed to determine the effectiveness of air suctioning during removal of biopsy forceps in reducing bacterial air contamination. This was a prospective single-blinded trial involving 50 patients who were undergoing elective nontherapeutic colonoscopy. During colonoscopy, endoscopists removed the biopsy forceps first without and then with suctioning following contact with the sigmoid mucosa. A total of 50 L of air was collected continuously for 30 seconds at 30-cm distance from the biopsy channel valve of the colonoscope, with time starting at forceps removal. Airborne bacteria were collected by an impactor air sampler (MAS-100). Standard Petri dishes with CNA blood agar were used to culture Gram-positive bacteria. Main outcome measure was the bacterial load in endoscopy room air. At the beginning and end of the daily colonoscopy program, the median (and interquartile [IQR] range) bioaerosol burden was 4 colony forming units (CFU)/m (3) (IQR 3 - 6) and 16 CFU/m (3) (IQR 13 - 18), respectively. Air suctioning during removal of the biopsy forceps reduced the bioaerosol burden from a median of 14 CFU/m (3) (IQR 11 - 29) to a median of 7 CFU/m (3) (IQR 4 - 16) ( P = 0.0001). Predominantly enterococci were identified on the agar plates. The bacterial aerosol burden during handling of biopsy forceps can be reduced by applying air suction while removing the forceps. This simple method may reduce transmission of infectious agents during gastrointestinal endoscopies. Copyright Georg Thieme Verlag KG Stuttgart . New York.
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Arsenic uptake in bacterial calcite
NASA Astrophysics Data System (ADS)
Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario
2018-02-01
Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and X-ray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03 Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.
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Baby Shampoo Versus Povidone-Iodine or Isopropyl Alcohol in Reducing Eyelid Skin Bacterial Load.
Garcia, Giancarlo A; Nguyen, Christine V; Yonkers, Marc A; Tao, Jeremiah P
Baby shampoo is used as an alternative surgical skin preparation, but the evidence supporting its use is scarce with no descriptions of efficacy in the periocular region. The authors compare the efficacy of baby shampoo, povidone-iodine (PI, Betadine) and isopropyl alcohol (IA) in reducing eyelid skin bacterial load. Prospective, randomized, comparative, and interventional trial. Bacterial load on adult, human eyelid skin was quantitated before and after cleansing with 1) dilute baby shampoo, 2) 10% PI, or 3) 70% IA. Paired skin swabs were collected from a 1 cm area of the upper eyelid of subjects before and after a standardized surgical scrub technique. Samples were cultured on 5% sheep blood agar for 24 hours. The number of colony forming units (CFU) was assessed and bacterial load per square centimeter of eyelid skin was quantified. Baseline and postcleansing samples were assessed from 42 eyelids of 42 subjects (n = 14 for each of baby shampoo, PI, and IA). Before cleansing, similar amounts of bacterial flora were grown from all specimens (median log CFU/cm = 2.04 before baby shampoo, 2.01 before PI, 2.11 before IA; p > 0.05). All 3 cleansing agents significantly reduced the bacterial load (p < 0.01 for each). There was no statistically significant difference in postcleansing bacterial load between the 3 cleansing agents (median log CFU/cm = 0.48 after baby shampoo, 0.39 after PI, 0.59 after IA; p > 0.05). Change from baseline in bacterial load was statistically similar for all 3 agents (median reduction in log CFU/cm = 1.28 with baby shampoo, 1.57 with PI, 1.40 with IA; p > 0.05). These corresponded to bacterial load reductions of 96.3%, 96.6%, and 98.4% for baby shampoo, PI, and IA, respectively. Baby shampoo achieved comparable diminution in eyelid skin bacterial load to PI or IA. These data suggest baby shampoo may be an effective preoperative cleansing agent.
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Arsenic uptake in bacterial calcite
DOE Office of Scientific and Technical Information (OSTI.GOV)
Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco
Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and Xray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the cmore » axis (by 0.03Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.« less
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Biruduganti, Munidhar S.; Gupta, Sreenath Borra; Sekar, R. Raj; McConnell, Steven S.
2008-11-25
A method and system for reducing nitrous oxide emissions from an internal combustion engine. An input gas stream of natural gas includes a nitrogen gas enrichment which reduces nitrous oxide emissions. In addition ignition timing for gas combustion is advanced to improve FCE while maintaining lower nitrous oxide emissions.
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Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.
Thoendel, Matthew; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Yao, Janet Z; Chia, Nicholas; Hanssen, Arlen D; Abdel, Matthew P; Patel, Robin
2016-08-01
Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing. Copyright © 2016 Elsevier B.V. All rights reserved.
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Environmental enrichment reduces signs of boredom in caged mink.
Meagher, Rebecca K; Mason, Georgia J
2012-01-01
be operationalized and assessed empirically in non-human animals. It can also be reduced by environmental enrichment.
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Environmental Enrichment Reduces Signs of Boredom in Caged Mink
Meagher, Rebecca K.; Mason, Georgia J.
2012-01-01
). Boredom can thus be operationalized and assessed empirically in non-human animals. It can also be reduced by environmental enrichment. PMID:23155462
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Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments
NASA Astrophysics Data System (ADS)
Nixon, Sophie L.; Telling, Jon P.; Wadham, Jemma L.; Cockell, Charles S.
2017-03-01
Subglacial environments are known to harbour metabolically diverse microbial communities. These microbial communities drive chemical weathering of underlying bedrock and influence the geochemistry of glacial meltwater. Despite its importance in weathering reactions, the microbial cycling of iron in subglacial environments, in particular the role of microbial iron reduction, is poorly understood. In this study we address the prevalence of viable iron-reducing microorganisms in subglacial sediments from five geographically isolated glaciers. Iron-reducing enrichment cultures were established with sediment from beneath Engabreen (Norway), Finsterwalderbreen (Svalbard), Leverett and Russell glaciers (Greenland), and Lower Wright Glacier (Antarctica). Rates of iron reduction were higher at 4 °C compared with 15 °C in all but one duplicated second-generation enrichment culture, indicative of cold-tolerant and perhaps cold-adapted iron reducers. Analysis of bacterial 16S rRNA genes indicates Desulfosporosinus were the dominant iron-reducing microorganisms in low-temperature Engabreen, Finsterwalderbreen and Lower Wright Glacier enrichments, and Geobacter dominated in Russell and Leverett enrichments. Results from this study suggest microbial iron reduction is widespread in subglacial environments and may have important implications for global biogeochemical iron cycling and export to marine ecosystems.
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Benbouzid, Fathalah; Kodjikian, Laurent; Hartmann, Daniel; Renaud, François; Baillif, Stéphanie
2016-02-01
To compare the anti-adhesive effect of cefuroxime and moxifloxacin on the primary attachment phase of Staphylococcus epidermidis on hydrophobic acrylic intraocular lenses (IOLs). Forty hydrophobic acrylic IOLs were used. Two groups of IOLs were soaked in a moxifloxacin (Mox-T1: 0.5 mg/0.1 ml) or a cefuroxime (Cef-T1: cefuroxime 1 mg/0.1 ml) solution before incubation in a S. epidermidis bacterial suspension. Two other groups were incubated in the bacterial suspension before antibiotics (Cef-T2 and Mox-T2) were added. The control group (Ctrl) consisted of IOLs incubated in the bacterial suspension. After incubation, IOLs were sonicated and vortexed. The resultant suspension was spread over a nutritive agar plate. Bacterial colonies were counted after 24 hr of incubation. Mean number of colony-forming units per IOL was Cef-T1: 184 × 10(3) (SE: 5.24; SD: 28.21), Cef-T2: 117 × 10(3) (SE: 5.74; SD: 30.37), Mox-T1: 1.27 × 10(3) (SE: 0.12; SD: 0.61), Mox-T2: 25 × 10(3) (SE:1.98; SD: 9.72) and Ctrl: 361 × 10(3) (SE: 26.9; SD: 107.6). The number of adhering bacteria did not vary whether cefuroxime was added before or after IOL incubation in the bacterial suspension (p = 0.132). Moxifloxacin was more effective in reducing the number of adhering bacteria when used before IOL incubation (p < 0.001). Overall for T1 and T2, moxifloxacin was more effective than cefuroxime in reducing bacterial adhesion on IOLs (p < 0.001). Moxifloxacin and cefuroxime significantly reduced S. epidermidis adhesion on hydrophobic acrylic IOLs. The anti-adhesive effect was superior with moxifloxacin. © 2015 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.
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Robinson, Andrew L; Lee, Hyun Jung; Kwon, Junehee; Todd, Ewen; Rodriguez, Fernando Perez; Ryu, Dojin
2016-02-01
Hand washing and glove use are the main methods for reducing bacterial cross-contamination from hands to ready-to-eat food in a food service setting. However, bacterial transfer from hands to gloves is poorly understood, as is the effect of different durations of soap rubbing on bacterial reduction. To assess bacterial transfer from hands to gloves and to compare bacterial transfer rates to food after different soap washing times and glove use, participants' hands were artificially contaminated with Enterobacter aerogenes B199A at ∼9 log CFU. Different soap rubbing times (0, 3, and 20 s), glove use, and tomato dicing activities followed. The bacterial counts in diced tomatoes and on participants' hands and gloves were then analyzed. Different soap rubbing times did not significantly change the amount of bacteria recovered from participants' hands. Dicing tomatoes with bare hands after 20 s of soap rubbing transferred significantly less bacteria (P < 0.01) to tomatoes than did dicing with bare hands after 0 s of soap rubbing. Wearing gloves while dicing greatly reduced the incidence of contaminated tomato samples compared with dicing with bare hands. Increasing soap washing time decreased the incidence of bacteria recovered from outside glove surfaces (P < 0.05). These results highlight that both glove use and adequate hand washing are necessary to reduce bacterial cross-contamination in food service environments.
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Flury, Sabine; Gessner, Mark O
2011-02-01
Atmospheric warming and increased nitrogen deposition can lead to changes of microbial communities with possible consequences for biogeochemical processes. We used an enclosure facility in a freshwater marsh to assess the effects on microbes associated with decomposing plant litter under conditions of simulated climate warming and pulsed nitrogen supply. Standard batches of litter were placed in coarse-mesh and fine-mesh bags and submerged in a series of heated, nitrogen-enriched, and control enclosures. They were retrieved later and analyzed for a range of microbial parameters. Fingerprinting profiles obtained by denaturing gradient gel electrophoresis (DGGE) indicated that simulated global warming induced a shift in bacterial community structure. In addition, warming reduced fungal biomass, whereas bacterial biomass was unaffected. The mesh size of the litter bags and sampling date also had an influence on bacterial community structure, with the apparent number of dominant genotypes increasing from spring to summer. Microbial respiration was unaffected by any treatment, and nitrogen enrichment had no clear effect on any of the microbial parameters considered. Overall, these results suggest that microbes associated with decomposing plant litter in nutrient-rich freshwater marshes are resistant to extra nitrogen supplies but are likely to respond to temperature increases projected for this century.
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Hsueh, P-R; Huang, H-C; Young, T-G; Su, C-Y; Liu, C-S; Yen, M-Y
2014-04-01
A contaminated hospital environment has been identified as an important reservoir of pathogens causing healthcare-associated infections. This study is to evaluate the efficacy of bacteria killing nanotechnology Bio-Kil on reducing bacterial counts in an intensive care unit (ICU). Two single-bed rooms (S-19 and S-20) in the ICU were selected from 7 April to 27 May 2011. Ten sets of new textiles (pillow cases, bed sheets, duvet cover, and patient clothing) used by patients in the two single-bed rooms were provided by the sponsors. In the room S-20, the 10 sets of new textiles were washed with Bio-Kil; the room walls, ceiling, and air-conditioning filters were treated with Bio-Kil; and the surfaces of instruments (respirator, telephone, and computer) were covered with Bio-Kil-embedded silicon pads. Room S-19 served as the control. We compared the bacterial count on textiles and environment surfaces as well as air samples between the two rooms. A total of 1,364 samples from 22 different sites in each room were collected. The mean bacterial count on textiles and environmental surfaces in room S-20 was significantly lower than that in room S-19 (10.4 vs 49.6 colony-forming units [CFU]/100 cm(2); P < 0.001). Room S-20 had lower bacterial counts in air samples than room S-19 (33.4-37.6 vs 21.6-25.7 CFU/hour/plate; P < 0.001). The density of microbial isolations was significantly greater among patients admitted to room S-19 than those to room S-20 (9.15 vs 5.88 isolates per 100 patient-days, P < 0.05). Bio-Kil can significantly reduce bacterial burden in the environment of the ICU.
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Effects of predation and nutrient enrichment on the success and microbiome of a foundational coral.
Shaver, Elizabeth C; Shantz, Andrew A; McMinds, Ryan; Burkepile, Deron E; Vega Thurber, Rebecca L; Silliman, Brian R
2017-03-01
By inflicting damage to prey tissues, consumer species may increase stress in prey hosts and reduce overall fitness (i.e., primary effects, such as growth or reproduction) or cause secondary effects by affecting prey interactions with other species such as microbes. However, little is known about how abiotic conditions affect the outcomes of these biotic interactions. In coral reef communities, both nutrient enrichment and predation have been linked to reduced fitness and disease facilitation in corals, yet no study to date has tested their combined effects on corals or their associated microbial communities (i.e., microbiomes). Here, we assess the effects of grazing by a prevalent coral predator (the short coral snail, Coralliophila abbreviata) and nutrient enrichment on staghorn coral, Acropora cervicornis, and its microbiomes using a factorial experiment and high-throughput DNA sequencing. We found that predation, but not nutrients, significantly reduced coral growth and increased mortality, tissue loss, and turf algae colonization. Partial predation and nutrient enrichment both independently altered coral microbiomes such that one bacterial genus came to dominate the microbial community. Nutrient-enriched corals were associated with significant increases in Rickettsia-like organisms, which are currently one of several microbial groups being investigated as a disease agent in this coral species. However, we found no effects of nutrient enrichment on coral health, disease, or their predators. This research suggests that in the several months following coral transplantation (i.e., restoration) or disturbance (i.e., recovery), Caribbean acroporid corals appear to be highly susceptible to negative effects caused by predators, but not or not yet susceptible to nutrient enrichment despite changes to their microbial communities. © 2016 by the Ecological Society of America.
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Jahn, Michael K.; Haderlein, Stefan B.; Meckenstock, Rainer U.
2005-01-01
Monoaromatic hydrocarbons such as benzene, toluene, ethylbenzene, and xylene (BTEX) are widespread contaminants in groundwater. We examined the anaerobic degradation of BTEX compounds with amorphous ferric oxide as electron acceptor. Successful enrichment cultures were obtained for all BTEX substrates both in the presence and absence of AQDS (9,10-anthraquinone-2,6-disulfonic acid). The electron balances showed a complete anaerobic oxidation of the aromatic compounds to CO2. This is the first report on the anaerobic degradation of o-xylene and ethylbenzene in sediment-free iron-reducing enrichment cultures. PMID:15933041
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Dellagnezze, Bruna Martins; Vasconcellos, Suzan Pantaroto de; Melo, Itamar Soares de; Santos Neto, Eugênio Vaz Dos; Oliveira, Valéria Maia de
2016-01-01
Unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. Despite the techniques developed in order to improve methodologies involving DNA extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environments with low cellular density for further microbiological analyses. This work aimed at the evaluation of different matrices (arenite, shale and polyurethane foam) as support materials for microbial growth and biofilm formation in enrichments using a biodegraded petroleum sample as inoculum in sulfate reducing condition. Subsequent microbial diversity characterization was carried out using Scanning Electronic Microscopy (SEM), Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA gene libraries in order to compare the microbial biomass yield, DNA recovery efficiency and diversity among the enrichments. The DNA from microbial communities in petroleum enrichments was purified according to a protocol established in this work and used for 16S rRNA amplification with bacterial generic primers. The PCR products were cloned, and positive clones were screened by Amplified Ribosomal DNA Restriction Analysis (ARDRA). Sequencing and phylogenetic analyses revealed that the bacterial community was mostly represented by members of the genera Petrotoga, Bacillus, Pseudomonas, Geobacillus and Rahnella. The use of different support materials in the enrichments yielded an increase in microbial biomass and biofilm formation, indicating that these materials may be employed for efficient biomass recovery from petroleum reservoir samples. Nonetheless, the most diverse microbiota were recovered from the biodegraded petroleum sample using polyurethane foam cubes as support material. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.
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Jaekel, Ulrike; Musat, Niculina; Adam, Birgit; Kuypers, Marcel; Grundmann, Olav; Musat, Florin
2013-05-01
The short-chain, non-methane hydrocarbons propane and butane can contribute significantly to the carbon and sulfur cycles in marine environments affected by oil or natural gas seepage. In the present study, we enriched and identified novel propane and butane-degrading sulfate reducers from marine oil and gas cold seeps in the Gulf of Mexico and Hydrate Ridge. The enrichment cultures obtained were able to degrade simultaneously propane and butane, but not other gaseous alkanes. They were cold-adapted, showing highest sulfate-reduction rates between 16 and 20 °C. Analysis of 16S rRNA gene libraries, followed by whole-cell hybridizations with sequence-specific oligonucleotide probes showed that each enrichment culture was dominated by a unique phylotype affiliated with the Desulfosarcina-Desulfococcus cluster within the Deltaproteobacteria. These phylotypes formed a distinct phylogenetic cluster of propane and butane degraders, including sequences from environments associated with hydrocarbon seeps. Incubations with (13)C-labeled substrates, hybridizations with sequence-specific probes and nanoSIMS analyses showed that cells of the dominant phylotypes were the first to become enriched in (13)C, demonstrating that they were directly involved in hydrocarbon degradation. Furthermore, using the nanoSIMS data, carbon assimilation rates were calculated for the dominant cells in each enrichment culture.
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Cuyàs, Elisabet; Martin-Castillo, Begoña; Corominas-Faja, Bruna; Massaguer, Anna; Bosch-Barrera, Joaquim; Menendez, Javier A
2015-01-01
Key players in translational regulation such as ribosomes might represent powerful, but hitherto largely unexplored, targets to eliminate drug-refractory cancer stem cells (CSCs). A recent study by the Lisanti group has documented how puromycin, an old antibiotic derived from Streptomyces alboniger that inhibits ribosomal protein translation, can efficiently suppress CSC states in tumorspheres and monolayer cultures. We have used a closely related approach based on Biolog Phenotype Microarrays (PM), which contain tens of lyophilized antimicrobial drugs, to assess the chemosensitivity profiles of breast cancer cell lines enriched for stem cell-like properties. Antibiotics directly targeting active sites of the ribosome including emetine, puromycin and cycloheximide, inhibitors of ribosome biogenesis such as dactinomycin, ribotoxic stress agents such as daunorubicin, and indirect inhibitors of protein synthesis such as acriflavine, had the largest cytotoxic impact against claudin-low and basal-like breast cancer cells. Thus, biologically aggressive, treatment-resistant breast cancer subtypes enriched for stem cell-like properties exhibit exacerbated chemosensitivities to anti-protozoal and anti-bacterial antibiotics targeting protein synthesis. These results suggest that old/existing microbicides might be repurposed not only as new cancer therapeutics, but also might provide the tools and molecular understanding needed to develop second-generation inhibitors of ribosomal translation to eradicate CSC traits in tumor tissues.
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Cuyàs, Elisabet; Martin-Castillo, Begoña; Corominas-Faja, Bruna; Massaguer, Anna; Bosch-Barrera, Joaquim; Menendez, Javier A
2015-01-01
Key players in translational regulation such as ribosomes might represent powerful, but hitherto largely unexplored, targets to eliminate drug-refractory cancer stem cells (CSCs). A recent study by the Lisanti group has documented how puromycin, an old antibiotic derived from Streptomyces alboniger that inhibits ribosomal protein translation, can efficiently suppress CSC states in tumorspheres and monolayer cultures. We have used a closely related approach based on Biolog Phenotype Microarrays (PM), which contain tens of lyophilized antimicrobial drugs, to assess the chemosensitivity profiles of breast cancer cell lines enriched for stem cell-like properties. Antibiotics directly targeting active sites of the ribosome including emetine, puromycin and cycloheximide, inhibitors of ribosome biogenesis such as dactinomycin, ribotoxic stress agents such as daunorubicin, and indirect inhibitors of protein synthesis such as acriflavine, had the largest cytotoxic impact against claudin-low and basal-like breast cancer cells. Thus, biologically aggressive, treatment-resistant breast cancer subtypes enriched for stem cell-like properties exhibit exacerbated chemosensitivities to anti-protozoal and anti-bacterial antibiotics targeting protein synthesis. These results suggest that old/existing microbicides might be repurposed not only as new cancer therapeutics, but also might provide the tools and molecular understanding needed to develop second-generation inhibitors of ribosomal translation to eradicate CSC traits in tumor tissues. PMID:25970790
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Acidification of calf bedding reduces fly development and bacterial abundance.
Calvo, M S; Gerry, A C; McGarvey, J A; Armitage, T L; Mitloehner, F M
2010-03-01
Environmental stressors, such as high fly density, can affect calf well-being. Sodium bisulfate (SBS) is an acidifier that reduces the pH of flooring and bedding, creating a medium that neither bacteria nor immature flies (also known as larvae or maggots) can thrive in. Two experiments were conducted to investigate the application of SBS to a mixture of rice hull calf bedding and calf slurry (BED) to reduce house fly (Musca domestica L.) larval density and the abundance of bacteria. In experiment 1, dish pans containing 1L of BED and 3,000 house fly eggs were treated with SBS at concentrations of 0, 8.9, 17.7, and 26.5g of SBS/0.05m(2) of BED (CON, LOW, MED, and HIGH, respectively), with each SBS concentration applied to 4 individual pans (16 pans total). Reapplication of the same SBS concentrations in each pan occurred 3 times/wk throughout the 23-d trial. Larval house fly survival was significantly reduced in all pans with SBS relative to CON pans, with lowest survival rates in the MED and HIGH pans (99% and 100% reduction, respectively). The mean pH for each treatment was inversely related to the SBS concentration. In experiment 2, pans containing 1L of BED and 3,000 house fly eggs were treated with either 0g of SBS (CON), 8.9g of SBS/0.05m(2) of BED with reapplication of the acidifier 3 times/wk (SB3x), or 8.9g of SBS/0.05m(2) of BED applied only once at 48h before the end of the 8 d-trial (SB48). Larval house fly survival and bacterial concentrations were reduced (90% larval reduction and 68% bacterial reduction) in the SB3x treatment relative to the CON. Mean pH was also reduced in SB3x pans relative to CON or SB48 pans. Overall, acidification of calf BED using the acidifier SBS resulted in a reduction of bacteria and house fly larval survival. This form of fly control might be expected to reduce adult fly production and, therefore, fly-related stress in calves.
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Bahi, Amine
2017-07-03
Previous research from our laboratory has shown that exposure to chronic psychosocial stress increased voluntary ethanol consumption and preference as well as acquisition of ethanol-induced conditioned place preference (CPP) in mice. This study was done to determine whether an enriched environment could have "curative" effects on chronic psychosocial stress-induced ethanol intake and CPP. For this purpose, experimental mice "intruders" were exposed to the chronic subordinate colony (CSC) housing for 19 consecutive days in the presence of an aggressive "resident" mouse. At the end of that period, mice were tested for their anxiety-like behavior using the elevated plus maze (EPM) test then housed in a standard or enriched environment (SE or EE respectively). Anxiety and ethanol-related behaviors were investigated using the open field (OF) test, a standard two-bottle choice drinking paradigm, and the CPP procedure. As expected, CSC exposure increased anxiety-like behavior and reduced weight gain as compared to single housed colony (SHC) controls. In addition, CSC exposure increased voluntary ethanol intake and ethanol-CPP. Interestingly, we found that EE significantly and consistently reduced anxiety and ethanol consumption and preference. However, neither tastants' (saccharin and quinine) intake nor blood ethanol metabolism were affected by EE. Finally, and most importantly, EE reduced the acquisition of CPP induced by 1.5g/kg ethanol. Taken together, these results support the hypothesis that EE can reduce voluntary ethanol intake and ethanol-induced conditioned reward and seems to be one of the strategies to reduce the behavioral deficits and the risk of anxiety-induced alcohol abuse. Copyright © 2017 Elsevier Inc. All rights reserved.
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Drago, Lorenzo; Boot, Willemijn; Dimas, Kostantinos; Malizos, Kostantinos; Hänsch, Gertrud M; Stuyck, Jos; Gawlitta, Debby; Romanò, Carlo L
2014-11-01
Implant-related infections represent one of the most severe complications in orthopaedics. A fast-resorbable, antibacterial-loaded hydrogel may reduce or prevent bacterial colonization and biofilm formation of implanted biomaterials. We asked: (1) Is a fast-resorbable hydrogel able to deliver antibacterial compounds in vitro? (2) Can a hydrogel (alone or antibacterial-loaded) coating on implants reduce bacterial colonization? And (3) is intraoperative coating feasible and resistant to press-fit implant insertion? We tested the ability of Disposable Antibacterial Coating (DAC) hydrogel (Novagenit Srl, Mezzolombardo, Italy) to deliver antibacterial agents using spectrophotometry and a microbiologic assay. Antibacterial and antibiofilm activity were determined by broth microdilution and a crystal violet assay, respectively. Coating resistance to press-fit insertion was tested in rabbit tibias and human femurs. Complete release of all tested antibacterial compounds was observed in less than 96 hours. Bactericidal and antibiofilm effect of DAC hydrogel in combination with various antibacterials was shown in vitro. Approximately 80% of the hydrogel coating was retrieved on the implant after press-fit insertion. Implant coating with an antibacterial-loaded hydrogel reduces bacterial colonization and biofilm formation in vitro. A fast-resorbable, antibacterial-loaded hydrogel coating may help prevent implant-related infections in orthopaedics. However, further validation in animal models and properly controlled human studies is required.
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Holmes, Dawn E; Giloteaux, Ludovic; Williams, Kenneth H; Wrighton, Kelly C; Wilkins, Michael J; Thompson, Courtney A; Roper, Thomas J; Long, Philip E; Lovley, Derek R
2013-07-01
The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.
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Holmes, Dawn E; Giloteaux, Ludovic; Williams, Kenneth H; Wrighton, Kelly C; Wilkins, Michael J; Thompson, Courtney A; Roper, Thomas J; Long, Philip E; Lovley, Derek R
2013-01-01
The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey–predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies. PMID:23446832
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Schreiber, Lars; Holler, Thomas; Knittel, Katrin; Meyerdierks, Anke; Amann, Rudolf
2010-08-01
The anaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor is mediated by consortia of methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Whereas three clades of ANME have been repeatedly studied with respect to phylogeny, key genes and genomic capabilities, little is known about their sulfate-reducing partner. In order to identify the partner of anaerobic methanotrophs of the ANME-2 clade, bacterial 16S rRNA gene libraries were constructed from cultures highly enriched for ANME-2a and ANME-2c in consortia with Deltaproteobacteria of the Desulfosarcina/Desulfococcus group (DSS). Phylogenetic analysis of those and publicly available sequences from AOM sites supported the hypothesis by Knittel and colleagues that the DSS partner belongs to the diverse SEEP-SRB1 cluster. Six subclusters of SEEP-SRB1, SEEP-SRB1a to SEEP-SRB1f, were proposed and specific oligonucleotide probes were designed. Using fluorescence in situ hybridization on samples from six different AOM sites, SEEP-SRB1a was identified as sulfate-reducing partner in up to 95% of total ANME-2 consortia. SEEP-SRB1a cells exhibited a rod-shaped, vibrioid, or coccoid morphology and were found to be associated with subgroups ANME-2a and ANME-2c. Moreover, SEEP-SRB1a was also detected in 8% to 23% of ANME-3 consortia in Haakon Mosby Mud Volcano sediments, previously described to be predominantly associated with SRB of the Desulfobulbus group. SEEP-SRB1a contributed to only 0.3% to 0.7% of all single cells in almost all samples indicating that these bacteria are highly adapted to a symbiotic relationship with ANME-2. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.
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Enriched environment reduces glioma growth through immune and non-immune mechanisms in mice
Garofalo, Stefano; D’Alessandro, Giuseppina; Chece, Giuseppina; Brau, Frederic; Maggi, Laura; Rosa, Alessandro; Porzia, Alessandra; Mainiero, Fabrizio; Esposito, Vincenzo; Lauro, Clotilde; Benigni, Giorgia; Bernardini, Giovanni; Santoni, Angela; Limatola, Cristina
2015-01-01
Mice exposed to standard (SE) or enriched environment (EE) were transplanted with murine or human glioma cells and differences in tumour development were evaluated. We report that EE exposure affects: (i) tumour size, increasing mice survival; (ii) glioma establishment, proliferation and invasion; (iii) microglia/macrophage (M/Mφ) activation; (iv) natural killer (NK) cell infiltration and activation; and (v) cerebral levels of IL-15 and BDNF. Direct infusion of IL-15 or BDNF in the brain of mice transplanted with glioma significantly reduces tumour growth. We demonstrate that brain infusion of IL-15 increases the frequency of NK cell infiltrating the tumour and that NK cell depletion reduces the efficacy of EE and IL-15 on tumour size and of EE on mice survival. BDNF infusion reduces M/Mφ infiltration and CD68 immunoreactivity in tumour mass and reduces glioma migration inhibiting the small G protein RhoA through the truncated TrkB.T1 receptor. These results suggest alternative approaches for glioma treatment. PMID:25818172
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Thermal breeder fuel enrichment zoning
Capossela, Harry J.; Dwyer, Joseph R.; Luce, Robert G.; McCoy, Daniel F.; Merriman, Floyd C.
1992-01-01
A method and apparatus for improving the performance of a thermal breeder reactor having regions of higher than average moderator concentration are disclosed. The fuel modules of the reactor core contain at least two different types of fuel elements, a high enrichment fuel element and a low enrichment fuel element. The two types of fuel elements are arranged in the fuel module with the low enrichment fuel elements located between the high moderator regions and the high enrichment fuel elements. Preferably, shim rods made of a fertile material are provided in selective regions for controlling the reactivity of the reactor by movement of the shim rods into and out of the reactor core. The moderation of neutrons adjacent the high enrichment fuel elements is preferably minimized as by reducing the spacing of the high enrichment fuel elements and/or using a moderator having a reduced moderating effect.
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Swept Away: Resuspension of Bacterial Mats Regulates Benthic-Pelagic Exchange of Sulfur
NASA Astrophysics Data System (ADS)
Grant, Jonathan; Bathmann, Ulrich V.
1987-06-01
Filaments and extracellular material from colorless sulfur bacteria (Beggiatoa spp.) form extensive white sulfur mats on surface sediments of coastal, oceanic, and even deep-sea environments. These chemoautotrophic bacteria oxidize soluble reduced sulfur compounds and deposit elemental sulfur, enriching the sulfur content of surface sediment fivefold over that of deeper sediments. Laboratory flume experiments with Beggiatoa mats from an intertidal sandflat (Nova Scotia) demonstrated that even slight erosion of sediment causes a flux of 160 millimoles of sulfur per square meter per hour, two orders of magnitude greater than the flux produced by sulfur transformations involving either sulfate reduction or sulfide oxidation by benthic bacteria. These experiments indicate that resuspension of sulfur bacterial mats by waves and currents is a rapid mechanism by which sediment sulfur is recycled to the water column. Benthic communities thus lose an important storage intermediate for reduced sulfur as well as a high-quality bacterial food source for benthic grazers.
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Liu, Juan; Xiang, Yanbing; Zhang, Zhiming; Ling, Wanting; Gao, Yanzheng
2017-06-01
Colonization by polycyclic aromatic hydrocarbon (PAH)-degrading endophytic bacteria (PAHDEB) can reduce the PAH contamination risk in plant. However, little information is available on the impact of PAHDEB colonization on the endophytic bacterial community of inner plant tissues. A phenanthrene-degrading endophytic bacterium (PDEB), Massilia sp. Pn2, was inoculated onto the roots of wheat and subjected to greenhouse container experiments. The endophytic bacterial community structure in wheat was investigated using high-throughput sequencing technology. The majority of endophytic bacteria in wheat were Proteobacteria, and the dominant genus was Pseudomonas. Phenanthrene contamination clearly increased the diversity of endophytic bacteria in wheat. The cultivable endophytic bacteria counts in wheat decreased with increasing the level of phenanthrene contamination; the endophytic bacterial community structure changed correspondingly, and the bacterial richness first increased and then decreased. Inoculation of strain Pn2 reduced the phenanthrene contamination in wheat, enlarged the biomass of wheat roots, changed the bacterial community structure and enhanced the cell counts, diversity and richness of endophytic bacteria in phenanthrene-contaminated wheat in a contamination level-dependent manner. The findings of this investigation provide insight into the responses of endophytic bacterial community in plant to external PAH contamination and PAHDEB colonization.
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Eronen-Rasimus, Eeva; Kaartokallio, Hermanni; Lyra, Christina; Autio, Riitta; Kuosa, Harri; Dieckmann, Gerhard S; Thomas, David N
2014-02-01
The structure of sea-ice bacterial communities is frequently different from that in seawater. Bacterial entrainment in sea ice has been studied with traditional microbiological, bacterial abundance, and bacterial production methods. However, the dynamics of the changes in bacterial communities during the transition from open water to frozen sea ice is largely unknown. Given previous evidence that the nutritional status of the parent water may affect bacterial communities during ice formation, bacterial succession was studied in under ice water and sea ice in two series of mesocosms: the first containing seawater from the North Sea and the second containing seawater enriched with algal-derived dissolved organic matter (DOM). The composition and dynamics of bacterial communities were investigated with terminal restriction fragment length polymorphism (T-RFLP), and cloning alongside bacterial production (thymidine and leucine uptake) and abundance measurements (measured by flow cytometry). Enriched and active sea-ice bacterial communities developed in ice formed in both unenriched and DOM-enriched seawater (0-6 days). γ-Proteobacteria dominated in the DOM-enriched samples, indicative of their capability for opportunistic growth in sea ice. The bacterial communities in the unenriched waters and ice consisted of the classes Flavobacteria, α- and γ-Proteobacteria, which are frequently found in natural sea ice in polar regions. Furthermore, the results indicate that seawater bacterial communities are able to adapt rapidly to sudden environmental changes when facing considerable physicochemical stress such as the changes in temperature, salinity, nutrient status, and organic matter supply during ice formation. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
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Uranium reduction and resistance to reoxidation under iron-reducing and sulfate-reducing conditions.
Boonchayaanant, Benjaporn; Nayak, Dipti; Du, Xin; Criddle, Craig S
2009-10-01
Oxidation and mobilization of microbially-generated U(IV) is of great concern for in situ uranium bioremediation. This study investigated the reoxidation of uranium by oxygen and nitrate in a sulfate-reducing enrichment and an iron-reducing enrichment derived from sediment and groundwater from the Field Research Center in Oak Ridge, Tennessee. Both enrichments were capable of reducing U(VI) rapidly. 16S rRNA gene clone libraries of the two enrichments revealed that Desulfovibrio spp. are dominant in the sulfate-reducing enrichment, and Clostridium spp. are dominant in the iron-reducing enrichment. In both the sulfate-reducing enrichment and the iron-reducing enrichment, oxygen reoxidized the previously reduced uranium but to a lesser extent in the iron-reducing enrichment. Moreover, in the iron-reducing enrichment, the reoxidized U(VI) was eventually re-reduced to its previous level. In both, the sulfate-reducing enrichment and the iron-reducing enrichment, uranium reoxidation did not occur in the presence of nitrate. The results indicate that the Clostridium-dominated iron-reducing communities created conditions that were more favorable for uranium stability with respect to reoxidation despite the fact that fewer electron equivalents were added to these systems. The likely reason is that more of the added electrons are present in a form that can reduce oxygen to water and U(VI) back to U(IV).
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Prado Lima, Mariza G; Schimidt, Helen L; Garcia, Alexandre; Daré, Letícia R; Carpes, Felipe P; Izquierdo, Ivan; Mello-Carpes, Pâmela B
2018-03-06
Recently, nongenetic animal models to study the onset and development of Alzheimer's disease (AD) have appeared, such as the intrahippocampal infusion of peptides present in Alzheimer amyloid plaques [i.e., amyloid-β (Aβ)]. Nonpharmacological approaches to AD treatment also have been advanced recently, which involve combinations of behavioral interventions whose specific effects are often difficult to determine. Here we isolate the neuroprotective effects of three of these interventions-environmental enrichment (EE), anaerobic physical exercise (AnPE), and social enrichment (SE)-on Aβ-induced oxidative stress and on impairments in learning and memory induced by Aβ. Wistar rats were submitted to 8 wk of EE, AnPE, or SE, followed by Aβ infusion in the dorsal hippocampus. Short-term memory (STM) and long-term memory (LTM) of object recognition (OR) and social recognition (SR) were evaluated. Biochemical assays determined hippocampal oxidative status: reactive oxygen species, lipid peroxidation by thiobarbituric acid reactive substance (TBARS) test, and total antioxidant capacity by ferric reducing/antioxidant power (FRAP), as well as acetylcholinesterase activity. Aβ infusion resulted in memory deficits and hippocampal oxidative damage. EE and AnPE prevented all memory deficits (STM and LTM of OR and SR) and lipid peroxidation (i.e., TBARS). SE prevented only the SR memory deficits and the decrease of total antioxidant capacity decrease (i.e., FRAP). Traditionally, findings obtained with EE protocols do not allow discrimination of the roles of the three individual factors involved. Here we demonstrate that EE and physical exercise have better neuroprotective effects than SE in memory deficits related to Aβ neurotoxicity in the AD model tested.
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Food-safe modification of stainless steel food processing surfaces to reduce bacterial biofilms.
Awad, Tarek Samir; Asker, Dalal; Hatton, Benjamin D
2018-06-11
Biofilm formation on stainless steel (SS) surfaces of food processing plants, leading to foodborne illness outbreaks, is enabled by the attachment and confinement within microscale cavities of surface roughness (grooves, scratches). We report Foodsafe Oil-based Slippery Coatings (FOSCs) for food processing surfaces that suppress bacterial adherence and biofilm formation by trapping residual oil lubricant within these surface cavities to block microbial growth. SS surfaces were chemically functionalized with alkylphosphonic acid to preferentially wet a layer of food grade oil. FOSCs reduced the effective surface roughness, the adhesion of organic food residue, and bacteria. FOSCs significantly reduced Pseudomonas aeruginosa biofilm formation on standard roughness SS-316 by 5 log CFU cm-2, and by 3 log CFU cm-2 for mirror-finished SS. FOSCs also enhanced surface cleanability, which we measured by bacterial counts after conventional detergent cleaning. Importantly, both SS grades maintained their anti-biofilm activity after erosion of the oil layer by surface wear with glass beads, which suggests there is a residual volume of oil that remains to block surface cavity defects. These results indicate the potential of such low-cost, scalable approaches to enhance the cleanability of SS food processing surfaces and improve food safety by reducing biofilm growth.
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Kato, Souichiro; Chino, Kanako; Kamimura, Naofumi; Masai, Eiji; Yumoto, Isao; Kamagata, Yoichi
2015-09-24
Anaerobic degradation of lignin-derived aromatics is an important metabolism for carbon and nutrient cycles in soil environments. Although there are some studies on degradation of lignin-derived aromatics by nitrate- and sulfate-reducing bacteria, knowledge on their degradation under methanogenic conditions are quite limited. In this study, methanogenic microbial communities were enriched from rice paddy field soil with lignin-derived methoxylated monoaromatics (vanillate and syringate) and their degradation intermediates (protocatechuate, catechol, and gallate) as the sole carbon and energy sources. Archaeal community analysis disclosed that both aceticlastic (Methanosarcina sp.) and hydrogenotrophic (Methanoculleus sp. and Methanocella sp.) methanogens dominated in all of the enrichments. Bacterial community analysis revealed the dominance of acetogenic bacteria (Sporomusa spp.) only in the enrichments on the methoxylated aromatics, suggesting that Sporomusa spp. initially convert vanillate and syringate into protocatechuate and gallate, respectively, with acetogenesis via O-demethylation. As the putative ring-cleavage microbes, bacteria within the phylum Firmicutes were dominantly detected from all of the enrichments, while the dominant phylotypes were not identical between enrichments on vanillate/protocatechuate/catechol (family Peptococcaceae bacteria) and on syringate/gallate (family Ruminococcaceae bacteria). This study demonstrates the importance of cooperation among acetogens, ring-cleaving fermenters/syntrophs and aceticlastic/hydrogenotrophic methanogens for degradation of lignin-derived aromatics under methanogenic conditions.
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Kato, Souichiro; Chino, Kanako; Kamimura, Naofumi; Masai, Eiji; Yumoto, Isao; Kamagata, Yoichi
2015-01-01
Anaerobic degradation of lignin-derived aromatics is an important metabolism for carbon and nutrient cycles in soil environments. Although there are some studies on degradation of lignin-derived aromatics by nitrate- and sulfate-reducing bacteria, knowledge on their degradation under methanogenic conditions are quite limited. In this study, methanogenic microbial communities were enriched from rice paddy field soil with lignin-derived methoxylated monoaromatics (vanillate and syringate) and their degradation intermediates (protocatechuate, catechol, and gallate) as the sole carbon and energy sources. Archaeal community analysis disclosed that both aceticlastic (Methanosarcina sp.) and hydrogenotrophic (Methanoculleus sp. and Methanocella sp.) methanogens dominated in all of the enrichments. Bacterial community analysis revealed the dominance of acetogenic bacteria (Sporomusa spp.) only in the enrichments on the methoxylated aromatics, suggesting that Sporomusa spp. initially convert vanillate and syringate into protocatechuate and gallate, respectively, with acetogenesis via O-demethylation. As the putative ring-cleavage microbes, bacteria within the phylum Firmicutes were dominantly detected from all of the enrichments, while the dominant phylotypes were not identical between enrichments on vanillate/protocatechuate/catechol (family Peptococcaceae bacteria) and on syringate/gallate (family Ruminococcaceae bacteria). This study demonstrates the importance of cooperation among acetogens, ring-cleaving fermenters/syntrophs and aceticlastic/hydrogenotrophic methanogens for degradation of lignin-derived aromatics under methanogenic conditions. PMID:26399549
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Successful enrichment of the ubiquitous freshwater acI Actinobacteria.
Garcia, Sarahi L; McMahon, Katherine D; Grossart, Hans-Peter; Warnecke, Falk
2014-02-01
Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for > 50% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acI Actinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Efficacy of a mouthrinse based on hydroxyapatite to reduce initial bacterial colonisation in situ.
Kensche, A; Holder, C; Basche, S; Tahan, N; Hannig, C; Hannig, M
2017-08-01
The present in situ - investigation aimed to specify the impact of pure hydroxyapatite microclusters on initial bioadhesion and bacterial colonization at the tooth surface. Pellicle formation was carried out in situ on bovine enamel slabs (9 subjects). After 1min of pellicle formation rinses with 8ml of hydroxyapatite (HA) microclusters (5%) in bidestilled water or chlorhexidine 0.2% were performed. As negative control no rinse was adopted. In situ biofilm formation was promoted by the intraoral slab exposure for 8h overnight. Afterwards initial bacterial adhesion was quantified by DAPI staining and bacterial viability was determined in vivo/in vitro by live/dead-staining (BacLight). SEM analysis evaluated the efficacy of the mouthrinse to accumulate hydroxyapatite microclusters at the specimens' surface and spit-out samples of the testsolution were investigated by TEM. Compared to the control (2.36×10 6 ±2.01×10 6 bacteria/cm 2 ), significantly reduced amounts of adherent bacteria were detected on specimens rinsed with chlorhexidine 0.2% (8.73×10 4 ±1.37×10 5 bacteria/cm 2 ) and likewise after rinses with the hydroxyapatite testsolution (2.08×10 5 ±2.85×10 5 bacteria/cm 2 , p<0.001). No demonstrable effect of HA-particles on Streptococcus mutans viability could be shown. SEM analysis confirmed the temporary adsorption of hydroxyapatite microclusters at the tooth surface. Adhesive interactions of HA-particles with oral bacteria were shown by TEM. Hydroxyapatite microclusters reduced initial bacterial adhesion to enamel in situ considerably and could therefore sensibly supplement current approaches in dental prophylaxis. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Sheng, Ping; Huang, Jiangli; Zhang, Zhihong; Wang, Dongsheng; Tian, Xiaojuan; Ding, Jiannan
2016-09-30
Degradation of rice straw by cooperative microbial activities is at present the most attractive alternative to fuels and provides a basis for biomass conversion. The use of microbial consortia in the biodegradation of lignocelluloses could reduce problems such as incomplete synergistic enzymes, end-product inhibition, and so on. In this study, a cellulolytic microbial consortium was enriched from the hindgut of Holotrichia parallela larvae via continuous subcultivation (20 subcultures in total) under static conditions. The degradation ratio for rice straw was about 83.1% after three days of cultivation, indicating its strong cellulolytic activity. The diversity analysis results showed that the bacterial diversity and richness decreased during the consortium enrichment process, and the consortium enrichment process could lead to a significant enrichment of phyla Proteobacteria and Spirochaetes, classes Clostridia, Epsilonproteobacteria, and Betaproteobacteria, and genera Arcobacter , Treponema , Comamonas , and Clostridium . Some of these are well known as typical cellulolytic and hemicellulolytic microorganisms. Our results revealed that the microbial consortium identified herein is a potential candidate for use in the degradation of waste lignocellulosic biomass and further highlights the hindgut of the larvae as a reservoir of extensive and specific cellulolytic and hemicellulolytic microbes.
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Krieger, Joseph R; Kourtev, Peter S
2012-03-01
Pitcher plants have been widely used in ecological studies of food webs; however, their bacterial communities are poorly characterized. Pitchers of Sarracenia purpurea contain several distinct sub-habitats, namely the bottom sediment, the liquid, and the internal pitcher wall. We hypothesized that those three sub-habitats within pitcher plants are inhabited by distinct bacterial populations. We used denaturing gradient gel electrophoresis and 16S rRNA gene sequencing to characterize bacterial populations in pitchers from three bogs. DGGE and sequencing revealed that in any given pitcher, the three sub-habitats contain significantly different bacterial populations. However, there was significant variability between bacterial populations inhabiting the same type of habitat in different pitchers, even at the same site. Therefore, no consistent set of bacterial populations was enriched in any of the three sub-habitats. All sub-habitats appeared to be dominated by alpha- and betaproteobacteria in differing proportions. In addition, sequences from the Bacteroidetes and Firmicutes were obtained from all three sub-habitats. We conclude that container aquatic habitats such as the pitchers of S. purpurea possess a very high bacterial diversity, with many unique bacterial populations enriched in individual pitchers. Within an individual pitcher, populations of certain bacterial families may be enriched in one of the three studied sub-habitats. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
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Distributions of Bacterial Generalists among the Guts of Birds ...
Complex distributions of bacterial taxa within diverse animal microbiomes have inspired ecological and biogeographical approaches to revealing the functions of taxa that may be most important for host health. Of particular interest are bacteria that find many diverse habitats suitable for growth and remain competitive amongst finely-tuned host specialists. While previous work has focused on identifying these specialists, here our aims were to 1) identify generalist taxa, 2) identify taxonomic clades with enriched generalist diversity, and 3) describe the distribution of the largest generalist groups among hosts. We analyzed existing bacterial rRNA tag-sequencing data (v6) available on VAMPs (vamps.mbl.edu) from the microbiomes of 12 host species (106 samples total) spanning birds, mammals, and fish for generalist taxa using the CLAM test. OTUs with approximately equal abundance and a minimum of 10 reads in two hosts were classified as generalists. Generalist OTUs (n=2,982) were found in all hosts tested. Bacterial families Alcaligenaceae and Burkholderiaceae were significantly enriched with generalists OTUs compared to other families. Bacterial families such as Bacteroidaceae and Lachnospiraceae significantly lacked generalists OTUs compared to other families. Enterobacteriaceae, Peptostreptococcaceae, and Erysipelotrichaceae more so than other bacterial families were widely distributed and abundant in birds, mammals, and fish suggesting that these taxa mainta
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Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Zhang, Wei-Peng; Bajic, Vladimir
2014-01-01
ABSTRACT Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. PMID:25370493
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Holmes, Dawn; Giloteaux, L.; Williams, Kenneth H.
2013-07-28
The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well-recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, acetate amendments initially promoted the growth of metal-reducing Geobacter species followed by the growthmore » of sulfate-reducers, as previously observed. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater prior to the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the amoeboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity, and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.« less
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Sabuncuoglu, Mehmet Zafer; Kismet, Kemal; Kilicoglu, Sibel Serin; Kilicoglu, Bulent; Erel, Serap; Muratoglu, Sabahattin; Sunay, Asli Elif; Erdemli, Esra; Akkus, Mehmet Ali
2007-01-01
AIM: To investigate the effects of propolis on bacterial translocation and ultrastructure of intestinal morphology in experimental obstructive jaundice. METHODS: Thirty Wistar-Albino male rats were randomly divided into three groups, each including 10 animals: groupI, sham-operated; group II, ligation and division of the common bile duct (BDL); group III, BDL followed by oral supplementation of propolis 100 mg/kg per day. Liver, blood, spleen, mesenteric lymph nodes, and ileal samples were taken for microbiological, light and transmission electron microscopic examination on postoperative 7th d after sacrification. RESULTS: The mean number of villi per centimeter and mean mucosal height of the propolis group were significantly different in the BDL group (P = 0.001 and 0.012, respectively). The electron microscopic changes were also different between these groups. Sham and BDL + propolis groups had similar incidence of bacterial translocation (BT). The BDL group had significantly higher rates of BT as compared with sham and BDL + propolis groups. BT was predominantly detected in MLNs and the most commonly isolated bacteria was Escherichia coli. CONCLUSION: Propolis showed a significant protective effect on ileal mucosa and reduced bacterial translocation in the experimental obstructive jaundice model. Further studies should be carried out to explain the mechanisms of these effects. PMID:17876893
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2014-01-01
Background The nuclear protein high-mobility group box 1 (HMGB1) is a key trigger for the inflammatory reaction during liver ischemia reperfusion injury (IRI). Hydrogen treatment was recently associated with down-regulation of the expression of HMGB1 and pro-inflammatory cytokines during sepsis and myocardial IRI, but it is not known whether hydrogen has an effect on HMGB1 in liver IRI. Methods A rat model of 60 minutes 70% partial liver ischemia reperfusion injury was used. Hydrogen enriched saline (2.5, 5 or 10 ml/kg) was injected intraperitoneally 10 minutes before hepatic reperfusion. Liver injury was assessed by serum alanine aminotransferase (ALT) enzyme levels and histological changes. We also measured malondialdehyde (MDA), hydroxynonenal (HNE) and 8-hydroxy-guanosine (8-OH-G) levels as markers of the peroxidation injury induced by reactive oxygen species (ROS). In addition, pro-inflammatory cytokines including TNF-α and IL-6, and high mobility group box B1 protein (HMGB1) were measured as markers of post ischemia-reperfusion inflammation. Results Hydrogen enriched saline treatment significantly attenuated the severity of liver injury induced by ischemia-reperfusion. The treatment group showed reduced serum ALT activity and markers of lipid peroxidation and post ischemia reperfusion histological changes were reduced. Hydrogen enriched saline treatment inhibited HMGB1 expression and release, reflecting a reduced local and systemic inflammatory response to hepatic ischemia reperfusion. Conclusion These results suggest that, in our model, hydrogen enriched saline treatment is protective against liver ischemia-reperfusion injury. This effect may be mediated by both the anti-oxidative and anti-inflammatory effects of the solution. PMID:24410860
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Forbes, Sarah; Cowley, Nicola; Mistry, Hitesh; Amézquita, Alejandro
2017-01-01
ABSTRACT The current investigation aimed to generate data to inform the development of risk assessments of biocide usage. Stabilized domestic drain biofilm microcosms were exposed daily over 6 months to increasing concentrations (0.01% to 1%) of the biocide benzalkonium chloride (BAC) in a simple aqueous solution (BAC-s) or in a complex formulation (BAC-f) representative of a domestic cleaning agent. Biofilms were analyzed by culture, differentiating by bacterial functional group and by BAC or antibiotic susceptibility. Bacterial isolates were identified by 16S rRNA sequencing, and changes in biofilm composition were assessed by high-throughput sequencing. Exposure to BAC-f resulted in significantly larger reductions in levels of viable bacteria than exposure to BAC-s, while bacterial diversity greatly decreased during exposure to both BAC-s and BAC-f, as evidenced by sequencing and viable counts. Increases in the abundance of bacteria exhibiting reduced antibiotic or BAC susceptibility following exposure to BAC at 0.1% were significantly greater for BAC-s than BAC-f. Bacteria with reduced BAC and antibiotic susceptibility were generally suppressed by higher BAC concentrations, and formulation significantly enhanced this effect. Significant decreases in the antimicrobial susceptibility of bacteria isolated from the systems before and after long-term BAC exposure were not detected. In summary, dose-dependent suppression of bacterial viability by BAC was enhanced by formulation. Biocide exposure decreased bacterial diversity and transiently enriched populations of organisms with lower antimicrobial susceptibility, and the effects were subsequently suppressed by exposure to 1% BAC-f, the concentration most closely reflecting deployment in formulated products. IMPORTANCE Assessment of the risks of biocide use has been based mainly on the exposure of axenic cultures of bacteria to biocides in simple aqueous solutions. The current investigation aimed to assess the
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Bioretention column study of bacteria community response to salt-enriched artificial stormwater.
Endreny, Theodore; Burke, David J; Burchhardt, Kathleen M; Fabian, Mark W; Kretzer, Annette M
2012-01-01
Cold climate cities with green infrastructure depend on soil bacteria to remove nutrients from road salt-enriched stormwater. Our research examined how bacterial communities in laboratory columns containing bioretention media responded to varying concentrations of salt exposure from artificial stormwater and the effect of bacteria and salt on column effluent concentrations. We used a factorial design with two bacteria treatments (sterile, nonsterile) and three salt concentrations (935, 315, and 80 ppm), including a deionized water control. Columns were repeatedly saturated with stormwater or deionized and then drained throughout 5 wk, with the last week of effluent analyzed for water chemistry. To examine bacterial communities, we extracted DNA from column bioretention media at time 0 and at week 5 and used molecular profiling techniques to examine bacterial community changes. We found that bacterial community taxa changed between time 0 and week 5 and that there was significant separation between taxa among salt treatments. Bacteria evenness was significantly affected by stormwater treatment, but there were no differences in bacterial richness or diversity. Soil bacteria and salt treatments had a significant effect on the effluent concentration of NO, PO, Cu, Pb, and Zn based on ANOVA tests. The presence of bacteria reduced effluent NO and Zn concentrations by as much as 150 and 25%, respectively, while having a mixed effect on effluent PO concentrations. Our results demonstrate how stormwater can affect bacterial communities and how the presence of soil bacteria improves pollutant removal by green infrastructure. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.
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Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi
2015-11-01
Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.
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Margot, H; Tasara, T; Zwietering, M H; Joosten, H; Stephan, R
2016-09-02
Sprouted seeds have been implicated in a number of serious outbreaks caused by Salmonella and Shiga toxin-producing Escherichia coli. Sprouts pose a very complex challenge to bacterial pathogen enrichment and detection since they naturally contain high levels of background microflora including members of the Enterobacteriaceae. As such, the currently used method cannot ensure reliable detection of STEC in sprouts. In this study, we compared different media for the enrichment of Enterobacteriaceae in their ability to promote the growth of stressed STEC at 37°C and 42°C. Mung bean sprouts were spiked with low levels of STEC and their growth was recorded over time. In addition, the microbiome of mung bean sprouts was analysed before and after enrichment. Our results indicate that the growth of dry-stressed STEC is comparable in all of the tested enrichment media except for mTSB+Novobiocin and not influenced by the incubation temperature. Low levels of STEC spiked into the sprouts resuspended in media only grew to levels of around 4logcfu/ml during enrichment, which could reduce the probability of detection. Proteobacteria was the dominant phylum detected within the microbiome of non-enriched mung bean sprouts. During enrichment in EE-broth, Proteobacteria remained the most abundant phylum. In contrast, during enrichment in BPW the relative abundance of Proteobacteria decreased whereas Firmicutes increased when compared to the non-enriched mung bean sprout microbiome. The microbiome composition was not significantly influenced by the incubation temperature during enrichment in both BPW and EE-broth. This is the first study to examine the microbiome on sprouted mung bean seeds during BPW and EE enrichment and relates the bacterial community composition changes to the enrichment of pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.
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Lin, L-H; Tsai, C-Y; Hung, M-H; Fang, Y-T; Ling, Q-D
2011-09-01
Although routine bacterial culture is the traditional reference standard method for the detection of Salmonella infection in children with diarrhoea, it is a time-consuming procedure that usually only gives results after 3-4 days. Some molecular detection methods can improve the turn-around time to within 24 h, but these methods are not applied directly from stool or rectal swab specimens as routine diagnostic methods for the detection of gastrointestinal pathogens. In this study, we tested the feasibility of a bacterial enrichment culture-based real-time PCR assay method for detecting and screening for diarrhoea in children caused by Salmonella. Our results showed that the minimum real-time PCR assay time required to detect enriched bacterial culture from a swab was 3 h. In all children with suspected Salmonella diarrhoea, the enrichment culture-based real-time PCR achieved 85.4% sensitivity and 98.1% specificity, as compared with the 53.7% sensitivity and 100% specificity of detection with the routine bacterial culture method. We suggest that rectal swab sampling followed by enrichment culture-based real-time PCR is suitable as a rapid method for detecting and screening for Salmonella in paediatric patients. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.
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Coupling Bacterial Activity Measurements with Cell Sorting by Flow Cytometry.
Servais; Courties; Lebaron; Troussellier
1999-08-01
> Abstract A new procedure to investigate the relationship between bacterial cell size and activity at the cellular level has been developed; it is based on the coupling of radioactive labeling of bacterial cells and cell sorting by flow cytometry after SYTO 13 staining. Before sorting, bacterial cells were incubated in the presence of tritiated leucine using a procedure similar to that used for measuring bacterial production by leucine incorporation and then stained with SYTO 13. Subpopulations of bacterial cells were sorted according to their average right-angle light scatter (RALS) and fluorescence. Average RALS was shown to be significantly related to the average biovolume. Experiments were performed on samples collected at different times in a Mediterranean seawater mesocosm enriched with nitrogen and phosphorus. At four sampling times, bacteria were sorted in two subpopulations (cells smaller and larger than 0.25 µm(3)). The results indicate that, at each sampling time, the growth rate of larger cells was higher than that of smaller cells. In order to confirm this tendency, cell sorting was performed on six subpopulations differing in average biovolume during the mesocosm follow-up. A clear increase of the bacterial growth rates was observed with increasing cell size for the conditions met in this enriched mesocosm.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p180.html
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Grissell, Terry V; Chang, Anne B; Gibson, Peter G
2007-04-01
Neuro-immune interactions are increasingly relevant to human health and disease. The neuropeptide Substance P also has antibacterial activity and bears similarities to the innate immune antibacterial defensins. This suggests possible co-regulation of neuropeptide and innate immune mediators. In this study, non-bronchoscopic bronchoalveolar lavage (BAL) was performed on 69 children. BAL was examined for cellular profile, microbiology (bacteria, virus) and gene expression for TLRs 2, 3, 4; chemokine receptors (CCR3, CCR5, CXCR1); neurotrophins and neurokinin genes (TAC1, TAC3, CGRP, NGF). In children with bacterial colonization (n=10) there was an airway inflammatory response with increased BAL neutrophils, IL-8 protein, and CXCR1 expression. Substance P (TAC1) and TLR4 RNA expression were reduced in children with bacterial colonization. TLR3 mRNA was increased in 7.2% (n=5) children with rhinovirus, and there was a non-significant trend to increased TLR2. There is evidence for co-regulation of neurokinin (TAC1) and TLR4 gene expression in airway cells from children with airway bacterial colonization and their reduced expression may be associated with an impaired bacterial clearance. (c) 2007 Wiley-Liss, Inc.
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Todd, Timothy C.; Blair, John M.; Herman, Michael A.
2013-01-01
Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs) experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion). The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have important
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Adams, Aaron S; Aylward, Frank O; Adams, Sandye M; Erbilgin, Nadir; Aukema, Brian H; Currie, Cameron R; Suen, Garret; Raffa, Kenneth F
2013-06-01
The mountain pine beetle, Dendroctonus ponderosae, is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability of D. ponderosae to overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated with D. ponderosae beetles and their galleries from their historical host, Pinus contorta, and their more recent host, hybrid P. contorta-Pinus banksiana. We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the genera Pseudomonas, Rahnella, Serratia, and Burkholderia, and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment.
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Clark, Neil R.; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D.; Jones, Matthew R.; Ma’ayan, Avi
2016-01-01
Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community. PMID:26848405
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Drought and host selection influence bacterial community dynamics in the grass root microbiome
Naylor, Dan; DeGraaf, Stephanie; Purdom, Elizabeth; Coleman-Derr, Devin
2017-01-01
Root endophytes have been shown to have important roles in determining host fitness under periods of drought stress, and yet the effect of drought on the broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles of bacterial communities associated with drought-treated root and rhizosphere tissues of 18 species of plants with varying degrees of drought tolerance belonging to the Poaceae family, including important crop plants. Through 16S rRNA gene profiling across two distinct watering regimes and two developmental time points, we demonstrate that there is a strong correlation between host phylogenetic distance and the microbiome dissimilarity within root tissues, and that drought weakens this correlation by inducing conserved shifts in bacterial community composition. We identify a significant enrichment in a wide variety of Actinobacteria during drought within the roots of all hosts, and demonstrate that this enrichment is higher within the root than it is in the surrounding environments. Furthermore, we show that this observed enrichment is the result of an absolute increase in Actinobacterial abundance and that previously hypothesized mechanisms for observed enrichments in Actinobacteria in drought-treated soils are unlikely to fully account for the phenomena observed here within the plant root. PMID:28753209
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Drought and host selection influence bacterial community dynamics in the grass root microbiome.
Naylor, Dan; DeGraaf, Stephanie; Purdom, Elizabeth; Coleman-Derr, Devin
2017-12-01
Root endophytes have been shown to have important roles in determining host fitness under periods of drought stress, and yet the effect of drought on the broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles of bacterial communities associated with drought-treated root and rhizosphere tissues of 18 species of plants with varying degrees of drought tolerance belonging to the Poaceae family, including important crop plants. Through 16S rRNA gene profiling across two distinct watering regimes and two developmental time points, we demonstrate that there is a strong correlation between host phylogenetic distance and the microbiome dissimilarity within root tissues, and that drought weakens this correlation by inducing conserved shifts in bacterial community composition. We identify a significant enrichment in a wide variety of Actinobacteria during drought within the roots of all hosts, and demonstrate that this enrichment is higher within the root than it is in the surrounding environments. Furthermore, we show that this observed enrichment is the result of an absolute increase in Actinobacterial abundance and that previously hypothesized mechanisms for observed enrichments in Actinobacteria in drought-treated soils are unlikely to fully account for the phenomena observed here within the plant root.
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Chave, Marie; Crozilhac, Patrice; Deberdt, Péninna; Plouznikoff, Katia; Declerck, Stéphane
2017-10-01
Bacterial wilt caused by Ralstonia solanacearum is one of the world's most important soil-borne plant diseases. In Martinique, French West Indies, a highly virulent new pathogenic variant of this bacterium (phylotype IIB/4NPB) severely impacts tomato production. Here we report on the effect of R. solanacearum CFBP 6783, classified in phytotype IIB/4NPB, on tomato plantlets grown under strict in vitro culture conditions in the presence or absence of the arbuscular mycorrhizal fungus Rhizophagus irregularis MUCL 41833. A mycelium donor plant (i.e. Crotalaria spectabilis) was used for rapid, uniform mycorrhization of tomato plantlets that were subsequently infected by the bacterium. Bacterial wilt was significantly delayed and the incidence of the disease consequently reduced in the mycorrhizal tomato plantlets. Conversely, R. solanacearum did not affect root colonization by the AMF within the 16 days of the experiment. These results suggested that the mycorrhizal fungus was able to reduce bacterial wilt symptoms, probably by eliciting defence mechanisms in the plant.
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Biodegradation of di-n-butyl phthalate by bacterial consortium LV-1 enriched from river sludge
Li, Fangfang; Ruan, Xinling; Song, Jian; Lv, Lv; Chai, Liyuan; Yang, Zhihui; Luo, Lin
2017-01-01
A stable bacterial consortium (LV-1) capable of degrading di-n-butyl phthalate (DBP) was enriched from river sludge. Community analysis revealed that the main families of LV-1 are Brucellaceae (62.78%) and Sinobacteraceae (14.83%), and the main genera of LV-1 are Brucella spp. (62.78%) and Sinobacter spp. (14.83%). The optimal pH and temperature for LV-1 to degrade DBP were pH 6.0 and 30°C, respectively. Inoculum size influenced the degradation ratio when the incubation time was < 24 h. The initial concentration of DBP also influenced the degradation rates of DBP by LV-1, and the degradation rates ranged from 69.0–775.0 mg/l/d in the first 24 h. Degradation of DBP was best fitted by first-order kinetics when the initial concentration was < 300 mg/l. In addition, Cd2+, Cr6+, and Zn2+ inhibited DBP degradation by LV-1 at all considered concentrations, but low concentrations of Pb2+, Cu2+, and Mn2+ enhanced DBP degradation. The main intermediates (mono-ethyl phthalate [MEP], mono-butyl phthalate [MBP], and phthalic acid [PA]) were identified in the DBP degradation process, thus a new biochemical pathway of DBP degradation is proposed. Furthermore, LV-1 also degraded other phthalates with shorter ester chains (DMP, DEP, and PA). PMID:28542471
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NASA Astrophysics Data System (ADS)
Han, R.; Zhang, L.; Fu, B.; Liu, H.
2014-12-01
Synthetic gases are usually generated from either cellulosic agricultural waste combustion or industrial release and could be subsequently transformed into acetate, ethanol, and/or butyrate by homoacetogenic bacteria, which commonly possess reductive acetyl-CoA synthesis pathway. Homoacetogen-based syngas fermentation technology provides an alternative solution to link greenhouse gas emission control and cellulosic solid waste treatment with biofuels production. The objective of our current project is to hunt for homoacetogens with capabilities of highly efficiently converting syngases to chemical solvents. In this study, we evaluated homoacetogens population dynamics during enrichments and pinpointed dominant homoacetogens representing diverse ecosystems enriched by different substrates. We enriched homoacetogens from four different samples including waste activate sludge, freshwater sediment, anaerobic methanogenic sludge, and cow manure using H2/CO2 (4:1) or formate as substrate for homoacetogen enrichment. Along with the formyltetrahydrofolate synthetase (FTHFS) gene (fhs gene)-specific real time qPCR assay and Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis, 16S rRNA based 454 high-throughput pyrosequencing was applied to reveal the population dynamic and community structure during enrichment from different origins. Enrichment of homoacetogenic populations coincided with accumulations of short chain fatty acids such as acetate and butyrate. 454 high-throughput pyrosequencing revealed Firmicutes and Spirochaetes populations became dominant while the overall microbial diversity decreased after enrichment. The most abundant sequences among the four origins belonged to the following phyla: Firmicutes, Spirochaetes, Proteobacteria, and Bacteroidetes, accounting for 62.1%-99.1% of the total reads. The major putative homoacetogenic species enriched on H2/CO2 or formate belonged to Clostridium spp., Acetobacterium spp., Acetoanaerobium spp
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Bacterial Cell Production from Hexadecane at High Temperatures
Sukatsch, Dieter A.; Johnson, Marvin J.
1972-01-01
On mineral medium with hexadecane as the sole carbon source, stable mixed bacterial enrichment cultures were obtained from soil inoculum at 25, 35, 45, 55, and 65 C. Cell yields (grams of dry cells per gram of hexadecane) were determined for each of the enrichment cultures grown at the temperature at which they were enriched, and also for the 55 and 65 C cultures grown at various temperatures. In all cases, cell yields decreased with increasing growth temperature. The highest yield obtained at 65 C was 0.26, and the lowest yield obtained at 25 or 35 C was 1.02. Slower growth was observed at higher temperatures. PMID:5021971
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Humic Acid-Oxidizing, Nitrate-Reducing Bacteria in Agricultural Soils
Van Trump, J. Ian; Wrighton, Kelly C.; Thrash, J. Cameron; Weber, Karrie A.; Andersen, Gary L.; Coates, John D.
2011-01-01
ABSTRACT This study demonstrates the prevalence, phylogenetic diversity, and physiology of nitrate-reducing microorganisms capable of utilizing reduced humic acids (HA) as electron donors in agricultural soils. Most probable number (MPN) enumeration of agricultural soils revealed large populations (104 to 106 cells g−1 soil) of microorganisms capable of reducing nitrate while oxidizing the reduced HA analog 2,6-anthrahydroquinone disulfonate (AH2DS) to its corresponding quinone. Nitrate-dependent HA-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups. Subsequent 16S rRNA gene-based high-density oligonucleotide microarray (PhyloChip) indicated that reduced HA columns supported the development of a bacterial community enriched with members of the Acidobacteria, Firmicutes, and Betaproteobacteria relative to the no-donor control and initial inoculum. This study identifies a previously unrecognized role for HA in stimulating denitrification processes in saturated soil systems. Furthermore, this study indicates that reduced humic acids impact soil geochemistry and the indigenous bacterial community composition. PMID:21750120
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Effect of Hydrogenase and Mixed Sulfate-Reducing Bacterial Populations on the Corrosion of Steel
Bryant, Richard D.; Jansen, Wayne; Boivin, Joe; Laishley, Edward J.; Costerton, J. William
1991-01-01
The importance of hydrogenase activity to corrosion of steel was assessed by using mixed populations of sulfate-reducing bacteria isolated from corroded and noncorroded oil pipelines. Biofilms which developed on the steel studs contained detectable numbers of sulfate-reducing bacteria (104 increasing to 107/0.5 cm2). However, the biofilm with active hydrogenase activity (i.e., corrosion pipeline organisms), as measured by a semiquantitative commercial kit, was associated with a significantly higher corrosion rate (7.79 mm/year) relative to noncorrosive biofilm (0.48 mm/year) with 105 sulfate-reducing bacteria per 0.5 cm2 but no measurable hydrogenase activity. The importance of hydrogenase and the microbial sulfate-reducing bacterial population making up the biofilm are discussed relative to biocorrosion. Images PMID:16348560
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Rasmussen, Mary L; Koziel, Jacek A; Jane, Jay-lin; Pometto, Anthony L
2015-06-03
Ozonation of uncooked corn mash from the POET BPX process was investigated as a potential disinfection method for reducing bacterial contamination prior to ethanol fermentation. Corn mash (200 g) was prepared from POET ground corn and POET corn slurry and was ozonated in 250 mL polypropylene bottles. Lactic and acetic acid levels were monitored daily during the fermentation of ozonated, aerated, and nontreated corn mash samples to evaluate bacterial activity. Glycerol and ethanol contents of fermentation samples were checked daily to assess yeast activity. No yeast supplementation, no addition of other antimicrobial agents (such as antibiotics), and spiking with a common lactic acid bacterium found in corn ethanol plants, Lactobacillus plantarum, amplified the treatment effects. The laboratory-scale ozone dosages ranged from 26-188 mg/L, with very low estimated costs of $0.0008-0.006/gal ($0.21-1.6/m(3)) of ethanol. Ozonation was found to decrease the initial pH of ground corn mash samples, which could reduce the sulfuric acid required to adjust the pH prior to ethanol fermentation. Lactic and acetic acid levels tended to be lower for samples subjected to increasing ozone dosages, indicating less bacterial activity. The lower ozone dosages in the range applied achieved higher ethanol yields. Preliminary experiments on ozonating POET corn slurry at low ozone dosages were not as effective as using POET ground corn, possibly because corn slurry samples contained recycled antimicrobials from the backset. The data suggest additional dissolved and suspended organic materials from the backset consumed the ozone or shielded the bacteria.
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Fahrenfeld, Nicole; Zoeckler, Jeffrey; Widdowson, Mark A; Pruden, Amy
2013-04-01
2,4,6-Trinitrotoluene (TNT) is a toxic and persistent explosive compound occurring as a contaminant at numerous sites worldwide. Knowledge of the microbial dynamics driving TNT biodegradation is limited, particularly in native aquifer sediments where it poses a threat to water resources. The purpose of this study was to quantify the effect of organic amendments on anaerobic TNT biodegradation rate and pathway in an enrichment culture obtained from historically contaminated aquifer sediment and to compare the bacterial community dynamics. TNT readily biodegraded in all microcosms, with the highest biodegradation rate obtained under the lactate amended condition followed by ethanol amended and naturally occurring organic matter (extracted from site sediment) amended conditions. Although a reductive pathway of TNT degradation was observed across all conditions, denaturing gradient gel electrophoresis (DGGE) analysis revealed distinct bacterial community compositions. In all microcosms, Gram-negative γ- or β-Proteobacteria and Gram-positive Negativicutes or Clostridia were observed. A Pseudomonas sp. in particular was observed to be stimulated under all conditions. According to non-metric multidimensional scaling analysis of DGGE profiles, the microcosm communities were most similar to heavily TNT-contaminated field site sediment, relative to moderately and uncontaminated sediments, suggesting that TNT contamination itself is a major driver of microbial community structure. Overall these results provide a new line of evidence of the key bacteria driving TNT degradation in aquifer sediments and their dynamics in response to organic carbon amendment, supporting this approach as a promising technology for stimulating in situ TNT bioremediation in the subsurface.
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Marine bacterial degradation of brominated methanes
Goodwin, K.D.; Lidstrom, M.E.; Oremland, R.S.
1997-01-01
Brominated methanes are ozone-depleting compounds whose natural sources include marine algae such as kelp. Brominated methane degradation by bacteria was investigated to address whether bacterial processes might effect net emission of these compounds to the atmosphere. Bacteria in seawater collected from California kelp beds degraded CH2Br2 but not CHBr3. Specific inhibitors showed that methanotrophs and nitrifiers did not significantly contribute to CH2Br2 removal. A seawater enrichment culture oxidized 14CH2Br2 to 14CO2 as well as 14CH3Br to 14CO2. The rates of CH2Br2 degradation in laboratory experiments suggest that bacterial degradation of CH2Br2 in a kelp bed accounts for <1% of the CH2Br2 produced by the kelp. However, the half-life of CH2Br2 due to bacterial removal appears faster than hydrolysis and within an order of magnitude of volatilization to the atmosphere.Brominated methanes are ozone-depleting compounds whose natural sources include marine algae such as kelp. Brominated methane degradation by bacteria was investigated to address whether bacterial processes might effect net emission of these compounds to the atmosphere. Bacteria in seawater collected from California kelp beds degraded CH2Br2 but not CHBr3. Specific inhibitors showed that methanotrophs and nitrifiers did not significantly contribute to CH2Br2 removal. A seawater enrichment culture oxidized 14CH2Br2 to 14CO2 as well as 14CH3Br to 14CO2. The rates of CH2Br2 degradation in laboratory experiments suggest that bacterial degradation of CH2Br2 in a kelp bed accounts for <1% of the CH2Br2 produced by the kelp. However, the half-life of CH2Br2 due to bacterial removal appears faster than hydrolysis and within an order of magnitude of volatilization to the atmosphere.
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Wang, Lirui; Fouts, Derrick E.; Stärkel, Peter; Hartmann, Phillipp; Chen, Peng; Llorente, Cristina; DePew, Jessica; Moncera, Kelvin; Ho, Samuel B.; Brenner, David A.; Hooper, Lora V.; Schnabl, Bernd
2016-01-01
Summary Approximately half of all deaths from liver cirrhosis, the 10th leading cause of mortality in the United States, are related to alcohol use. Chronic alcohol consumption is accompanied by intestinal dysbiosis and bacterial overgrowth, yet little is known about the factors that alter the microbial composition or their contribution to liver disease. We previously associated chronic alcohol consumption with lower intestinal levels of the antimicrobial-regenerating islet-derived (REG)-3 lectins. Here, we demonstrate that intestinal deficiency in REG3B or REG3G increases numbers of mucosa-associated bacteria and enhances bacterial translocation to the mesenteric lymph nodes and liver, promoting the progression of ethanol-induced fatty liver disease toward steatohepatitis. Overexpression of Reg3g in intestinal epithelial cells restricts bacterial colonization of mucosal surfaces, reduces bacterial translocation, and protects mice from alcohol-induced steatohepatitis. Thus, alcohol appears to impair control of the mucosa-associated microbiota, and subsequent breach of the mucosal barrier facilitates progression of alcoholic liver disease. PMID:26867181
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Wang, Zhao; Yang, Yuyin; Dai, Yu; Xie, Shuguang
2015-04-09
Nonylphenol (NP) is a commonly detected pollutant in aquatic ecosystem and can be harmful to aquatic organisms. Anaerobic degradation is of great importance for the clean-up of NP in sediment. However, information on anaerobic NP biodegradation in the environment is still very limited. The present study investigated the shift in bacterial community structure associated with NP degradation in river sediment microcosms under nitrate- or sulfate-reducing conditions. Nearly 80% of NP (100 mg kg(-1)) could be removed under these two anaerobic conditions after 90 or 110 days' incubation. Illumina MiSeq sequencing analysis indicated that Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi became the dominant phylum groups with NP biodegradation. The proportion of Gammaproteobacteria, Deltaproteobacteria and Choloroflexi showed a marked increase in nitrate-reducing microcosm, while Gammaproteobacteria and Firmicutes in sulfate-reducing microcosm. Moreover, sediment bacterial diversity changed with NP biodegradation, which was dependent on type of electron acceptor. Copyright © 2014 Elsevier B.V. All rights reserved.
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Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem.
Northrop, Amanda C; Brooks, Rachel; Ellison, Aaron M; Gotelli, Nicholas J; Ballif, Bryan A
2017-10-01
Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic-matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea . Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states.
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Clusters of antibiotic resistance genes enriched together stay together in swine agriculture
Johnson, Timothy A.; Stedtfeld, Robert D.; Wang, Qiong; ...
2016-04-12
Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundancemore » of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance
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Clusters of antibiotic resistance genes enriched together stay together in swine agriculture
DOE Office of Scientific and Technical Information (OSTI.GOV)
Johnson, Timothy A.; Stedtfeld, Robert D.; Wang, Qiong
Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundancemore » of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance
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Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture.
Johnson, Timothy A; Stedtfeld, Robert D; Wang, Qiong; Cole, James R; Hashsham, Syed A; Looft, Torey; Zhu, Yong-Guan; Tiedje, James M
2016-04-12
Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk. Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance genes if
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López-Nicolás, Rubén; González-Bermúdez, Carlos A; Ros-Berruezo, Gaspar; Frontela-Saseta, Carmen
2014-08-15
The selective antimicrobial effect of fruit juices enriched with pine bark extract (PBE) (0.5 g/L) has been studied before and after in vitro gastrointestinal digestion. PBE (a concentrate of water-soluble bioflavonoids, mainly including phenolic compounds) has been proven to have high stability to the digestion process. Pure phenolic compounds such as gallic acid had a high antimicrobial effect on Staphylococcus aureus and Escherichia coli, maintaining the lactic acid bacteria population (≈100%). Otherwise, E. coli O157:H7 only growth 50% when PBE was added to the culture media, while a slight increase on the growth of lactobacilli and bifidobacteria was observed after exposition to the bark extract. Fresh fruit juices enriched with PBE showed the highest inhibitory effect on pathogenic intestinal bacterial growth, mainly E. coli and Enterococcus faecalis. The in vitro digestion process reduced the antibacterial effect of juices against most pathogenic bacteria in approximately 10%. However, the beneficial effect of fruit juices enriched with PBE (0.5 g/L) on gut microbiota is still considerable after digestion. Copyright © 2014 Elsevier Ltd. All rights reserved.
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de Carvalho, Cristiane Ribeiro; Pandolfo, Pablo; Pamplona, Fabrício Alano; Takahashi, Reinaldo Naoto
2010-03-17
The present study investigated the consequences of environmental enrichment on the impact of novelty and motivational properties of ethanol in spontaneously hypertensive rats (SHR), a validated model of attention deficit hyperactivity disorder (ADHD). This rat strain displays increased sensitivity to distinct classes of abused drugs, which makes it an interesting model for the study of the association between ADHD and drug abuse. Female SHR reared from weaning to adulthood in standard (SE) or enriched (EE) environment were tested on novelty-induced locomotion, saccharin consumption, ethanol consumption (forced and free-choice schedules) and ethanol-induced conditioned place preference (CPP). SHR reared in an EE showed reduced novelty-induced locomotion, consumed less saccharin and ethanol in a forced schedule and showed less ethanol preference in a free-choice schedule compared to SE rats. Moreover, EE rats did not develop CPP, whereas SE rats developed preference for ethanol (1.2g/kg). These results show that exposure to stimuli mimicking positive life experiences (environmental enrichment) induces persistent changes in the reward/motivational system of female SHR, suggesting an important role of the familiar environment during early stages of the neurodevelopment on the co-morbidity of ADHD and drug abuse. Copyright 2009 Elsevier B.V. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Edlund, A.; Jansson, J.
The aim of this study was to enrich and identify psychrotolerant phenanthrenedegrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and thismore » reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella,Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.« less
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Feliciano, Lizanel; Lee, Jaesung; Lopes, John A; Pascall, Melvin A
2010-05-01
This study investigated the efficacy of sanitized ice for the reduction of bacteria in the water collected from the ice that melted during storage of whole and filleted Tilapia fish. Also, bacterial reductions on the fish fillets were investigated. The sanitized ice was prepared by freezing solutions of PRO-SAN (an organic acid formulation) and neutral electrolyzed water (NEW). For the whole fish study, the survival of the natural microflora was determined from the water of the melted ice prepared with PRO-SAN and tap water. These water samples were collected during an 8 h storage period. For the fish fillet study, samples were inoculated with Escherichia coli K12, Listeria innocua, and Pseudomonas putida then stored on crushed sanitized ice. The efficacies of these were tested by enumerating each bacterial species on the fish fillet and in the water samples at 12 and 24 h intervals for 72 h, respectively. Results showed that each bacterial population was reduced during the test. However, a bacterial reduction of < 1 log CFU was obtained for the fillet samples. A maximum of approximately 2 log CFU and > 3 log CFU reductions were obtained in the waters sampled after the storage of whole fish and the fillets, respectively. These reductions were significantly (P < 0.05) higher in the water from sanitized ice when compared with the water from the unsanitized melted ice. These results showed that the organic acid formulation and NEW considerably reduced the bacterial numbers in the melted ice and thus reduced the potential for cross-contamination.
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Fodelianakis, Stilianos; Papageorgiou, Nafsika; Pitta, Paraskevi; Kasapidis, Panagiotis; Karakassis, Ioannis
2014-01-01
A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. PMID:24747897
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Quantitative chemical biosensing by bacterial chemotaxis in microfluidic chips.
Roggo, Clémence; Picioreanu, Cristian; Richard, Xavier; Mazza, Christian; van Lintel, Harald; van der Meer, Jan Roelof
2018-01-01
Whole-cell bacterial bioreporters are proposed as alternatives to chemical analysis of, for example, pollutants in environmental compartments. Commonly based on reporter gene induction, bioreporters produce a detectable signal within 30 min to a few hours after exposure to the chemical target, which is impractical for applications aiming at a fast response. In an attempt to attain faster readout but maintain flexibility of chemical targeting, we explored the concept for quantitative chemical sensing by bacterial chemotaxis. Chemotaxis was quantified from enrichment of cells across a 600 µm-wide chemical gradient stabilized by parallel flow in a microfluidic chip, further supported by transport and chemotaxis steady state and kinetic modelling. As proof-of-concept, we quantified Escherichia coli chemotaxis towards serine, aspartate and methylaspartate as a function of attractant concentration and exposure time. E. coli chemotaxis enrichment increased sharply between 0 and 10 µM serine, before saturating at 100 µM. The chemotaxis accumulation rate was maximal at 10 µM serine, leading to observable cell enrichment within 5 min. The potential application for biosensing of environmental toxicants was investigated by quantifying chemotaxis of Cupriavidus pinatubonensis JMP134 towards the herbicide 2,4-dichlorophenoxyacetate. Our results show that bacterial chemotaxis can be quantified on a scale of minutes and may be used for developing faster bioreporter assays. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
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Webster, Gordon; Watt, Lynsey C; Rinna, Joachim; Fry, John C; Evershed, Richard P; Parkes, R John; Weightman, Andrew J
2006-09-01
Marine sediment slurries enriched for anaerobic, sulfate-reducing prokaryotic communities utilizing glucose and acetate were used to provide the first comparison between stable-isotope probing (SIP) of phospholipid fatty acids (PLFA) and DNA (16S rRNA and dsrA genes) biomarkers. Different 13C-labelled substrates (glucose, acetate and pyruvate) at low concentrations (100 microM) were used over a 7-day incubation to follow and identify carbon flow into different members of the community. Limited changes in total PLFA and bacterial 16S rRNA gene DGGE profiles over 7 days suggested the presence of a stable bacterial community. A broad range of PLFA were rapidly labelled (within 12 h) in the 13C-glucose slurry but this changed with time, suggesting the presence of an active glucose-utilizing population and later development of another population able to utilize glucose metabolites. The identity of the major glucose-utilizers was unclear as 13C-enriched PLFA were common (16:0, 16:1, 18:1omega7, highest incorporation) and there was little difference between 12C- and 13C-DNA 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles. Seemingly glucose, a readily utilizable substrate, resulted in widespread incorporation consistent with the higher extent of 13C-incorporation (approximately 10 times) into PLFA compared with 13C-acetate or 13C-pyruvate. 13C-PLFA in the 13C-acetate and 13C-pyruvate slurries were similar to each other and to those that developed in the 13C-glucose slurry after 4 days. These were more diagnostic, with branched odd-chain fatty acids (i15:0, a15:0 and 15:1omega6) possibly indicating the presence of Desulfococcus or Desulfosarcina sulfate-reducing bacteria (SRB) and sequences related to these SRB were in the 13C-acetate-DNA dsrA gene library. The 13C-acetate-DNA 16S rRNA gene library also contained sequences closely related to SRB, but these were the acetate-utilizing Desulfobacter sp., as well as a broad range of uncultured Bacteria. In
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Hussain, Sabir; Sørensen, Sebastian R; Devers-Lamrani, Marion; El-Sebai, Talaat; Martin-Laurent, Fabrice
2009-11-01
The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized by a bacterial culture isolated from an agricultural soil regularly exposed to IPU. Molecular analysis of the bacterial culture by DNA fingerprinting, cloning and sequencing of the 16S rRNA genes revealed that it consisted of six different members among whom the dominant was related to Sphingomonas sp. Six bacterial strains belonging to genera Ancylobacter, Pseudomonas, Stenotrophomonas, Methylobacterium, Variovorax and Agrobacterium were isolated from the IPU-degrading culture. None of these were able to degrade IPU in pure culture and only the intact culture sustained the ability to mineralize IPU. The composition of the culture appeared stable suggesting that yet unknown interactions are involved in the IPU mineralization. IPU degradation involved the transitory accumulation of three known IPU metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, and 4-isopropylaniline and their further degradation. Thus, it indicates a metabolic pathway initiated by two successive N-demethylations, followed by cleavage of the urea side chain. This culture did not degrade other structurally related phenylurea herbicides. The degrading activity of the bacterial culture was deeply influenced by the pH, being completely inhibited at pH 5.5 and optimal at pH 7.5.
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Acute Consumption of Flavan-3-ol-Enriched Dark Chocolate Affects Human Endogenous Metabolism.
Ostertag, Luisa M; Philo, Mark; Colquhoun, Ian J; Tapp, Henri S; Saha, Shikha; Duthie, Garry G; Kemsley, E Kate; de Roos, Baukje; Kroon, Paul A; Le Gall, Gwénaëlle
2017-07-07
Flavan-3-ols and methylxanthines have potential beneficial effects on human health including reducing cardiovascular risk. We performed a randomized controlled crossover intervention trial to assess the acute effects of consumption of flavan-3-ol-enriched dark chocolate, compared with standard dark chocolate and white chocolate, on the human metabolome. We assessed the metabolome in urine and blood plasma samples collected before and at 2 and 6 h after consumption of chocolates in 42 healthy volunteers using a nontargeted metabolomics approach. Plasma samples were assessed and showed differentiation between time points with no further separation among the three chocolate treatments. Multivariate statistics applied to urine samples could readily separate the postprandial time points and distinguish between the treatments. Most of the markers responsible for the multivariate discrimination between the chocolates were of dietary origin. Interestingly, small but significant level changes were also observed for a subset of endogenous metabolites. 1 H NMR revealed that flavan-3-ol-enriched dark chocolate and standard dark chocolate reduced urinary levels of creatinine, lactate, some amino acids, and related degradation products and increased the levels of pyruvate and 4-hydroxyphenylacetate, a phenolic compound of bacterial origin. This study demonstrates that an acute chocolate intervention can significantly affect human metabolism.
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Bacterial population dynamics in recycled mushroom compost leachate.
Safianowicz, Katarzyna; Bell, Tina L; Kertesz, Michael A
2018-06-01
Mushrooms are an important food crop throughout the world. The most important edible mushroom is the button mushroom (Agaricus bisporus), which comprises about 30% of the global mushroom market. This species is cultivated commercially on a selective compost that is produced predominantly from wheat straw/stable bedding and chicken manure, at a moisture content of around 70% (w/w) and temperatures of up to 80 °C. Large volumes of water are required to achieve this moisture content, and many producers therefore collect leachate from the composting windrows and bunkers (known in the industry as "goody water") and reuse it to wet the raw ingredients. This has the benefit of recycling and saving water and has the potential to enrich beneficial microorganisms that stimulate composting, but also the risk of enhancing pathogen populations that could reduce productivity. Here, we show by 16S rRNA gene sequencing that mushroom compost leachate contains a high diversity of unknown microbes, with most of the species found affiliated with the phyla Firmicutes and Proteobacteria. However, by far the most abundant species was the thermophile Thermus thermophilus, which made up approximately 50% of the bacterial population present. Although the leachate was routinely collected and stored in an aerated central storage tank, many of the bacterial species found in leachate were facultative anaerobes. However, there was no evidence for sulfide production, and no sulfate-reducing bacterial species were detected. Because T. thermophilus is important in the high temperature phase of composting, the use of recycled leachate as an inoculum for the raw materials is likely to be beneficial for the composting process.
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Degradation of trimethylbenzene isomers by an enrichment culture under N{sub 2}O-reducing conditions
DOE Office of Scientific and Technical Information (OSTI.GOV)
Haener, A.; Hoehener, P.; Zeyer, J.
1997-03-01
In mineral oil-contaminated soils and aquifers, monoaromatic hydrocarbons are often a major concern because of high water solubility and toxicity. Under aerobic conditions, these compounds are rapidly mineralized. However, only limited data are available on the anaerobic degradation. This study reports on the growth of an enrichment culture on 1,3,5-trimethylbenzene (TMB) and 1,2,4-TMB under N2O-reducing conditions, and provides carbon mass and electron balances for the biodegradation of 1,3,5-TMB. 43 refs., 3 figs.
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Chróst, Ryszard J; Adamczewski, Tomasz; Kalinowska, Krystyna; Skowrońska, Agnieszka
2009-01-01
Effects of mesotrophic lake water enrichment with organic phosphorus and nitrogen substrates (DNA and model protein, bovine serum albumin--BSA) on dynamics and diversity of natural microbial communities (bacteria, heterotrophic nanoflagellates, ciliates) were studied in mesocosm experiments. Simultaneous enrichment with DNA and BSA strongly increased the abundance and biomass of all studied groups of microorganisms and induced changes in their morphological and taxonomic structure. The increased participation of large heterotrophic nanoflagellates cells (larger than 10 microm) in their total numbers and shifts in taxonomic and trophic structure of the ciliates, from algivorous to small bacterivorous, species were observed. Grazing caused changes in bacterial size distribution in all enriched mesocosms. Large (10-50 microm) filamentous bacteria significantly contributed to the total bacterial numbers and biomass. Pronounced increase in populations of beta- and gamma-Proteobacteria was found in lake water enriched with organic P and N sources, whereas alpha-Proteobacteria did not change markedly in the studied mesocosms. DNA additions stimulated the rates of bacterial secondary production. BSA shortened the rates of bacterial biomass turnover in lake water. Relatively high and constant (approximately 30%) percentage contribution of active bacteria (MEM+) in two mesocosms enriched with DNA and DNA+BSA suggested the important role of nucleic acids as a source of phosphorus for bacterial growth, activity and production. Numerous and statistically significant correlations between bacteria and protists indicated the direct and selective predator-prey relationship.
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Grossmann, S
1994-07-01
Metabolic activity of bacteria was investigated in open water, newly forming sea ice, and successive stages of pack ice in the Weddell Sea. Microautoradiography, using [(3)H]leucine as substrate, was compared with incorporation rates of [(3)H]leucine into proteins. Relation of [(3)H]leucine incorporation to the biomass of active bacteria provides information about changes of specific metabolic activity of cells. During a phytoplankton bloom in an ice-free, stratified water column, total numbers of bacteria in the euphotic zone averaged 2.3 × 10(5) ml(-1), but only about 13% showed activity via leucine uptake. Growth rate of the active bacteria was estimated as 0.3-0.4 days(-1). Total cell concentration of bacteria in 400 m depth was 6.6 × 10(4) ml(-1). Nearly 50% of these cells were active, although biomass production and specific growth rate were only about one-tenth that of the surface populations. When sea ice was forming in high concentrations of phytoplankton, bacterial biomass in the newly formed ice was 49.1 ng C ml(-1), exceeding that in open water by about one order of magnitude. Attachment of large bacteria to algal cells seems to cause their enrichment in the new ice, since specific bacterial activity was reduced during ice formation, and enrichment of bacteria was not observed when ice formed at low algal concentration. During growth of pack ice, biomass of bacteria increased within the brine channel system. Specific activity was still reduced at these later stages of ice development, and percentages of active cells were as low as 3-5%. In old, thick pack ice, bacterial activity was high and about 30% of cells were active. However, biomass-specific activity of bacteria remained significantly lower than that in open water. It is concluded that bacterial assemblages different to those of open water developed within the ice and were dominated by bacteria with lower average metabolic activity than those of ice-free water.
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McMahon, Tanis C.; Blais, Burton W.; Wong, Alex; Carrillo, Catherine D.
2017-01-01
Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0–2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of
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McMahon, Tanis C; Blais, Burton W; Wong, Alex; Carrillo, Catherine D
2017-01-01
Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin ( stx ) and intimin ( eae )]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae -negative STEC and eae -positive E. coli , but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets ( stx and eae ) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli . By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae -negative STEC and eae -positive E. coli (0-2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and
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Application of 57Fe-enriched synthetic ferrihydrite to speciate the product of bacterial reduction
NASA Astrophysics Data System (ADS)
Larsen, Ole; Bender Koch, Chr.
2000-07-01
We have sampled a clay lens with evidence of sulfide reduction from a texturally stratified sandy aquifer at Rømø, Denmark. A minor amount of synthetic, pure 57Fe ferrihydrite was added to this sample and allowed to react for up to three months. The initial sample, the 57Fe ferrihydrite, and samples taken from the reaction mixture were investigated by Mössbauer spectroscopy at temperatures between 15 and 298 K as sampled and following exposure to oxygen. The initial sample only contained Fe(II) (33% of the iron) and Fe(III) in silicates. The Fe(III) in the ferrihydrite is reduced to Fe(II) as evidenced by an increase of this component by bacterial activity. The Fe(II) component remains paramagnetic at temperatures down to 15 K. Similarly to naturally reduced sediments the new-formed Fe(II) is extremely reactive towards molecular oxygen. Following oxidation the reformed Fe(III) is found as ferrihydrite. The bonding of the Fe(II) is by electrostatical bonding (adsorbed) to the layer silicates as evidenced by a temperature scanning of the sample between 80 and 270 K.
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Tzanetakis, Giorgos N; Azcarate-Peril, M Andrea; Zachaki, Sophia; Panopoulos, Panos; Kontakiotis, Evangelos G; Madianos, Phoebus N; Divaris, Kimon
2015-08-01
Elucidating the microbial ecology of endodontic infections (EIs) is a necessary step in developing effective intracanal antimicrobials. The aim of the present study was to investigate the bacterial composition of symptomatic and asymptomatic primary and persistent infections in a Greek population using high-throughput sequencing methods. 16S amplicon pyrosequencing of 48 root canal bacterial samples was conducted, and sequencing data were analyzed using an oral microbiome-specific and a generic (Greengenes) database. Bacterial abundance and diversity were examined by EI type (primary or persistent), and statistical analysis was performed by using non-parametric and parametric tests accounting for clustered data. Bacteroidetes was the most abundant phylum in both infection groups. Significant, albeit weak associations of bacterial diversity were found, as measured by UniFrac distances with infection type (analyses of similarity, R = 0.087, P = .005) and symptoms (analyses of similarity, R = 0.055, P = .047). Persistent infections were significantly enriched for Proteobacteria and Tenericutes compared with primary ones; at the genus level, significant differences were noted for 14 taxa, including increased enrichment of persistent infections for Lactobacillus, Streptococcus, and Sphingomonas. More but less abundant phyla were identified using the Greengenes database; among those, Cyanobacteria (0.018%) and Acidobacteria (0.007%) were significantly enriched among persistent infections. Persistent infections showed higher phylogenetic diversity (PD) (asymptomatic: PD = 9.2, standard error [SE] = 1.3; symptomatic: PD = 8.2, SE = 0.7) compared with primary infections (asymptomatic: PD = 5.9, SE = 0.8; symptomatic: PD = 7.4, SE = 1.0). The present study revealed a high bacterial diversity of EI and suggests that persistent infections may have more diverse bacterial communities than primary infections. Copyright © 2015 American Association of Endodontists. Published by
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Natsuga, Ken; Cipolat, Sara; Watt, Fiona M
2016-01-01
Mice lacking three epidermal barrier proteins-envoplakin, periplakin, and involucrin (EPI-/- mice)-have a defective cornified layer, reduced epidermal γδ T cells, and increased dermal CD4(+) T cells. They are also resistant to developing skin tumors. The tumor-protective mechanism involves signaling between Rae-1 expressing keratinocytes and the natural killer group 2D receptor on immune cells, which also plays a role in host defenses against infection. Given the emerging link between bacteria and cancer, we investigated whether EPI-/- mice have an altered skin microbiota. The bacterial phyla were similar in wild-type and EPI-/- skin. However, bacteria were threefold more abundant in EPI-/- skin and penetrated deeper into the epidermis. The major epithelial defense mechanism against bacteria is production of antimicrobial proteins (AMPs). EPI-/- skin exhibited enhanced expression of antimicrobial peptides. However, reducing the bacterial load by antibiotic treatment or breeding mice under specific pathogen-free conditions did not reduce AMP expression or alleviate the abnormalities in T-cell populations. We conclude that the atopic characteristics of EPI-/- skin are a consequence of the defective barrier rather than a response to the increased bacterial load. It is therefore unlikely that the increase in skin microbiota contributes directly to the observed cancer resistance. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
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Zhu, Jinyong; Dai, Wenfang; Qiu, Qiongfen; Dong, Chunming; Zhang, Jinjie; Xiong, Jinbo
2016-11-01
Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphaproteobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.
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Morphomechanics of bacterial biofilms undergoing anisotropic differential growth
NASA Astrophysics Data System (ADS)
Zhang, Cheng; Li, Bo; Huang, Xiao; Ni, Yong; Feng, Xi-Qiao
2016-10-01
Growing bacterial biofilms exhibit a number of surface morphologies, e.g., concentric wrinkles, radial ridges, and labyrinthine networks, depending on their physiological status and nutrient access. We explore the mechanisms underlying the emergence of these greatly different morphologies. Ginzburg-Landau kinetic method and Fourier spectral method are integrated to simulate the morphological evolution of bacterial biofilms. It is shown that the morphological instability of biofilms is triggered by the stresses induced by anisotropic and heterogeneous bacterial expansion, and involves the competition between membrane energy and bending energy. Local interfacial delamination further enriches the morphologies of biofilms. Phase diagrams are established to reveal how the anisotropy and spatial heterogeneity of growth modulate the surface patterns. The mechanics of three-dimensional microbial morphogenesis may also underpin self-organization in other development systems and provide a potential strategy for engineering microscopic structures from bacterial aggregates.
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Degnim, Amy C.; Scow, Jeffrey S.; Hoskin, Tanya L.; Miller, Joyce P.; Loprinzi, Margie; Boughey, Judy C.; Jakub, James W.; Throckmorton, Alyssa; Patel, Robin; Baddour, Larry M.
2014-01-01
Objective To determine if bacterial colonization of drains can be reduced by local antiseptic interventions. Summary Background Drains are a potential source of bacterial entry into surgical wounds and may contribute to surgical site infection (SSI) after breast surgery. Methods Following IRB approval, patients undergoing total mastectomy and/or axillary lymph node dissection were randomized to standard drain care (control) or drain antisepsis (treated). Standard drain care comprised twice daily cleansing with alcohol swabs. Antisepsis drain care included 1) a chlorhexidine disc at the drain exit site and 2) irrigation of the drain bulb twice daily with dilute sodium hypochlorite (Dakin’s) solution. Cultures results of drain fluid and tubing were compared between control and antisepsis groups. Results Overall, 100 patients with 125 drains completed the study with 48 patients (58 drains) in the control group and 52 patients (67 drains) in the antisepsis group. Cultures of drain bulb fluid at one week were positive (1+ or greater growth) in 66% (38/58) of control drains compared to 21% of antisepsis drains (14/67), (p=0.0001). Drain tubing cultures demonstrated >50 CFU in 19% (8/43) of control drains versus 0% (0/53) of treated drains (p=0.004). SSI was diagnosed in 6 patients (6%) - 5 patients in the control group and 1 patient in the antisepsis group (p=0.06). Conclusions Simple and inexpensive local antiseptic interventions with a chlorhexidine disc and hypochlorite solution reduce bacterial colonization of drains. Based on these data, further study of drain antisepsis and its potential impact on SSI rate is warranted. PMID:23518704
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Thomas, Stephanie; Palmer, Rish; Phillipo, Edward; Chipungu, Geoffrey
2016-05-31
All surgical procedures have the potential for infection and some of the main sources are contamination from airborne particles, theatre personnel and the theatre environment. There is strong evidence that the use of ultra-clean air flow systems in orthopedic operating theatres reduces the incidence of deep sepsis after surgery. In the developing world however, this is often an unrealistic solution. The aim of this study was to establish baseline levels of contamination in a working orthopedic theatre, at the Queen Elizabeth Central Hospital, Blantyre, Malawi. To feedback results to the theatre team, promote infection prevention discussion and work with the team to implement workable and realistic goals to improve the intra-operative environment. Samples were collected from theatre equipment available at the time of surgery, from theatre water and theatre air using passive air sampling techniques. Samples were immediately transferred to the Central Microbiology Laboratory for culture on basic culture media. Bacterial contamination of theatre equipment, intra-operative theatre air and water was detected. Results were discussed with the theatre and infection prevention team who were receptive to feedback with regards to infection prevention strategies and keen to develop simple measures which could be put in place to change practice. In this setting, we suggest that implementing workable and realistic goals such as, establishing baseline rates of bacterial contamination and introduction of strict protocols for asepsis and theatre etiquette, may reduce bacterial contamination rates and subsequent intra-operative infection in the absence of expensive engineering solutions.
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Grace, Mary H.; Guzman, Ivette; Roopchand, Diana E.; Moskal, Kristin; Cheng, Diana M.; Pogrebnyak, Natasha; Raskin, Ilya; Howell, Amy; Lila, Mary Ann
2013-01-01
Defatted soy flour (DSF), soy protein isolate (SPI), hemp protein isolate (HPI), medium roast peanut flour (MPF) and pea protein isolate (PPI) stably bind and concentrate cranberry (CB) polyphenols, creating protein/polyphenol-enriched matrices. Proanthocyanidins (PAC) in the enriched matrices ranged from 20.75 mg/g (CB-HPI) to 10.68 mg/g (CB-SPI). Anthocyanins (ANC) ranged from 3.19 mg/g (CB-DSF) to 1.68 mg/g (CB-SPI), while total phenolics (TP) ranged from 37.61 mg/g (CB-HPI) to 21.29 mg/g (CB-SPI). LC-MS indicated that the enriched matrices contained all identifiable ANC, PAC and flavonols present in CB juice. Complexation with SPI stabilized and preserved the integrity of the CB polyphenolic components for at least 15 weeks at 37 °C. PAC isolated from enriched matrices demonstrated comparable anti-adhesion bioactivity to PAC isolated directly from CB juice (MIC 0.4 to 0.16 mg/mL), indicating their potential utility for maintenance of urinary tract health. Approximately 1.0 g of polyphenol-enriched matrix delivered the same amount of PAC available in one cup (300 mL) of commercial CB juice cocktail; which has been shown clinically to be the prophylactic dose for reducing recurring urinary tract infections. CB-SPI inhibited gram- positive and gram-negative bacterial growth. Nutritional and sensory analyses indicated that the targeted CB-matrix combinations have high potential for incorporation in functional food formulations. PMID:23786629
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Maraccini, P A; Wenk, J; Boehm, A B
2016-08-01
To investigate the UVB-independent and exogenous indirect photoinactivation of eight human health-relevant bacterial species in the presence of photosensitizers. Eight bacterial species were exposed to simulated sunlight with greatly reduced UVB light intensity in the presence of three synthetic photosensitizers and two natural photosensitizers. Inactivation curves were fit with shoulder log-linear or first-order kinetic models, from which the presence of a shoulder and magnitude of inactivation rate constants were compared. Eighty-four percent reduction in the UVB light intensity roughly matched a 72-95% reduction in the overall bacterial photoinactivation rate constants in sensitizer-free water. With the UVB light mostly reduced, the exogenous indirect mechanism contribution was evident for most bacteria and photosensitizers tested, although most prominently with the Gram-positive bacteria. Results confirm the importance of UVB light in bacterial photoinactivation and, with the reduction of the UVB light intensity, that the Gram-positive bacteria are more vulnerable to the exogenous indirect mechanism than Gram-negative bacteria. UVB is the most important range of the sunlight spectrum for bacterial photoinactivation. In aquatic environments where photosensitizers are present and there is high UVB light attenuation, UVA and visible wavelengths can contribute to exogenous indirect photoinactivation. © 2016 The Society for Applied Microbiology.
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Zhang, Ping; Lapara, Timothy M; Goslan, Emma H; Xie, Yuefeng; Parsons, Simon A; Hozalski, Raymond M
2009-05-01
Biodegradation is a potentially important loss process for haloacetic acids (HAAs), a class of chlorination byproducts, in water treatment and distribution systems, but little is known about the organisms involved (i.e., identity, substrate range, biodegradation kinetics). In this research, 10 biomass samples (i.e., tap water, distribution system biofilms, and prechlorinated granular activated carbon filters) from nine drinking water systems were used to inoculate a total of thirty enrichment cultures fed monochloroacetic acid (MCAA), dichloroacetic acid (DCAA), or trichloroacetic (TCAA) as sole carbon and energy source. HAA degraders were successfully enriched from the biofilm samples (GAC and distribution system) but rarely from tap water. Half of the MCAA and DCAA enrichment cultures were positive, whereas only one TCAA culture was positive (two were inconclusive). Eight unique HAA-degrading isolates were obtained including several Afipia spp. and a Methylobacterium sp.; all isolates were members of the phylum Proteobacteria. MCAA, monobromoacetic acid (MBAA), and monoiodoacetic acid (MIAA) were rapidly degraded by all isolates, and DCAA and tribromoacetic (TBAA) were also relatively labile. TCAA and dibromoacetic acid (DBAA)were degraded by only three isolates and degradation lagged behind the other HAAs. Detailed DCAA biodegradation kinetics were obtained for two selected isolates and two enrichment cultures. The maximum biomass-normalized degradation rates (Vm) were 0.27 and 0.97 microg DCAA/ microg protein/h for Methylobacterium fujisawaense strain PAWDI and Afipia felis strain EMD2, respectively, which were comparable to the values obtained for the enrichment cultures from which those organisms were isolated (0.39 and 1.37 microg DCAN/microg protein/h, respectively). The half-saturation constant (Km) values ranged from 4.38 to 77.91 microg DCAA/L and the cell yields ranged from 14.4 to 36.1 mg protein/g DCAA.
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Lee, Wen-Sen; Hsieh, Tai-Chin; Shiau, Justine C; Ou, Tsong-Yih; Chen, Fu-Lun; Liu, Yu-Hsin; Yen, Muh-Yong; Hsueh, Po-Ren
2017-10-01
This prospective before-after study was intended to investigate the effect of Bio-Kil on reducing environmental bacterial burden and healthcare-associated infections (HAIs) in intensive care units (ICUs) at the Municipal Wan-Fang Hospital, Taipei, Taiwan in 2014. Four rooms in the medical and surgical ICUs were investigated and designated as study rooms (n = 2) or control rooms (n = 2). Routine disinfection was performed during the pre-intervention period in both room types. Bio-Kil was applied to the fomites and surroundings of the study rooms during the intervention period. Total bacterial burden and proportion of colonization of fomites and surroundings by multidrug-resistance organisms (MDROs) were determined before and after the intervention. The demographic characteristics, underlying conditions, and clinical outcomes of patients were analyzed. After application of Bio-Kil, the bacterial burden declined in both groups, although the reduction was greater in the study rooms as compared with the control rooms (p = 0.001). During the pre-intervention period, 16 patients were admitted to control rooms and 18 patients to study rooms. After the intervention, 22 patients were admitted to control rooms and 21 patients to study rooms. The number of cases of new-onset sepsis declined in the intervention group (from 33% to 23.8%), but increased in the control group (from 25% to 40.9%); however, there was no significant difference in incidence of new-onset sepsis between the study and control rooms after intervention. Application of Bio-Kil reduced the environmental bacterial burden and MDROs in ICUs. Further studies are needed to evaluate the efficacy of this nanotechnology-based disinfectant in reducing HAIs. Copyright © 2016. Published by Elsevier B.V.
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Microbial biomass, community structure and metal tolerance of a naturally Pb-enriched forest soil.
Bååth, E; Díaz-Raviña, M; Bakken, L R
2005-11-01
The effect of long-term elevated soil Pb levels on soil microbiota was studied at a forest site in Norway, where the soil has been severely contaminated with Pb since the last period of glaciation (several thousand years). Up to 10% Pb (total amount, w/w) has been found in the top layer. The microbial community was drastically affected, as judged from changes in the phospholipid fatty acid (PLFA) pattern. Specific PLFAs that were high in Pb-enriched soil were branched (especially br17:0 and br18:0), whereas PLFAs common in eukaryotic organisms such as fungi (18:2omega6,9 and 20:4) were low compared with levels at adjacent, uncontaminated sites. Congruent changes in the PLFA pattern were found upon analyzing the culturable part of the bacterial community. The high Pb concentrations in the soil resulted in increased tolerance to Pb of the bacterial community, measured using both thymidine incorporation and plate counts. Furthermore, changes in tolerance were correlated to changes in the community structure. The bacterial community of the most contaminated soils showed higher specific activity (thymidine and leucine incorporation rates) and higher culturability than that of control soils. Fungal colony forming units (CFUs) were 10 times lower in the most Pb-enriched soils, the species composition was widely different from that in control soils, and the isolated fungi had high Pb tolerance. The most commonly isolated fungus in Pb-enriched soils was Tolypocladium inflatum. Comparison of isolates from Pb-enriched soil and isolates from unpolluted soils showed that T. inflatum was intrinsically Pb-tolerant, and that the prolonged conditions with high Pb had not selected for any increased tolerance.
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Dimethylamine biodegradation by mixed culture enriched from drinking water biofilter.
Liao, Xiaobin; Chen, Chao; Zhang, Jingxu; Dai, Yu; Zhang, Xiaojian; Xie, Shuguang
2015-01-01
Dimethylamine (DMA) is one of the important precursors of drinking water disinfection by-product N-nitrosodimethylamine (NDMA). Reduction of DMA to minimize the formation of carcinogenic NDMA in drinking water is of practical importance. Biodegradation plays a major role in elimination of DMA pollution in the environment, yet information on DMA removal by drinking water biofilter is still lacking. In this study, microcosms with different treatments were constructed to investigate the potential of DMA removal by a mixed culture enriched from a drinking water biofilter and the effects of carbon and nitrogen sources. DMA could be quickly mineralized by the enrichment culture. Amendment of a carbon source, instead of a nitrogen source, had a profound impact on DMA removal. A shift in bacterial community structure was observed with DMA biodegradation, affected by carbon and nitrogen sources. Proteobacteria was the predominant phylum group in DMA-degrading microcosms. Microorganisms from a variety of bacterial genera might be responsible for the rapid DMA mineralization. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Bhardwaj, Garima; Webster, Thomas J
2017-01-01
The attachment and initial growth of bacteria on an implant surface dictates the progression of infection. Treatment often requires aggressive antibiotic use, which does not always work. To overcome the difficulties faced in systemic and local antibiotic delivery, scientists have forayed into using alternative techniques, which includes implant surface modifications that prevent initial bacterial adhesion, foreign body formation, and may offer a controlled inflammatory response. The current study focused on using electrophoretic deposition to treat titanium with a nanophase titanium dioxide surface texture to reduce bacterial adhesion and growth. Two distinct nanotopographies were analyzed, Ti-160, an antimicrobial surface designed to greatly reduce bacterial colonization, and Ti-120, an antimicrobial surface with a topography that upregulates osteoblast activity while reducing bacterial colonization; the number following Ti in the nomenclature represents the atomic force microscopy root-mean-square roughness value in nanometers. There was a 95.6% reduction in Staphylococcus aureus (gram-positive bacteria) for the Ti-160-treated surfaces compared to the untreated titanium alloy controls. There was a 90.2% reduction in Pseudomonas aeruginosa (gram-negative bacteria) on Ti-160-treated surfaces compared to controls. For ampicillin-resistant Escherichia coli , there was an 81.1% reduction on the Ti-160-treated surfaces compared to controls. Similarly for surfaces treated with Ti-120, there was an 86.8% reduction in S. aureus , an 82.1% reduction in P. aeruginosa , and a 48.6% reduction in ampicillin-resistant E. coli . The Ti-120 also displayed a 120.7% increase at day 3 and a 168.7% increase at day 5 of osteoblast proliferation over standard titanium alloy control surfaces. Compared to untreated surfaces, Ti-160-treated titanium surfaces demonstrated a statistically significant 1 log reduction in S. aureus and P. aeruginosa , whereas Ti-120 provided an additional
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Effect of NO2(-) on stable isotope fractionation during bacterial sulfate reduction.
Einsiedl, Florian
2009-01-01
The effects of low NO2(-) concentrations on stable isotope fractionation during dissimilatory sulfate reduction by strain Desulfovibrio desulfuricans were investigated. Nitrite, formed as an intermediate during nitrification and denitrification processes in marine and freshwater habitats, inhibits the reduction of the sulfuroxy intermediate SO3(2-) to H2S even at low concentrations. To gain an understanding of the inhibition effect of the reduction of the sulfuroxy intermediate on stable isotope fractionation in sulfur and oxygen during bacterial sulfate reduction, nitrite was added in the form of short pulses. In the batch experiments that contained 0.02, 0.05, and 0.1 mM nitrite, sulfur enrichment factors epsilon of -12 +/- 1.6, -15 +/- 1.1, and -26 +/- 1.3 per thousand, respectively were observed. In the control experiment (no addition of nitrite) a sulfur enrichment factor epsilon of around -11 per thousand was calculated. In the experiments that contained no 18O enriched water (delta18O: -10 per thousand) and nitrite concentrations of 0.02, 0.05, and 0.1 mM, delta18O values in the remaining sulfate were fairly constant during the experiments (delta18O sulfate: approximately equal to 10 per thousand) and were similar to those obtained from the control experiment (no nitrite and no enriched water). However, in the batch experiments that contained 18O enriched water (+700 per thousand) and nitrite concentrations of 0.05 and 0.1 mM increasing delta18O values in the remaining sulfate from around 15 per thousand to approximately 65 and 85 per thousand, respectively, were found. Our experiments that contained isotopic enriched water and nitrite show clear evidence that the ratio of forward and backward fluxes regulated by adenosine-5'-phosphosulfate reductase (APSR) controls the extent of sulfur isotope fractionation during bacterial sulfate reduction in strain Desulfovibrio desulfuricans. Since the metabolic sulfuroxy intermediate SO3(2-) exchanges with water
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Production and characterisation of reduced-fat and PUFA-enriched Burrata cheese.
Trani, Antonio; Gambacorta, Giuseppe; Gomes, Tommaso F; Loizzo, Pasqua; Cassone, Angela; Faccia, Michele
2016-05-01
Burrata is an Italian fresh 'pasta filata' cheese made from cow's milk and cream that is rapidly spreading in Europe. It has very high caloric content, and a technological protocol was developed for producing a reduced-fat type and fortifying it with polyunsaturated fatty acids (PUFA) of vegetable origin. A satisfactory reduced-fat prototype was obtained by using a 14% fat cream, which was specifically developed by diluting double cream with a suspension of carob seed flour. The composition of the new cheese changed with respect to the control, but the sensory characteristics were not impaired. Moisture increased from 62·6 to 68·4%, fat on dry matter decreased from 59·1 to 34·7%, and the caloric content decreased from 1060·8 to 718 J/100 g. Proteolysis and lipolysis were not affected by the technological modifications: after 7 d storage, the electrophoretic pattern of caseins and the free fatty acids profile of experimental and control cheeses were not significantly different. Fortification of reduced-fat Burrata with PUFA was obtained by using two commercial formulates available at a compatible price with the current economic values of the cheese. The two formulates derived from flaxseeds and Carthamus tinctorius oil and allowed enrichment in C18 :3 : n3 (α-linolenic acid, ALA), and 9cis,11trans- and 10trans,12cis- conjugated linoleic acid (CLA), respectively. Fortification was easy to perform under a technical point of view, but the negative sensory impact limited fortification at a maximum of 7·0 mg g-1 fat ALA and 6·8 g-1 fat CLA.
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A Summary of Actinide Enrichment Technologies and Capability Gaps
DOE Office of Scientific and Technical Information (OSTI.GOV)
Patton, Bradley D.; Robinson, Sharon M.
2017-01-01
The evaluation performed in this study indicates that a new program is needed to efficiently provide a national actinide radioisotope enrichment capability to produce milligram-to-gram quantities of unique materials for user communities. This program should leverage past actinide enrichment, the recent advances in stable isotope enrichment, and assessments of the future requirements to cost effectively develop this capability while establishing an experience base for a new generation of researchers in this vital area. Preliminary evaluations indicate that an electromagnetic isotope separation (EMIS) device would have the capability to meet the future needs of the user community for enriched actinides. Themore » EMIS technology could be potentially coupled with other enrichment technologies, such as irradiation, as pre-enrichment and/or post-enrichment systems to increase the throughput, reduce losses of material, and/or reduce operational costs of the base EMIS system. Past actinide enrichment experience and advances in the EMIS technology applied in stable isotope separations should be leveraged with this new evaluation information to assist in the establishment of a domestic actinide radioisotope enrichment capability.« less
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Lal, Devyani; Keim, Paul; Delisle, Josie; Barker, Bridget; Rank, Matthew A; Chia, Nicholas; Schupp, James M; Gillece, John D; Cope, Emily K
2017-06-01
The role of microbiota in sinonasal inflammation can be further understood by targeted sampling of healthy and diseased subjects. We compared the microbiota of the middle meatus (MM) and inferior meatus (IM) in healthy, allergic rhinitis (AR), and chronic rhinosinusitis (CRS) subjects to characterize intrasubject, intersubject, and intergroup differences. Subjects were recruited in the office, and characterized into healthy, AR, and CRS groups. Endoscopically-guided swab samples were obtained from the MM and IM bilaterally. Bacterial microbiota were characterized by sequencing the V3-V4 region of the 16S ribosomal RNA (rRNA) gene. Intersubject microbiome analyses were conducted in 65 subjects: 8 healthy, 11 AR, and 46 CRS (25 CRS with nasal polyps [CRSwNP]; 21 CRS without nasal polyps [CRSsNP]). Intrasubject analyses were conducted for 48 individuals (4 controls, 11 AR, 8 CRSwNP, and 15 CRSwNP). There was considerable intersubject microbiota variability, but intrasubject profiles were similar (p = 0.001, nonparametric t test). Intrasubject bacterial diversity was significantly reduced in MM of CRSsNP subjects compared to IM samples (p = 0.022, nonparametric t test). CRSsNP MM samples were enriched in Streptococcus, Haemophilus, and Fusobacterium spp. but exhibited loss of diversity compared to healthy, CRSwNP, and AR subject-samples (p < 0.05; nonparametric t test). CRSwNP patients were enriched in Staphylococcus, Alloiococcus, and Corynebacterium spp. This study presents the sinonasal microbiome profile in one of the larger populations of non-CRS and CRS subjects, and is the first office-based cohort in the literature. In contrast to healthy, AR, and CRSwNP subjects, CRSsNP MM samples exhibited decreased microbiome diversity and anaerobic enrichment. CRSsNP MM samples had reduced diversity compared to same-subject IM samples, a novel finding. © 2017 ARS-AAOA, LLC.
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Effect of red clay on diesel bioremediation and soil bacterial community.
Jung, Jaejoon; Choi, Sungjong; Hong, Hyerim; Sung, Jung-Suk; Park, Woojun
2014-08-01
Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.
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Reduced Set of Virulence Genes Allows High Accuracy Prediction of Bacterial Pathogenicity in Humans
Iraola, Gregorio; Vazquez, Gustavo; Spangenberg, Lucía; Naya, Hugo
2012-01-01
Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of different virulence-related genes among more than finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes () is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at ), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions. PMID:22916122
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Rogers, Jake; Li, Shanshan; Lanfumey, Laurence; Hannan, Anthony J; Renoir, Thibault
2017-08-14
Along with being the main target of many antidepressant medications, the serotonin transporter (5-HTT) is known to be involved in the pathophysiology of depression and anxiety disorders. In line with this, mice with varying 5-HTT genotypes are invaluable tools to study depression- and anxiety-like behaviours as well as the mechanisms mediating potential therapeutics. There is clear evidence that both genetic and environmental factors play a role in the aetiology of psychiatric disorders. In that regard, housing paradigms which seek to enhance cognitive stimulation and physical activity have been shown to exert beneficial effects in animal models of neuropsychiatric disorders. In the present study, we examined the effects of environmental enrichment on affective-like behaviours and sensorimotor gating function of 5-HTT knock-out (KO) mice. Using the elevated-plus maze and the light-dark box, we found that environmental enrichment ameliorated the abnormal innate anxiety of 5-HTT KO mice on both tests. In contrast, environmental enrichment did not rescue the depression-like behaviour displayed by 5-HTT KO mice in the forced-swim test. Finally, measuring pre-pulse inhibition, we found no effect of genotype or treatment on sensorimotor gating. In conclusion, our data suggest that environmental enrichment specifically reduces innate anxiety of 5-HTT KO mice with no amelioration of the depression-like behaviour. This has implications for the current use of clinical interventions for patients with symptoms of both anxiety and depression. Copyright © 2017 Elsevier B.V. All rights reserved.
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Bacterial mobilization and transport through manure enriched soils: Experiment and modeling.
Sepehrnia, N; Memarianfard, L; Moosavi, A A; Bachmann, J; Guggenberger, G; Rezanezhad, F
2017-10-01
A precise evaluation of bacteria transport and mathematical investigations are useful for best management practices in agroecosystems. In this study, using laboratory experiments and modeling approaches, we assess the transport of bacteria released from three types of manure (cow, sheep, and poultry) to find the importance of the common manures in agricultural activities in soil and water pollution. Thirty six intact soil columns with different textures (sandy, loamy, and silty clay loam) were sampled. Fecal coliform leaching from layers of the manures on the soil surface was conducted under steady-state saturated flow conditions at 20 °C for up to four Pore Volumes (PVs). Separate leaching experiments were conducted to obtain the initial concentrations of bacteria released from the manures (Co). Influent (Co) and effluent (C) bacteria concentrations were measured by the plate-count method and the normalized concentrations (C/C0) were plotted versus PV representing the breakthrough curves (BTCs). Transport parameters were predicted using the attachment/detachment model (two-kinetic site) in HYDRUS-1D. Simulations fitted well the experimental data (R 2 = 0.50-0.96). The attachment, detachment, and straining coefficients of bacteria were more influenced by the soils treated with cow manure compared to the sheep and poultry manures. Influent curves of fecal coliforms from the manures (leached without soil) illustrated that the poultry manure had the highest potential to pollute the effluent water from the soils in term of concentration, but the BTCs and simulated data related to the treated soils illustrated that the physical shape of cow manure was more important to both straining and detachment of bacteria back into the soil solution. Detachment trends of bacteria were observed through loam and silty clay loam soils treated with cow manure compared to the cow manure enriched sandy soil. We conclude that management strategies must specifically minimize the
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Chikere, Chioma B; Surridge, Karen; Okpokwasili, Gideon C; Cloete, Thomas E
2012-03-01
Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The
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Jamal, Mamdoh T; Pugazhendi, Arulazhagan
2018-06-01
A halophilic bacterial consortium was enriched from Red Sea saline water and sediment samples collected from Abhor, Jeddah, Saudi Arabia. The consortium potentially degraded different low (above 90% for phenanthrene and fluorene) and high (69 ± 1.4 and 56 ± 1.8% at 50 and 100 mg/L of pyrene) molecular weight polycyclic aromatic hydrocarbons (PAHs) at different concentrations under saline condition (40 g/L NaCl concentration). The cell hydrophobicity (91° ± 1°) and biosurfactant production (30 mN/m) confirmed potential bacterial cell interaction with PAHs to facilitate biodegradation process. Co-metabolic study with phenanthrene as co-substrate during pyrene degradation recorded 90% degradation in 12 days. The consortium in continuous stirred tank reactor with petroleum refinery wastewater showed complete and 90% degradation of low and high molecular weight PAHs, respectively. The reactor study also revealed 94 ± 1.8% chemical oxygen demand removal by the halophilic consortium under saline condition (40 g/L NaCl concentration). The halophilic bacterial strains present in the consortium were identified as Ochrobactrum halosaudis strain CEES1 (KX377976), Stenotrophomonas maltophilia strain CEES2 (KX377977), Achromobacter xylosoxidans strain CEES3 (KX377978) and Mesorhizobium halosaudis strain CEES4 (KX377979). Thus, the promising halophilic consortium was highly recommended to be employed in petroleum saline wastewater treatment process.
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Brouwer, M C; van de Beek, D
2012-05-01
Bacterial meningitis is a severe disease which affects 35.000 Europeans each year and has a mortality rate of about 20%. During the past 25 years the epidemiology of bacterial meningitis has changed significantly due to the implementation of vaccination against Haemophilus influenzae, Neisseria meningtidis group C and Streptococcus pneumoniae. Due to these vaccines, meningitis is now predominantly a disease occurring in adults, caused especially by Streptococcus pneumoniae, while it was formerly a child disease which was largely caused by Haemophilus influenzae. Bacterial meningitis is often difficult to recognize since the classical presentation with neck stiffness, reduced awareness and fever occurs in less than half of the patients. The only way to diagnose or exclude bacterial meningitis is by performing low-threshold cerebrospinal fluid examination with a suspicion of bacterial meningitis. The treatment consists of the prescription of antibiotics and dexamethasone.
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Berasategi, Izaskun; Navarro-Blasco, Iñigo; Calvo, Maria Isabel; Cavero, Rita Yolanda; Astiasarán, Iciar; Ansorena, Diana
2014-03-01
Reduced-energy and reduced-fat Bologna products enriched with ω-3 polyunsaturated fatty acids were formulated by replacing the pork back-fat by an oil-in-water emulsion containing a mixture of linseed-algae oil stabilized with a lyophilized Melissa officinalis extract. Healthier composition and lipid profile was obtained: 85 kcal/100 g, 3.6% fat, 0.6 g ALA and 0.44 g DHA per 100 g of product and ω-6/ω-3 ratio of 0.4. Technological and sensory problems were not detected in the new formulations. Reformulation did not cause oxidation problems during 32 days of storage under refrigeration. The results suggest that it is possible to obtain reduced-fat Bologna-type sausages rich in ALA and DHA and stabilized with natural antioxidants, applying the appropriate technology without significant effects on the sensory quality, yielding interesting products from a nutritional point of view. © 2013.
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Maternal presence and environmental enrichment affect food neophobia of piglets
Oostindjer, Marije; Muñoz, Julia Mas; Van den Brand, Henry; Kemp, Bas; Bolhuis, J. Elizabeth
2011-01-01
Young omnivores show food neophobia in order to avoid the potential harmful effects of ingesting unfamiliar food items. We investigated whether the presence of the mother and an enriched rearing environment would reduce food neophobia in piglets. A mother may provide information on suitable food types to include in the diet, whereas an enriched environment may stimulate behavioural development and reduce reactivity towards novel stimuli (including food). Five barren-reared or enriched-reared piglets per litter were exposed to two novel food items in the presence, and the other five per litter in the absence, of the mother in a 7 min test. Maternal presence reduced food neophobia profoundly as reflected in a reduced latency to touching the food, a higher proportion of piglets sampling the two different food items and a higher intake. Latency to touch the food, however, was affected by maternal presence more strongly for barren-reared piglets than for enriched-reared piglets, and in the absence of the sow, consumption of one novel food type and time spent in the feeding area were higher for enriched-reared piglets. Environmental enrichment does have the potential to reduce food neophobia, but the presence of the mother during the encounter with novel food seems more efficient in decreasing food neophobia of piglets. PMID:20554557
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de Aguiar, Sílvia Cristina; Zeoula, Lucia Maria; do Prado, Odimari Pricila Pires; Arcuri, Pedro Braga; Forano, Evelyne
2014-11-01
Propolis presents many biological properties, including antibacterial activities, and has been proposed as an additive in ruminant nutrition. Twenty bacterial strains, previously isolated from enrichments of Brazilian cow rumen contents in the presence of different propolis extracts (LLOS), were characterized using phenotyping and 16S rRNA identification. Seven strains were assigned to Streptococcus sp., most likely S. bovis, and were all degrading starch. One amylolytic lactate-utilizing strain of Selenomonas ruminantium was also found. Two strains of Clostridium bifermentans were identified and showed proteolytic activity. Two strains were assigned to Mitsuokella jalaludinii and were saccharolytic. One strain belonged to a Bacillus species and seven strains were affiliated with Escherichia coli. All of the 20 strains were able to use many sugars, but none of them were able to degrade the polysaccharides carboxymethylcellulose and xylans. The effect of three propolis extracts (LLOS B1, C1 and C3) was tested on the in vitro growth of four representative isolates of S. bovis, E. coli, M. jalaludinii and C. bifermentans. The growth of S. bovis, E. coli and M. jalaludinii was not affected by the three propolis extracts at 1 mg ml(-1). C. bifermentans growth was completely inhibited at this LLOS concentration, but this bacterium was partially resistant at lower concentrations. LLOS C3, with the lower concentration of phenolic compounds, was a little less inhibitory than B1 and C1 on this strain.
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Bowling, Frank L; Stickings, Daryl S; Edwards-Jones, Valerie; Armstrong, David G; Boulton, Andrew Jm
2009-05-08
The purpose of this study was to assess the level of air contamination with bacteria after surgical hydrodebridement and to determine the effectiveness of hydro surgery on bacterial reduction of a simulated infected wound. Four porcine samples were scored then infected with a broth culture containing a variety of organisms and incubated at 37 degrees C for 24 hours. The infected samples were then debrided with the hydro surgery tool (Versajet, Smith and Nephew, Largo, Florida, USA). Samples were taken for microbiology, histology and scanning electron microscopy pre-infection, post infection and post debridement. Air bacterial contamination was evaluated before, during and after debridement by using active and passive methods; for active sampling the SAS-Super 90 air sampler was used, for passive sampling settle plates were located at set distances around the clinic room. There was no statistically significant reduction in bacterial contamination of the porcine samples post hydrodebridement. Analysis of the passive sampling showed a significant (p < 0.001) increase in microbial counts post hydrodebridement. Levels ranging from 950 colony forming units per meter cubed (CFUs/m3) to 16780 CFUs/m3 were observed with active sampling of the air whilst using hydro surgery equipment compared with a basal count of 582 CFUs/m3. During removal of the wound dressing, a significant increase was observed relative to basal counts (p < 0.05). Microbial load of the air samples was still significantly raised 1 hour post-therapy. The results suggest a significant increase in bacterial air contamination both by active sampling and passive sampling. We believe that action might be taken to mitigate fallout in the settings in which this technique is used.
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Enrichment of clinical study populations.
Temple, R
2010-12-01
Those who conduct clinical trials "enrich" study populations in a variety of ways in order to identify a population of patients in whom a drug effect, if present, is more likely to be demonstrable. The principal ways to do this are as follows: (i) practical enrichment, i.e., generally seeking to reduce noise (variability of measurement) and heterogeneity (by avoiding the enrollment of patients with other diseases and individuals in whom the disease disappears spontaneously), (ii) prognostic enrichment, i.e., finding patients who are likely to have the event of interest when enrolling for risk-reduction studies, and (iii) predictive enrichment, i.e., finding the individuals who are more likely to respond. Enrichment fits well into the growing interest in "individualization" of therapy but creates some tension with another trend, namely, the desire for "real-world studies" with less restrictive entry criteria and other requirements.
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Long, Rachel M; Lappin-Scott, Hilary M; Stevens, Jamie R
2009-07-01
The degradation of polycyclic aromatic compounds (PACs) has been widely studied. Knowledge of the degradation of PACs by microbial populations can be utilized in the remediation of contaminated sites. To isolate and identify PAC-degrading bacteria for potential use in future bioremediation programmes, we established a series of PAC enrichments under the same experimental conditions from a single sediment sample taken from a highly polluted estuarine site. Enrichment cultures were established using the pollutants: anthracene, phenanthrene and dibenzothiophene as a sole carbon source. The shift in microbial community structure on each of these carbon sources was monitored by analysis of a time series of samples from each culture using 16S rRNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Significantly, our findings demonstrate that shifts in the constituent species within each degradative community are directly attributable to enrichment with different PACs. Subsequently, we characterized the microorganisms comprising the degradative communities within each enrichment using 16S rRNA sequence data. Our findings demonstrate that the ability to degrade PACs is present in five divisions of the Proteobacteria and Actinobacteria. By determining the precise identity of the PAC-degrading bacterial species isolated from a single sediment sample, and by comparing our findings with previously published research, we demonstrate how bacteria with similar PAC degrading capabilities and 16S rRNA signatures are found in similarly polluted environments in geographically very distant locations, e.g., China, Italy, Japan and Hawaii. Such a finding suggests that geographical barriers do not limit the distribution of key PAC-degrading bacteria; this finding is in accordance with the Baas-Becking hypothesis "everything is everywhere; the environment selects" and may have significant consequences for the global distribution of PAC-degrading bacteria and
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NASA Astrophysics Data System (ADS)
Coelho, Francisco J. R. C.; Louvado, António; Domingues, Patrícia M.; Cleary, Daniel F. R.; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R.; Cunha, Ângela; Gomes, Newton C. M.
2016-10-01
The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.
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Coelho, Francisco J. R. C.; Louvado, António; Domingues, Patrícia M.; Cleary, Daniel F. R.; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R.; Cunha, Ângela; Gomes, Newton C. M.
2016-01-01
The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults. PMID:27762306
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Coelho, Francisco J R C; Louvado, António; Domingues, Patrícia M; Cleary, Daniel F R; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R; Cunha, Ângela; Gomes, Newton C M
2016-10-20
The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.
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Status of reduced enrichment programs for research reactors in Japan
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kanda, Keiji; Nishihara, Hedeaki; Shirai, Eiji
1997-08-01
The reduced enrichment programs for the JRR-2, JRR-3, JRR-4 and JMTR of Japan Atomic Energy Research Institute (JAERI), and the KUR of Kyoto University Research Reactor Institute (KURRI) have been partially completed and are mostly still in progress under the Joint Study Programs with Argonne National Laboratory (ANL). The JMTR and JRR-2 have been already converted to use MEU aluminide fuels in 1986 and 1987, respectively. The operation of the upgraded JRR-3(JRR-3M) has started in March 1990 with the LEU aluminide fuels. Since May 1992, the two elements have been inserted in the KUR. The safety review application for themore » full core conversion to use LEU silicide in the JMTR was approved in February 1992 and the conversion has been done in January 1994. The Japanese Government approved a cancellation of the KUHFR Project in February 1991, and in April 1994 the U.S. Government gave an approval to utilize HEU in the KUR instead of the KUHFR. Therefore, the KUR will be operated with HEU fuel until 2001. Since March 1994, Kyoto University is continuing negotiation with UKAEA Dounreay on spent fuel reprocessing and blending down of recovered uranium, in addition to that with USDOE.« less
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Enhanced delignification of steam-pretreated poplar by a bacterial laccase
Singh, Rahul; Hu, Jinguang; Regner, Matthew R.; ...
2017-02-07
The recalcitrance of woody biomass, particularly its lignin component, hinders its sustainable transformation to fuels and biomaterials. Although the recent discovery of several bacterial ligninases promises the development of novel biocatalysts, these enzymes have largely been characterized using model substrates: direct evidence for their action on biomass is lacking. Herein, we report the delignification of woody biomass by a small laccase (sLac) from Amycolatopsis sp. 75iv3. Incubation of steam-pretreated poplar (SPP) with sLac enhanced the release of acid-precipitable polymeric lignin (APPL) by ~6-fold, and reduced the amount of acid-soluble lignin by ~15%. NMR spectrometry revealed that the APPL was significantlymore » syringyl-enriched relative to the original material (~16:1 vs. ~3:1), and that sLac preferentially oxidized syringyl units and altered interunit linkage distributions. sLac’s substrate preference among monoaryls was also consistent with this observation. In addition, sLac treatment reduced the molar mass of the APPL by over 50%, as determined by gel-permeation chromatography coupled with multi-angle light scattering. Finally, sLac acted synergistically with a commercial cellulase cocktail to increase glucose production from SPP ~8%. Altogether, this study establishes the lignolytic activity of sLac on woody biomass and highlights the biocatalytic potential of bacterial enzymes.« less
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Enhanced delignification of steam-pretreated poplar by a bacterial laccase
DOE Office of Scientific and Technical Information (OSTI.GOV)
Singh, Rahul; Hu, Jinguang; Regner, Matthew R.
The recalcitrance of woody biomass, particularly its lignin component, hinders its sustainable transformation to fuels and biomaterials. Although the recent discovery of several bacterial ligninases promises the development of novel biocatalysts, these enzymes have largely been characterized using model substrates: direct evidence for their action on biomass is lacking. Herein, we report the delignification of woody biomass by a small laccase (sLac) from Amycolatopsis sp. 75iv3. Incubation of steam-pretreated poplar (SPP) with sLac enhanced the release of acid-precipitable polymeric lignin (APPL) by ~6-fold, and reduced the amount of acid-soluble lignin by ~15%. NMR spectrometry revealed that the APPL was significantlymore » syringyl-enriched relative to the original material (~16:1 vs. ~3:1), and that sLac preferentially oxidized syringyl units and altered interunit linkage distributions. sLac’s substrate preference among monoaryls was also consistent with this observation. In addition, sLac treatment reduced the molar mass of the APPL by over 50%, as determined by gel-permeation chromatography coupled with multi-angle light scattering. Finally, sLac acted synergistically with a commercial cellulase cocktail to increase glucose production from SPP ~8%. Altogether, this study establishes the lignolytic activity of sLac on woody biomass and highlights the biocatalytic potential of bacterial enzymes.« less
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Parental material and cultivation determine soil bacterial community structure and fertility.
Sun, Li; Gao, Jusheng; Huang, Ting; Kendall, Joshua R A; Shen, Qirong; Zhang, Ruifu
2015-01-01
Microbes are the key components of the soil environment, playing important roles during soil development. Soil parent material provides the foundation elements that comprise the basic nutritional environment for the development of microbial community. After 30 years artificial maturation of cultivation, the soil developments of three different parental materials were evaluated and bacterial community compositions were investigated using the high-throughput sequencing approach. Thirty years of cultivation increased the soil fertility and soil microbial biomass, richness and diversity, greatly changed the soil bacterial communities, the proportion of phylum Actinobacteria decreased significantly, while the relative abundances of the phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Armatimonadetes and Nitrospira were significantly increased. Soil bacterial communities of parental materials were separated with the cultivated ones, and comparisons of different soil types, granite soil and quaternary red clay soil were similar and different with purple sandy shale soil in both parental materials and cultivated treatments. Bacterial community variations in the three soil types were affected by different factors, and their alteration patterns in the soil development also varied with soil type. Soil properties (except total potassium) had a significant effect on the soil bacterial communities in all three soil types and a close relationship with abundant bacterial phyla. The amounts of nitrogen-fixing bacteria as well as the abundances of the nifH gene in all cultivated soils were higher than those in the parental materials; Burkholderia and Rhizobacte were enriched significantly with long-term cultivation. The results suggested that crop system would not deplete the nutrients of soil parental materials in early stage of soil maturation, instead it increased soil fertility and changed bacterial community, specially enriched the nitrogen-fixing bacteria to accumulate
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Uppal, Lipi; Singhi, Sunit; Singhi, Pratibha; Aggarwal, Ritu
2017-06-01
Treatment of acute bacterial meningitis in children with bactericidal antibiotics causes cell wall lysis and a surge in inflammatory cascade, which in turn contributes to neuronal damage and morbidity. Pretreatment with a nonbacteriolytic antibiotic, such as rifampin, has been shown to attenuate the inflammatory response in experimental models of bacterial meningitis. In a pilot study, in children with bacterial meningitis, we have studied markers of inflammatory response and neuronal damage in 2 groups of children with bacterial meningitis; one group received rifampin pretreatment with ceftriaxone and the other group received ceftriaxone alone. Forty children with bacterial meningitis, who were 3 months to 12 years of age, were randomly assigned to receive either a single dose rifampin (20 mg/kg) 30 minutes before ceftriaxone or ceftriaxone alone was given. The primary outcome variables were cerebrospinal fluid (CSF) concentrations of tumor necrosis factor alpha (TNFα), S100B and neuron-specific enolase on day 1 and day 5, and secondary outcome variables were the values of TNFα and interleukin 6 in serum on day 1 and day 5; hearing and neurologic sequelae at 3 months after recovery from the illness. Children in rifampin pretreatment group had significantly lower CSF TNFα concentrations [median (interquartile range [IQR]): 15.5 (7.2-22.0) vs. 53.0 (9.0-87.5) pg/mL, P = 0.019] and S100B [median (IQR): 145.0 (54.7-450.0) vs. 447.5 (221.0-804.6) pg/mL, P = 0.033] on day 1 and S100B [median (IQR): 109.7 (64.0-287.0) vs. 322 (106.7-578.0) pg/mL, P = 0.048] and neuron-specific enolase [median (IQR): 8.6 (5-14.75) vs. 18.2 (7.0-28.75) ng/mL, P = 0.035] on day 5 when compared with ceftriaxone alone group. The rifampin-treated group also had reduced morbidity and neurologic sequelae; however, these were not statistically significant. Pretreatment with single dose rifampin 30 minutes before ceftriaxone administration reduced the CSF concentrations of markers of
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Environmental enrichment for aquatic animals.
Corcoran, Mike
2015-05-01
Aquatic animals are the most popular pets in the United States based on the number of owned pets. They are popular display animals and are increasingly used in research settings. Enrichment of captive animals is an important element of zoo and laboratory medicine. The importance of enrichment for aquatic animals has been slower in implementation. For a long time, there was debate over whether or not fish were able to experience pain or form long-term memories. As that debate has reduced and the consciousness of more aquatic animals is accepted, the need to discuss enrichment for these animals has increased. Copyright © 2015 Elsevier Inc. All rights reserved.
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USDA-ARS?s Scientific Manuscript database
The effectiveness of pre-evisceration, skin-on carcass sanitation on reducing bacterial contamination of beef carcasses was tested using 3 cattle per treatment and 3 cattle as controls at each of 3 abattoirs in southern Wisconsin. The sanitation procedure included stunning, bleeding, tying off the e...
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Over four years (1998-2001), we examined the effects of CO2 enrichment on stomatal conductance (gs) of sun and shade leaves of overstory sweetgum (Liquidambar styraciflua L.) grown at the Duke Forest Free Air Carbon CO2 Enrichment (FACE) experiment. Gas exchange measurements were...
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Bacterial diversity in the feces of dogs with CPV infection.
Zheng, Yun; Hao, Xiangqi; Lin, Xi; Zheng, Qingxu; Zhang, Wenyan; Zhou, Pei; Li, Shoujun
2018-04-27
Canine parvovirus (CPV) is a contagious disease in dogs that has high morbidity and mortality. In cases of infection, the pups tend to have a higher mortality and more severe clinical symptoms than the adult dogs because the dehydration is difficult for pups to bear. Following the natural infection, there is a rapid antibody response neutralizing the extracellular virus. As a result, virus titers in tissue and feces become markedly reduced. Hence, it is important to have an effective symptomatic therapy of supporting animals to survive in the early stages of CPV infection. Furthermore, the co-infection with bacteria could increase the severity of lesions and clinical signs as well. In this paper, we obtained the bacterial diversity in feces of CPV infected dogs with the enrichment of five bacteria genera (Shigella, Peptoclostridium, Peptostreptococcus, Streptococcus, Fusobacterium). These microorganisms may partly result in the intestinal pathology of the infection. In summary, the discussion of the bacterial biodiversity in feces of CPV infected dogs provides further insights into the pathology of CPV disease and the targets of developing more effective treatment strategies. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Cr(VI) remediation by enriched sediment with anthraquinone-2,6-disulfonate as electron shuttles
NASA Astrophysics Data System (ADS)
Chen, Hong; Li, Xiaojuan; Xu, Zhiwei
Hexavalent chromium (Cr(VI)) is a priority pollutant in the USA and many other countries. This study investigated the simultaneous remediation of Cr(VI) in sediment enriched with quinone-reducing microorganisms via a closely coupled, biotic-abiotic pathway. The results showed that Cr(VI) remediation was achieved by sediment adsorption and reduction of quinone-reducing microorganism. Moreover, microorganism reduction of Cr(VI) could be continued when sediment adsorption was saturated after long-term Cr(VI) remediation. The acetate and anthraquinone-2,6-disulfonate (AQDS), which acted as exogenous carbon and electron shuttle, respectively, were two crucial factors. The optimum concentrations of acetate and AQDS were 5 mM and 1 mM when the initial Cr(VI) concentration was 10 mg/L. AQDS was recycled, and it acted in a catalytic-type manner for the bacterial reduction of Cr(VI). Thus, biological humus reduction might provide an extensive pathway for the sequestration and detoxification of Cr(VI) in anaerobic soils, water, and industrial effluents.
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Penedo, Letícia A; Nunes, Juliana C; Gama, Marco Antônio S; Leite, Paulo Emilio C; Quirico-Santos, Thereza F; Torres, Alexandre G
2013-12-01
A conjugated linoleic acid (CLA) depletion-repletion study was carried out to investigate the effects of dietary c9,t11 CLA on C-reactive protein, transcription factor NFκB, metalloproteinases 2 and 9, inflammatory mediators (adiponectin, TNFα, IL-2, IL-4, IL-8, IL-10), body composition, and erythrocyte membrane composition in healthy normal-weight human adults. CLA depletion was achieved through an 8-week period of restricted dairy fat intake (depletion phase; CLA intake was 5.2±5.8 mg/day), followed by an 8-week period in which individuals consumed 20 g/day of butter naturally enriched with c9,t11 CLA (repletion phase; CLA intake of 1020±167 mg/day). The participants were 29 healthy adult volunteers (19 women and 10 men, aged 22 to 36 years), with body mass index between 18.0 and 29.9 kg m(-2). Blood samples were collected at baseline and at the end of both depletion and repletion phases. The content of CLA in erythrocytes decreased during CLA-depletion and increased during CLA-repletion. Intake of CLA-enriched butter increased the serum levels of anti-inflammatory IL-10 but reduced transcription factor NFκB in blood and serum levels of TNFα, IL-2, IL-8 and inactive metalloproteinase-9. Moreover, reduced activity of metalloproteinases 2 and 9 in serum was observed during the CLA-repletion period. In contrast, intake of CLA-enriched butter had no effects on body composition (DXA analysis) as well as on serum levels of adiponectin, C-reactive protein, and IL-4. Taken together, our results indicate that the intake of a c9,t11 CLA-enriched butter by normal-weight subjects induces beneficial changes in immune modulators associated with sub-clinical inflammation in overweight individuals. © 2013.
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de Andrade Gagheggi Ravanini, Guilherme; Portari Filho, Pedro Eder; Abrantes Luna, Renato; Almeida de Oliveira, Vinicius
2015-08-01
this study aims to assess the organic inflammatory response of the video laparoscopic cholecystectomy, with abbreviation of the preoperative fasting to 2h using a carbohydrate and protein enriched solution. this is a randomized, prospective study with patients divided into the following 2 groups: group A, conventional fasting and group B, 2h abbreviated fasting with oral ingestion of a carbohydrate and protein solution. Serum glucose, insulin, interleukin 1, and TNF-α were mesasured before ingestion of the solution, during induction of anesthesia, and 4 h after the end of surgery. thirty-eight patients completed the study without presenting pulmonary complications associated with bronchoaspiration. The postoperative HOMA-IR variance was greater in group A (p = 0.001). the abbreviation of preoperative fasting for 2 h, using carbohydrate and protein enriched solutions, is safe, reduces insulin resistance, and does not increase the risk of bronchoaspiration. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.
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Review of environmental enrichment for broiler chickens.
Riber, A B; van de Weerd, H A; de Jong, I C; Steenfeldt, S
2018-02-01
Welfare problems are commonly found in both conventional and organic production of broiler chickens. In order to reduce the extent of welfare problems, it has been suggested to provide stimulating, enriched environments. The aim of the present paper is to provide a review of the effect on behavior and welfare of the different kinds of environmental enrichments in the production of broilers that have been described in the scientific literature. Environmental enrichment is defined as an improvement of the environment of captive animals, which increases the behavioral opportunities of the animal and leads to improvements of the biological function. This definition has been broadened to include practical and economic aspects, as any enrichment strategy that adversely affects the health of animals or that has too many economic or practical constraints will never be implemented on commercial farms and thus never benefit animals. Environmental enrichment for broilers often has the purpose of satisfying behavioral needs and/or stimulating the broilers to an increased level of activity, which among others will reduce the occurrence of leg problems. Potentially successful environmental enrichments for broiler chickens are elevated resting-places, panels, barriers, and bales of straw ("point-source enrichment"), as well as covered verandas and outdoor ranges ("complex enriched environments"). Many of the ideas for environmental enrichment for broilers need to be further developed and studied, preferably in commercial trials, with respect to the use, the effect on behavior and on other welfare aspects such as leg health, and the interaction with genotype, production system, stocking density, light, and flock size. In addition, information on the practical application and the economics of the production system is often lacking, although it is important for application in practice. © 2017 Poultry Science Association Inc.
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Zhang, Zhongming; Chen, Hong; Liu, Jin; Ali, Muhammad; Liu, Fan; Li, Lin
2013-01-01
Manganese-oxidizing bacteria in the aquatic environment have been comprehensively investigated. However, little information is available about the distribution and biogeochemical significance of these bacteria in terrestrial soil environments. In this study, stratified soils were initially examined to investigate the community structure and diversity of manganese-oxidizing bacteria. Total 344 culturable bacterial isolates from all substrata exhibited Mn(II)-oxidizing activities at the range of 1 µM to 240 µM of the equivalent MnO2. The high Mn(II)-oxidizing isolates (>50 mM MnO2) were identified as the species of phyla Actinobacteria, Firmicutes and Proteobacteria. Seven novel Mn(II)-oxidizing bacterial genera (species), namely, Escherichia, Agromyces, Cellulomonas, Cupriavidus, Microbacterium, Ralstonia, and Variovorax, were revealed via comparative phylogenetic analysis. Moreover, an increase in the diversity of soil bacterial community was observed after the combined enrichment of Mn(II) and carbon-rich complex. The phylogenetic classification of the enriched bacteria represented by predominant denaturing gradient gel electrophoresis bands, was apparently similar to culturable Mn(II)-oxidizing bacteria. The experiments were further undertaken to investigate the properties of the Mn oxide aggregates formed by the bacterial isolates with high Mn(II)-oxidizing activity. Results showed that these bacteria were closely encrusted with their Mn oxides and formed regular microspherical aggregates under prolonged Mn(II) and carbon-rich medium enrichment for three weeks. The biotic oxidation of Mn(II) to Mn(III/IV) by these isolates was confirmed by kinetic examinations. X-ray diffraction assays showed the characteristic peaks of several Mn oxides and rhodochrosite from these aggregates. Leucoberbelin blue tests also verified the Mn(II)-oxidizing activity of these aggregates. These results demonstrated that Mn oxides were formed at certain amounts under the enrichment
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Blue Light Enhances Bacterial Clearance and Reduces Organ Injury During Sepsis.
Lewis, Anthony J; Zhang, Xianghong; Griepentrog, John E; Yuan, Du; Collage, Richard D; Waltz, Paul K; Angus, Derek C; Zuckerbraun, Brian S; Rosengart, Matthew R
2018-05-04
The physiology of nearly all mammalian organisms are entrained by light and exhibit circadian rhythm. The data derived from animal studies show that light influences immunity, and these neurophysiologic pathways are maximally entrained by the blue spectrum. Here, we hypothesize that bright blue light reduces acute kidney injury by comparison with either bright red or standard, white fluorescent light in mice subjected to sepsis. To further translational relevance, we performed a pilot clinical trial of blue light therapy in human subjects with appendicitis. Laboratory animal research, pilot human feasibility trial. University basic science laboratory and tertiary care hospital. Male C57BL/6J mice, adult (> 17 yr) patients with acute appendicitis. Mice underwent cecal ligation and puncture and were randomly assigned to a 24-hour photoperiod of bright blue, bright red, or ambient white fluorescent light. Subjects with appendicitis were randomized to receive postoperatively standard care or standard care plus high-illuminance blue light. Exposure to bright blue light enhanced bacterial clearance from the peritoneum, reduced bacteremia and systemic inflammation, and attenuated the degree of acute kidney injury. The mechanism involved an elevation in cholinergic tone that augmented tissue expression of the nuclear orphan receptor REV-ERBα and occurred independent of alterations in melatonin or corticosterone concentrations. Clinically, exposure to blue light after appendectomy was feasible and reduced serum interleukin-6 and interleukin-10 concentrations. Modifying the spectrum of light may offer therapeutic utility in sepsis.
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Fairhurst, Graham D.; Frey, Matthew D.; Reichert, James F.; Szelest, Izabela; Kelly, Debbie M.; Bortolotti, Gary R.
2011-01-01
Enrichment is widely used as tool for managing fearfulness, undesirable behaviors, and stress in captive animals, and for studying exploration and personality. Inconsistencies in previous studies of physiological and behavioral responses to enrichment led us to hypothesize that enrichment and its removal are stressful environmental changes to which the hormone corticosterone and fearfulness, activity, and exploration behaviors ought to be sensitive. We conducted two experiments with a captive population of wild-caught Clark's nutcrackers (Nucifraga columbiana) to assess responses to short- (10-d) and long-term (3-mo) enrichment, their removal, and the influence of novelty, within the same animal. Variation in an integrated measure of corticosterone from feathers, combined with video recordings of behaviors, suggests that how individuals perceive enrichment and its removal depends on the duration of exposure. Short- and long-term enrichment elicited different physiological responses, with the former acting as a stressor and birds exhibiting acclimation to the latter. Non-novel enrichment evoked the strongest corticosterone responses of all the treatments, suggesting that the second exposure to the same objects acted as a physiological cue, and that acclimation was overridden by negative past experience. Birds showed weak behavioral responses that were not related to corticosterone. By demonstrating that an integrated measure of glucocorticoid physiology varies significantly with changes to enrichment in the absence of agonistic interactions, our study sheds light on potential mechanisms driving physiological and behavioral responses to environmental change. PMID:21412426
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NASA Technical Reports Server (NTRS)
Tunlid, A.; Odham, G.; Findlay, R. H.; White, D. C.
1985-01-01
Sensitive detection of cellular components from specific groups of microbes can be utilized as 'signatures' in the examination of microbial consortia from soils, sediments or biofilms. Utilizing capillary gas chromatography/mass spectrometry and stereospecific derivatizing agents, D-alanine, a component localized in the prokaryotic (bacterial) cell wall, can be detected reproducibly. Enrichments of D-[15N]alanine determined in E. coli grown with [15N]ammonia can be determined with precision at 1.0 atom%. Chemical ionization with methane gas and the detection of negative ions (M - HF)- and (M - F or M + H - HF)- formed from the heptafluorobutyryl D-2 butanol ester of D-alanine allowed as little as 8 pg (90 fmol) to be detected reproducibly. This method can be utilized to define the metabolic activity in terms of 15N incorporation at the level of 10(3)-10(4) cells, as a function of the 15N-14N ratio.
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Wang, Jianjun; Pan, Feiyan; Soininen, Janne; Heino, Jani; Shen, Ji
2016-12-21
Climate effects and human impacts, that is, nutrient enrichment, simultaneously drive spatial biodiversity patterns. However, there is little consensus about their independent effects on biodiversity. Here we manipulate nutrient enrichment in aquatic microcosms in subtropical and subarctic regions (China and Norway, respectively) to show clear segregation of bacterial species along temperature gradients, and decreasing alpha and gamma diversity toward higher nutrients. The temperature dependence of species richness is greatest at extreme nutrient levels, whereas the nutrient dependence of species richness is strongest at intermediate temperatures. For species turnover rates, temperature effects are strongest at intermediate and two extreme ends of nutrient gradients in subtropical and subarctic regions, respectively. Species turnover rates caused by nutrients do not increase toward higher temperatures. These findings illustrate direct effects of temperature and nutrients on biodiversity, and indirect effects via primary productivity, thus providing insights into how nutrient enrichment could alter biodiversity under future climate scenarios.
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Nutrient enrichment modifies temperature-biodiversity relationships in large-scale field experiments
NASA Astrophysics Data System (ADS)
Wang, Jianjun; Pan, Feiyan; Soininen, Janne; Heino, Jani; Shen, Ji
2016-12-01
Climate effects and human impacts, that is, nutrient enrichment, simultaneously drive spatial biodiversity patterns. However, there is little consensus about their independent effects on biodiversity. Here we manipulate nutrient enrichment in aquatic microcosms in subtropical and subarctic regions (China and Norway, respectively) to show clear segregation of bacterial species along temperature gradients, and decreasing alpha and gamma diversity toward higher nutrients. The temperature dependence of species richness is greatest at extreme nutrient levels, whereas the nutrient dependence of species richness is strongest at intermediate temperatures. For species turnover rates, temperature effects are strongest at intermediate and two extreme ends of nutrient gradients in subtropical and subarctic regions, respectively. Species turnover rates caused by nutrients do not increase toward higher temperatures. These findings illustrate direct effects of temperature and nutrients on biodiversity, and indirect effects via primary productivity, thus providing insights into how nutrient enrichment could alter biodiversity under future climate scenarios.
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Zouch, Hana; Karray, Fatma; Armougom, Fabrice; Chifflet, Sandrine; Hirschler-Réa, Agnès; Kharrat, Hanen; Kamoun, Lotfi; Ben Hania, Wajdi; Ollivier, Bernard; Sayadi, Sami; Quéméneur, Marianne
2017-01-01
Anaerobic biotechnology using sulfate-reducing bacteria (SRB) is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG), an acidic (pH ~3) by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate) and sulfate sources (i.e., sodium sulfate or PG) as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia). Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures) was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB. PMID:28871244
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Ozbayram, E Gozde; Kleinsteuber, Sabine; Nikolausz, Marcell; Ince, Bahar; Ince, Orhan
2017-08-01
The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen microbiota to enhance the anaerobic digestion of lignocellulosic feedstock. An anaerobic cellulolytic culture was enriched from sheep rumen fluid using wheat straw as substrate under mesophilic conditions. To investigate the effects of bioaugmentation on methane production from straw, the enrichment culture was added to batch reactors in proportions of 2% (Set-1) and 4% (Set-2) of the microbial cell number of the standard inoculum slurry. The methane production in the bioaugmented reactors was higher than in the control reactors. After 30 days of batch incubation, the average methane yield was 154 mL N CH 4 g VS -1 in the control reactors. Addition of 2% enrichment culture did not enhance methane production, whereas in Set-2 the methane yield was increased by 27%. The bacterial communities were examined by 454 amplicon sequencing of 16S rRNA genes, while terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of mcrA genes was applied to analyze the methanogenic communities. The results highlighted that relative abundances of Ruminococcaceae and Lachnospiraceae increased during the enrichment. However, Cloacamonaceae, which were abundant in the standard inoculum, dominated the bacterial communities of all batch reactors. T-RFLP profiles revealed that Methanobacteriales were predominant in the rumen fluid, whereas the enrichment culture was dominated by Methanosarcinales. In the batch rectors, the most abundant methanogens were affiliated to Methanobacteriales and Methanomicrobiales. Our results suggest that bioaugmentation with sheep rumen enrichment cultures can enhance the performance of digesters treating lignocellulosic feedstock. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture
Johnson, Timothy A.; Stedtfeld, Robert D.; Wang, Qiong; Cole, James R.; Hashsham, Syed A.; Looft, Torey; Zhu, Yong-Guan
2016-01-01
ABSTRACT Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk. PMID:27073098
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Braikat, Mohamed; Barkia, Abdelaziz; El Mdaghri, Naima; Rainey, Jeanette J; Cohen, Adam L; Teleb, Nadia
2012-03-28
Haemophilus influenzae type b (Hib) is a leading cause of bacterial meningitis and pneumonia and can be prevented by Hib vaccine. We conducted a vaccine impact evaluation to support continued use of Hib vaccine in Morocco following introduction in 2007. Bacterial meningitis surveillance data from 2004 to 2009 were obtained from 11 sentinel hospitals located in eight provinces and one prefecture in Morocco to examine Hi meningitis reporting for cases aged <5 years. We defined the years of 2004-2006 as the pre-vaccine period and 2008-2009 as the post-vaccine period and compared the mean annual number of confirmed Hi meningitis cases for these time periods using a Chi-square test. We calculated the minimum incidence of Hi meningitis during the evaluation period in Grand Casa Prefecture, where the catchment population could be estimated. From 2004 to 2009, 1844 suspected meningitis case-patients aged <5 years were reported; 354 (19.2%) were confirmed with bacterial meningitis, including 105 (29.7%) Hi cases. The mean annual number of confirmed Hi meningitis cases decreased by 75%, from 24 in the pre-vaccine period to 6 during the post-vaccine period (p<0.001). Assuming Hi cases with unknown age were <5 years of age, the estimated minimum incidence of confirmed Hi meningitis in Grand Casa Prefecture decreased by 93%, from 15 cases per 100,000 children in the pre-vaccine period to 1 case per 100,000 children in the post-vaccine period. Hib vaccine introduction likely significantly reduced the occurrence of Hi meningitis among children aged <5 years at the 11 sentinel hospitals included in this evaluation in Morocco, suggesting that continued use of Hib vaccine in Morocco would be beneficial. Published by Elsevier Ltd.
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Ozbayram, Emine Gozde; Kleinsteuber, Sabine; Nikolausz, Marcell; Ince, Bahar; Ince, Orhan
2018-01-01
The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters treating lignocellulosic biomass such as straw. For that purpose, lignocellulose-degrading methanogenic communities were enriched on wheat straw from cow and goat rumen fluid as well as from a biogas reactor acclimated to lignocellulosic biomass (sorghum as mono-substrate). The bacterial communities of the enriched cultures and the different inocula were examined by 454 amplicon sequencing of 16S rRNA genes while the methanogenic archaeal communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the mcrA gene. Bacteroidetes was the most abundant phylum in all samples. Within the Bacteroidetes phylum, Bacteroidaceae was the most abundant family in the rumen-derived enrichment cultures, whereas Porphyromonadaceae was the predominant one in the reactor-derived culture. Additionally, the enrichment procedure increased the relative abundance of Ruminococcaceae (phylum: Firmicutes) in all cultures. T-RFLP profiles of the mcrA gene amplicons highlighted that the ruminal methanogenic communities were composed of hydrogenotrophic methanogens dominated by the order Methanobacteriales regardless of the host species. The methanogenic communities changed significantly during the enrichment procedure, but still the strict hydrogenotrophic Methanobacteriales and Methanomicrobiales were the predominant orders in the enrichment cultures. The bioaugmentation potential of the enriched methanogenic cultures will be evaluated in further studies.
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Grossmann, S; Dieckmann, G S
1994-08-01
Bacterial response to formation and growth of sea ice was investigated during autumn in the northeastern Weddell Sea. Changes in standing stock, activity, and carbon production of bacteria were determined in successive stages of ice development. During initial ice formation, concentrations of bacterial cells, in the order of 1 x 10 to 3 x 10 liter, were not enhanced within the ice matrix. This suggests that physical enrichment of bacteria by ice crystals is not effective. Due to low concentrations of phytoplankton in the water column during freezing, incorporation of bacteria into newly formed ice via attachment to algal cells or aggregates was not recorded in this study. As soon as the ice had formed, the general metabolic activity of bacterial populations was strongly suppressed. Furthermore, the ratio of [H]leucine incorporation into proteins to [H]thymidine incorporation into DNA changed during ice growth. In thick pack ice, bacterial activity recovered and growth rates up to 0.6 day indicated actively dividing populations. However, biomass-specific utilization of organic compounds remained lower than in open water. Bacterial concentrations of up to 2.8 x 10 cells liter along with considerably enlarged cell volumes accumulated within thick pack ice, suggesting reduced mortality rates of bacteria within the small brine pores. In the course of ice development, bacterial carbon production increased from about 0.01 to 0.4 mug of C liter h. In thick ice, bacterial secondary production exceeded primary production of microalgae.
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NASA Astrophysics Data System (ADS)
Kewcharoenwong, Chidchamai; Rinchai, Darawan; Utispan, Kusumawadee; Suwannasaen, Duangchan; Bancroft, Gregory J.; Ato, Manabu; Lertmemongkolchai, Ganjana
2013-11-01
Type 2 diabetes mellitus is a major risk factor for melioidosis, which is caused by Burkholderia pseudomallei. Our previous study has shown that polymorphonuclear neutrophils (PMNs) from diabetic subjects exhibited decreased functions in response to B. pseudomallei. Here we investigated the mechanisms regulating cytokine secretion of PMNs from diabetic patients which might contribute to patient susceptibility to bacterial infections. Purified PMNs from diabetic patients who had been treated with glibenclamide (an ATP-sensitive potassium channel blocker for anti-diabetes therapy), showed reduction of interleukin (IL)-1β and IL-8 secretion when exposed to B. pseudomallei. Additionally, reduction of these pro-inflammatory cytokines occurred when PMNs from diabetic patients were treated in vitro with glibenclamide. These findings suggest that glibenclamide might be responsible for the increased susceptibility of diabetic patients, with poor glycemic control, to bacterial infections as a result of its effect on reducing IL-1β production by PMNs.
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Xu, Jia; Sun, Jinling; Xue, Zhaoxia; Li, Xinwang
2014-06-18
This study investigated the relationships among an enriched environment, stress levels, and drug addiction. Mice were divided randomly into four treatment groups (n=12 each): enriched environment without restraint stress (EN), standard environment without restraint stress (SN), enriched environment with restraint stress (ES), and standard environment with restraint stress (SS). Mice were reared in the respective environment for 45 days. Then, the ES and SS groups were subjected to restraint stress daily (2 h/day) for 14 days, whereas the EN and SN groups were not subjected to restraint stress during this stage. The stress levels of all mice were tested in the elevated plus maze immediately after exposure to restraint stress. After the 2-week stress testing period, mice were administered acute or chronic morphine (5 mg/kg) treatment for 7 days. Then, after a 7-day withdrawal period, the mice were injected with saline (1 ml/kg) or morphine (5 mg/kg) daily for 2 days to observe locomotor activity. The results indicated that the enriched environment reduced the stress and locomotor activity induced by acute morphine administration or saline after chronic morphine treatment. However, the enriched environment did not significantly inhibit locomotor activity induced by morphine challenge. In addition, the stress level did not mediate the effect of the enriched environment on drug-induced locomotor activity after acute or chronic morphine treatment.
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Faisal, Muhammad; Hasnain, Shahida
2005-01-01
This study deals with the use of three chromium-resistant bacterial strains (Ochrobactrum intermedium CrT-1, Brevibacterium CrT-13, and CrM-1) in conjunction with Eichornia crassipes for the removal of toxic chromium from wastewater. Bacterial strains resulted in reduced uptake of chromate into inoculated plants as compared to noninoculated control plants. In the presence of different heavy metals, chromium uptake into the plants was 28.7 and 7.15% less at an initial K2CrO4 concentration of 100 and 500 microg ml(-1) in comparison to a metal free chromium solution. K2CrO4 uptake into the plant occurred at different pHs tested, but maximum uptake was observed at pH 5. Nevertheless, the bacterial strains caused some decrease in chromate uptake into the plants, but the combined effect of plants and bacterial strains conduce more removal of Cr(VI) from the solution.
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Minard, G.; Tran, F. H.; Van, Van Tran; Goubert, C.; Bellet, C.; Lambert, G.; Kim, Khanh Ly Huynh; Thuy, Trang Huynh Thi; Mavingui, P.; Valiente Moro, C.
2015-01-01
The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype) and bacterial diversity (16S rDNA metabarcoding) were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects. PMID:26441903
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Bacterial Infection of Fly Ovaries Reduces Egg Production and Induces Local Hemocyte Activation
Brandt, Stephanie M.; Schneider, David S.
2009-01-01
Summary Morbidity, the state of being diseased, is an important aspect of pathogenesis that has gone relatively unstudied in fruit flies. Our interest is in characterizing how bacterial pathogenesis affects various physiologies of the fly. We chose to examine the fly ovary because we found bacterial infection had a striking effect on fly reproduction. We observed decreased egg laying after bacterial infection that correlated with increased bacterial virulence. We also found that bacteria colonized the ovary in a previously undescribed manner; bacteria were found in the posterior of the ovary, adjacent to the lateral oviduct. This local infection in the ovary resulted in melanization and activation of the cellular immune response at the site of infection. PMID:17400292
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NASA Astrophysics Data System (ADS)
Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.
2016-12-01
Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.
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Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.
2016-01-01
Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated. PMID:27941918
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Nutrient enrichment modifies temperature-biodiversity relationships in large-scale field experiments
Wang, Jianjun; Pan, Feiyan; Soininen, Janne; Heino, Jani; Shen, Ji
2016-01-01
Climate effects and human impacts, that is, nutrient enrichment, simultaneously drive spatial biodiversity patterns. However, there is little consensus about their independent effects on biodiversity. Here we manipulate nutrient enrichment in aquatic microcosms in subtropical and subarctic regions (China and Norway, respectively) to show clear segregation of bacterial species along temperature gradients, and decreasing alpha and gamma diversity toward higher nutrients. The temperature dependence of species richness is greatest at extreme nutrient levels, whereas the nutrient dependence of species richness is strongest at intermediate temperatures. For species turnover rates, temperature effects are strongest at intermediate and two extreme ends of nutrient gradients in subtropical and subarctic regions, respectively. Species turnover rates caused by nutrients do not increase toward higher temperatures. These findings illustrate direct effects of temperature and nutrients on biodiversity, and indirect effects via primary productivity, thus providing insights into how nutrient enrichment could alter biodiversity under future climate scenarios. PMID:28000677
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Bent, Zachary W.; Poorey, Kunal; LaBauve, Annette E.; ...
2016-12-21
When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich formore » pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Bent, Zachary W.; Poorey, Kunal; LaBauve, Annette E.
When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich formore » pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs.« less
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Omrani, Rahma; Spini, Giulia; Puglisi, Edoardo; Saidane, Dalila
2018-04-01
Environmental microbial communities are key players in the bioremediation of hydrocarbon pollutants. Here we assessed changes in bacterial abundance and diversity during the degradation of Tunisian Zarzatine oil by four indigenous bacterial consortia enriched from a petroleum station soil, a refinery reservoir soil, a harbor sediment and seawater. The four consortia were found to efficiently degrade up to 92.0% of total petroleum hydrocarbons after 2 months of incubation. Illumina 16S rRNA gene sequencing revealed that the consortia enriched from soil and sediments were dominated by species belonging to Pseudomonas and Acinetobacter genera, while in the seawater-derived consortia Dietzia, Fusobacterium and Mycoplana emerged as dominant genera. We identified a number of species whose relative abundances bloomed from small to high percentages: Dietzia daqingensis in the seawater microcosms, and three OTUs classified as Acinetobacter venetianus in all two soils and sediment derived microcosms. Functional analyses on degrading genes were conducted by comparing PCR results of the degrading genes alkB, ndoB, cat23, xylA and nidA1 with inferences obtained by PICRUSt analysis of 16S amplicon data: the two data sets were partly in agreement and suggest a relationship between the catabolic genes detected and the rate of biodegradation obtained. The work provides detailed insights about the modulation of bacterial communities involved in petroleum biodegradation and can provide useful information for in situ bioremediation of oil-related pollution.
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Choi, Young-Jun; Fuchs, Jeremy F.; Mayhew, George F.; Yu, Helen E.; Christensen, Bruce M.
2012-01-01
Hemocytes are integral components of mosquito immune mechanisms such as phagocytosis, melanization, and production of antimicrobial peptides. However, our understanding of hemocyte-specific molecular processes and their contribution to shaping the host immune response remains limited. To better understand the immunophysiological features distinctive of hemocytes, we conducted genome-wide analysis of hemocyte-enriched transcripts, and examined how tissue-enriched expression patterns change with the immune status of the host. Our microarray data indicate that the hemocyte-enriched trascriptome is dynamic and context-dependent. Analysis of transcripts enriched after bacterial challenge in circulating hemocytes with respect to carcass added a dimension to evaluating infection-responsive genes and immune-related gene families. We resolved patterns of transcriptional change unique to hemocytes from those that are likely shared by other immune responsive tissues, and identified clusters of genes preferentially induced in hemocytes, likely reflecting their involvement in cell type specific functions. In addition, the study revealed conserved hemocyte-enriched molecular repertoires which might be implicated in core hemocyte function by cross-species meta-analysis of microarray expression data from Anopheles gambiae and Drosophila melanogaster. PMID:22796331
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Bacterial-biota dynamics of eight bryophyte species from different ecosystems
Koua, Faisal Hammad Mekky; Kimbara, Kazuhide; Tani, Akio
2014-01-01
Despite the importance of bryophyte-associated microorganisms in various ecological aspects including their crucial roles in the soil-enrichment of organic mass and N2 fixation, nonetheless, little is known about the microbial diversity of the bryophyte phyllospheres (epi-/endophytes). To get insights into bacterial community structures and their dynamics on the bryophyte habitats in different ecosystems and their potential biological roles, we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan. Forty-two bacterial species belonging to γ-proteobacteria and Firmicutes with 71.4% and 28.6%, respectively, were identified among 90 DGGE gel band population. These DGGE-bands were assigned to 13 different genera with obvious predomination the genus Clostridium with 21.4% from the total bacterial community. These analyses provide new insights into bryophyte-associated bacteria and their relations to the ecosystems. PMID:25737654
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Fuentes, Sebastián; Barra, Bárbara; Caporaso, J Gregory; Seeger, Michael
2016-02-01
Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼ 0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
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From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation
Fuentes, Sebastián; Barra, Bárbara; Caporaso, J. Gregory
2015-01-01
Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of “conditionally rare taxa,” in which rareness is a temporary state conditioned by environmental constraints. PMID:26590285
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He, Jing; Yi, Li; Hai, Le; Ming, Liang; Gao, Wanting; Ji, Rimutu
2018-01-12
The bacterial community plays important roles in the gastrointestinal tracts (GITs) of animals. However, our understanding of the microbial communities in the GIT of Bactrian camels remains limited. Here, we describe the bacterial communities from eight different GIT segments (rumen, reticulum, abomasum, duodenum, ileum, jejunum, caecum, colon) and faeces determined from 11 Bactrian camels using 16S rRNA gene amplicon sequencing. Twenty-seven bacterial phyla were found in the GIT, with Firmicutes, Verrucomicrobia and Bacteroidetes predominating. However, there were significant differences in microbial community composition between segments of the GIT. In particular, a greater proportion of Akkermansia and Unclassified Ruminococcaceae were found in the large intestine and faecal samples, while more Unclassified Clostridiales and Unclassified Bacteroidales were present in the in forestomach and small intestine. Comparative analysis of the microbiota from different GIT segments revealed that the microbial profile in the large intestine was like that in faeces. We also predicted the metagenomic profiles for the different GIT regions. In forestomach, there was enrichment associated with replication and repair and amino acid metabolism, while carbohydrate metabolism was enriched in the large intestine and faeces. These results provide profound insights into the GIT microbiota of Bactrian camels.
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Duncan, Sylvia H; Russell, Wendy R; Quartieri, Andrea; Rossi, Maddalena; Parkhill, Julian; Walker, Alan W; Flint, Harry J
2016-07-01
Cereal fibres such as wheat bran are considered to offer human health benefits via their impact on the intestinal microbiota. We show here by 16S rRNA gene-based community analysis that providing amylase-pretreated wheat bran as the sole added energy source to human intestinal microbial communities in anaerobic fermentors leads to the selective and progressive enrichment of a small number of bacterial species. In particular, OTUs corresponding to uncultured Lachnospiraceae (Firmicutes) related to Eubacterium xylanophilum and Butyrivibrio spp. were strongly enriched (by five to 160 fold) over 48 h in four independent experiments performed with different faecal inocula, while nine other Firmicutes OTUs showed > 5-fold enrichment in at least one experiment. Ferulic acid was released from the wheat bran during degradation but was rapidly converted to phenylpropionic acid derivatives via hydrogenation, demethylation and dehydroxylation to give metabolites that are detected in human faecal samples. Pure culture work using bacterial isolates related to the enriched OTUs, including several butyrate-producers, demonstrated that the strains caused substrate weight loss and released ferulic acid, but with limited further conversion. We conclude that breakdown of wheat bran involves specialist primary degraders while the conversion of released ferulic acid is likely to involve a multi-species pathway. © 2015 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
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Rosas-Trigueros, A P; Candanosa-Aranda, I E; Ducoing-Watty, A E; Gutiérrez-Molotla, J; Galindo, F; Sisto-Burt, A M
2017-12-01
Intensive production systems can negatively affect the welfare of goats. Environmental enrichment techniques can be used to reduce stress. The aim of this study was analyze the effect of environmental enrichment on the histological characteristics of adrenal glands, cortisol levels and weekly weight gain of suckling Alpine French male kids under confinement. A randomised design was used to test the effect of the treatment. The animals (n=20) were randomly assigned to two treatments (enriched and non-enriched) with two replicates each. Enrichment elements included elevated sacks of henequen, trunks, tires and coconuts. The cortisol levels were measured weekly. Male kids were euthanized when their weight reached 10kg, and immediately after euthanasia, samples of the adrenal glands were collected. The adrenal glands were weighed and measured, and histological sections were taken and fixed. Four hundred cells were measured from each animal, with two blind measurements taken from each sample. There were no significant differences between experimental groups (P>0.05) in the weigh, size, the area of cells from the glomerulosa and fasciculata areas of the adrenal glands, the cortisol levels and weekly weight gain. However, there were histological differences between the glomerular and fascicular zones of the left and right adrenal glands of the different groups (P<0.05). These findings suggest that adrenal glands of animals in non-enriched environment, contained histological changes, suggestive of increased activity. We suggest testing adrenal histology as an indicator of stress and recommend the use of environmental enrichment as a means to reduce stress. Copyright © 2017 Elsevier Ltd. All rights reserved.
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GOMA: functional enrichment analysis tool based on GO modules
Huang, Qiang; Wu, Ling-Yun; Wang, Yong; Zhang, Xiang-Sun
2013-01-01
Analyzing the function of gene sets is a critical step in interpreting the results of high-throughput experiments in systems biology. A variety of enrichment analysis tools have been developed in recent years, but most output a long list of significantly enriched terms that are often redundant, making it difficult to extract the most meaningful functions. In this paper, we present GOMA, a novel enrichment analysis method based on the new concept of enriched functional Gene Ontology (GO) modules. With this method, we systematically revealed functional GO modules, i.e., groups of functionally similar GO terms, via an optimization model and then ranked them by enrichment scores. Our new method simplifies enrichment analysis results by reducing redundancy, thereby preventing inconsistent enrichment results among functionally similar terms and providing more biologically meaningful results. PMID:23237213
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Detection of Pseudomonas savastanoi pv. savastanoi in olive plants by enrichment and PCR.
Penyalver, R; García, A; Ferrer, A; Bertolini, E; López, M M
2000-06-01
The sequence of the gene iaaL of Pseudomonas savastanoi EW2009 was used to design primers for PCR amplification. The iaaL-derived primers directed the amplification of a 454-bp fragment from genomic DNA isolated from 70 strains of P. savastanoi, whereas genomic DNA from 93 non-P. savastanoi isolates did not yield this amplified product. A previous bacterial enrichment in the semiselective liquid medium PVF-1 improved the PCR sensitivity level, allowing detection of 10 to 100 CFU/ml of plant extract. P. savastanoi was detected by the developed enrichment-PCR method in knots from different varieties of inoculated and naturally infected olive trees. Moreover, P. savastanoi was detected in symptomless stem tissues from naturally infected olive plants. This enrichment-PCR method is more sensitive and less cumbersome than the conventional isolation methods for detection of P. savastanoi.
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Tian, Ren-Mao; Lee, On On; Wang, Yong; Cai, Lin; Bougouffa, Salim; Chiu, Jill Man Ying; Wu, Rudolf Shiu Sun; Qian, Pei-Yuan
2014-01-01
Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2′,4,4′-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge. PMID:25642227
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Schoolwide Enrichment Model: Challenging All Children to Excel
ERIC Educational Resources Information Center
Beecher, Margaret
2010-01-01
This article summarizes how the components of the Schoolwide Enrichment Model were used to dramatically reduce the achievement gap in a school with a high at-risk student population. The theories of enrichment and instructional differentiation replaced an existing remedial paradigm and a strength-based methodology was embraced by the school…
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NASA Astrophysics Data System (ADS)
Scarratt, M. G.; Marchetti, A.; Hale, M. S.; Rivkin, R. B.; Michaud, S.; Matthews, P.; Levasseur, M.; Sherry, N.; Merzouk, A.; Li, W. K. W.; Kiyosawa, H.
2006-10-01
A microcosm experiment was conducted in the NE Pacific in July 2002 to compare the microbial response between microcosms and the Subarctic Ecosystem Response to Iron-Enrichment Study (SERIES) in situ iron-enrichment experiment. Seawater microcosms (20 L) were incubated aboard ship under natural light using three treatments: (1) low-iron seawater amended with 4 nmol l -1 FeSO 4 (+Fe); (2) low-iron seawater amended with 4 nmol l -1 FeSO 4 and 86 nmol l -1 GeO 2 (+Fe+Ge); (3) seawater collected from the in situ Fe-enriched patch (PW). The +Fe+Ge treatment used germanium to control diatom growth to assess the role of diatoms in dimethylsulfoniopropionate (DMSP) production. The following variables were measured in the microcosms and in situ: chlorophyll a (chl a), nitrate ( NO3-), silicic acid (Si(OH) 4), phytoplankton abundance and species identification, bacterial abundance (including estimates of low- and high-DNA bacteria), bacterial production, bacterial specific growth rate, particulate and dissolved DMSP and dimethylsulfide (DMS) concentrations. There was little or no significant difference (ANCOVA) in the response of most variables between the +Fe and PW microcosms, but large differences were observed between both these treatments and the in situ data from the enriched patch. Chl a in all microcosms increased from ambient levels (approx. 0.5-1 μg l -1) to approx. 4.5-6.2 μg l -1 after 11 d incubation, when NO3- was fully depleted from all microcosms. During this same period, in situ chl a increased more slowly to a maximum of 2.9 μg l -1 on day 11. Nanophytoplankton and picophytoplankton were more abundant in the microcosms relative to the in situ community, which became dominated by large diatoms. Bacterial abundance was similar in the microcosms and in situ, but bacterial production was significantly higher in the microcosms. While neither DMSP d nor DMS accumulation showed significant differences between the microcosms and in situ , particulate DMSP
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Environmental enrichment as a potential intervention for heroin seeking.
Galaj, E; Manuszak, M; Ranaldi, R
2016-06-01
Heroin-related cues can trigger craving and relapse in addicts or heroin seeking in rats. In the present study we investigated whether environmental enrichment (EE) implemented after heroin exposure can reduce cue-induced reinstatement of heroin seeking and expression of heroin conditioned place preference. In Experiment 1, male Long Evans rats that already acquired a heroin self-administration habit, were housed in enriched or non-enriched environments, underwent extinction training and later were tested for cue-induced reinstatement of heroin seeking. In Experiment 2, rats were conditioned with heroin in one compartment of a CPP apparatus and saline in the other, exposed to 30days of enrichment or no enrichment and were later tested for heroin CPP. The results showed that exposure to EE significantly reduced responding during the reinstatement test (Experiment 1) and prevented the expression of heroin CPP (Experiment 2). Our findings suggest that EE can be an effective behavioral approach to diminish the effects of conditioned cues on heroin seeking. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
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Sulfate-reducing bacteria are common members of bacterial communities in Altamira Cave (Spain).
Portillo, M Carmen; Gonzalez, Juan M
2009-01-15
The conservation of paleolithic paintings such as those in Altamira Cave (Spain) is a primary objective. Recent molecular studies have shown the existence of unknown microbial communities in this cave including anaerobic microorganisms on cave walls. Herein, we analyzed an anaerobic microbial group, the sulfate-reducing bacteria (SRB), from Altamira Cave with potential negative effects on painting conservation. In the present work, the communities of bacteria and SRB were studied through PCR-DGGE analysis. Data suggest that SRB communities represent a significant, highly diverse bacterial group in Altamira Cave. These findings represent a first report on this physiological group on caves with paleolithic paintings and their potential biodegradation consequences. Expanding our knowledge on microbial communities in Altamira Cave is a priority to design appropriate conservation strategies.
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Drury, Bradley; Rosi-Marshall, Emma
2013-01-01
In highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the composition of WWTP effluent to match the composition of the receiving system, the potential exists for effluent to significantly impact the chemical and biological characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and composition of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chemical characteristics and in the composition of their sediment bacterial communities. Although effluent resulted in significant increases in inorganic nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community composition in both rivers, including decreases in abundances of Deltaproteobacteria, Desulfococcus, Dechloromonas, and Chloroflexi sequences and increases in abundances of Nitrospirae and Sphingobacteriales sequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chemical and biological properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization. PMID:23315724
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Jellyfish modulate bacterial dynamic and community structure.
Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina
2012-01-01
Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in
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NASA Astrophysics Data System (ADS)
Benard, L. D.; Tuah, P. M.; Suadin, E. G.; Jamian, N.
2015-04-01
The distribution of hydrocarbon-utilizing bacterial may vary between surface and subsurface of the seawater. One of the identified contributors is the Total Petroleum Hydrocarbon. The isolation and characterization of bacteria using Direct and Enrichment techniques helps in identifying dominant bacterial populations in seawater of Mantanani Island, Kota Belud, Sabah, potential of further investigation as hydrocarbon degrader. Crude oil (5% v/v) was added as the carbon source for bacteria in Enrichment technique. For surface seawater, the highest population of bacteria identified for both Direct and Enrichment technique were 2.60 × 107 CFU/mL and 3.84 × 106 CFU/mL respectively. Meanwhile, for subsurface seawater, the highest population of bacteria identified for both Direct and Enrichment technique were 5.21 × 106 CFU/mL and 8.99 × 107 CFU/mL respectively. Dominant species in surface seawater were characterized as Marinobacter hydrocarbonoclasticus-RMSF-C1 and RMSF-C2 and Alcanivorax borkumensis-RMSF-C3, RMSF-C4 and RMSF-C5. As for subsurface seawater, dominant species were characterized as Pseudomonas luteola-SSBR-W1, Burkholderia cepacia-SSBR-C1, Rhizobium radiobacter- SSBR-C3 and Leuconostoc-cremois -SSBR-C4.
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Tracking the flow of bacterially derived 13C and 15N through soil faunal feeding channels.
Crotty, F V; Blackshaw, R P; Murray, P J
2011-06-15
The soil food web has been referred to as a 'black box', a 'poor man's tropical rainforest' and an 'enigma', due to its opacity, diversity and the limited insight into feeding specificity. Here we investigate the flow of C and N through the soil food web as a way to gain understanding of the feeding interactions occurring. A bacterium, Pseudomonas lurida, was introduced to soil cores from two different habitats, a grassland and a woodland with the same soil type, enriched to 99 atom% in (13)C and (15)N, to trace the flow of bacterial C and N through the soil food web. Throughout the experiment the soil remained enriched in (13)C and (15)N. Almost all the invertebrates tested gained C and N enrichment indicative of the labelled bacteria, implying that bacterial feeding is a common mechanism within the soil. Only three groups were significantly enriched in both (13)C and (15)N in both habitats. These were Collembola (Entomobryomorpha), Acari (Oribatida), and Nematoda, indicating that these organisms are consuming the most bacteria within both systems. When the invertebrates were grouped into hypothesised trophic levels, those considered secondary decomposers were gaining the most enrichment across all invertebrates tested. This enrichment was also high in the micro-predators within the soil, implying that their main food source was the secondary decomposers, particularly the Collembola. Using an enriched bacterium to track the trophic transfer between organisms within the soil food web is a novel way of empirically showing that interactions are occurring, which normally cannot be seen. Copyright © 2011 John Wiley & Sons, Ltd.
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Wiles, Travis J.; Norton, J. Paul; Russell, Colin W.; Dalley, Brian K.; Fischer, Kael F.; Mulvey, Matthew A.
2013-01-01
Strains of Extraintestinal Pathogenic Escherichia c oli (ExPEC) exhibit an array of virulence strategies and are a major cause of urinary tract infections, sepsis and meningitis. Efforts to understand ExPEC pathogenesis are challenged by the high degree of genetic and phenotypic variation that exists among isolates. Determining which virulence traits are widespread and which are strain-specific will greatly benefit the design of more effective therapies. Towards this goal, we utilized a quantitative genetic footprinting technique known as transposon insertion sequencing (Tn-seq) in conjunction with comparative pathogenomics to functionally dissect the genetic repertoire of a reference ExPEC isolate. Using Tn-seq and high-throughput zebrafish infection models, we tracked changes in the abundance of ExPEC variants within saturated transposon mutant libraries following selection within distinct host niches. Nine hundred and seventy bacterial genes (18% of the genome) were found to promote pathogen fitness in either a niche-dependent or independent manner. To identify genes with the highest therapeutic and diagnostic potential, a novel Trait Enrichment Analysis (TEA) algorithm was developed to ascertain the phylogenetic distribution of candidate genes. TEA revealed that a significant portion of the 970 genes identified by Tn-seq have homologues more often contained within the genomes of ExPEC and other known pathogens, which, as suggested by the first axiom of molecular Koch's postulates, is considered to be a key feature of true virulence determinants. Three of these Tn-seq-derived pathogen-associated genes—a transcriptional repressor, a putative metalloendopeptidase toxin and a hypothetical DNA binding protein—were deleted and shown to independently affect ExPEC fitness in zebrafish and mouse models of infection. Together, the approaches and observations reported herein provide a resource for future pathogenomics-based research and highlight the diversity of
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Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure.
Ma, Xiao; Vikram, Amit; Casson, Leonard; Bibby, Kyle
2017-07-05
Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.
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USDA-ARS?s Scientific Manuscript database
The intestinal microbiota allows mammals to recover energy stored in plant biomass through fermentation of plant cell walls, primarily cellulose and hemicellulose. Bacteria were isolated from 8 week continuous culture enrichments with cellulose and xylan/pectin from cow (C, n=4), goat (G, n=4), huma...
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SanMiguel, Adam J.; Meisel, Jacquelyn S.; Horwinski, Joseph; Zheng, Qi
2017-01-01
ABSTRACT The skin microbiome is a complex ecosystem with important implications for cutaneous health and disease. Topical antibiotics and antiseptics are often employed to preserve the balance of this population and inhibit colonization by more pathogenic bacteria. However, despite their widespread use, the impact of these interventions on broader microbial communities remains poorly understood. Here, we report the longitudinal effects of topical antibiotics and antiseptics on skin bacterial communities and their role in Staphylococcus aureus colonization resistance. In response to antibiotics, cutaneous populations exhibited an immediate shift in bacterial residents, an effect that persisted for multiple days posttreatment. By contrast, antiseptics elicited only minor changes to skin bacterial populations, with few changes to the underlying microbiota. While variable in scope, both antibiotics and antiseptics were found to decrease colonization by commensal Staphylococcus spp. by sequencing- and culture-based methods, an effect which was highly dependent on baseline levels of Staphylococcus. Because Staphylococcus residents have been shown to compete with the skin pathogen S. aureus, we also tested whether treatment could influence S. aureus levels at the skin surface. We found that treated mice were more susceptible to exogenous association with S. aureus and that precolonization with the same Staphylococcus residents that were previously disrupted by treatment reduced S. aureus levels by over 100-fold. In all, the results of this study indicate that antimicrobial drugs can alter skin bacterial residents and that these alterations can have critical implications for cutaneous host defense. PMID:28630195
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Bacterial methane oxidation in sea-floor gas hydrate: Significance to life in extreme environments
NASA Astrophysics Data System (ADS)
Sassen, Roger; MacDonald, Ian R.; Guinasso, Norman L., Jr.; Joye, Samantha; Requejo, Adolfo G.; Sweet, Stephen T.; Alcalá-Herrera, Javier; Defreitas, Debra A.; Schink, David R.
1998-09-01
Samples of thermogenic hydrocarbon gases, from vents and gas hydrate mounds within a sea-floor chemosynthetic community on the Gulf of Mexico continental slope at about 540 m depth, were collected by research submersible. Our study area is characterized by low water temperature (mean =7 °C), high pressure (about 5400 kPa), and abundant structure II gas hydrate. Bacterial oxidation of hydrate-bound methane (CH4) is indicated by three isotopic properties of gas hydrate samples. Relative to the vent gas from which the gas hydrate formed, (1) methane-bound methane is enriched in 13C by as much as 3.8‰ PDB (Peedee belemnite), (2) hydrate-bound methane is enriched in deuterium (D) by as much as 37‰ SMOW (standard mean ocean water), and (3) hydrate-bound carbon dioxide (CO2) is depleted in 13C by as much as 22.4‰ PDB. Hydrate-associated authigenic carbonate rock is also depleted in 13C. Bacterial oxidation of methane is a driving force in chemosynthetic communities, and in the concomitant precipitation of authigenic carbonate rock that modifies sea-floor geology. Bacterial oxidation of hydrate-bound methane expands the potential boundaries of life in extreme environments.
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NASA Astrophysics Data System (ADS)
Brodie, E. L.; Beller, H. R.; Goldfarb, K. C.; Han, R.; Santee, C. A.
2009-12-01
In situ reductive immobilization, whereby highly soluble Cr(VI) species are reduced to poorly soluble Cr(III) species, is a favored approach for remediating Cr-contaminated groundwater. How microbial populations respond phylogenetically and functionally to the injection of an organic electron donor to stimulate Cr(VI) reduction is unclear, as are the relative contributions of direct enzymatic Cr(VI) reduction versus indirect (e.g. sulfide-mediated) reduction. In this study, we inoculated anaerobic microcosms with groundwater from the Cr-contaminated Hanford 100H site (WA) and supplemented them with lactate and the electron acceptors nitrate, sulfate, and amorphous ferric oxyhydroxide. The microcosms progressed successively through nitrate-reducing, sulfate-reducing, and Fe(III)-reducing conditions, and after a second nitrate amendment, nitrate-dependent Fe(II)-oxidizing conditions. Cr(VI) reduction occurred during both the denitrification and the sulfate/iron reduction phases. DNA and RNA were harvested during each major biogeochemical phase and were subjected to PhyloChip analysis, qPCR, and transcript sequencing. Bacterial community succession followed a trajectory related to the sequential use of electron acceptors. During denitrification, bacterial communities were enriched in known denitrifiers within the Beta- and Gamma-proteobacteria and became phylogenetically clustered. Fermenters became enriched following nitrate reduction, preceding both iron and sulfate reduction. Iron reduction was stoichiometrically related to the formation of hydrogen sulfide and, although iron reducers were detected during this phase, their iron-reducing activity was not confirmed. Following the depletion of lactate and sulfate, iron reduction rates decreased and acetate and propionate concentrations stabilized, indicating a marginal contribution of acetate-coupled iron reduction. Rapid Fe(II) oxidation occurred following the nitrate amendment with a concomitant reduction of nitrate
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Romero-Perdomo, Felipe; Abril, Jorge; Camelo, Mauricio; Moreno-Galván, Andrés; Pastrana, Iván; Rojas-Tapias, Daniel; Bonilla, Ruth
The aim of this research was to evaluate whether the application of two plant growth-promoting (rhizo)bacteria might reduce nitrogen fertilization doses in cotton. We used strains Azotobacter chroococcum AC1 and AC10 for their proven ability to promote seed germination and cotton growth. These microorganisms were characterized by their plant growth-promoting activities. Then, we conducted a glasshouse study to evaluate the plant growth promoting ability of these strains with reduced doses of urea fertilization in cotton. Results revealed that both strains are capable of fixing nitrogen, solubilizing phosphorus, synthesizing indole compounds and producing hydrolytic enzymes. After 12 weeks, the glasshouse experiment showed that cotton growth was positively influenced due to bacterial inoculation with respect to chemical fertilization. Notably, we observed that microbial inoculation further influenced plant biomass (p<0.05) than nitrogen content. Co-inoculation, interestingly, exhibited a greater beneficial effect on plant growth parameters compared to single inoculation. Moreover, similar results without significant statistical differences were observed among bacterial co-inoculation plus 50% urea and 100% fertilization. These findings suggest that co-inoculation of A. chroococcum strains allow to reduce nitrogen fertilization doses up to 50% on cotton growth. Our results showed that inoculation with AC1 and AC10 represents a viable alternative to improve cotton growth while decreasing the N fertilizer dose and allows to alleviate the environmental deterioration related to N pollution. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.
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Suzuki, Kei; Kato, Yutaka; Yui, Arashi; Yamamoto, Shuji; Ando, Syota; Rubaba, Owen; Tashiro, Yosuke; Futamata, Hiroyuki
2018-05-01
We investigated how bacterial communities adapted to external resistances and exhibited the performance of electricity production in microbial fuel cells (MFCs) with external resistance of 10 Ω (LR-MFC) and 1000 Ω (HR-MFC). The HR-MFC exhibited better performance than the LR-MFC. The power densities of the LR-MFC and the HR-MFC were 5.2 ± 1.6 mW m -2 and 28 ± 9.6 mW m -2 after day 197, respectively. Low-scan cyclic voltammetry analyses indicated that the onset potential of the HR-MFC was more negative than that of the LR-MFC, suggesting that the higher external resistance led to enrichment of the highly current producing bacteria on the anode surface. All clones of Geobacter retrieved from the LR-MFC and the HR-MFC were members of the Geobacter metallireducens clade. Although the population density of Geobacter decreased from days 366-427 in the HR-MFC, the current density was almost maintained. Multidimensional scaling analyses based on denaturing gradient gel electrophoresis profiles indicated that the dynamics of the biofilm and anolytic communities changed synchronously in the two MFCs, but the dynamics of the bacterial communities in the LR-MFC and the HR-MFC were different from each other, reflecting different processes in adaptation to the different external resistances. The results suggest that the microbial community structure was formed by adapting to higher external resistance, exhibiting more negative onset potential and higher performance of the HR-MFC through collaborating with anode-respiring bacteria and fermenters. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.
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Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome.
Beckers, Bram; Op De Beeck, Michiel; Weyens, Nele; Van Acker, Rebecca; Van Montagu, Marc; Boerjan, Wout; Vangronsveld, Jaco
2016-02-23
Cinnamoyl-CoA reductase (CCR), an enzyme central to the lignin biosynthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. However, silencing of the CCR gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. Here, we evaluated host genotype-dependent effects of field-grown, CCR-down-regulated poplar trees (Populus tremula × Populus alba) on the bacterial rhizosphere microbiome and the endosphere microbiome, namely the microbiota present in roots, stems, and leaves. Plant-associated bacteria were isolated from all plant compartments by selective isolation and enrichment techniques with specific phenolic carbon sources (such as ferulic acid) that are up-regulated in CCR-deficient poplar trees. The bacterial microbiomes present in the endosphere were highly responsive to the CCR-deficient poplar genotype with remarkably different metabolic capacities and associated community structures compared with the WT trees. In contrast, the rhizosphere microbiome of CCR-deficient and WT poplar trees featured highly overlapping bacterial community structures and metabolic capacities. We demonstrate the host genotype modulation of the plant microbiome by minute genetic variations in the plant genome. Hence, these interactions need to be taken into consideration to understand the full consequences of plant metabolic pathway engineering and its relation with the environment and the intended genetic improvement.
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Tan, Michelle S F; Rahman, Sadequr; Dykes, Gary A
2017-04-01
This study investigated the removal of bacterial surface structures, particularly flagella, using sonication, and examined its effect on the attachment of Salmonella Typhimurium ATCC 14028 cells to plant cell walls. S. Typhimurium ATCC 14028 cells were subjected to sonication at 20 kHz to remove surface structures without affecting cell viability. Effective removal of flagella was determined by staining flagella of sonicated cells with Ryu's stain and enumerating the flagella remaining by direct microscopic counting. The attachment of sonicated S. Typhimurium cells to bacterial cellulose-based plant cell wall models and cut plant material (potato, apple, lettuce) was then evaluated. Varying concentrations of pectin and/or xyloglucan were used to produce a range of bacterial cellulose-based plant cell wall models. As compared to the non-sonicated controls, sonicated S. Typhimurium cells attached in significantly lower numbers (between 0.5 and 1.0 log CFU/cm 2 ) to all surfaces except to the bacterial cellulose-only composite without pectin and xyloglucan. Since attachment of S. Typhimurium to the bacterial cellulose-only composite was not affected by sonication, this suggests that bacterial surface structures, particularly flagella, could have specific interactions with pectin and xyloglucan. This study indicates that sonication may have potential applications for reducing Salmonella attachment during the processing of fresh produce. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Selection of peptidoglycan-specific aptamers for bacterial cells identification.
Ferreira, Iêda Mendes; de Souza Lacerda, Camila Maria; de Faria, Lígia Santana; Corrêa, Cristiane Rodrigues; de Andrade, Antero Silva Ribeiro
2014-12-01
Peptidoglycan is a highly complex and essential macromolecule of bacterial outer cell wall; it is a heteropolymer made up of linear glycan strands cross-linked by peptides. Peptidoglycan has a particular composition which makes it a possible target for specific bacterial recognition. Aptamers are single-stranded DNA or RNA oligonucleotides that bind to target molecules with high affinity and specificity. Aptamers can be labeled with different radioisotopes and possess several properties that make them suitable for molecular imaging. The purpose of this study was to obtain aptamers for use as radiopharmaceutical in bacterial infection diagnosis. Two aptamers (Antibac1 and Antibac2) against peptidoglycan were selected through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology. The dissociation constant (Kd) for Antibac1 was 0.415 + 0.047 μM and for Antibac2 was 1.261 + 0.280 μM. These aptamers labeled with (32)P showed high affinity for Staphylococcus aureus cells. The binding to S. aureus and Escherichia coli in vitro were significantly higher than for Candida albicans and human fibroblasts, demonstrating their specificity for bacterial cells. These results point Antibac1 and Antibac2 as promising tools for bacterial infections identification.
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Merlino, Giuseppe; Marzorati, Massimo; Rizzi, Aurora; Lavazza, Davide; de Ferra, Francesca; Carpani, Giovanna
2015-01-01
The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales. Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community. PMID:26273600
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Manios, Yannis; Moschonis, George; Mavrogianni, Christina; van den Heuvel, Eghm; Singh-Povel, Cécile M; Kiely, Mairead; Cashman, Kevin D
2017-10-01
The primary aim of the present study was to examine the effectiveness of daily consumption of vitamin D 3 -enriched, reduced-fat Gouda-type cheese on 25-hydroxyvitamin D (25(OH)D) concentration in postmenopausal women. Health-related quality of life (HRQL) indices were examined as secondary outcomes. This is a single-blinded (i.e., to study participants), randomized, controlled food-based dietary intervention study. A sample of 79 postmenopausal women (55-75 years old) was randomized either to a control group (CG: n = 39) or an intervention group (IG: n = 40) that consumed, as part of their usual diet, 60 g of either non-enriched or vitamin D 3 enriched Gouda-type cheese, respectively, for eight consecutive weeks (i.e., from January to March 2015). Sixty grams of enriched cheese provided a daily dose of 5.7 μg of vitamin D 3 . There was a differential response of mean (95 % CI) serum 25(OH)D levels in the IG and CG, with the former increasing and the latter decreasing significantly over the eight weeks of the trial [i.e., by 5.1 (3.4, 6.9) nmol/L vs. -4.6 (-6.4, -2.8) nmol/L, P < 0.001, respectively]. The percentages of study participants with 25(OH)D levels <30 (deficiency) and <50 nmol/L (insufficiency) were significantly higher at follow-up in the CG compared to the IG (41.0 vs. 0 %, P < 0.001 and 74.4 vs. 47.5 %, P < 0.001, respectively). The emotional well-being scale of the HRQL score increased in the IG compared to a decrease in the CG (3.2 vs. -3.8, P = 0.028). However, none of the other seven scales of the HRQL score significantly differentiated between study groups (P > 0.1). Consumption of 60 g of vitamin D 3 -enriched, reduced-fat Gouda-type cheese provided a daily dose of 5.7 μg of additional vitamin D 3 and was effective in increasing mean serum 25(OH)D concentration and in counteracting vitamin D deficiency during winter months in postmenopausal women in Greece.
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Pérez, Alexander J; Wesche, Frank; Adihou, Hélène; Bode, Helge B
2016-01-11
Many methods have been devised over the decades to trace precursors of specific molecules in cellular environments as, for example, in biosynthesis studies. The advent of click chemistry has facilitated the powerful combination of tracing and at the same time sieving the highly complex metabolome for compounds derived from simple or complex starting materials, especially when the click reaction takes place on a solid support. While the principle of solid-phase click reactions has already been successfully applied for selective protein and peptide enrichment, the successful enrichment of much smaller primary and secondary metabolites, showing great structural diversity and undergoing many different biosynthetic steps, has seen only little development. For bacterial secondary metabolism, a far broader tolerance for "clickable" precursors was observed than in ribosomal proteinogenesis, thus making this method a surprisingly valuable tool for the tracking and discovery of compounds within the cellular biochemical network. The implementation of this method has led to the identification of several new compounds from the bacterial genera Photorhabdus and Xenorhabdus, clearly proving its power. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Lovelock, Sarah L; Turner, Nicholas J
2014-10-15
Phenylalanine ammonia lyases (PALs) catalyse the regio- and stereoselective hydroamination of cinnamic acid analogues to yield optically enriched α-amino acids. Herein, we demonstrate that a bacterial PAL from Anabaena variabilis (AvPAL) displays significantly higher activity towards a series of non-natural substrates than previously described eukaryotic PALs. Biotransformations performed on a preparative scale led to the synthesis of the 2-chloro- and 4-trifluoromethyl-phenylalanine derivatives in excellent ee, highlighting the enormous potential of bacterial PALs as biocatalysts for the synthesis of high value, non-natural amino acids. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage
Mesa, Victoria; Gallego, Jose L. R.; González-Gil, Ricardo; Lauga, Béatrice; Sánchez, Jesús; Méndez-García, Celia; Peláez, Ana I.
2017-01-01
Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats. PMID:28955322
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Zhu, Baoli; van Dijk, Gijs; Fritz, Christian; Smolders, Alfons J. P.; Pol, Arjan; Jetten, Mike S. M.
2012-01-01
The importance of anaerobic oxidation of methane (AOM) as a methane sink in freshwater systems is largely unexplored, particularly in peat ecosystems. Nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and reported to be catalyzed by the bacterium “Candidatus Methylomirabilis oxyfera,” which is affiliated with the NC10 phylum. So far, several “Ca. Methylomirabilis oxyfera” enrichment cultures have been obtained using a limited number of freshwater sediments or wastewater treatment sludge as the inoculum. In this study, using stable isotope measurements and porewater profiles, we investigated the potential of n-damo in a minerotrophic peatland in the south of the Netherlands that is infiltrated by nitrate-rich ground water. Methane and nitrate profiles suggested that all methane produced was oxidized before reaching the oxic layer, and NC10 bacteria could be active in the transition zone where countergradients of methane and nitrate occur. Quantitative PCR showed high NC10 bacterial cell numbers at this methane-nitrate transition zone. This soil section was used to enrich the prevalent NC10 bacteria in a continuous culture supplied with methane and nitrite at an in situ pH of 6.2. An enrichment of nitrite-reducing methanotrophic NC10 bacteria was successfully obtained. Phylogenetic analysis of retrieved 16S rRNA and pmoA genes showed that the enriched bacteria were very similar to the ones found in situ and constituted a new branch of NC10 bacteria with an identity of less than 96 and 90% to the 16S rRNA and pmoA genes of “Ca. Methylomirabilis oxyfera,” respectively. The results of this study expand our knowledge of the diversity and distribution of NC10 bacteria in the environment and highlight their potential contribution to nitrogen and methane cycles. PMID:23042166
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Predicting effects of structural stress in a genome-reduced model bacterial metabolism
NASA Astrophysics Data System (ADS)
Güell, Oriol; Sagués, Francesc; Serrano, M. Ángeles
2012-08-01
Mycoplasma pneumoniae is a human pathogen recently proposed as a genome-reduced model for bacterial systems biology. Here, we study the response of its metabolic network to different forms of structural stress, including removal of individual and pairs of reactions and knockout of genes and clusters of co-expressed genes. Our results reveal a network architecture as robust as that of other model bacteria regarding multiple failures, although less robust against individual reaction inactivation. Interestingly, metabolite motifs associated to reactions can predict the propagation of inactivation cascades and damage amplification effects arising in double knockouts. We also detect a significant correlation between gene essentiality and damages produced by single gene knockouts, and find that genes controlling high-damage reactions tend to be expressed independently of each other, a functional switch mechanism that, simultaneously, acts as a genetic firewall to protect metabolism. Prediction of failure propagation is crucial for metabolic engineering or disease treatment.
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SanMiguel, Adam J; Meisel, Jacquelyn S; Horwinski, Joseph; Zheng, Qi; Grice, Elizabeth A
2017-09-01
The skin microbiome is a complex ecosystem with important implications for cutaneous health and disease. Topical antibiotics and antiseptics are often employed to preserve the balance of this population and inhibit colonization by more pathogenic bacteria. However, despite their widespread use, the impact of these interventions on broader microbial communities remains poorly understood. Here, we report the longitudinal effects of topical antibiotics and antiseptics on skin bacterial communities and their role in Staphylococcus aureus colonization resistance. In response to antibiotics, cutaneous populations exhibited an immediate shift in bacterial residents, an effect that persisted for multiple days posttreatment. By contrast, antiseptics elicited only minor changes to skin bacterial populations, with few changes to the underlying microbiota. While variable in scope, both antibiotics and antiseptics were found to decrease colonization by commensal Staphylococcus spp. by sequencing- and culture-based methods, an effect which was highly dependent on baseline levels of Staphylococcus Because Staphylococcus residents have been shown to compete with the skin pathogen S. aureus , we also tested whether treatment could influence S. aureus levels at the skin surface. We found that treated mice were more susceptible to exogenous association with S. aureus and that precolonization with the same Staphylococcus residents that were previously disrupted by treatment reduced S. aureus levels by over 100-fold. In all, the results of this study indicate that antimicrobial drugs can alter skin bacterial residents and that these alterations can have critical implications for cutaneous host defense. Copyright © 2017 American Society for Microbiology.
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A polyphenol-enriched cocoa extract reduces free radicals produced by mycotoxins.
Corcuera, L A; Amézqueta, S; Arbillaga, L; Vettorazzi, A; Touriño, S; Torres, J L; López de Cerain, A
2012-03-01
Polyphenols are characterized by the presence of phenol units in the molecules. These compounds may show antioxidant ability by scavenging reactive oxygen species (ROS) of the free radical type. A polyphenol enriched cocoa extract (PECE) was obtained from cocoa seeds with 28% of procyanidins which were mainly epicatechin oligomers. PECE was very active as free radical scavenger against 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid (ABTS), 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) and tris(2,4,6-trichloro-3,5-dinitrophenyl)methyl (HNTTM) radicals; and the tris(2,3,5,6-tetrachloro-4-nitrophenyl)methyl (TNPTM) assay showed that the PECE might not be pro-oxidant. Thus it was considered a good candidate to be tested in in vitro models. It showed mild cytotoxic power on Hep G2 cells and induced ROS in a dose-dependent manner being weak oxidant only at high concentrations near the limit of solubility. The antioxidant properties were assayed in Hep G2 treated with the mycotoxins ochratoxin A (OTA) and/or aflatoxin B1 (AFB1). The PECE was not effective against AFB1 but it increased the cell viability and reduced significantly the amounts of ROS in cells treated with OTA or mixtures of AFB1+OTA. These results are coherent with the role of oxidative pathways in the mechanism of OTA and indicate that polyphenols extracted from cocoa may be good candidates as antioxidant agents. Copyright © 2011 Elsevier Ltd. All rights reserved.
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Zhu, Chenghui; Ling, Qinjie; Cai, Zhihui; Wang, Yun; Zhang, Yibo; Hoffmann, Peter R; Zheng, Wenjie; Zhou, Tianhong; Huang, Zhi
2016-06-22
Selenium (Se) plays an important role in fine-tuning immune responses. Inflammatory bowel disease (IBD) involves hyperresponsive immunity of the digestive tract, and a low Se level might aggravate IBD progression; however, the beneficial effects of natural Se-enriched diets on IBD remain unknown. Previously, we developed high-yield Se-enriched Spirulina platensis (Se-SP) as an excellent organic nutritional Se source. Here we prepared Se-containing phycocyanin (Se-PC) from Se-SP and observed that Se-PC administration effectively reduced the extent of colitis in mouse induced by dextran sulfate sodium. Supplementation with Se-PC resulted in significant protective effects, including mitigation of body weight loss, bloody diarrhea, and colonic inflammatory damage. The anti-inflammatory effects of Se-PC supplementation were found to involve modulation of cytokines, including IL-6, TNF-α, MCP-1, and IL-10. Mechanistically, Se-PC inhibited the activation of macrophages by suppressing the nuclear translocation of NF-κB, which is involved in the transcription of these pro-inflammatory cytokines. These results together suggest potential benefits of Se-PC as a functional Se supplement to reduce the symptoms of IBD.
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Coelho, Carlyle Mendes; de Azevedo, Cristiano Schetini; Guimarães, Marcelo Alcino de Barros Vaz; Young, Robert John
2016-01-01
Environmental enrichment is a technique that may reduce the stress of nonhuman animals in captivity. Stress may interfere with normal behavioral expression and affect cognitive decision making. Noninvasive hormonal studies can provide important information about the stress statuses of animals. This study evaluated the effectiveness of different environmental enrichment treatments in the diminution of fecal glucocorticoid metabolites (stress indicators) of three captive maned wolves (Chrysocyon brachyurus). Correlations of the fecal glucocorticoid metabolite levels with expressed behaviors were also determined. Results showed that environmental enrichment reduced fecal glucocorticoid metabolite levels. Furthermore, interspecific and foraging enrichment items were most effective in reducing stress in two of the three wolves. No definite pattern was found between behavioral and physiological responses to stress. In conclusion, these behavioral and physiological data showed that maned wolves responded positively from an animal well being perspective to the enrichment items presented.
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Luo, Yuheng; Zhang, Ling; Li, Hua; Smidt, Hauke; Wright, André-Denis G.; Zhang, Keying; Ding, Xuemei; Zeng, Qiufeng; Bai, Shiping; Wang, Jianping; Li, Jian; Zheng, Ping; Tian, Gang; Cai, Jingyi; Chen, Daiwen
2017-01-01
Soluble dietary fibers (SDF) are fermented more than insoluble dietary fibers (IDF), but their effect on colonic bacterial community structure and function remains unclear. Thus, bacterial community composition and function in the colon of BALB/c mice (n = 7) fed with a high level (approximately 20%) of typical SDF, oat-derived β-glucan (G), microcrystalline cellulose (M) as IDF, or their mixture (GM), were compared. Mice in group G showed a lowest average feed intake (p < 0.05) but no change on the average body weight gain (p > 0.05) compared to other groups, which may be associated with the highest concentration of colonic propionate (p < 0.05) in these mice. The bacterial α-diversity of group G was significantly lower than other groups (p < 0.01). In group G, the relative abundance of bacteria belonging to the phylum Bacteroidetes was significantly increased, whereas bacteria from the phylum Firmicutes were significantly decreased (p < 0.01). The core bacteria for different treatments showed distinct differences. Bacteroides, Dehalobacterium, and Prevotella, including known acetogens and carbohydrate fermenting organisms, were significantly increased in relative abundance in group G. In contrast, Adlercreutzia, Odoribacter, and Coprococcus were significantly more abundant in group M, whereas Oscillospira, Desulfovibrio, and Ruminoccaceae, typical hydrogenotrophs equipped with multiple carbohydrate active enzymes, were remarkably enriched in group GM (p < 0.05). The relative abundance of bacteria from the three classes of Proteobacteria, Betaproteobacteria, Gammaproteobacteria (including Enterobacteriaceae) and Deltaproteobacteria, were significantly more abundant in group G, indicating a higher ratio of conditional pathogenic bacteria in mice fed dietary β-glucan in current study. The predicted colonic microbial function showed an enrichment of “Energy metabolism” and “Carbohydrate metabolism” pathways in mice from group G and M, suggesting that the
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Luo, Yuheng; Zhang, Ling; Li, Hua; Smidt, Hauke; Wright, André-Denis G; Zhang, Keying; Ding, Xuemei; Zeng, Qiufeng; Bai, Shiping; Wang, Jianping; Li, Jian; Zheng, Ping; Tian, Gang; Cai, Jingyi; Chen, Daiwen
2017-01-01
Soluble dietary fibers (SDF) are fermented more than insoluble dietary fibers (IDF), but their effect on colonic bacterial community structure and function remains unclear. Thus, bacterial community composition and function in the colon of BALB/c mice ( n = 7) fed with a high level (approximately 20%) of typical SDF, oat-derived β-glucan (G), microcrystalline cellulose (M) as IDF, or their mixture (GM), were compared. Mice in group G showed a lowest average feed intake ( p < 0.05) but no change on the average body weight gain ( p > 0.05) compared to other groups, which may be associated with the highest concentration of colonic propionate ( p < 0.05) in these mice. The bacterial α-diversity of group G was significantly lower than other groups ( p < 0.01). In group G, the relative abundance of bacteria belonging to the phylum Bacteroidetes was significantly increased, whereas bacteria from the phylum Firmicutes were significantly decreased ( p < 0.01). The core bacteria for different treatments showed distinct differences. Bacteroides , Dehalobacterium , and Prevotella , including known acetogens and carbohydrate fermenting organisms, were significantly increased in relative abundance in group G. In contrast, Adlercreutzia , Odoribacter , and Coprococcus were significantly more abundant in group M, whereas Oscillospira , Desulfovibrio , and Ruminoccaceae , typical hydrogenotrophs equipped with multiple carbohydrate active enzymes, were remarkably enriched in group GM ( p < 0.05). The relative abundance of bacteria from the three classes of Proteobacteria , Betaproteobacteria , Gammaproteobacteria (including Enterobacteriaceae ) and Deltaproteobacteria , were significantly more abundant in group G, indicating a higher ratio of conditional pathogenic bacteria in mice fed dietary β-glucan in current study. The predicted colonic microbial function showed an enrichment of "Energy metabolism" and "Carbohydrate metabolism" pathways in mice from group G and M, suggesting
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USDA-ARS?s Scientific Manuscript database
In the present study, populations of equine cecal microbes enriched for enhanced rates of 3-nitro-1-propionic acid (NPA) or nitrate metabolism were diluted and cultured for NPA-metabolizing bacteria on a basal enrichment medium (BEM) or tryptose soy agar (TSA) medium supplemented with either 5 mM NP...
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Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment
Ponce-Soto, Gabriel Y.; Aguirre-von-Wobeser, Eneas; Eguiarte, Luis E.; Elser, James J.; Lee, Zarraz M.-P.; Souza, Valeria
2015-01-01
The increase of nutrients in water bodies, in particular nitrogen (N) and phosphorus (P) due to the recent expansion of agricultural and other human activities is accelerating environmental degradation of these water bodies, elevating the risk of eutrophication and reducing biodiversity. To evaluate the ecological effects of the influx of nutrients in an oligotrophic and stoichiometrically imbalanced environment, we performed a replicated in situ mesocosm experiment. We analyzed the effects of a N- and P-enrichment on the bacterial interspecific interactions in an experiment conducted in the Cuatro Cienegas Basin (CCB) in Mexico. This is a desert ecosystem comprised of several aquatic systems with a large number of microbial endemic species. The abundance of key nutrients in this basin exhibits strong stoichiometric imbalance (high N:P ratios), suggesting that species diversity is maintained mostly by competition for resources. We focused on the biofilm formation and antibiotic resistance of 960 strains of cultivated bacteria in two habitats, water and sediment, before and after 3 weeks of fertilization. The water habitat was dominated by Pseudomonas, while Halomonas dominated the sediment. Strong antibiotic resistance was found among the isolates at time zero in the nutrient-poor bacterial communities, but resistance declined in the bacteria isolated in the nutrient-rich environments, suggesting that in the nutrient-poor original environment, negative inter-specific interactions were important, while in the nutrient-rich environments, competitive interactions are not so important. In water, a significant increase in the percentage of biofilm-forming strains was observed for all treatments involving nutrient addition. PMID:25883593
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Kang, Shifei; Huang, Wei; Zhang, Lu; He, Maofen; Xu, Suyun; Sun, Di; Jiang, Xia
2018-04-25
Delamination treatment is crucial in promoting the activity of bulk graphitic carbon nitride (g-C 3 N 4 ). However, most of the currently used methods of exfoliating bulk g-C 3 N 4 to achieve g-C 3 N 4 thin layers suffer from low yield and environmental pollution. Herein, we developed a facile bacterial etching approach for the preparation of high-quality g-C 3 N 4 nanosheets by exfoliating bulk g-C 3 N 4 under room temperature. Morphology and physicochemical characterizations show that the bacteria-treated g-C 3 N 4 (BT-CN) samples, especially BT-CN-2d, have a lamina-like two-dimensional (2D) in-plane porous structure, a significantly enlarged specific surface area (82.61 m 2 g -1 ), and a remarkable narrow band gap (2.11 eV). X-ray photoelectron spectroscopy and electron paramagnetic resonance spectra confirm the dramatic enrichment of unpaired electron in the BT-CN-2d g-C 3 N 4 nanosheets. EIS spectra and photocurrent tests indicate the fast electron transportation. As a result, the representative BT-CN-2d g-C 3 N 4 photocatalyst shows an optimal visible light-driven photocatalytic performance in water disinfection (fourfold higher than bulk g-C 3 N 4 ), as well as good cycle stability. This moderate and clean bacterial etching process can be realized in tens of gram scale in the laboratory and should be readily extended to kilogram scale. The present work provides fundamental knowledge about the scalable production of high-quality g-C 3 N 4 by bioengineering method, offering extendable availability for designing and fabricating other functional 2D materials.
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Ito, Hiroyuki; Tanabe, Hiroki; Kawagishi, Hirokazu; Tadashi, Wada; Yasuhiko, Tomono; Sugiyama, Kimio; Kiriyama, Shuhachi; Morita, Tatsuya
2009-10-01
Anti-inflammatory effects of short-chain inulin-like fructans (SCF) on trinitrobenzene sulfonic acid (TNBS)-induced colitis were investigated in rats, focusing specifically on endotoxin and bacterial translocations. SCF with degrees of polymerization (DP) of 4 and 8 were used. Rats were fed either control diet or diets including 60 g DP4 or DP8 per kilogram for 7 days, and then received intracolonic TNBS and were fed the respective diets for a further 10 days. DP4 and DP8 significantly reduced colonic injuries as assessed by damage score, but the reduction of colonic myeloperoxidase activity was manifest solely with DP8. At 3 days after colitis induction, bacterial translocation to the mesenteric lymph node was significantly lower in the DP4 and DP8 groups, but significant reduction in the portal endotoxin concentration was achieved solely in the DP8 group. Immediately prior to colitis induction, cecal immunoglobulin A and mucin concentrations were higher in the DP4 and DP8 groups, but these changes were abolished at 10 days post colitis induction. The data suggest that SCF exert prophylactic effects against TNBS colitis, presumably as a result of inhibitory effects on endotoxin and bacterial translocations.
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Bare below elbows: does this policy affect handwashing efficacy and reduce bacterial colonisation?
Burger, A; Wijewardena, C; Clayson, S; Greatorex, RA
2010-01-01
INTRODUCTION UK Department of Health guidelines recommend that clinical staff are ‘bare below the elbows’. There is a paucity of evidence to support this policy. One may hypothesise that absence of clothing around wrists facilitates more effective handwashing: this study aims to establish whether dress code affects bacterial colonisation before and after handwashing. SUBJECTS AND METHODS Sixty-six clinical staff volunteered to take part in the study, noting whether they were bare below the elbows (BBE) or not bare (NB). Using a standardised technique, imprints of left and right fingers, palms, wrists and forearms were taken onto mini agar plates. Imprints were repeated after handwashing. After incubation, colonies per plate were counted, and subcultures taken. RESULTS Thirty-eight staff were BBE and 28 were not. A total of 1112 plates were cultured. Before handwashing there was no significant difference in number of colonies between BBE and NB groups (Mann–Whitney, P < 0.05). Handwashing reduced the colony count, with greatest effect on fingers, palms and dominant wrists (t-test, P < 0.05). Comparing the two groups again after handwashing revealed no significant difference (Mann–Whitney, P < 0.05). Subcultures revealed predominantly skin flora. CONCLUSIONS There was a large variation in number of colonies cultured. Handwashing resulted in a statistically significant reduction in colony count on fingers, palms and dominant wrist regardless of clothing. We conclude that handwashing produces a significant reduction in number of bacterial colonies on staff hands, and that clothing that is not BBE does not impede this reduction. PMID:20727253
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The Heterotrophic Bacterial Response During the Meso-scale Southern Ocean Iron Experiment (SOFeX)
NASA Astrophysics Data System (ADS)
Oliver, J. L.; Barber, R. T.; Ducklow, H. W.
2002-12-01
Previous meso-scale iron enrichments have demonstrated the stimulatory effect of iron on primary productivity and the accelerated flow of carbon into the surface ocean foodweb. In stratified waters, heterotrophic activity can work against carbon export by remineralizing POC and/or DOC back to CO2, effectively slowing the biological pump. To assess the response of heterotrophic activity to iron enrichment, we measured heterotrophic bacterial production and abundance during the Southern Ocean Iron Experiment (SOFeX). Heterotrophic bacterial processes primarily affect the latter of the two carbon export mechanisms, removal of DOC to the deep ocean. Heterotrophic bacterial production (BP), measured via tritiated thymidine (3H-TdR) and leucine (3H-Leu) incorporation, increased ~40% over the 18-d observation period in iron fertilized waters south of the Polar Front (South Patch). Also, South Patch BP was 61% higher than in the surrounding unfertilized waters. Abundance, measured by flow cytometry (FCM) and acridine orange direct counts (AODC), also increased in the South Patch from 3 to 5 x 108 cells liter-1, a 70% increase. Bacterial biomass increased from ~3.6 to 6.3 μg C liter-1, a clear indication that production rates exceeded removal rates (bactivory, viral lysis) over the course of 18 days. Biomass within the fertilized patch was 11% higher than in surrounding unfertilized waters reflecting a similar trend. This pattern is in contrast to SOIREE where no accumulation of biomass was observed. High DNA-containing (HDNA) cells detected by FCM also increased over time in iron fertilized waters from 20% to 46% relative to the total population suggesting an active subpopulation of cells that were growing faster than the removal rates. In iron fertilized waters north of the Polar Front (North Patch), BP and abundance were ~90% and 80% higher, respectively, than in unfertilized waters. Our results suggest an active bacterial population that responded to iron fertilization
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Akimkin, V G; Kalmykov, A A; Aminev, R M; Polyakov, V S; Artebyakin, S V
2016-02-01
The authors defined epidemiological efficacy and safety of the use of bacteriophages(streptococcal, staphylococcal, piobakferiophage multipartial) and bitsillin-5 to reduce tonsillitis morbidityand other respiratory diseases with bacterial etiology in groups of servicemen during their formationagainst increase of seasonal morbidity. The results of the use of these preventive agents were evaluatedby a comparative analysis of this disease in experimental and control groups. In total 510 healthy conscriptswere involved into the study. The effectiveness of prophylactic use of bacteriophages and bitsillin-5, whichprovided a reduction in the incidence of respiratory infections of bacterial ethiology, tonsillitis, and otherrespiratory diseases is showed. Recommendations on the choice of drugsfor the prevention of these infections,methods and organization of their application in organized groups are given.
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Roopchand, Diana E; Kuhn, Peter; Rojo, Leonel E; Lila, Mary Ann; Raskin, Ilya
2013-02-01
Defatted soybean flour (DSF) can sorb and concentrate blueberry anthocyanins and other polyphenols, but not sugars. In this study blueberry polyphenol-enriched DSF (BB-DSF) or DSF were incorporated into very high fat diet (VHFD) formulations and provided ad libitum to obese and hyperglycemic C57BL/6 mice for 13 weeks to investigate anti-diabetic effects. Compared to the VHFD containing DSF, the diet supplemented with BB-DSF reduced weight gain by 5.6%, improved glucose tolerance, and lowered fasting blood glucose levels in mice within 7 weeks of intervention. Serum cholesterol of mice consuming the BB-DSF-supplemented diet was 13.2% lower than mice on the diet containing DSF. Compounds were eluted from DSF and BB-DSF for in vitro assays of glucose production and uptake. Compared to untreated control, doses of BB-DSF eluate containing 0.05-10μg/μL of blueberry anthocyanins significantly reduced glucose production by 24-74% in H4IIE rat hepatocytes, but did not increase glucose uptake in L6 myotubes. The results indicate that delivery of blueberry polyphenols stabilized in a high-protein food matrix may be useful for the dietary management of pre-diabetes and/or diabetes. Copyright © 2012 Elsevier Ltd. All rights reserved.
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Roopchand, Diana E.; Kuhn, Peter; Rojo, Leonel E.; Lila, Mary Ann; Raskin, Ilya
2013-01-01
Defatted soybean flour (DSF) can sorb and concentrate blueberry anthocyanins and other polyphenols, but not sugars. In this study blueberry polyphenol-enriched DSF (BB-DSF) or DSF were incorporated into very high fat diet (VHFD) formulations and provided ad libitum to obese and hyperglycemic C57BL/6 mice for 13 weeks to investigate anti-diabetic effects. Compared to the VHFD containing DSF, the diet supplemented with BB-DSF reduced weight gain by 5.6%, improved glucose tolerance, and lowered fasting blood glucose levels in mice within 7 weeks of intervention. Serum cholesterol of mice consuming the BB-DSF-supplemented diet was 13.2% lower than mice on the diet containing DSF. Compounds were eluted from DSF and BB-DSF for in vitro assays of glucose production and uptake. Compared to untreated control, doses of BB-DSF eluate containing 0.05 – 10 μg/μL of blueberry anthocyanins significantly reduced glucose production by 24% - 74% in H4IIE rat hepatocytes, but did not increase glucose uptake in L6 myotubes. The results indicate that delivery of blueberry polyphenols stabilized in a high-protein food matrix may be useful for the dietary management of pre-diabetes and/or diabetes. PMID:23220243
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Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm
Probst, Alexander J; Holman, Hoi-Ying N; DeSantis, Todd Z; Andersen, Gary L; Birarda, Giovanni; Bechtel, Hans A; Piceno, Yvette M; Sonnleitner, Maria; Venkateswaran, Kasthuri; Moissl-Eichinger, Christine
2013-01-01
Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging. PMID:23178669
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Opdahl, Lee James; Gonda, Michael G.
2018-01-01
The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6–50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers (Ruminococcus flavefaciens and Fibrobacter succinogenes), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides. PMID:29495256
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Opdahl, Lee James; Gonda, Michael G; St-Pierre, Benoit
2018-02-24
The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6-50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers ( Ruminococcus flavefaciens and Fibrobacter succinogenes ), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides.
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Dezsi, Gabi; Ozturk, Ezgi; Salzberg, Michael R; Morris, Margaret; O'Brien, Terence J; Jones, Nigel C
2016-09-01
The absence epilepsies are presumed to be caused by genetic factors, but the influence of environmental exposures on epilepsy development and severity, and whether this influence is transmitted to subsequent generations, is not well known. We assessed the effects of environmental enrichment on epilepsy and anxiety outcomes in multiple generations of GAERS - a genetic rat model of absence epilepsy that manifests comorbid elevated anxiety-like behaviour. GAERS were exposed to environmental enrichment or standard housing beginning either prior to, or after epilepsy onset, and underwent EEG recordings and anxiety testing. Then, we exposed male GAERS to early enrichment or standard housing and generated F1 progeny, which also underwent EEG recordings. Hippocampal CRH mRNA expression and DNA methylation were assessed using RT-PCR and pyrosequencing, respectively. Early environmental enrichment delayed the onset of epilepsy in GAERS, and resulted in fewer seizures in adulthood, compared with standard housed GAERS. Enrichment also reduced the frequency of seizures when initiated in adulthood. Anxiety levels were reduced by enrichment, and these anti-epileptogenic and anxiolytic effects were heritable into the next generation. We also found reduced expression of CRH mRNA in GAERS exposed to enrichment, but this was not due to changes in DNA methylation. Environmental enrichment produces disease-modifying effects on genetically determined absence epilepsy and anxiety, and these beneficial effects are transferable to the subsequent generation. Reduced CRH expression was associated with these phenotypic improvements. Environmental stimulation holds promise as a naturalistic therapy for genetically determined epilepsy which may benefit subsequent generations. Copyright © 2016 Elsevier Inc. All rights reserved.
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Sulakvelidze, Alexander
2013-10-01
Bacteriophages (also called 'phages') are viruses that kill bacteria. They are arguably the oldest (3 billion years old, by some estimates) and most ubiquitous (total number estimated to be 10(30) -10(32) ) known organisms on Earth. Phages play a key role in maintaining microbial balance in every ecosystem where bacteria exist, and they are part of the normal microflora of all fresh, unprocessed foods. Interest in various practical applications of bacteriophages has been gaining momentum recently, with perhaps the most attention focused on using them to improve food safety. That approach, called 'phage biocontrol', typically includes three main types of applications: (i) using phages to treat domesticated livestock in order to reduce their intestinal colonization with, and shedding of, specific bacterial pathogens; (ii) treatments for decontaminating inanimate surfaces in food-processing facilities and other food establishments, so that foods processed on those surfaces are not cross-contaminated with the targeted pathogens; and (iii) post-harvest treatments involving direct applications of phages onto the harvested foods. This mini-review primarily focuses on the last type of intervention, which has been gaining the most momentum recently. Indeed, the results of recent studies dealing with improving food safety, and several recent regulatory approvals of various commercial phage preparations developed for post-harvest food safety applications, strongly support the idea that lytic phages may provide a safe, environmentally-friendly, and effective approach for significantly reducing contamination of various foods with foodborne bacterial pathogens. However, some important technical and nontechnical problems may need to be addressed before phage biocontrol protocols can become an integral part of routine food safety intervention strategies implemented by food industries in the USA. © 2013 Society of Chemical Industry.
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Detergent-compatible bacterial amylases.
Niyonzima, Francois N; More, Sunil S
2014-10-01
Proteases, lipases, amylases, and cellulases are enzymes used in detergent formulation to improve the detergency. The amylases are specifically supplemented to the detergent to digest starchy stains. Most of the solid and liquid detergents that are currently manufactured contain alkaline enzymes. The advantages of using alkaline enzymes in the detergent formulation are that they aid in removing tough stains and the process is environmentally friendly since they reduce the use of toxic detergent ingredients. Amylases active at low temperature are preferred as the energy consumption gets reduced, and the whole process becomes cost-effective. Most microbial alkaline amylases are used as detergent ingredients. Various reviews report on the production, purification, characterization, and application of amylases in different industry sectors, but there is no specific review on bacterial or fungal alkaline amylases or detergent-compatible amylases. In this mini-review, an overview on the production and property studies of the detergent bacterial amylases is given, and the stability and compatibility of the alkaline bacterial amylases in the presence of the detergents and the detergent components are highlighted.
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Antibiotics for treating bacterial vaginosis in pregnancy.
McDonald, H M; Brocklehurst, P; Gordon, A
2007-01-24
Bacterial vaginosis is an imbalance of the normal vaginal flora with an overgrowth of anaerobic bacteria and a lack of the normal lactobacillary flora. Bacterial vaginosis during pregnancy has been associated with poor perinatal outcome and, in particular, preterm birth (PTB). Identification and treatment may reduce the risk of PTB and its consequences. To assess the effects of antibiotic treatment of bacterial vaginosis in pregnancy. We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (May 2006). Randomized trials comparing antibiotic treatment with placebo or no treatment, or comparing two or more antibiotic regimens in pregnant women with bacterial vaginosis or intermediate vaginal flora. Two review authors assessed trials and extracted data independently. We contacted study authors for additional information. We included fifteen trials of good quality, involving 5888 women. Antibiotic therapy was effective at eradicating bacterial vaginosis during pregnancy (Peto odds ratio (OR) 0.17, 95% confidence interval (CI) 0.15 to 0.20; 10 trials, 4357 women). Treatment did not reduce the risk of PTB before 37 weeks (Peto OR 0.91, 95% CI 0.78 to 1.06; 15 trials, 5888 women), or the risk of preterm prelabour rupture of membranes (PPROM) (Peto OR 0.88, 95% CI 0.61 to 1.28; four trials, 2579 women). However, treatment before 20 weeks' gestation may reduce the risk of preterm birth less than 37 weeks (Peto OR 0.63, 95% CI 0.48 to 0.84; five trials, 2387 women). In women with a previous PTB, treatment did not affect the risk of subsequent PTB (Peto OR 0.83, 95% CI 0.59 to 1.17, five trials of 622); however, it may decrease the risk of PPROM (Peto OR 0.14, 95% CI 0.05 to 0.38) and low birthweight (Peto OR 0.31, 95% CI 0.13 to 0.75)(two trials, 114 women). In women with abnormal vaginal flora (intermediate flora or bacterial vaginosis) treatment may reduce the risk of PTB before 37 weeks (Peto OR 0.51, 95% CI 0.32 to 0.81; two trials, 894 women
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Champagne, C P; Raymond, Y; Gonthier, J; Audet, P
2009-04-01
Pasteurized and unfermented milks supplemented with probiotic bacteria are appearing on the market. It then becomes a challenge to ascertain the undesirable contamination microbiota in the presence of a largely superior population of probiotic bacteria. A method to enumerate the contaminating microbial microbiota in such probiotic-enriched milks was developed. The probiotic cultures, Lactobacillus rhamnosus Lb-Immuni-T and Bifidobacterium animalis subsp. lactis BB-12(R), were added to a pasteurized unfermented milk to reach a minimum of 1 billion CFU per 250 mL portion, as ascertained by plating on de Man - Rogosa - Sharpe (MRS) agar in anaerobic conditions. No growth of B. animalis subsp. lactis BB-12 was noted on plate count agar (PCA) or Petrifilm plates, and the presence of this culture did not affect standard plate counts (SPC) of contaminating bacteria. However, L. rhamnosus formed colonies on PCA and Petrifilm plates. Attempts were thus made to inhibit the growth of the probiotic lactobacilli in PCA. The addition of 2% sodium phosphate (SP) or 5% glycerophosphate (GP) inhibited the growth of the lactobacilli in broths, but pin-point colonies of L. rhamnosus Lb-Immuni-T nevertheless appeared on PCA supplemented with phosphates. SPC could be obtained on PCA + 2% SP by only counting the large colonies, but this resulted in a significant (4.4 fold) underestimation of SPC values. On Petrifilm AC, at dilutions 0 to 2, all colonies were considered as being contaminants, while at dilutions 3 and 4, only large colonies were counted for SPC determinations. There was a direct correlation (R2 = 0.99) between SPC values with Petrifilm in uninoculated milks and those obtained on probiotic-enriched milks. The high correlation obtained over the 102 to 106 CFU/mL range of SPC values show that this Petrifilm method is appropriate to evaluate the microbiological quality of pasteurized milks enriched with L. rhamnosus Lb-Immuni-T and B. animalis subsp. lactis BB-12.
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Yang, Jiajun; Qian, Kun; Zhang, Wei; Xu, Yayuan; Wu, Yijing
2016-11-08
Both chromium (Cr) and probiotic bacillus own the virtues of regulating animal metabolism and meat quality. Purpose of this study was to evaluate the efficiency of supplemental Cr and bacillus in the form of chromium-enriched Bacillus subtilis KT260179 (CEBS) on chicken growth performance, plasma lipid parameters, tissue chromium levels, cecal bacterial composition and breast meat quality. Six hundred of 1-day-old Chinese Huainan Partridge chickens were divided into four groups randomly: Control, inorganic Cr, Bacillus subtilis, and CEBS. The feed duration was 56 days. After 28 days of treatment, broiler feed CEBS or normal B. subtilis had higher body weights than control broiler, and after 56 days, chickens given either CEBS or B. subtilis had greater body weights than control broiler or those given inorganic Cr. Plasma total cholesterol, triglycerides, and low density lipoprotein cholesterol levels declined significantly in the CEBS group compared with the control, whereas plasma high density lipoprotein cholesterol levels increased significantly. The concentration of Cr in blood and breast muscle increased after CEBS and inorganic Cr supplementation. B. subtilis and CEBS supplementation caused a significant increase in the numbers of Lactobacillus and Bifidobacterium in the caecum, while the numbers of Escherichia coli and Salmonella decreased significantly compared to the control. Feed adding CEBS increased the lightness, redness, and yellowness of breast meat, improved the water-holding capacity, decreased the shear force and cooking loss. In all, CEBS supplementation promoted body growth, improved plasma lipid parameters, increased tissue Cr concentrations, altered cecal bacterial composition and improved breast meat quality.
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Liu, Wenjun; Zheng, Yi; Kwok, Lai-Yu; Sun, Zhihong; Zhang, Jiachao; Guo, Zhuang; Hou, Qiangchuan; Menhe, Bilige; Zhang, Heping
2015-02-22
Traditional fermented dairy products are major components of the typical Mongolian diet since ancient times. However, almost all the previous studies on the microbial composition of traditional Mongolian fermented dairy products analyzed food samples from the Chinese Mongolian region and Mongolia but not the Russian Mongolian region. In this study, the bacterial and fungal community diversity of nineteen naturally fermented cow's milk (NFCM) samples from local Mongolian families residing in Kalmykia and Chita of Russia was investigated with pyrosequencing. Firmicutes and Ascomycota were the predominant phyla respectively for bacteria and fungi. The abundance of the bacterial phylum Acidobacteria was considerably different between the samples from the two regions. At genus level, Lactobacillus and Pichia were the predominating bacterial and fungal genera, respectively, while six bacterial genera significantly differed between the Kalmykia (enrichment of Aeromonas, Bacillus, Clostridium, Streptococcus, Vogesella) and Chita (enrichment of Lactococcus) samples. The results of principal coordinate analysis (PCoA) based on the bacterial or fungal composition of the Kalmykia and Chita samples revealed a different microbiota structure between the samples collected in these two locations. The redundancy analysis (RDA) identified 60 bacterial and 21 fungal OTUs as the key variables responsible for such microbiota structural difference. Our results suggest that structural differences existed in the microbiota of NFCM between Kalmykia and Chita. The difference in geographic environment may be an important factor influencing the microbial diversity of NFCM made by the Mongolians in Russia.
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Bacterial diversity at different stages of the composting process
2010-01-01
Background Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. Results Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. Conclusions Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants. PMID:20350306
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Tao, Kaiyun; Liu, Xiaoyan; Chen, Xueping; Hu, Xiaoxin; Cao, Liya; Yuan, Xiaoyu
2017-01-01
The aim of this work was to study biodegradation of crude oil by defined co-cultures of indigenous bacterial consortium and exogenous Bacillus subtilis. Through residual oil analysis, it is apparent that the defined co-culture displayed a degradation ratio (85.01%) superior to indigenous bacterial consortium (71.32%) after 7days of incubation when ratio of inoculation size of indigenous bacterial consortium and Bacillus subtilis was 2:1. Long-chain n-alkanes could be degraded markedly by Bacillus subtilis. Result analysis of the bacterial community showed that a decrease in bacterial diversity in the defined co-culture and the enrichment of Burkholderiales order (98.1%) degrading hydrocarbons. The research results revealed that the promising potential of the defined co-culture for application to degradation of crude oil. Copyright © 2016 Elsevier Ltd. All rights reserved.
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2011-01-01
Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat. PMID:21812946
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Jurelevicius, Diogo; Alvarez, Vanessa Marques; Marques, Joana Montezano; de Sousa Lima, Laryssa Ribeiro Fonseca; Dias, Felipe de Almeida
2013-01-01
Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that Acinetobacter and Cloacibacterium were the dominant genera in freshwater microcosms; the Oceanospirillales order and the Marinobacter, Pseudomonas, and Cycloclasticus genera predominated in marine microcosms; and the Oceanospirillales order and the Marinobacter genus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination. PMID:23872573
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USDA-ARS?s Scientific Manuscript database
One of the fascinating functions of the mammalian intestinal microbiota is the fermentation of plant cell wall components. Eight week continuous culture enrichments of cow feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were ...
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Lynnes, Ty; Horne, S M; Prüß, B M
2014-01-01
Bacterial infection by Escherichia coli O157:H7 through the consumption of beef meat or meat products is an ongoing problem, in part because bacteria develop resistances towards chemicals aimed at killing them. In an approach that uses bacterial nutrients to manipulate bacteria into behaviors or cellular phenotypes less harmful to humans, we screened a library of 95 carbon and 95 nitrogen sources for their effect on E. coli growth, cell division, and biofilm formation. In the initial screening experiment using the Phenotype MicroArray(TM) technology from BioLog (Hayward, CA), we narrowed the 190 starting nutrients down to eight which were consecutively tested as supplements in liquid beef broth medium. Acetoacetic acid (AAA) and ß-phenylethylamine (PEA) performed best in this experiment. On beef meat pieces, PEA reduced the bacterial cell count by 90% after incubation of the PEA treated and E. coli contaminated meat pieces at 10°C for one week. © 2013.
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Yang, Sizhong; Wen, Xi; Zhao, Liang; Shi, Yulan; Jin, Huijun
2014-01-01
The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils.
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Yang, Sizhong; Wen, Xi; Zhao, Liang; Shi, Yulan; Jin, Huijun
2014-01-01
The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils. PMID:24794099
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Application of polyimide membranes for biogas purification and enrichment.
Harasimowicz, M; Orluk, P; Zakrzewska-Trznadel, G; Chmielewski, A G
2007-06-18
Biogas is a clean environment friendly fuel that is produced by bacterial conversion of organic matter under anaerobic (oxygen-free) conditions. Raw biogas contains about 55-65% methane (CH(4)), 30-45% carbon dioxide (CO(2)), traces of hydrogen sulphide (H(2)S) and fractions of water vapour. Pure methane has a calorific value of 9100 kcal/m(3) at 15.5 degrees C and 1 atm; the calorific value of biogas varies from 4800 to 6900 kcal/m(3). To achieve the standard composition of the biogas and calorific value of 5500 kcal/m(3) the treatment techniques like absorption or membrane separation should be applied. In the paper the results of the tests of the CH(4) enrichment in simulated biogas mixture consisted of methane, carbon dioxide and hydrogen sulphide were presented. It was showed that using the capillary module with polyimide membranes it was possible to achieve the enrichment of CH(4) from the concentrations of 55-85% up to 91-94.4%. The membrane material was resistant to the small concentrations of sour gases and assured the reduction of H(2)S and water vapour concentrations, as well. The required enrichment was achieved in the single module, however to prevent CH(4) losses the multistage or hybrid systems should be used to improve process efficiency.
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Kovačević, Sanja; Nestorov, Jelena; Matić, Gordana; Elaković, Ivana
2017-02-01
The consumption of refined, fructose-enriched food continuously increases and has been linked to development of obesity, especially in young population. Low-grade inflammation and increased oxidative stress have been implicated in the pathogenesis of obesity-related disorders including type 2 diabetes. In this study, we examined alterations in inflammation and antioxidative defense system in the visceral adipose tissue (VAT) of fructose-fed young female rats, and related them to changes in adiposity and insulin sensitivity. We examined the effects of 9-week fructose-enriched diet applied immediately after weaning on nuclear factor κB (NF-κB) intracellular distribution, and on the expression of pro-inflammatory cytokines (IL-1β and TNFα) and key antioxidative enzymes in the VAT of female rats. Insulin signaling in the VAT was evaluated at the level of insulin receptor substrate-1 (IRS-1) protein and its inhibitory phosphorylation on Ser 307 . Fructose-fed rats had increased VAT mass along with increased NF-κB nuclear accumulation and elevated IL-1β, but not TNFα expression. The protein levels of antioxidative defense enzymes, mitochondrial manganese superoxide dismutase 2, and glutathione peroxidase, were reduced, while the protein content of IRS-1 and its inhibitory phosphorylation were not altered by fructose diet. The results suggest that fructose overconsumption-related alterations in pro-inflammatory markers and antioxidative capacity in the VAT of young female rats can be implicated in the development of adiposity, but do not affect inhibitory phosphorylation of IRS-1.
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Screening host proteins required for bacterial adherence after H9N2 virus infection.
Ma, Li-Li; Sun, Zhen-Hong; Xu, Yu-Lin; Wang, Shu-Juan; Wang, Hui-Ning; Zhang, Hao; Hu, Li-Ping; Sun, Xiao-Mei; Zhu, Lin; Shang, Hong-Qi; Zhu, Rui-Liang; Wei, Kai
2018-01-01
H9N2 subtype low pathogenic avian influenza virus (LPAIV) is distributed worldwide and causes great economic losses in the poultry industry, especially when complicated with other bacterial infections. Tissue damages caused by virus infection provide an opportunity for bacteria invasion, but this mechanism is not sufficient for low pathogenic strains. Moreover, although H9N2 virus infection was demonstrated to promote bacterial infection in several studies, its mechanism remained unclear. In this study, infection experiments in vivo and in vitro demonstrated that the adhesion of Escherichia coli (E. coli) to host cells significantly increased after H9N2 virus infection, and this increase was not caused by pathological damages. Subsequently, we constructed a late chicken embryo infection model and used proteomics techniques to analyze the expression of proteins associated with bacterial adhesion after H9N2 virus infection. A total of 279 significantly differential expressed proteins were detected through isobaric tags for relative and absolute quantitation (iTRAQ) coupled with nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) analysis. The results of Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that differentially expressed proteins were enriched in host innate immunity; cell proliferation, differentiation, and apoptosis; and pathogenicity-related signaling pathways. Finally, we screened out several proteins, such as TGF-β1, integrins, cortactin, E-cadherin, vinculin, and fibromodulin, which were probably associated with bacterial adhesion. The study analyzed the mechanism of secondary bacterial infection induced by H9N2 virus infection from a novel perspective, which provided theoretical and data support for investigating the synergistic infection mechanism between the H9N2 virus and bacteria. Copyright © 2017 Elsevier B.V. All rights reserved.
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Patrick, T E; Goodwin, T L; Collins, J A; Wyche, R C; Love, B E
1972-04-01
A comparison of two types of scalders was conducted to determine their effectiveness in reducing bacterial contamination of poultry carcasses. A conventional hot-water scalder and a prototype model of a steam scalder were tested under commercial conditions. Total plate counts from steam-scalded birds were significantly lower than the counts of water-scalded birds immediately after scalding and again after picking. No differences in the two methods could be found after chilling. Coliform counts from steam-scalded birds were significantly lower than the counts from water-scalded birds immediately after scalding. No significant differences in coliform counts were detected when the two scald methods were compared after defeathering and chilling.
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Bacterial respiration of arsenic and selenium
Stolz, J.F.; Oremland, R.S.
1999-01-01
Oxyanions of arsenic and selenium can be used in microbial anaerobic respiration as terminal electron acceptors. The detection of arsenate and selenate respiring bacteria in numerous pristine and contaminated environments and their rapid appearance in enrichment culture suggest that they are widespread and metabolically active in nature. Although the bacterial species that have been isolated and characterized are still few in number, they are scattered throughout the bacterial domain and include Gram- positive bacteria, beta, gamma and epsilon Proteobacteria and the sole member of a deeply branching lineage of the bacteria, Chrysiogenes arsenatus. The oxidation of a number of organic substrates (i.e. acetate, lactate, pyruvate, glycerol, ethanol) or hydrogen can be coupled to the reduction of arsenate and selenate, but the actual donor used varies from species to species. Both periplasmic and membrane-associated arsenate and selenate reductases have been characterized. Although the number of subunits and molecular masses differs, they all contain molybdenum. The extent of the environmental impact on the transformation and mobilization of arsenic and selenium by microbial dissimilatory processes is only now being fully appreciated.
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Bräuer, Suzanna L; Yashiro, Erika; Ueno, Norikiyo G; Yavitt, Joseph B; Zinder, Stephen H
2006-08-01
Two methanogenic cultures were enriched from acidic peat soil using a growth medium buffered to c. pH 5. One culture, 6A, was obtained from peat after incubation with H(2)/CO(2), whereas culture NTA was derived from a 10(-4) dilution of untreated peat into a modified medium. 16S rRNA gene clone libraries from each culture contained one methanogen and two bacterial sequences. The methanogen 16S rRNA gene sequences were 99% identical with each other and belonged to the novel "R-10/Fen cluster" family of the Methanomicrobiales, whereas their mcrA sequences were 96% identical. One bacterial 16S rRNA gene sequence from culture 6A belonged to the Bacteroidetes and showed 99% identity with sequences from methanogenic enrichments from German and Russian bogs. The other sequence belonged to the Firmicutes and was identical to a thick rod-shaped citrate-utilizing organism isolated from culture 6A, the numbers of which decreased when the Ti (III) chelator was switched from citrate to nitrilotriacetate. Bacterial clones from the NTA culture clustered in the Delta- and Betaproteobacteria. Both cultures contained thin rods, presumably the methanogens, as the predominant morphotype, and represent a significant advance in characterization of the novel acidiphilic R-10 family methanogens.
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Growth of Serratia liquefaciens under 7 mbar, 0°C, and CO2-Enriched Anoxic Atmospheres
Ulrich, Richard; Berry, Bonnie J.; Nicholson, Wayne L.
2013-01-01
Abstract Twenty-six strains of 22 bacterial species were tested for growth on trypticase soy agar (TSA) or sea-salt agar (SSA) under hypobaric, psychrophilic, and anoxic conditions applied singly or in combination. As each factor was added to multi-parameter assays, the interactive stresses decreased the numbers of strains capable of growth and, in general, reduced the vigor of the strains observed to grow. Only Serratia liquefaciens strain ATCC 27592 exhibited growth at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres. To discriminate between the effects of desiccation and hypobaria, vegetative cells of Bacillus subtilis strain 168 and Escherichia coli strain K12 were grown on TSA surfaces and simultaneously in liquid Luria-Bertani (LB) broth media. Inhibition of growth under hypobaria for 168 and K12 decreased in similar ways for both TSA and LB assays as pressures were reduced from 100 to 25 mbar. Results for 168 and K12 on TSA and LB are interpreted to indicate a direct low-pressure effect on microbial growth with both species and do not support the hypothesis that desiccation alone on TSA was the cause of reduced growth at low pressures. The growth of S. liquefaciens at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres was surprising since S. liquefaciens is ecologically a generalist that occurs in terrestrial plant, fish, animal, and food niches. In contrast, two extremophiles tested in the assays, Deinococcus radiodurans strain R1 and Psychrobacter cryohalolentis strain K5, failed to grow under hypobaric (25 mbar; R1 only), psychrophilic (0°C; R1 only), or anoxic (<0.1% ppO2; both species) conditions. Key Words: Habitable zone—Hypobaria—Extremophiles—Special regions—Planetary protection. Astrobiology 13, 115–131. PMID:23289858
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Foraging enrichment modulates open field response to monosodium glutamate in mice.
Onaolapo, Olakunle J; Onaolapo, Adejoke Y; Akanmu, Moses A; Olayiwola, Gbola
2015-07-01
Environmental enrichment can enhance expression of species-specific behaviour. While foraging enrichment is encouraged in laboratory animals, its impact on novelty induced behaviour remain largely unknown. Here, we studied behavioural response of mice to acute and subchronic oral monosodium glutamate (MSG) in an open field with /without foraging enrichment. Adult male mice, assigned to five groups were administered vehicle (distilled water), or one of four selected doses of MSG (10, 20, 40 and 80 mg/kg) for 21 days. Open field novelty induced behaviours i.e. horizontal locomotion, rearing and grooming were assessed after the first and last doses of MSG. Results were analysed using MANOVA followed by Tukey HSD multiple comparison test and expressed as mean ± S.E.M. Following acute MSG administration without enrichment, locomotor activity reduced, grooming increased, while rearing activity reduced at lower doses and increased at higher doses. Subchronic administration without enrichment was associated with increased locomotor activity and reduction in grooming, rearing activity however still showed a biphasic response. Addition of enrichment with acute administration resulted in sustained reduction in locomotor and rearing activities with a biphasic grooming response. Subchronically, there was reduction in horizontal locomotion, biphasic rearing response and sustained increase in grooming activity. Behavioural response to varying doses of MSG as observed in the open field is affected by modifications such as foraging enrichment, which can reverse or dampen the central effects seen irrespective of duration of administration.
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Bioactive glass fillers reduce bacterial penetration into marginal gaps for composite restorations
Khvostenko, D.; Hilton, T. J.; Ferracane, J. L.; Mitchell, J. C.; Kruzic, J. J.
2015-01-01
Objectives Bioactive glass (BAG) is known to possess antimicrobial and remineralizing properties; however, the use of BAG as a filler for resin based composite restorations to slow recurrent caries has not been studied. Accordingly, the objective of this study was to investigate the effect of 15 wt% BAG additions to a resin composite on bacterial biofilms penetrating into marginal gaps of simulated tooth fillings in vitro during cyclic mechanical loading. Methods Human molars were machined into approximately 3 mm thick disks of dentin and 1.5–2 mm deep composite restorations were placed. A narrow 15–20 micrometer wide dentin-composite gap was allowed to form along half of the margin by not applying dental adhesive to that region. Two different 72 wt% filled composites were used, one with 15 wt% BAG filler (15BAG) and the balance silanated strontium glass and one filled with OX-50 and silanated strontium glass without BAG (0BAG – control). Samples of both groups had Streptococcus mutans biofilms grown on the surface and were tested inside a bioreactor for two weeks while subjected to periods of cyclic mechanical loading. After post-test biofilm viability was confirmed, each specimen was fixed in glutaraldehyde, gram positive stained, mounted in resin and cross-sectioned to reveal the gap profile. Depth of biofilm penetration for 0BAG and 15BAG was quantified as the fraction of gap depth. The data were compared using a Student’s t-test. Results The average depth of bacterial penetration into the marginal gap for the 15BAG samples was significantly smaller (~61%) in comparison to 0BAG, where 100% penetration was observed for all samples with the biofilm penetrating underneath of the restoration in some cases. Significance BAG containing resin dental composites reduce biofilm penetration into marginal gaps of simulated tooth restorations. This suggests BAG containing composites may have the potential to slow the development and propagation of secondary tooth
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Update on bacterial meningitis: epidemiology, trials and genetic association studies.
Kasanmoentalib, E Soemirien; Brouwer, Matthijs C; van de Beek, Diederik
2013-06-01
Bacterial meningitis is a life-threatening disease that continues to inflict a heavy toll. We reviewed recent advances in vaccination, randomized studies on treatment, and genetic association studies in bacterial meningitis. The incidence of bacterial meningitis has decreased after implementation of vaccines, and further implementation of existing conjugate vaccines particularly in low-income countries is expected to reduce the global disease burden. Several randomized studies have been performed recently in this field. Clinical studies showed that short duration (5 days) of antibiotic treatment is as effective as longer duration treatment in low-income countries, and that dexamethasone decreases death and neurological sequelae in high-income countries. Ongoing trials will further define the role of paracetamol, glycerol and hypothermia in bacterial meningitis. Genetic association studies identified pathophysiological mechanisms that could be counteracted in experimental meningitis, providing promising leads for future treatments. Conjugate vaccines have reduced the burden of bacterial meningitis in high-income countries, but implementation of available vaccines in low-income countries is necessary to reduce disease burden worldwide. Adjunctive dexamethasone therapy has beneficial effects in patients with bacterial meningitis but only in high-income countries. Genetic association studies may reveal targets for new treatment strategies.
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NASA Technical Reports Server (NTRS)
Peslier, A. H.; Hnatyshin, D.; Herd, C. D. K.; Walton, E. L.; Brandon, A. D.; Lapen, T. J.; Shafer, J.
2010-01-01
A detailed petrographic study of melt inclusions and Cr-Fe-Ti oxides of LAR 06319 leads to two main conclusions: 1) this enriched oxidized olivine- phyric shergottite represents nearly continuous crystallization of a basaltic shergottite melt, 2) the melt became more oxidized during differentiation. The first crystallized mineral assemblages record the oxygen fugacity which is closest to that of the melt s mantle source, and which is lower than generally attributed to the enriched shergottite group.
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Goevert, Dennis; Conrad, Ralf
2008-11-01
Acetate is a key intermediate in the anaerobic degradation of organic matter. In anoxic environments, available acetate is a competitive substrate for sulfate-reducing bacteria (SRB) and methane-producing archaea. Little is known about the fractionation of carbon isotopes by sulfate reducers. Therefore, we determined carbon isotope compositions in cultures of three acetate-utilizing SRB, Desulfobacter postgatei, Desulfobacter hydrogenophilus, and Desulfobacca acetoxidans. We found that these species showed strong differences in their isotope enrichment factors (epsilon) of acetate. During the consumption of acetate and sulfate, acetate was enriched in 13C by 19.3% per hundred in Desulfobacca acetoxidans. By contrast, both D. postgatei and D. hydrogenophilus showed a slight depletion of 13C resulting in epsilon(ac)-values of 1.8 and 1.5% per hundred, respectively. We suggest that the different isotope fractionation is due to the different metabolic pathways for acetate oxidation. The strongly fractionating Desulfobacca acetoxidans uses the acetyl-CoA/carbon monoxide dehydrogenase pathway, which is also used by acetoclastic methanogens that show a similar fractionation of acetate (epsilon(ac) = -21 to -27% per hundred). In contrast, Desulfobacter spp. oxidize acetate to CO2 via the tricarboxylic acid (TCA) cycle and apparently did not discriminate against 13C. Our results suggestthat carbon isotope fractionation in environments with sulfate reduction will strongly depend on the composition of the sulfate-reducing bacterial community oxidizing acetate.
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Fate of di (2‑ethylhexyl) phthalate in different soils and associated bacterial community changes.
Zhu, Fengxiao; Zhu, Changyin; Doyle, Evelyn; Liu, Hailong; Zhou, Dongmei; Gao, Juan
2018-05-10
Di (2‑ethylhexyl) phthalate (DEHP) is a ubiquitous organic pollutant, which has caused considerable pollution in arable soils. In this study, the relationship between DEHP degradation potential and soil properties in 12 agricultural soils (S1-S12) was examined in a microcosm based experiment. Six of these soils were then selected to monitor patterns in bacterial community responses. It was found that DEHP degradation was positively correlated with bacterial counts in the original soils, suggesting a key role for bacteria in degradation. However, DEHP metabolism did not always lead to complete degradation. Its monoester metabolite, mono (2‑ethylhexyl) phthalate (MEHP), was present at appreciable levels in the two acidic soils (S1 and S2) during the incubation period of 35 days. Based on high-throughput sequencing data, we observed a greater impact of DEHP contamination on bacterial community structure in acidic soils than in the other soils. Nocardioides, Ramlibacter and unclassified Sphingomonadaceae were enriched in the two near-neutral soils where degradation was highest (S4 and S7), suggesting that these organisms might be efficient degraders. The relative abundance of Tumibacillus was greatly reduced in 50% of the six soils examined, demonstrating a high sensitivity to DEHP contamination. Furthermore, putative organic-matter decomposing bacteria (including Tumebacillus and other bacteria taxa such as members from Micromonosporaceae) were greatly reduced in the two acidic soils (S1 and S2), possibly due to the accumulation of MEHP. These results suggest a crucial role of soil acidity in determining the fate and impact of DEHP in soil ecosystems, which deserves further investigation. This work contributes to a better understanding of the environmental behavior of DEHP in soil and should facilitate the development of appropriate remediation technologies. Copyright © 2018 Elsevier B.V. All rights reserved.
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Swidsinski, Alexander; Loening-Baucke, Vera; Schulz, Stefan; Manowsky, Julia; Verstraelen, Hans; Swidsinski, Sonja
2016-02-01
Sections of fecal cylinders were analyzed using fluorescence in situ hybridization targeting 180 bacterial groups. Samples were collected from three groups of women (N=20 each) treated for bacterial vaginosis with ciprofloxacin+metronidazole. Group A only received the combined antibiotic regimen, whereas the A/Sb group received concomitant Saccharomyces boulardii CNCM I-745 treatment, and the A_Sb group received S. boulardii prophylaxis following the 14-day antibiotic course. The number of stool cylinders analyzed was 188 out of 228 in group A, 170 out of 228 in group A/Sb, and 172 out of 216 in group A_Sb. The colonic biomass was organized into a separate mucus layer with no bacteria, a 10-30μm broad unstirred transitional layer enriched with bacteria, and a patchy fermentative area that mixed digestive leftovers with bacteria. The antibiotics suppressed bacteria mainly in the fermentative area, whereas abundant bacterial clades retreated to the transitional mucus and survived. As a result, the total concentration of bacteria decreased only by one order. These effects were lasting, since the overall recovery of the microbial mass, bacterial diversity and concentrations were still below pre-antibiotic values 4 months after the end of antibiotic treatment. Sb-prophylaxis markedly reduced antibiotic effects and improved the recovery rates. Since the colon is a sophisticated bioreactor, the study indicated that the spatial anatomy of its biomass was crucial for its function. Copyright © 2015 The Authors. Published by Elsevier GmbH.. All rights reserved.
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Proteolysis and utilization of albumin by enrichment cultures of subgingival microbiota.
Wei, G X; van der Hoeven, J S; Smalley, J W; Mikx, F H; Fan, M W
1999-12-01
Subgingival dental plaque consists mainly of microorganisms that derive their energy from amino acid fermentation. Their nutrient requirements are met by the subgingival proteolytic system, which includes proteases from microorganism and inflammatory cells, and substrate proteins from sulcus exudate, including albumin. To determine the selective effect of individual proteins on microbiota, we used albumin as the main substrate for growth. Eight subgingval plaque samples from untreated periodontal pockets of patients with adult periodontitis were inoculated in peptone yeast medium with bovine albumin (9 g/l). After three subculture steps, cell yields of the enrichment cultures at the medium with 0, 1.25, 2.5, 5, 10, and 20 g/l albumin were determined. Proteolytic activity (U/absorbance at 550 nm) of the enrichment cultures and different isolates derived from the cultures was estimated by the degradation of resorufin-labeled casein. It was observed that the yield of the mixed culture was albumin limited, and the proteolytic activities of the cultures in albumin broth were higher than in control (peptone broth). Among the isolates from the enrichment cultures, Peptostreptococcus micros, Prevotella melaninogenica, Prevotella buccae and Prevotella bivia demonstrated proteolysis. The frequent occurrence of Streptococcus gordonii and Streptococcus anginosus in the albumin cultures is explained by their ability to utilize arginine as an energy source for growth. Albumin in the medium was partly degraded by pure cultures but completely consumed in enrichment cultures, indicating synergy of bacterial proteinases. It is concluded that the subgingival microbiota possesses proteolytic activity and may use albumin as a substrate for their growth. Enrichment cultures on albumin may serve as a relatively simple in vitro model to evaluate the effects of proteinase inhibitors.
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Nutrient enrichment reduces constraints on material flows in a detritus-based food web
Wyatt F. Cross; Bruce Wallace; Amy D. Rosemond
2007-01-01
Most aquatic and terrestrial ecosystems are experiencing increased nutrient availability, which is affecting their structure and function. By altering community composition and productivity of consumers, enrichment can indirectly cause changes in the pathways and magnitude of material flows in food webs. These changes, in turn, have major consequences for material...
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Vázquez-Velasco, Miguel; González-Torres, Laura; García-Fernández, Rosa A; Méndez, María Teresa; Bastida, Sara; Benedí, Juana; González-Muñoz, María José; Sánchez-Muniz, Francisco J
2017-06-01
Glucomannan-enriched squid surimi improves cholesterolemia and liver antioxidant status. The effect of squid surimi enriched with glucomannan or glucomannan plus spirulina on liver and heart structures and cell damage markers was tested in fa/fa rats fed highly saturated-hyper-energetic diets. Animals were fed 70% AIN-93M rodent diet plus six versions of 30% squid surimi for 7 weeks: control (C), glucomannan (G), and glucomannan plus spirulina (GS). The cholesterol-control (HC), cholesterol-glucomannan (HG), and cholesterol-glucomannan plus spirulina (HGS) groups were given similar diets that were enriched with 2% cholesterol and 0.4% cholic acid. G and GS diets versus C diet significantly inhibited weight gain and lowered plasma alanine aminotransferase and aspartate aminotransferase, liver steatosis, lipogranulomas, and total inflammation and alteration scores. The hypercholesterolemic agent significantly increased the harmful effects of the C diet. Liver weight, the hepatosomatic index, all damage markers, and total histological scoring rose for HC versus C (at least P < .05). The addition of glucomannan (HG vs. HC) improved these biomarkers, and non-additional effects from spirulina were observed except for the total liver alteration score. In conclusion, glucomannan and glucomannan plus spirulina blocked the highly saturated-hyper-energetic diet negative effects both with and without added cholesterol. Results suggest the usefulness of including these functional ingredients in fish products.
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Enrichment options for African painted dogs (Lycaon pictus).
Cloutier, Tammy L; Packard, Jane M
2014-01-01
Best practices for carnivore enrichment encourage the diversity of species-typical behaviors, increased activity, and reduced stereotypic behavior; ideally considering the life-history and behavior of each species. African wild dogs (Lycaon pictus), or painted dogs, are social carnivores that have large home ranges and complex pack dynamics (e.g., variation in group size, relatedness, etc.). As there are relatively few studies on painted dog enrichment, the goal of this study was to compile a list of enrichment options used by institutions participating in the species survival plan (SSP). Representatives were asked to describe social groups (n = 45), enclosures (n = 21), enrichment practices (options, delivery frequency, perceived success), and overall best practices. Respondents (61%, n = 23) reported using options for all six enrichment categories recommended by the Canid Taxon Advisory Group: environmental enrichment devices, habitat, sensory, food, behavioral, and social. Perceived success was significantly higher for the food category, followed by the sensory and behavioral categories. All respondents reported delivering enrichment at least multiple times a month, and most reported multiple times per week. Enclosure size did not differ significantly for mixed-sex groups (n = 28) compared to single-sex groups (n = 17). We discuss respondents' suggestions for best practices and the need to record data to compare perceived success with actual behavioral effects, controlling for variation in group size and composition. Overall, respondents recommended a flexible approach, since not all painted dogs and groups respond in the same way to the enrichment options. © 2014 Wiley Periodicals, Inc.
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Patrick, Thomas E.; Goodwin, T. L.; Collins, J. A.; Wyche, R. C.; Love, B. E.
1972-01-01
A comparison of two types of scalders was conducted to determine their effectiveness in reducing bacterial contamination of poultry carcasses. A conventional hot-water scalder and a prototype model of a steam scalder were tested under commercial conditions. Total plate counts from steam-scalded birds were significantly lower than the counts of water-scalded birds immediately after scalding and again after picking. No differences in the two methods could be found after chilling. Coliform counts from steam-scalded birds were significantly lower than the counts from water-scalded birds immediately after scalding. No significant differences in coliform counts were detected when the two scald methods were compared after defeathering and chilling. PMID:4553146
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Horn, Hannes; Slaby, Beate M.; Jahn, Martin T.
Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, clustered regularly interspaced short palindromic repeats, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defensemore » is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. Furthermore, this study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.« less
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Horn, Hannes; Slaby, Beate M.; Jahn, Martin T.; ...
2016-11-08
Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, clustered regularly interspaced short palindromic repeats, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defensemore » is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. Furthermore, this study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.« less
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Bacterial communities in sediment of a Mediterranean marine protected area.
Catania, Valentina; Sarà, Gianluca; Settanni, Luca; Quatrini, Paola
2017-04-01
Biodiversity is crucial in preservation of ecosystems, and bacterial communities play an indispensable role for the functioning of marine ecosystems. The Mediterranean marine protected area (MPA) "Capo Gallo-Isola delle Femmine" was instituted to preserve marine biodiversity. The bacterial diversity associated with MPA sediment was compared with that from sediment of an adjacent harbour exposed to intense nautical traffic. The MPA sediment showed higher diversity with respect to the impacted site. A 16S rDNA clone library of the MPA sediment allowed the identification of 7 phyla: Proteobacteria (78%), Firmicutes (11%), Acidobacteria (3%), Actinobacteria (3%), Bacteroidetes (2%), Planctomycetes (2%), and Cyanobacteria (1%). Analysis of the hydrocarbon (HC)-degrading bacteria was performed using enrichment cultures. Most of the MPA sediment isolates were affiliated with Gram-positive G+C rich bacteria, whereas the majority of taxa in the harbour sediment clustered with Alpha- and Gammaproteobacteria; no Gram-positive HC degraders were isolated from the harbour sediment. Our results show that protection probably has an influence on bacterial diversity, and suggest the importance of monitoring the effects of protection at microbial level as well. This study creates a baseline of data that can be used to assess changes over time in bacterial communities associated with a Mediterranean MPA.
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Poessel, S.A.; Biggins, D.E.; Santymire, R.M.; Livieri, T.M.; Crooks, K.R.; Angeloni, L.
2011-01-01
Potential stressors of wildlife living in captivity, such as artificial living conditions and frequent human contact, may lead to a higher occurrence of disease and reduced reproductive function. One successful method used by wildlife managers to improve general well-being is the provision of environmental enrichment, which is the practice of providing animals under managed care with environmental stimuli. The black-footed ferret (Mustela nigripes) is a highly-endangered carnivore species that was rescued from extinction by removal of the last remaining individuals from the wild to begin an ex situ breeding program. Our goal was to examine the effect of environmental enrichment on adrenocortical activity in ferrets by monitoring fecal glucocorticoid metabolites (FGM). Results demonstrated that enrichment lowered FGM in juvenile male ferrets, while increasing it in adult females; enrichment had no effect on FGM in juvenile females and adult males. These results correspond with our findings that juvenile males interacted more with the enrichment items than did adult females. However, we did not detect an impact of FGM on the incidence of disease or on the ability of ferrets to become reproductive during the following breeding season. We conclude that an environmental enrichment program could benefit captive juvenile male ferrets by reducing adrenocortical activity. ?? 2011 Elsevier Inc.
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Poessel, Sharon A; Biggins, Dean E; Santymire, Rachel M; Livieri, Travis M; Crooks, Kevin R; Angeloni, Lisa
2011-07-01
Potential stressors of wildlife living in captivity, such as artificial living conditions and frequent human contact, may lead to a higher occurrence of disease and reduced reproductive function. One successful method used by wildlife managers to improve general well-being is the provision of environmental enrichment, which is the practice of providing animals under managed care with environmental stimuli. The black-footed ferret (Mustela nigripes) is a highly-endangered carnivore species that was rescued from extinction by removal of the last remaining individuals from the wild to begin an ex situ breeding program. Our goal was to examine the effect of environmental enrichment on adrenocortical activity in ferrets by monitoring fecal glucocorticoid metabolites (FGM). Results demonstrated that enrichment lowered FGM in juvenile male ferrets, while increasing it in adult females; enrichment had no effect on FGM in juvenile females and adult males. These results correspond with our findings that juvenile males interacted more with the enrichment items than did adult females. However, we did not detect an impact of FGM on the incidence of disease or on the ability of ferrets to become reproductive during the following breeding season. We conclude that an environmental enrichment program could benefit captive juvenile male ferrets by reducing adrenocortical activity. Copyright © 2011 Elsevier Inc. All rights reserved.
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Closing the Achievement Gap with Curriculum Enrichment and Differentiation: One School's Story
ERIC Educational Resources Information Center
Beecher, Margaret; Sweeny, Sheelah M.
2008-01-01
This article summarizes a unique approach to reducing the achievement gap that strategically blended differentiated curriculum with schoolwide enrichment teaching and learning. The theories of enrichment and instructional differentiation were translated into practice in an elementary school that had previously embraced a remedial paradigm. This…
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Environmental Enrichment for Broiler Breeders: An Undeveloped Field.
Riber, Anja B; de Jong, Ingrid C; van de Weerd, Heleen A; Steenfeldt, Sanna
2017-01-01
Welfare problems, such as hunger, frustration, aggression, and abnormal sexual behavior, are commonly found in broiler breeder production. To prevent or reduce these welfare problems, it has been suggested to provide stimulating enriched environments. We review the effect of the different types of environmental enrichment for broiler breeders, which have been described in the scientific literature, on behavior and welfare. Environmental enrichment is defined as an improvement of the environment of captive animals, which increases the behavioral opportunities of the animal and leads to improvements in biological function. This definition has been broadened to include practical and economic aspects as any enrichment strategy that adversely affects the health of animals (e.g., environmental hygiene), or that has too many economic or practical constraints will never be implemented on commercial farms and thus never benefit animals. Environmental enrichment for broiler breeders often has the purpose of satisfying the behavioral motivations for feeding and foraging, resting, and/or encouraging normal sexual behavior. Potentially successful enrichments for broiler breeders are elevated resting places, cover panels, and substrate (for broiler breeders housed in cage systems). However, most of the ideas for environmental enrichment for broiler breeders need to be further developed and studied with respect to the use, the effect on behavior and welfare, and the interaction with genotype and production system. In addition, information on practical use and the economics of the production system is often lacking although it is important for application in practice.
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Harvey, R.W.; Lion, Leonard W.; Young, L.Y.; Leckie, J.O.
1982-01-01
The particle-laden surface layer (approx 150-370 mu m) and subsurface waters of a South San Francisco Bay salt marsh were sampled over 2 tidal cycles and analyzed for particle numbers and particulate-associated and total concentrations of Pb and bacteria. Laboratory studies examined the ability of a bacterial isolate from the surface layer and a bacterial 'film-former' to sorb Pb at environmentally significant concentrations in seawater. Degrees by which Pb concentrated in the surface layer relative to the subsurface strongly correlated with enrichments of surface layer bacteria (bacterioneuston). A significant fraction of the bacterioneuston and surface layer Pb were associated with particles. Particle-bound bacterioneuston may interact with Pb at particulate surfaces in this microenvironment.
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Zaheer, Rahat; Dugat-Bony, Eric; Holman, Devon; Cousteix, Elodie; Xu, Yong; Munns, Krysty; Selinger, Lorna J; Barbieri, Rutn; Alexander, Trevor; McAllister, Tim A; Selinger, L Brent
2017-01-01
Escherichia coli O157:H7 is a foodborne pathogen that colonizes ruminants. Cattle are considered the primary reservoir of E. coli O157:H7 with super-shedders, defined as individuals excreting > 104 E. coli O157:H7 CFU g-1 feces. The mechanisms leading to the super-shedding condition are largely unknown. Here, we used 16S rRNA gene pyrosequencing to examine the composition of the fecal bacterial community in order to investigate changes in the bacterial microbiota at several locations along the digestive tract (from the duodenum to the rectal-anal junction) in 5 steers previously identified as super-shedders and 5 non-shedders. The overall bacterial community structure did not differ by E. coli O157:H7 shedding status; but several differences in the relative abundance of taxa and OTUs were noted between the two groups. The genus Prevotella was most enriched in the non-shedders while the genus Ruminococcus and the Bacteroidetes phylum were notably enriched in the super-shedders. There was greater bacterial diversity and richness in samples collected from the lower- as compared to the upper gastrointestinal tract (GI). The spiral colon was the only GI location that differed in terms of bacterial diversity between super-shedders and non-shedders. These findings reinforced linkages between E. coli O157:H7 colonization in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders.
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Cousteix, Elodie; Xu, Yong; Munns, Krysty; Selinger, Lorna J.; Barbieri, Rutn; Alexander, Trevor; McAllister, Tim A.; Selinger, L. Brent
2017-01-01
Escherichia coli O157:H7 is a foodborne pathogen that colonizes ruminants. Cattle are considered the primary reservoir of E. coli O157:H7 with super-shedders, defined as individuals excreting > 104 E. coli O157:H7 CFU g-1 feces. The mechanisms leading to the super-shedding condition are largely unknown. Here, we used 16S rRNA gene pyrosequencing to examine the composition of the fecal bacterial community in order to investigate changes in the bacterial microbiota at several locations along the digestive tract (from the duodenum to the rectal-anal junction) in 5 steers previously identified as super-shedders and 5 non-shedders. The overall bacterial community structure did not differ by E. coli O157:H7 shedding status; but several differences in the relative abundance of taxa and OTUs were noted between the two groups. The genus Prevotella was most enriched in the non-shedders while the genus Ruminococcus and the Bacteroidetes phylum were notably enriched in the super-shedders. There was greater bacterial diversity and richness in samples collected from the lower- as compared to the upper gastrointestinal tract (GI). The spiral colon was the only GI location that differed in terms of bacterial diversity between super-shedders and non-shedders. These findings reinforced linkages between E. coli O157:H7 colonization in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders. PMID:28141846
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Juvenile psittacine environmental enrichment.
Simone-Freilicher, Elisabeth; Rupley, Agnes E
2015-05-01
Environmental enrichment is of great import to the emotional, intellectual, and physical development of the juvenile psittacine and their success in the human home environment. Five major types of enrichment include social, occupational, physical, sensory, and nutritional. Occupational enrichment includes exercise and psychological enrichment. Physical enrichment includes the cage and accessories and the external home environment. Sensory enrichment may be visual, auditory, tactile, olfactory, or taste oriented. Nutritional enrichment includes variations in appearance, type, and frequency of diet, and treats, novelty, and foraging. Two phases of the preadult period deserve special enrichment considerations: the development of autonomy and puberty. Copyright © 2015 Elsevier Inc. All rights reserved.
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Antibiotics for treating bacterial vaginosis in pregnancy
McDonald, Helen Margaret; Brocklehurst, Peter; Gordon, Adrienne
2014-01-01
Background Bacterial vaginosis is an imbalance of the normal vaginal flora with an overgrowth of anaerobic bacteria and a lack of the normal lactobacillary flora. Bacterial vaginosis during pregnancy has been associated with poor perinatal outcome and, in particular, preterm birth (PTB). Identification and treatment may reduce the risk of PTB and its consequences. Objectives To assess the effects of antibiotic treatment of bacterial vaginosis in pregnancy. Search methods We searched the Cochrane Pregnancy and Childbirth Group’s Trials Register (May 2006). We updated this search on 18 November 2010 and added the results to the awaiting classification section. Selection criteria Randomized trials comparing antibiotic treatment with placebo or no treatment, or comparing two or more antibiotic regimens in pregnant women with bacterial vaginosis or intermediate vaginal flora. Data collection and analysis Two review authors assessed trials and extracted data independently. We contacted study authors for additional information. Main results We included fifteen trials of good quality, involving 5888 women. Antibiotic therapy was effective at eradicating bacterial vaginosis during pregnancy (Peto odds ratio (OR) 0.17, 95% confidence interval (CI) 0.15 to 0.20; 10 trials, 4357 women). Treatment did not reduce the risk of PTB before 37 weeks (Peto OR 0.91, 95% CI 0.78 to 1.06; 15 trials, 5888 women), or the risk of preterm prelabour rupture of membranes (PPROM) (Peto OR 0.88, 95% CI 0.61 to 1.28; four trials, 2579 women). However, treatment before 20 weeks’ gestation may reduce the risk of preterm birth less than 37 weeks (Peto OR 0.72, 95% CI 0.55 to 0.95; five trials, 2387 women). In women with a previous PTB, treatment did not affect the risk of subsequent PTB (Peto OR 0.83, 95% CI 0.59 to 1.17, five trials of 622); however, it may decrease the risk of PPROM (Peto OR 0.14, 95% CI 0.05 to 0.38) and low birthweight (Peto OR 0.31, 95% CI 0.13 to 0.75)(two trials, 114
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[Efficacy of five disinfectants to reduce bacterial load in the household].
Stambullian, Julián; Rossotti, Daniel; Fridman, Diego; Luchetti, Pablo; Cheade, Yamila; Stamboulian, Daniel
2011-01-01
The proper use of products containing sodium hypochlorite,ammonium salts and triclosan has proved to be effective in the elimination of infectious agents in the household environment. Our objective was to evaluate the immediate, one-week and one-month efficacy of controlled use of five products containing these components, compared to other commonly used products. Within a six month period, thirty two middle-class homes from Buenos Aires City and suburbs were included in this open-label, randomized, parallel-group intervention study. Sixteen homes were randomized to use products containing sodium hypochlorite, ammonia and triclosan in the kitchen and bathroom during one month. The remaining maintained usual practices for domestic cleaning. Bacterial counts and identification were performed from samples taken from each study site. Baseline samples (no group discrimination) contained a mean bacterial count in kitchen of 66.0 CFU/cm2, and in bathroom 40.1 CFU/cm2. Samples taken immediately after-cleaning (no group discrimination) contained: kitchen 0.8 CFU/cm2; bathroom < 1 CFU/cm2. After one week (intervention group vs. control group) contained: kitchen 18.0 vs. 32.5 CFU/cm2; bathroom 12.7 vs. 7.7 CFU/cm2. After one month (intervention group vs. control group): kitchen 60.1 vs. 62.1 CFU/cm2; bathroom 37.0 vs. 42.0 CFU/cm2. A remarkable decrease of bacterial load was observed in both groups, which suggests that not only product quality but also education for suitable use plays a key role in successful house disinfection. This approach could be an important tool for improving prevention of foodborne infections since fecal coliforms widely predominated in all analyzed samples.
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Reducing DNA context dependence in bacterial promoters
Carr, Swati B.; Densmore, Douglas M.
2017-01-01
Variation in the DNA sequence upstream of bacterial promoters is known to affect the expression levels of the products they regulate, sometimes dramatically. While neutral synthetic insulator sequences have been found to buffer promoters from upstream DNA context, there are no established methods for designing effective insulator sequences with predictable effects on expression levels. We address this problem with Degenerate Insulation Screening (DIS), a novel method based on a randomized 36-nucleotide insulator library and a simple, high-throughput, flow-cytometry-based screen that randomly samples from a library of 436 potential insulated promoters. The results of this screen can then be compared against a reference uninsulated device to select a set of insulated promoters providing a precise level of expression. We verify this method by insulating the constitutive, inducible, and repressible promotors of a four transcriptional-unit inverter (NOT-gate) circuit, finding both that order dependence is largely eliminated by insulation and that circuit performance is also significantly improved, with a 5.8-fold mean improvement in on/off ratio. PMID:28422998
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Luo, Fei; Gitiafroz, Roya; Devine, Cheryl E.; Gong, Yunchen; Hug, Laura A.; Raskin, Lutgarde
2014-01-01
The enzymes involved in the initial steps of anaerobic benzene catabolism are not known. To try to elucidate this critical step, a metatranscriptomic analysis was conducted to compare the genes transcribed during the metabolism of benzene and benzoate by an anaerobic benzene-degrading, nitrate-reducing enrichment culture. RNA was extracted from the mixed culture and sequenced without prior mRNA enrichment, allowing simultaneous examination of the active community composition and the differential gene expression between the two treatments. Ribosomal and mRNA sequences attributed to a member of the family Peptococcaceae from the order Clostridiales were essentially only detected in the benzene-amended culture samples, implicating this group in the initial catabolism of benzene. Genes similar to each of two subunits of a proposed benzene-carboxylating enzyme were transcribed when the culture was amended with benzene. Anaerobic benzoate degradation genes from strict anaerobes were transcribed only when the culture was amended with benzene. Genes for other benzoate catabolic enzymes and for nitrate respiration were transcribed in both samples, with those attributed to an Azoarcus species being most abundant. These findings indicate that the mineralization of benzene starts with its activation by a strict anaerobe belonging to the Peptococcaceae, involving a carboxylation step to form benzoate. These data confirm the previously hypothesized syntrophic association between a benzene-degrading Peptococcaceae strain and a benzoate-degrading denitrifying Azoarcus strain for the complete catabolism of benzene with nitrate as the terminal electron acceptor. PMID:24795366
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Rowe, Annette R; Yoshimura, Miho; LaRowe, Doug E; Bird, Lina J; Amend, Jan P; Hashimoto, Kazuhito; Nealson, Kenneth H; Okamoto, Akihiro
2017-06-01
Serpentinization is a geologic process that produces highly reduced, hydrogen-rich fluids that support microbial communities under high pH conditions. We investigated the activity of microbes capable of extracellular electron transfer in a terrestrial serpentinizing system known as 'The Cedars'. Measuring current generation with an on-site two-electrode system, we observed daily oscillations in current with the current maxima and minima occurring during daylight hours. Distinct members of the microbial community were enriched. Current generation in lab-scale electrochemical reactors did not oscillate, but was correlated with carbohydrate amendment in Cedars-specific minimal media. Gammaproteobacteria and Firmicutes were consistently enriched from lab electrochemical systems on δ-MnO 2 and amorphous Fe(OH) 3 at pH 11. However, isolation of an electrogenic strain proved difficult as transfer cultures failed to grow after multiple rounds of media transfer. Lowering the bulk pH in the media allowed us to isolate a Firmicutes strain (Paenibacillus sp.). This strain was capable of electrode and mineral reduction (including magnetite) at pH 9. This report provides evidence of the in situ activity of microbes using extracellular substrates as sinks for electrons at The Cedars, but also highlights the potential importance of community dynamics for supporting microbial life through either carbon fixation, and/or moderating pH stress. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
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Dong, Yiran; Sanford, Robert A.; Locke, Randall A.; Cann, Isaac K.; Mackie, Roderick I.; Fouke, Bruce W.
2014-01-01
The Cambrian-age Mt. Simon Sandstone, deeply buried within the Illinois Basin of the midcontinent of North America, contains quartz sand grains ubiquitously encrusted with iron-oxide cements and dissolved ferrous iron in pore-water. Although microbial iron reduction has previously been documented in the deep terrestrial subsurface, the potential for diagenetic mineral cementation to drive microbial activity has not been well studied. In this study, two subsurface formation water samples were collected at 1.72 and 2.02 km, respectively, from the Mt. Simon Sandstone in Decatur, Illinois. Low-diversity microbial communities were detected from both horizons and were dominated by Halanaerobiales of Phylum Firmicutes. Iron-reducing enrichment cultures fed with ferric citrate were successfully established using the formation water. Phylogenetic classification identified the enriched species to be related to Vulcanibacillus from the 1.72 km depth sample, while Orenia dominated the communities at 2.02 km of burial depth. Species-specific quantitative analyses of the enriched organisms in the microbial communities suggest that they are indigenous to the Mt. Simon Sandstone. Optimal iron reduction by the 1.72 km enrichment culture occurred at a temperature of 40°C (range 20–60°C) and a salinity of 25 parts per thousand (range 25–75 ppt). This culture also mediated fermentation and nitrate reduction. In contrast, the 2.02 km enrichment culture exclusively utilized hydrogen and pyruvate as the electron donors for iron reduction, tolerated a wider range of salinities (25–200 ppt), and exhibited only minimal nitrate- and sulfate-reduction. In addition, the 2.02 km depth community actively reduces the more crystalline ferric iron minerals goethite and hematite. The results suggest evolutionary adaptation of the autochthonous microbial communities to the Mt. Simon Sandstone and carries potentially important implications for future utilization of this reservoir for CO2
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Salcedo-Sandoval, Lorena; Cofrades, Susana; Ruiz-Capillas, Claudia; Jiménez-Colmenero, Francisco
2014-12-01
The effect of cooking methods (electric grilling and pan-frying in olive oil) on the composition of reduced-fat and reduced-fat/PUFA enriched pork patties was studied. Fat reduction was performed by replacing pork backfat (38% and 100%) with konjac gel and PUFA-enrichment by replacing pork backfat (49%) with a konjac-based oil bulking system stabilizing a healthier oil combination (olive, linseed and fish oils). Cooking losses (13%-27%) were affected (p<0.05) by formulation and cooking procedure. Compared with raw products, cooked samples had higher (p<0.05) concentrations of MUFAs and PUFAs (both n-3 and n-6); the difference was greater (p<0.05) in the pan-fried patties. Fatty acid retention was generally better in pan-fried than in grilled samples. When cooked, the PUFA levels in the medium-fat/improved sample containing the oil bulking system ranged between 1.4 and 1.6g/100g (0.47-0.51 from n-3 PUFAs), with EPA+DHA concentrations of around 75mg/100g. Konjac materials were successfully used to produce pork patties with a better lipid composition. Copyright © 2014. Published by Elsevier Ltd.
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Chen, Junfeng; Zhang, Lihua; Hu, Yongyou; Huang, Wantang; Niu, Zhuyu; Sun, Jian
2017-10-01
In this work, bacterial community shift and incurred performance of graphene modified bioelectrode (GM-BE) in microbial fuel cell (MFC) were illustrated by high throughput sequencing technology and electrochemical analysis. The results showed that Firmicutes occupied 48.75% in graphene modified bioanode (GM-BA), while Proteobacteria occupied 62.99% in graphene modified biocathode (GM-BC), both were dominant bacteria in phylum level respectively. Typical exoelectrogens, including Geobacter, Clostridium, Pseudomonas, Geothrix and Hydrogenophaga, were counted 26.66% and 17.53% in GM-BA and GM-BC. GM-BE was tended to decrease the bacterial diversity and enrich the dominant species. Because of the enrichment of exoelectrogens and excellent electrical conductivity of graphene, the maximum power density of MFC with GM-BA and GM-BC increased 33.1% and 21.6% respectively, and the transfer resistance decreased 83.8% and 73.6% compared with blank bioelectrode. This study aimed to enrich the microbial study in MFC and broaden the development and application for bioelectrode. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S
2016-02-01
Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.
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Chin, Wai Hoe; Sun, Yi; Høgberg, Jonas; Quyen, Than Linh; Engelsmann, Pia; Wolff, Anders; Bang, Dang Duong
2017-04-01
Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture method is time consuming. In response to the demand for rapid on line or at site detection of pathogens, in this study, we developed a multiplex Direct PCR method for rapid detection of different Salmonella serotypes directly from pork meat samples without any DNA purification steps. An inhibitor-resistant Phusion Pfu DNA polymerase was used to overcome PCR inhibition. Four pairs of primers including a pair of newly designed primers targeting Salmonella spp. at subtype level were incorporated in the multiplex Direct PCR. To maximize the efficiency of the Direct PCR, the ratio between sample and dilution buffer was optimized. The sensitivity and specificity of the multiplex Direct PCR were tested using naturally contaminated pork meat samples for detecting and subtyping of Salmonella spp. Conventional bacterial culture methods were used as reference to evaluate the performance of the multiplex Direct PCR. Relative accuracy, sensitivity and specificity of 98.8%; 97.6% and 100%, respectively, were achieved by the method. Application of the multiplex Direct PCR to detect Salmonella in pork meat at slaughter reduces the time of detection from 5 to 6 days by conventional bacterial culture and serotyping methods to 14 h (including 12 h enrichment time). Furthermore, the method poses a possibility of miniaturization and integration into a point-of-need Lab-on-a-chip system for rapid online pathogen detection. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Ferrari, Belinda C.; Tujula, Niina; Stoner, Kate; Kjelleberg, Staffan
2006-01-01
Advances in the growth of hitherto unculturable soil bacteria have emphasized the requirement for rapid bacterial identification methods. Due to the slow-growing strategy of microcolony-forming soil bacteria, successful fluorescence in situ hybridization (FISH) requires an rRNA enrichment step for visualization. In this study, catalyzed reporter deposition (CARD)-FISH was employed as an alternative method to rRNA enhancement and was found to be superior to conventional FISH for the detection of microcolonies that are cultivated by using the soil substrate membrane system. CARD-FISH enabled real-time identification of oligophilic microcolony-forming soil bacteria without the requirement for enrichment on complex media and the associated shifts in community composition. PMID:16391135
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Synthetic analogs of bacterial quorum sensors
Iyer, Rashi [Los Alamos, NM; Ganguly, Kumkum [Los Alamos, NM; Silks, Louis A [Los Alamos, NM
2011-12-06
Bacterial quorum-sensing molecule analogs having the following structures: ##STR00001## and methods of reducing bacterial pathogenicity, comprising providing a biological system comprising pathogenic bacteria which produce natural quorum-sensing molecule; providing a synthetic bacterial quorum-sensing molecule having the above structures and introducing the synthetic quorum-sensing molecule into the biological system comprising pathogenic bacteria. Further is provided a method of targeted delivery of an antibiotic, comprising providing a synthetic quorum-sensing molecule; chemically linking the synthetic quorum-sensing molecule to an antibiotic to produce a quorum-sensing molecule-antibiotic conjugate; and introducing the conjugate into a biological system comprising pathogenic bacteria susceptible to the antibiotic.
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Synthetic analogs of bacterial quorum sensors
Iyer, Rashi S.; Ganguly, Kumkum; Silks, Louis A.
2013-01-08
Bacterial quorum-sensing molecule analogs having the following structures: ##STR00001## and methods of reducing bacterial pathogenicity, comprising providing a biological system comprising pathogenic bacteria which produce natural quorum-sensing molecule; providing a synthetic bacterial quorum-sensing molecule having the above structures and introducing the synthetic quorum-sensing molecule into the biological system comprising pathogenic bacteria. Further is provided a method of targeted delivery of an antibiotic, comprising providing a synthetic quorum-sensing molecule; chemically linking the synthetic quorum-sensing molecule to an antibiotic to produce a quorum-sensing molecule-antibiotic conjugate; and introducing the conjugate into a biological system comprising pathogenic bacteria susceptible to the antibiotic.
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Chaskiel, Léa; Paul, Flora; Gerstberger, Rüdiger; Hübschle, Thomas; Konsman, Jan Pieter
2016-08-01
During infection-induced inflammation food intake is reduced. Vagal and brainstem pathways are important both in feeding regulation and immune-to-brain communication. Glutamate is released by vagal afferent terminals in the nucleus of the solitary tract and by its neurons projecting to the parabrachial nuclei. We therefore studied the role of brainstem glutamate receptors in spontaneous food intake of healthy animals and during sickness-associated hypophagia after peripheral administration of bacterial lipopolysaccharides or interleukin-1beta. Brainstem group I and II metabotropic, but not ionotropic, glutamate receptor antagonism increased food intake both in saline- and lipopolysaccharide-treated rats. In these animals, expression of the cellular activation marker c-Fos in the lateral parabrachial nuclei and lipopolysaccharide-induced activation of the nucleus of the solitary tract rostral to the area postrema were suppressed. Group I metabotropic glutamate receptors did not colocalize with c-Fos or neurons regulating gastric function in these structures. Group I metabotropic glutamate receptors were, however, found on raphé magnus neurons that were part of the brainstem circuit innervating the stomach and on trigeminal and hypoglossal motor neurons. In conclusion, our findings show that brainstem metabotropic glutamate receptors reduce food intake and activate the lateral parabrachial nuclei as well as the rostral nucleus of the solitary tract after peripheral bacterial lipopolysaccharide administration. They also provide insight into potential group I metabotropic glutamate receptor-dependent brainstem circuits mediating these effects. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Ma, Qin-Yun; Huang, Da-Yu; Zhang, Hui-Jun; Wang, Shaohua; Chen, Xiao-Feng
2017-11-01
The microbial community in the mucosal surfaces is involved in the development of human cancers, including gastric cancer and colorectal cancer. The respiratory tract in the lung also hosts a distinctive microbial community, but the correlation between this community and lung cancer is largely unknown. Here, we examined the Th1 and Th17 responses toward several bacterial antigens, in CD4 + T cells sourced from the peripheral blood (PB), the lung cancer (LC) tissue, and the gastrointestinal (GI) tract of non-small cell lung cancer (NSCLC) patients. Compared to healthy controls, the NSCLC patients presented significantly higher frequencies of Th1 and Th17 cells reacting to Streptococcus salivarius and S. agalactiae, in the PB, LC, and GI tract. Further investigation showed that the upregulation in anti-bacteria response was likely antigen-specific for two reasons. Firstly, the frequencies of Th1 and Th17 cells reacting to Escherichia coli, a typical GI bacterium, were not upregulated in the PB and the LC of NSCLC patients. Secondly, the S. salivarius and S. agalactiae responses could be partially blocked by Tü39, a MHC class II blocking antibody, suggesting that antigen-specific interaction between CD4 + T cells and antigen-presenting cells was required. We also found that S. salivarius and S. agalactiae could potently activate the monocytes to secrete higher levels of interleukin (IL)-6, IL-12, and tumor necrosis factor, which were Th1- and Th17-skewing cytokines. Interestingly, whereas CXCR5 + CD4 + T cells represented <20% of total CD4 + T cells, they represented 17%-82% of bacteria-specific Th1 or Th17 cells. Together, these data demonstrated that NSCLC patients presented a significant upregulation of bacterial-specific Th1 and Th17 responses that were enriched in CXCR5 + CD4 + T cells. Copyright © 2017 Elsevier B.V. All rights reserved.
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Simplifying Collection of Corneal Specimens in Cases of Suspected Bacterial Keratitis
Kaye, Stephen B.; Rao, Prasad G.; Smith, Godfrey; Scott, John A.; Hoyles, Sharon; Morton, Clare E.; Willoughby, Colin; Batterbury, Mark; Harvey, Graham
2003-01-01
Identification of the causative organisms in suspected bacterial keratitis traditionally involves collecting multiple corneal scrapes, which are plated directly onto different solid agar culture media. Difficulties have been reported with this practice, so the development of a simpler diagnostic method in suspected bacterial keratitis would be useful. It is unclear whether a single corneal scrape sent to the microbiology laboratory in a liquid transport culture medium (indirect method) is as reliable for the diagnosis of bacterial keratitis as inoculation of multiple scrapes directly onto agar plates (direct method). To investigate this, bacterial recovery was assessed following transfer and transport of different concentrations and types of bacteria from an artificially contaminated surgical blade into brain heart infusion (BHI). Bacterial recovery rates between the proposed (indirect) and standard (direct) method were then compared after the in vitro inoculation of pig corneas and following specimen collection in patients with presumed bacterial ulcerative keratitis. Recovery of bacteria from contaminated surgical blades was found to be the same from both solid and liquid culture media. There was no significant difference in the numbers of positive cultures from solid (direct) and liquid (indirect) culture media, both in the experimental pig cornea inoculation study (P = 0.34) and in experiments with patients with clinical infections (P = 0.4), with an 85.2% agreement between methods (kappa = 0.61, P < 0.0001). In conclusion, therefore, the collection of two corneal scrapes, one used for Gram staining and the other transported in BHI followed by plating and subculturing in an enrichment medium, provides a simple method for the investigation of presumed bacterial keratitis. PMID:12843063
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Dutta, Anirban; Vasudevan, Venugopal; Nain, Lata; Singh, Neera
2016-01-01
An enrichment culture was used to study atrazine degradation in mineral salt medium (MSM) (T1), MSM+soil extract (1:1, v/v) (T2) and soil extract (T3). Results suggested that enrichment culture required soil extract to degrade atrazine, as after second sequential transfer only partial atrazine degradation was observed in T1 treatment while atrazine was completely degraded in T2 and T3 treatments even after fourth transfer. Culture independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique confirmed selective enrichment of genus Bacillus along with Pseudomonas and Burkholderia. Degradation of atrazine/metabolites in the industrial wastewater was studied at different initial concentrations of the contaminants [wastewater-water (v/v) ratio: T1, 1:9; T2, 2:8; T3, 3:7; T4, 5:5 and T5, undiluted effluent]. The initial concentrations of atrazine, cyanuric acid and biuret ranged between 5.32 and 53.92 µg mL(-1), 265.6 and 1805.2 µg mL(-1) and 1.85 and 16.12 µg mL(-1), respectively. The enrichment culture was able to completely degrade atrazine, cyanuric acid and biuret up to T4 treatment, while no appreciable degradation of contaminants was observed in the undiluted effluent (T5). Inability of enrichment culture to degrade atrazine/metabolites might be due to high concentrations of cyanuric acid. Therefore, a separate study on cyanuric acid degradation suggested: (i) no appreciable cyanuric acid degradation with accumulation of an unidentified metabolite in the medium where cyanuric acid was supplemented as the sole source of carbon and nitrogen; (ii) partial cyanuric acid degradation with accumulation of unidentified metabolite in the medium containing additional nitrogen source; and (iii) complete cyanuric acid degradation in the medium supplemented with an additional carbon source. This unidentified metabolite observed during cyanuric acid degradation and also detected in the enrichment culture inoculated wastewater samples
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Bacteriophages and Bacterial Plant Diseases
Buttimer, Colin; McAuliffe, Olivia; Ross, R. P.; Hill, Colin; O’Mahony, Jim; Coffey, Aidan
2017-01-01
Losses in crop yields due to disease need to be reduced in order to meet increasing global food demands associated with growth in the human population. There is a well-recognized need to develop new environmentally friendly control strategies to combat bacterial crop disease. Current control measures involving the use of traditional chemicals or antibiotics are losing their efficacy due to the natural development of bacterial resistance to these agents. In addition, there is an increasing awareness that their use is environmentally unfriendly. Bacteriophages, the viruses of bacteria, have received increased research interest in recent years as a realistic environmentally friendly means of controlling bacterial diseases. Their use presents a viable control measure for a number of destructive bacterial crop diseases, with some phage-based products already becoming available on the market. Phage biocontrol possesses advantages over chemical controls in that tailor-made phage cocktails can be adapted to target specific disease-causing bacteria. Unlike chemical control measures, phage mixtures can be easily adapted for bacterial resistance which may develop over time. In this review, we will examine the progress and challenges for phage-based disease biocontrol in food crops. PMID:28163700
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Ishii, Kento; Fujitani, Hirotsugu; Soh, Kentaro; Nakagawa, Tatsunori; Takahashi, Reiji
2017-01-01
ABSTRACT Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of “Candidatus Nitrotoga arctica,” which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (Km) and the generation time were determined to be 25 μM NO2− and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH4Cl but completely inhibited at 50 mM NH4Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of Nitrotoga. IMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we
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Ishii, Kento; Fujitani, Hirotsugu; Soh, Kentaro; Nakagawa, Tatsunori; Takahashi, Reiji; Tsuneda, Satoshi
2017-07-15
Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of " Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant ( K m ) and the generation time were determined to be 25 μM NO 2 - and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH 4 Cl but completely inhibited at 50 mM NH 4 Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of Nitrotoga IMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully
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Metal enrichments in solid bitumens: A review
NASA Astrophysics Data System (ADS)
Parnell, J.
1988-07-01
The association of oils and solid bitumens with ore deposits is widely recorded. The oils and bitumens may actually be enriched with metals. Unlike oils, metal enrichments within bitumens do not reflect the role of petroleum as a transporting agent for metals. By contrast, they may be a result of the reduction of metal ions on contact with bitumen, and may reach levels so high that ore mineral inclusions are precipitated. Metal determinations of British bitumens suggest that new metal anomalies can be detected by this approach, that some metal anomalies within bitumens may be related to ore mineralization, and that bitumens from different sources may be distinguished by their metal contents. The potential use of bitumen distribution and/or metal enrichment within bitumen for ore exploration is dependent on the metal concerned, and in particular whether the metal is transported by association with organic materials or reduced in the presence of organic materials.
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Selenium Enrichment of Horticultural Crops.
Puccinelli, Martina; Malorgio, Fernando; Pezzarossa, Beatrice
2017-06-04
The ability of some crops to accumulate selenium (Se) is crucial for human nutrition and health. Selenium has been identified as a cofactor of the enzyme glutathione peroxidase, which is a catalyzer in the reduction of peroxides that can damage cells and tissues, and can act as an antioxidant. Plants are the first link in the food chain, which ends with humans. Increasing the Se quantity in plant products, including leafy and fruity vegetables, and fruit crops, without exceeding the toxic threshold, is thus a good way to increase animal and human Se intake, with positive effects on long-term health. In many Se-enriched plants, most Se is in its major organic form. Given that this form is more available to humans and more efficient in increasing the selenium content than inorganic forms, the consumption of Se-enriched plants appears to be beneficial. An antioxidant effect of Se has been detected in Se-enriched vegetables and fruit crops due to an improved antioxidative status and to a reduced biosynthesis of ethylene, which is the hormone with a primary role in plant senescence and fruit ripening. This thus highlights the possible positive effect of Se in preserving a longer shelf-life and longer-lasting quality.
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Kraupner, Nadine; Ebmeyer, Stefan; Bengtsson-Palme, Johan; Fick, Jerker; Kristiansson, Erik; Flach, Carl-Fredrik; Larsson, D G Joakim
2018-04-25
There is concern that antibiotics in the environment can select for and enrich bacteria carrying acquired antibiotic resistance genes, thus increasing the potential of those genes to emerge in a clinical context. A critical question for understanding and managing such risks is what levels of antibiotics are needed to select for resistance in complex bacterial communities. Here, we address this question by examining the phenotypic and genotypic profiles of aquatic communities exposed to ciprofloxacin, also evaluating the within-species selection of resistant E. coli in complex communities. The taxonomic composition was significantly altered at ciprofloxacin exposure concentrations down to 1 μg/L. Shotgun metagenomic analysis indicated that mobile quinolone resistance determinants (qnrD, qnrS and qnrB) were enriched as a direct consequence of ciprofloxacin exposure from 1 μg/L or higher. Only at 5-10 μg/L resistant E.coli increased relative to their sensitive counterparts. These resistant E. coli predominantly harbored non-transferrable, chromosomal triple mutations (gyrA S83 L, D87N and parC S80I), which confer high-level resistance. In a controlled experimental setup such as this, we interpret effects on taxonomic composition and enrichment of mobile quinolone resistance genes as relevant indicators of risk. Hence, the lowest observed effect concentration for resistance selection in complex communities by ciprofloxacin was 1 μg/L and the corresponding no observed effect concentration 0.1 μg/L. These findings can be used to define and implement discharge or surface water limits to reduce risks for selection of antibiotic resistance in the environment. Copyright © 2018 Elsevier Ltd. All rights reserved.
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An, Xinli; Baker, Paul; Li, Hu; Su, Jianqiang; Yu, Changping; Cai, Chao
2016-11-01
Microorganisms are the primary agents responsible for the modification, degradation, and/or detoxification of pollutants, and thus, they play a major role in their natural attenuation; yet, little is known about the structure and diversity of the subsurface community and relationships between microbial community and groundwater hydrochemistry. In this study, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) allowed a comparative microbial community analysis of sulfate-contaminated groundwater samples from nine different wells in the region of Baogang rare earth tailings. Using real-time PCR, the abundance of total bacteria and the sulfate-reducing genes of aprA and dsrB were quantified. Statistical analyses showed a clear distinction of the microbial community diversity between the contaminated and uncontaminated samples, with Proteobacteria being the most dominant members of the microbial community. SO 4 2- concentrations exerted a significant effect on the variation of the bacterial community (P < 0.05), with higher concentrations of sulfate reducing the microbial diversity (H' index), indicating that human activity (e.g., mining industries) was a possible factor disturbing the structure of the bacterial community. Quantitative analysis of the functional genes showed that the proportions of dsrB to total bacteria were 0.002-2.85 %, and the sulfate-reducing bacteria (SRB) were predominant within the prokaryotic community in the groundwater. The uncontaminated groundwater with low sulfate concentration harbored higher abundance of SRB than that in the polluted samples, while no significant correlation was observed between sulfate concentrations and SRB abundances in this study, suggesting other environmental factors possibly contributed to different distributions and abundances of SRB in the different sites. The results should facilitate expanded studies to identify robust microbe
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Siciliano, Steven D; Laird, B D; Lemieux, C L
2010-08-01
The health risk associated with exposure to urban brownfields is often driven by the incidental ingestion of soil by humans. Recent evidence found that humans likely ingest the fraction of soil that passes a 45-microm sieve, which is the particle size adhered to the hands. We evaluated if PAH concentrations were enriched in this soil fraction compared to the bulk soil and if this enrichment lead to an increase in bioaccessibility and thus an increase in incremental lifetime cancer risk for exposed persons. Soils (n=18) with PAH concentrations below the current Canadian soil quality guidelines for human health were collected from an Arctic urban site and were sieved to pass a 45-microm sieve. Soil PAH profiles were measured and bioaccessibility was assessed using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). PAHs were significantly enriched in the <45 microm size fraction (3.7-fold) and this enrichment could be predicted according to the fugacity capacity of soil (Enrichment=2.18-0.055Zsoil, r2=0.65, p<0.001). PAH release in the stomach and small intestine compartments of the SHIME was low (8%) and could not be predicted by PAH concentrations in 45-microm sieved soil. In fact, PAH release in the SHIME was lower from the <45 microm size fraction despite the fact that this fraction had higher levels of PAHs than the bulk soil. We postulate that this occurs because PAHs adsorbed to soil did not reach equilibrium with the small intestinal fluid. In contrast, PAH release in the colonic compartment of the SHIME reached equilibrium and was linked to soil concentration. Bioaccessibility in the SHIME colon could be predicted by the ratio of fugacity capacity of soil to water for a PAH (Bioaccessibility=0.15e(-6.4x10E-7Zsoil/Zwater), r2=0.53, p<0.01). The estimated incremental lifetime cancer risk was significantly greater for the <45 microm soil fraction compared to the bulk fraction; however, when bioaccessible PAH concentrations in a simulated small
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Tissue enrichment analysis for C. elegans genomics.
Angeles-Albores, David; N Lee, Raymond Y; Chan, Juancarlos; Sternberg, Paul W
2016-09-13
Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available for Caenorhabditis elegans, it does not include anatomical information. We have developed a tool for identifying enrichment of C. elegans tissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection in C. elegans. Our Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python's standard pip installer. It tests a slimmed-down C. elegans tissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results.
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Patel, Jasmine D; Ebert, Michael; Stokes, Ken; Ward, Robert; Anderson, James M
2003-01-01
Biomaterial-centered infections, initiated by bacterial adhesion, persist due to a compromised host immune response. Altering implant materials with surface modifying endgroups (SMEs) may enhance their biocompatibility by reducing bacterial and inflammatory cell adhesion. A rotating disc model, which generates shear stress within physiological ranges, was used to characterize adhesion of leukocytes and Staphylococcus epidermidis on polycarbonate-urethanes and polyetherurethanes modified with SMEs (polyethylene oxide, fluorocarbon and dimethylsiloxane) under dynamic flow conditions. Bacterial adhesion in the absence of serum was found to be mediated by shear stress and surface chemistry, with reduced adhesion exhibited on materials modified with polydimethylsiloxane and polyethylene oxide SMEs. In contrast, bacterial adhesion was enhanced on materials modified with fluorocarbon SMEs. In the presence of serum, bacterial adhesion was primarily neither material nor shear dependent. However, bacterial adhesion in serum was significantly reduced to < or = 10% compared to adhesion in serum-free media. Leukocyte adhesion in serum exhibited a shear dependency with increased adhesion occurring in regions exposed to lower shear-stress levels of < or = 7 dyne/cm2. Additionally, polydimethylsiloxane and polyethylene oxide SMEs reduced leukocyte adhesion on polyether-urethanes. In conclusion, these results suggest that surface chemistry and shear stress can mediate bacterial and cellular adhesion. Furthermore, materials modified with polyethylene oxide SMEs are capable of inhibiting bacterial adhesion, consequently minimizing the probability of biomaterial-centered infections.
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Antibiotics for treating bacterial vaginosis in pregnancy.
McDonald, H; Brocklehurst, P; Parsons, J; Vigneswaran, R
2003-01-01
Bacterial vaginosis is an imbalance of the normal vaginal flora with an overgrowth of anaerobic bacteria and a lack of the normal lactobacillary flora. Bacterial vaginosis during pregnancy has been associated with poor perinatal outcome and, in particular, preterm birth. Identification and treatment may reduce the risk of preterm birth and its consequences. To assess the effects of antibiotic treatment of bacterial vaginosis in pregnancy. We searched the Cochrane Pregnancy and Childbirth Group trials register (September 2002). Randomized trials comparing antibiotic treatment with placebo or no treatment, or comparing two or more antibiotic regimens in pregnant women with bacterial vaginosis. Two reviewers assessed trials and extracted data independently. Study authors were contacted for additional information. Ten trials involving 4249 women were included; all were of good quality. Antibiotic therapy was effective at eradicating bacterial vaginosis during pregnancy (odds ratio (OR) 0.21, 95% confidence interval (CI) 0.18 to 0.24, eight trials of 3825 women). Treatment did not significantly reduce the risk of preterm birth before 37 weeks (OR 0.95, 95% CI 0.82 to 1.10, eight trials of 4062 women), 34 weeks (OR 1.20, 95% CI 0.69 to 2.07, five trials of 851 women), or 32 weeks (OR 1.08, 95% CI 0.70 to 1.68, three trials of 3080 women). However, antibiotic treatment did significantly decrease the risk of preterm prelabour rupture of membranes (OR 0.32, 95% CI 0.15 to 0.67, three trials of 562 women). In women with a previous preterm birth, treatment did not affect the risk of subsequent preterm birth (OR 0.83, 95% CI 0.59 to 1.17, five trials of 622 women) but it did decrease the risk of preterm prelabour rupture of membranes (OR 0.14, 95% CI 0.05 to 0.38, two trials of 114 women) and low birthweight (OR 0.31, 95% CI 0.13 to 0.75, five trials of 622 women). Antibiotic treatment can eradicate bacterial vaginosis in pregnancy. However, the current evidence does not
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Katsimichas, Themistoklis; Ohtani, Tomohito; Motooka, Daisuke; Tsukamoto, Yasumasa; Kioka, Hidetaka; Nakamoto, Kei; Konishi, Shozo; Chimura, Misato; Sengoku, Kaoruko; Miyawaki, Hiroshi; Sakaguchi, Taiki; Okumura, Ryu; Theofilis, Konstantinos; Iida, Tetsuya; Takeda, Kiyoshi; Nakamura, Shota; Sakata, Yasushi
2018-05-25
Research suggests that heart failure with reduced ejection fraction (HFrEF) is a state of systemic inflammation that may be triggered by microbial products passing into the bloodstream through a compromised intestinal barrier. However, whether the intestinal microbiota exhibits dysbiosis in HFrEF patients is largely unknown.Methods and Results:Twenty eight non-ischemic HFrEF patients and 19 healthy controls were assessed by 16S rRNA analysis of bacterial DNA extracted from stool samples. After processing of sequencing data, bacteria were taxonomically classified, diversity indices were used to examine microbial ecology, and relative abundances of common core genera were compared between groups. Furthermore, we predicted gene carriage for bacterial metabolic pathways and inferred microbial interaction networks on multiple taxonomic levels.Bacterial communities of both groups were dominated by the Firmicutes and Bacteroidetes phyla. The most abundant genus in both groups wasBacteroides. Although α diversity did not differ between groups, ordination by β diversity metrics revealed a separation of the groups across components of variation.StreptococcusandVeillonellawere enriched in the common core microbiota of patients, whileSMB53was depleted. Gene families in amino acid, carbohydrate, vitamin, and xenobiotic metabolism showed significant differences between groups. Interaction networks revealed a higher degree of correlations between bacteria in patients. Non-ischemic HFrEF patients exhibited multidimensional differences in intestinal microbial communities compared with healthy subjects.
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Sludge bio-drying: Effective to reduce both antibiotic resistance genes and mobile genetic elements.
Zhang, Junya; Sui, Qianwen; Tong, Juan; Buhe, Chulu; Wang, Rui; Chen, Meixue; Wei, Yuansong
2016-12-01
Sewage sludge is considered as one of major contributors to the increased environmental burden of ARGs. Sludge bio-drying was increasingly adopted due to its faster sludge reduction compared with composting. The fate of ARGs during full-scale sludge bio-drying was investigated to determine whether it could effectively reduce ARGs, and the contributions of bacterial community, horizontal gene transfer (HGT) through mobile genetic elements (MGEs) and co-selection from heavy metals to ARGs profiles were discussed in detail. Two piles with different aeration strategies (Pile I, the improved and Pile II, the control) were operated to elucidate effects of aeration strategy on ARGs profiles. Results showed that sludge bio-drying could effectively reduce both most of targeted ARGs (0.4-3.1 logs) and MGEs (0.8-3.3 logs) by the improved aeration strategy, which also enhanced both the sludge bio-drying performance and ARGs reduction. The enrichment of ARGs including ermF, tetX and sulII could be well explained by the evolution of bioavailable heavy metals, not HGT through MGEs, and their potential host bacteria mainly existed in Bacteroidetes. Although changes of bacterial community contributed the most to ARGs profiles, HGT through MGEs should be paid more attention especially in the thermophilic stage of sludge bio-drying. Copyright © 2016 Elsevier Ltd. All rights reserved.
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The bacterial communities associated with fecal types and body weight of rex rabbits
Zeng, Bo; Han, Shushu; Wang, Ping; Wen, Bin; Jian, Wensu; Guo, Wei; Yu, Zhiju; Du, Dan; Fu, Xiangchao; Kong, Fanli; Yang, Mingyao; Si, Xiaohui; Zhao, Jiangchao; Li, Ying
2015-01-01
Rex rabbit is an important small herbivore for fur and meat production. However, little is known about the gut microbiota in rex rabbit, especially regarding their relationship with different fecal types and growth of the hosts. We characterized the microbiota of both hard and soft feces from rex rabbits with high and low body weight by using the Illumina MiSeq platform targeting the V4 region of the 16S rDNA. High weight rex rabbits possess distinctive microbiota in hard feces, but not in soft feces, from the low weight group. We detected the overrepresentation of several genera such as YS2/Cyanobacteria, and Bacteroidales and underrepresentation of genera such as Anaeroplasma spp. and Clostridiaceae in high weight hard feces. Between fecal types, several bacterial taxa such as Ruminococcaceae, and Akkermansia spp. were enriched in soft feces. PICRUSt analysis revealed that metabolic pathways such as “stilbenoid, diarylheptanoid, gingerol biosynthesis” were enriched in high weight rabbits, and pathways related to “xenobiotics biodegradation” and “various types of N-glycan biosynthesis” were overrepresented in rabbit soft feces. Our study provides foundation to generate hypothesis aiming to test the roles that different bacterial taxa play in the growth and caecotrophy of rex rabbits. PMID:25791609
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Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics
Delmont, Tom O.; Eren, A. Murat; Maccario, Lorrie; Prestat, Emmanuel; Esen, Özcan C.; Pelletier, Eric; Le Paslier, Denis; Simonet, Pascal; Vogel, Timothy M.
2015-01-01
Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for 4 months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540 Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n = 2), Rhodanobacter (n = 5), Acidobacteria (n = 2), Sporolactobacillus (n = 2, novel nitrogen fixing taxon), Ktedonobacter (n = 1, second representative of the family Ktedonobacteraceae), Streptomyces (n = 3, novel polyketide synthase modules), and Burkholderia (n = 2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9 Mb, with relative abundances ranging from rare (<0.0001%) to relatively abundant (>0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment. PMID:25983722
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.
Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed
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Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.
2016-04-18
Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed
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Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J
2016-01-01
Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co
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Mell, Joshua Chang; Viadas, Cristina; Moleres, Javier; Sinha, Sunita; Fernández-Calvet, Ariadna; Porsch, Eric A; St Geme, Joseph W; Nislow, Corey; Redfield, Rosemary J; Garmendia, Junkal
2016-04-01
Many bacterial species actively take up and recombine homologous DNA into their genomes, called natural competence, a trait that offers a means to identify the genetic basis of naturally occurring phenotypic variation. Here, we describe "transformed recombinant enrichment profiling" (TREP), in which natural transformation is used to generate complex pools of recombinants, phenotypic selection is used to enrich for specific recombinants, and deep sequencing is used to survey for the genetic variation responsible. We applied TREP to investigate the genetic architecture of intracellular invasion by the human pathogen Haemophilus influenzae, a trait implicated in persistence during chronic infection. TREP identified the HMW1 adhesin as a crucial factor. Natural transformation of the hmw1 operon from a clinical isolate (86-028NP) into a laboratory isolate that lacks it (Rd KW20) resulted in ~1,000-fold increased invasion into airway epithelial cells. When a distinct recipient (Hi375, already possessing hmw1 and its paralog hmw2) was transformed by the same donor, allelic replacement of hmw2AHi375 by hmw1A86-028NP resulted in a ~100-fold increased intracellular invasion rate. The specific role of hmw1A86-028NP was confirmed by mutant and western blot analyses. Bacterial self-aggregation and adherence to airway cells were also increased in recombinants, suggesting that the high invasiveness induced by hmw1A86-028NP might be a consequence of these phenotypes. However, immunofluorescence results found that intracellular hmw1A86-028NP bacteria likely invaded as groups, instead of as individual bacterial cells, indicating an emergent invasion-specific consequence of hmw1A-mediated self-aggregation.
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Method and apparatus for reducing cold-phase emissions by utilizing oxygen-enriched intake air
Poola, Ramesh B.; Sekar, Ramanujam R.; Stork, Kevin C.
1997-01-01
An oxygen-enriched air intake control system for an internal combustion engine includes air directing apparatus to control the air flow into the intake of the engine. During normal operation of the engine, ambient air flowing from an air filter of the engine flows through the air directing apparatus into the intake of the engine. In order to decrease the amount of carbon monoxide (CO) and hydrocarbon (HC) emissions that tend to be produced by the engine during a short period of time after the engine is started, the air directing apparatus diverts for a short period of time following the start up of the engine at least a portion of the ambient air from the air filter through a secondary path. The secondary path includes a selectively permeable membrane through which the diverted portion of the ambient air flows. The selectively permeable membrane separates nitrogen and oxygen from the diverted air so that oxygen enriched air containing from about 23% to 25% oxygen by volume is supplied to the intake of the engine.
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Impacts of CO2 Enrichment on Productivity and Light Requirements of Eelgrass.
Zimmerman, R. C.; Kohrs, D. G.; Steller, D. L.; Alberte, R. S.
1997-10-01
Seagrasses, although well adapted for submerged existence, are CO2-limited and photosynthetically inefficient in seawater. This leads to high light requirements for growth and survival and makes seagrasses vulnerable to light limitation. We explored the long-term impact of increased CO2 availability on light requirements, productivity, and C allocation in eelgrass (Zostera marina L.). Enrichment of seawater CO2 increased photosynthesis 3-fold, but had no long-term impact on respiration. By tripling the rate of light-saturated photosynthesis, CO2 enrichment reduced the daily period of irradiance-saturated photosynthesis (Hsat) that is required for the maintenance of positive whole-plant C balance from 7 to 2.7 h, allowing plants maintained under 4 h of Hsat to perform like plants growing in unenriched seawater with 12 h of Hsat. Eelgrass grown under 4 h of Hsat without added CO2 consumed internal C reserves as photosynthesis rates and chlorophyll levels dropped. Growth ceased after 30 d. Leaf photosynthesis, respiration, chlorophyll, and sucrose-phosphate synthase activity of CO2-enriched plants showed no acclimation to prolonged enrichment. Thus, the CO2-stimulated improvement in photosynthesis reduced light requirements in the long term, suggesting that globally increasing CO2 may enhance seagrass survival in eutrophic coastal waters, where populations have been devastated by algal proliferation and reduced water-column light transparency.
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Enrichment and characterization of anaerobic TNT-degrading bacteria
DOE Office of Scientific and Technical Information (OSTI.GOV)
Roberts, D.J.; Pendharkar, S.
1995-12-31
Three media constitutions were used to enrich for mixed cultures capable of degrading 2,4,6-trinitrotoluene (TNT) under strictly anaerobic conditions. The media were derived from a mineral salts solution buffered to pH 7 with CO{sub 2}/bicarbonate and all contained TNT. The cultures were enriched in the TNT mineral salts medium or the TNT mineral salts medium supplemented with glucose, yeast extract, or ammonia in various combinations. Inocula were obtained from a treated soil, previously contaminated with dinoseb and then treated using anaerobic procedures, or from a bench-top aqueous culture, maintained with an extract from a munitions-contaminated soil for more than 4more » years. Several cultures reduced TNT, producing 4-amino-2,6-dinitrotoluene and 2,4-diamino-6-nitrotoluene as the major products. The cultures were unable to effectively remove TNT when cross-transferred to the media they were not enriched on, suggesting that different media had enriched different subcultures form the original inoculum. The treated soil provided the most successful inoculum. Two media were chosen for further studies. Medium 1 contained TNT and glucose and produced a culture that might have used TNT as a nitrogen source. Medium 2, containing TNT and yeast extract, enriched cultures that degraded TNT, accumulating small amounts of p-cresol during the degradation.« less
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Cultivar selection for bacterial root rot in sugar beet
USDA-ARS?s Scientific Manuscript database
Bacterial root rot of sugar beet caused by Leuconostoc mesenteroides subsp. dextranicum is a disease problem recently described in the United States, which has frequently been found in association with Rhizoctonia root rot. To reduce the impact of bacterial root rot on sucrose loss in the field, st...
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Proceedings of the 1994 international meeting on reduced enrichment for research and test reactors
DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
1997-08-01
This meeting brought together participants in the international effort to minimize and eventually eliminate the use of highly enriched uranium in civilian nuclear programs. Papers cover the following topics: National programs; fuel cycle; nuclear fuels; analyses; advanced reactors; and reactor conversions. Selected papers have been indexed separately for inclusion to the Energy Science and Technology Database.
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Jia, Yangyang; Wilkins, David; Lu, Hongyuan; Cai, Mingwei
2015-01-01
Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose- or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus Methanobacterium) and bacterial (order Clostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose- and xylan-digesting functions given appropriate enrichment conditions. PMID:26712547
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Zhou, Guo-Wei; Yang, Xiao-Ru; Marshall, Christopher W.; Li, Hu; Zheng, Bang-Xiao; Yan, Yu; Su, Jian-Qiang; Zhu, Yong-Guan
2017-01-01
Biochar contains quinones and aromatic structures that facilitate extracellular electron transfer between microbial cells and insoluble minerals. In this study, granulated biochar (1.2–2 mm) and powdered biochar (<0.15 mm) were amended to two ferrihydrite (in situ ferrihydrite and ex situ ferrihydrite) enrichments to investigate the effect of biochar with different particle sizes on dissimilatory iron(III)-reducing bacteria (DIRB) and methanogens. Biochar addition significantly stimulated the reduction of both in situ ferrihydrite and ex situ ferrihydrite and the production of methane. Powdered biochar amendments increased iron reduction compared to granulated biochar amendment in both the in situ ferrihydrite and ex situ ferrihydrite enrichments. However, no significant difference was observed in methane production between the powdered biochar and granulated biochar amendments in the two ferrihydrite enrichments. Analysis of 16S rRNA gene sequences showed that both DIRB and methanogens were enriched after biochar amendments in the in situ ferrihydrite and ex situ ferrihydrite enrichments. Taxa belonging to the Geobacteraceae and methanogenic genus affiliated to Methanosarcina were detected with significantly higher relative abundances in powdered biochar amendments than those in granulated biochar amendments in both the ferrihydrite enrichments. X-ray diffraction analysis indicated green rust [Fe2(CO3) (OH)] and vivianite [Fe3(PO4)2 8(H2O)] formed in the ex situ ferrihydrite and in situ ferrihydrite enrichments without biochar addition, respectively. After granulated biochar amendment, the mineral phase changed from the green rust to vivianite in the ex situ ferrihydrite enrichment, while crystalline vivianite and iron oxide (γ-Fe2O3) were detected simultaneously in the in situ ferrihydrite enrichment. No crystalline iron compound was found in the powdered biochar amendments in both ferrihydrite enrichments. Overall, our study illustrated that the addition of
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Boltaña, Sebastian; Castellana, Barbara; Goetz, Giles; Tort, Lluis; Teles, Mariana; Mulero, Victor; Novoa, Beatriz; Figueras, Antonio; Goetz, Frederick W; Gallardo-Escarate, Cristian; Planas, Josep V; Mackenzie, Simon
2017-02-03
This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS) and peptidoglycan (PGN)). Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO) showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs), carrier proteins/membrane transport (approximately 15%), effectors/modulators and cell communication (approximately 11%), nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5%) and intracellular transducers/signal transduction (approximately 5%). Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ) that provides a platform enriched for the study of gene
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Bacterial conjunctivitis in childhood: etiology, clinical manifestations, diagnosis, and management.
Leung, Alexander Kc; Hon, Kam Lun; Wong, Alex H C; Wong, Andrew S
2018-01-29
Bacterial conjunctivitis is a common reason for children to be seen in pediatric practices A correct diagnosis is important so that appropriate treatment can be instituted. To provide an update on the evaluation, diagnosis, and treatment of bacterial conjunctivitis in children. A PubMed search was completed in Clinical Queries using the key term "bacterial conjunctivitis". Patents were searched using the key term "bacterial conjunctivitis" from www.freepatentsonline.com and www.google.com/patents. In the neonatal period, bacterial conjunctivitis is rare and the most common cause of organism is Staphylococcus aureus, followed by Chlamydia trachomatis. In infants and older children, bacterial conjunctivitis is most often caused by Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis. Clinically, bacterial conjunctivitis is characterized by a purulent eye discharge, or sticky eyes on awakening, a foreign body sensation and conjunctival injection (pink eye). The diagnosis is made clinically. Cultures are unnecessary. Some authors suggest a watchful observation approach as most cases of bacterial conjunctivitis are self-limited. A Cochrane review suggests the use of antibiotic eye drops is associated with modestly improved rates of clinical and microbiological omission as compared to the use of placebo. Various investigators have also disclosed patents for the treatment of conjunctivitis. The present consensus supports the use of topical antibiotics for bacterial conjunctivitis. Topical antibiotics shorten the course of the disease, reduce discomfort, prevent person-to-person transmission and reduce the rate of reinfection. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
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Behavioral responses of three lemur species to different food enrichment devices.
Shapiro, Morgan E; Shapiro, Hannah G; Ehmke, Erin E
2018-05-01
Environmental enrichment is a tool used to promote the welfare and well-being of captive animals by encouraging the display of species-specific behaviors and reducing the stress or boredom induced by captive environments. Lemurs are highly endangered, yet few studies have analyzed the behavioral impacts of enrichment on captive populations. We studied the impacts of two novel enrichment devices on three lemur species (ring-tailed lemurs [Lemur catta], red-ruffed lemurs [Varecia rubra], and Coquerel's sifaka [Propithecus coquereli]) to determine both the overall and species-specific impacts of enrichment on lemur behavior. We recorded lemur behavior using the continuous sampling method to obtain behavior duration and analyzed our results using ANOVA Repeated Measures. Results showed enrichment effectiveness differed for each species and that different enrichment devices had varying impacts on lemur behavior across all species. We attributed the differences in species-specific responses to the unique locomotor patterns and methods of diet acquisition of each species, and the variances in behavioral responses across all species to the characteristics of each device. Our study highlights the importance of species-specific enrichment and encourages further research in this field in order to maximize the positive effects of enrichment, which in turn has the potential to affect the overall well-being of captive populations. © 2018 Wiley Periodicals, Inc.
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NASA Technical Reports Server (NTRS)
Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.
2003-01-01
The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at -9 degrees C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at -2 degrees C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years.
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Multi-stage combustion using nitrogen-enriched air
Fischer, Larry E.; Anderson, Brian L.
2004-09-14
Multi-stage combustion technology combined with nitrogen-enriched air technology for controlling the combustion temperature and products to extend the maintenance and lifetime cycles of materials in contact with combustion products and to reduce pollutants while maintaining relatively high combustion and thermal cycle efficiencies. The first stage of combustion operates fuel rich where most of the heat of combustion is released by burning it with nitrogen-enriched air. Part of the energy in the combustion gases is used to perform work or to provide heat. The cooled combustion gases are reheated by additional stages of combustion until the last stage is at or near stoichiometric conditions. Additional energy is extracted from each stage to result in relatively high thermal cycle efficiency. The air is enriched with nitrogen using air separation technologies such as diffusion, permeable membrane, absorption, and cryogenics. The combustion method is applicable to many types of combustion equipment, including: boilers, burners, turbines, internal combustion engines, and many types of fuel including hydrogen and carbon-based fuels including methane and coal.
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Bacterial community changes in an industrial algae production system.
Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T
2018-04-01
While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.
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Souday, Vincent; Koning, Nick J; Perez, Bruno; Grelon, Fabien; Mercat, Alain; Boer, Christa; Seegers, Valérie; Radermacher, Peter; Asfar, Pierre
2016-01-01
To test the hypothesis whether enriched air nitrox (EAN) breathing during simulated diving reduces decompression stress when compared to compressed air breathing as assessed by intravascular bubble formation after decompression. Human volunteers underwent a first simulated dive breathing compressed air to include subjects prone to post-decompression venous gas bubbling. Twelve subjects prone to bubbling underwent a double-blind, randomized, cross-over trial including one simulated dive breathing compressed air, and one dive breathing EAN (36% O2) in a hyperbaric chamber, with identical diving profiles (28 msw for 55 minutes). Intravascular bubble formation was assessed after decompression using pulmonary artery pulsed Doppler. Twelve subjects showing high bubble production were included for the cross-over trial, and all completed the experimental protocol. In the randomized protocol, EAN significantly reduced the bubble score at all time points (cumulative bubble scores: 1 [0-3.5] vs. 8 [4.5-10]; P < 0.001). Three decompression incidents, all presenting as cutaneous itching, occurred in the air versus zero in the EAN group (P = 0.217). Weak correlations were observed between bubble scores and age or body mass index, respectively. EAN breathing markedly reduces venous gas bubble emboli after decompression in volunteers selected for susceptibility for intravascular bubble formation. When using similar diving profiles and avoiding oxygen toxicity limits, EAN increases safety of diving as compared to compressed air breathing. ISRCTN 31681480.
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The bacterial community composition of the surface microlayer in a high mountain lake.
Hörtnagl, Paul; Pérez, Maria Teresa; Zeder, Michael; Sommaruga, Ruben
2010-09-01
The existence of bacterioneuston in aquatic ecosystems is well established, but little is known about its composition and dynamics, particularly in lakes. The bacterioneuston underlies extreme conditions at the air-water boundary, which may influence its dynamics in a different way compared with the bacterioplankton. In this study, we assessed quantitative changes in major bacterial groups of the surface microlayer (SML) (upper 900 microm) and the underlying water (ULW) (0.2-0.5 m depth) of an alpine lake during two consecutive ice-free seasons. Analysis of the bacterial community composition was done using catalyzed reporter deposition FISH with oligonucleotide probes. In addition, several physicochemical parameters were measured to characterize these two water layers. Dissolved organic carbon was consistently enriched in the SML and the dissolved organic matter pool presented clear signals of photodegradation and photobleaching. The water temperature was generally colder in the SML than in the subsurface. The bacterial community of the SML and the ULW was dominated by Betaproteobacteria and Actinobacteria. The bacterial community composition was associated with different combinations of physicochemical factors in these two layers, but temporal changes showed similar trends in both layers over the two seasons. Our results identify the SML of alpine lakes as a microhabitat where specific bacterial members such as of Betaproteobacteria seem to be efficient colonizers.
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Aerobic cyanide degradation by bacterial isolates from cassava factory wastewater
Kandasamy, Sujatha; Dananjeyan, Balachandar; Krishnamurthy, Kumar; Benckiser, Gero
2015-01-01
Ten bacterial strains that utilize cyanide (CN) as a nitrogen source were isolated from cassava factory wastewater after enrichment in a liquid media containing sodium cyanide (1 mM) and glucose (0.2% w/v). The strains could tolerate and grow in cyanide concentrations of up to 5 mM. Increased cyanide levels in the media caused an extension of lag phase in the bacterial growth indicating that they need some period of acclimatisation. The rate of cyanide removal by the strains depends on the initial cyanide and glucose concentrations. When initial cyanide and glucose concentrations were increased up to 5 mM, cyanide removal rate increased up to 63 and 61 per cent by Bacillus pumilus and Pseudomonas putida. Metabolic products such as ammonia and formate were detected in culture supernatants, suggesting a direct hydrolytic pathway without an intermediate formamide. The study clearly demonstrates the potential of aerobic treatment with cyanide degrading bacteria for cyanide removal in cassava factory wastewaters. PMID:26413045
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Aerobic cyanide degradation by bacterial isolates from cassava factory wastewater.
Kandasamy, Sujatha; Dananjeyan, Balachandar; Krishnamurthy, Kumar; Benckiser, Gero
2015-01-01
Ten bacterial strains that utilize cyanide (CN) as a nitrogen source were isolated from cassava factory wastewater after enrichment in a liquid media containing sodium cyanide (1 mM) and glucose (0.2% w/v). The strains could tolerate and grow in cyanide concentrations of up to 5 mM. Increased cyanide levels in the media caused an extension of lag phase in the bacterial growth indicating that they need some period of acclimatisation. The rate of cyanide removal by the strains depends on the initial cyanide and glucose concentrations. When initial cyanide and glucose concentrations were increased up to 5 mM, cyanide removal rate increased up to 63 and 61 per cent by Bacillus pumilus and Pseudomonas putida. Metabolic products such as ammonia and formate were detected in culture supernatants, suggesting a direct hydrolytic pathway without an intermediate formamide. The study clearly demonstrates the potential of aerobic treatment with cyanide degrading bacteria for cyanide removal in cassava factory wastewaters.
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Comparing Multi-Step IMAC and Multi-Step TiO2 Methods for Phosphopeptide Enrichment
Yue, Xiaoshan; Schunter, Alissa; Hummon, Amanda B.
2016-01-01
Phosphopeptide enrichment from complicated peptide mixtures is an essential step for mass spectrometry-based phosphoproteomic studies to reduce sample complexity and ionization suppression effects. Typical methods for enriching phosphopeptides include immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO2) beads, which have selective affinity and can interact with phosphopeptides. In this study, the IMAC enrichment method was compared with the TiO2 enrichment method, using a multi-step enrichment strategy from whole cell lysate, to evaluate their abilities to enrich for different types of phosphopeptides. The peptide-to-beads ratios were optimized for both IMAC and TiO2 beads. Both IMAC and TiO2 enrichments were performed for three rounds to enable the maximum extraction of phosphopeptides from the whole cell lysates. The phosphopeptides that are unique to IMAC enrichment, unique to TiO2 enrichment, and identified with both IMAC and TiO2 enrichment were analyzed for their characteristics. Both IMAC and TiO2 enriched similar amounts of phosphopeptides with comparable enrichment efficiency. However, phosphopeptides that are unique to IMAC enrichment showed a higher percentage of multi-phosphopeptides, as well as a higher percentage of longer, basic, and hydrophilic phosphopeptides. Also, the IMAC and TiO2 procedures clearly enriched phosphopeptides with different motifs. Finally, further enriching with two rounds of TiO2 from the supernatant after IMAC enrichment, or further enriching with two rounds of IMAC from the supernatant TiO2 enrichment does not fully recover the phosphopeptides that are not identified with the corresponding multi-step enrichment. PMID:26237447
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Enrichment and Training Improve Cognition in Rats with Cortical Malformations
Jenks, Kyle R.; Lucas, Marcella M.; Duffy, Ben A.; Robbins, Ashlee A.; Gimi, Barjor; Barry, Jeremy M.; Scott, Rod C.
2013-01-01
Children with malformations of cortical development (MCD) frequently have associated cognitive impairments which reduce quality of life. We hypothesized that cognitive deficits associated with MCD can be improved with environmental manipulation or additional training. The E17 methylazoxymethanol acetate (MAM) exposure model bears many anatomical hallmarks seen in human MCDs as well as similar behavioral and cognitive deficits. We divided control and MAM exposed Sprague-Dawley rats into enriched and non-enriched groups and tested performance in the Morris water maze. Another group similarly divided underwent sociability testing and also underwent Magnetic Resonance Imaging (MRI) scans pre and post enrichment. A third group of control and MAM rats without enrichment were trained until they reached criterion on the place avoidance task. MAM rats had impaired performance on spatial tasks and enrichment improved performance of both control and MAM animals. Although MAM rats did not have a deficit in sociability they showed similar improvement with enrichment as controls. MRI revealed a whole brain volume decrease with MAM exposure, and an increase in both MAM and control enriched volumes in comparison to non-enriched animals. In the place avoidance task, MAM rats required approximately 3 times as long to reach criterion as control animals, but with additional training were able to reach control performance. Environmental manipulation and additional training can improve cognition in a rodent MCD model. We therefore suggest that patients with MCD may benefit from appropriate alterations in educational strategies, social interaction and environment. These factors should be considered in therapeutic strategies. PMID:24358362
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Yousefshahi, Fardin; Azimpour, Khashayar; Boroumand, Mohammad Ali; Najafi, Mahdi; Barkhordari, Khosro; Vaezi, Mitra; Rouhipour, Nahid
2013-04-01
Central venous (CV) catheters play an essential role in the management of critically ill patients in the Intensive Care Unit (ICU). CV lines are, however, allied to catheter-associated blood stream infections. Bacterial colonization of CV lines is deemed the main cause of catheter-associated infection. The purpose of our study was to compare bacterial colony counts in the catheter site before CV line insertion in two groups of post-cardiac surgery patients: a group receiving Sanosil (an antiseptic agent composed of H2O2 and silver) and a control group. This interventional prospective double-blinded clinical trial recruited the patients in three post-cardiac surgery ICUs of a heart center. The participants were divided into interventional (113 patients) and control (136 patients) groups. Sanosil was added to the routine preparation procedure (Chlorhexidine bath one day before and scrub with Povidone-Iodine just before the CV line insertion). After the removal of the CV lines, the catheters tips were sent for culture and evaluation of colony counts. Catheter colonization occurred in 55 (22.1%) patients: 26 (23%) patients in the Sanosil group and 29 (21.3%) in the control group; there was no significant statistical difference between the two groups (p value = 0.75, RR = 1.05, 95% CI: 0.76-1.45). The most common organism having colonized in the cultures of the catheter tips was staphylococcus epidermis: 20 cases in the control group and 16 cases in the intervention group. Catheter colonization frequently occurs in post-cardiac surgery patients. However, our results did not indicate the effectiveness of adding Sanosil to the routine preparation procedure with respect to reducing catheter bacterial colonization.
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Antibiotics for treating bacterial vaginosis in pregnancy.
McDonald, H; Brocklehurst, P; Parsons, J
2005-01-25
Bacterial vaginosis is an imbalance of the normal vaginal flora with an overgrowth of anaerobic bacteria and a lack of the normal lactobacillary flora. Bacterial vaginosis during pregnancy has been associated with poor perinatal outcome and, in particular, preterm birth. Identification and treatment may reduce the risk of preterm birth and its consequences. To assess the effects of antibiotic treatment of bacterial vaginosis in pregnancy. We searched the Cochrane Pregnancy and Childbirth Group trials register (May 2004). Randomized trials comparing antibiotic treatment with placebo or no treatment, or comparing two or more antibiotic regimens in pregnant women with bacterial vaginosis or intermediate vaginal flora. Two reviewers assessed trials and extracted data independently. We contacted study authors for additional information. Thirteen trials involving 5300 women were included; all were of good quality. Antibiotic therapy was effective at eradicating bacterial vaginosis during pregnancy (odds ratio (OR) 0.21, 95% confidence interval (CI) 0.19 to 0.24, nine trials of 3895 women). Treatment was not significant in reducing the risk of preterm birth before 37 weeks (OR 0.87, 95% CI 0.74 to 1.03, thirteen trials of 5300 women, and there was significant heterogeneity between trials, p-value 0.002), preterm birth before 34 weeks (OR 1.22, 95% CI 0.67 to 2.19, five trials of 851 women), preterm birth before 32 weeks (OR 1.14, 95% CI 0.76 to 1.70, four trials of 3565 women), or the risk of preterm prelabour rupture of membranes (OR 0.88, 95% CI 0.61 to 1.28, four trials of 2579 women). In women with a previous preterm birth, treatment did not affect the risk of subsequent preterm birth (OR 0.83, 95% CI 0.59 to 1.17, five trials of 622 women, with significant heterogeneity between these trials); however, it may decrease the risk of preterm prelabour rupture of membranes (OR 0.14, 95% CI 0.05 to 0.38, two trials of 114 women, and low birthweight (OR 0.31, 95% CI 0.13 to
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Crossroads between Bacterial and Mammalian Glycosyltransferases
Brockhausen, Inka
2014-01-01
Bacterial glycosyltransferases (GT) often synthesize the same glycan linkages as mammalian GT; yet, they usually have very little sequence identity. Nevertheless, enzymatic properties, folding, substrate specificities, and catalytic mechanisms of these enzyme proteins may have significant similarity. Thus, bacterial GT can be utilized for the enzymatic synthesis of both bacterial and mammalian types of complex glycan structures. A comparison is made here between mammalian and bacterial enzymes that synthesize epitopes found in mammalian glycoproteins, and those found in the O antigens of Gram-negative bacteria. These epitopes include Thomsen–Friedenreich (TF or T) antigen, blood group O, A, and B, type 1 and 2 chains, Lewis antigens, sialylated and fucosylated structures, and polysialic acids. Many different approaches can be taken to investigate the substrate binding and catalytic mechanisms of GT, including crystal structure analyses, mutations, comparison of amino acid sequences, NMR, and mass spectrometry. Knowledge of the protein structures and functions helps to design GT for specific glycan synthesis and to develop inhibitors. The goals are to develop new strategies to reduce bacterial virulence and to synthesize vaccines and other biologically active glycan structures. PMID:25368613
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Yeshurun, Shlomo; Short, Annabel K; Bredy, Timothy W; Pang, Terence Y; Hannan, Anthony J
2017-03-01
Recent studies have demonstrated that paternal stress in rodents can result in modification of offspring behavior. Environmental enrichment, which enhances cognitive stimulation and physical activity, modifies various behaviors and reduces stress responses in adult rodents. We investigated the transgenerational influence of paternal environmental enrichment on offspring behavior and physiological stress response. Adult C57BL/6J male mice (F0) were exposed to either environmental enrichment or standard housing for four weeks and then pair-mated with naïve females. The F2 generation was generated using F1 male offspring. Male and female F1 and F2 offspring were tested for anxiety using the elevated-plus maze and large open field at 8 weeks of age. Depression-related behavior was assessed using the forced-swim test. Hypothalamic-pituitary-adrenal (HPA) axis function was determined by quantification of serum corticosterone and adrenocorticotropic hormone (ACTH) levels at baseline and after forced-swim stress. Paternal environmental enrichment was associated with increased body weights of male F1 and F2 offspring. There was no significant effect on F1 offspring anxiety and depression-related behaviors. There were no changes in anxiety-related behaviors in the F2 offspring, however these mice displayed a reduced latency to immobility in the forced-swim test. Furthermore, F2 females had significantly higher serum corticosterone levels post-stress, but not ACTH. These results show that paternal environmental enrichment exerts a sex-specific transgenerational impact on the behavioral and physiological response to stress. Our findings have implications for the modelling of psychiatric disorders in rodents. Copyright © 2017 Elsevier Ltd. All rights reserved.
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[Revised Japanese guidelines for the clinical management of bacterial meningitis].
Ishikawa, Harumi; Kamei, Satoshi
2014-01-01
Improvement of outcomes represents the most important problem in the treatment of bacterial meningitis. To achieve such improvement, revision of the guidelines for the clinical management of bacterial meningitis in Japan has been carried out, and these revised Japanese guidelines will soon be published. The choice of specific antimicrobial agents for initial treatment in bacterial meningitis is influenced by a number of factors, including patient age, systemic symptoms, and local patterns of bacterial resistance. In the revised Japanese guidelines, antimicrobial agents based on current knowledge of the epidemiology in Japan are recommended. Bacterial meningitis is a medical emergency, and patients with this disease require immediate medical assessment and appropriate treatment. Rapid diagnosis and treatment of bacterial meningitis reduces mortality and neurological sequelae. We describe the revised Japanese guidelines for the clinical management of bacterial meningitis 2014, with a focus on adults.
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Bacterial growth and substrate degradation by BTX-oxidizing culture in response to salt stress.
Lee, Chi-Yuan; Lin, Ching-Hsing
2006-01-01
Interactions between microbial growth and substrate degradation are important in determining the performance of trickle-bed bioreactors (TBB), especially when salt is added to reduce biomass formation in order to alleviate media clogging. This study was aimed at quantifying salinity effects on bacterial growth and substrate degradation, and at acquiring kinetic information in order to improve the design and operation of TBB. Experiment works began by cultivating a mixed culture in a chemostat reactor receiving artificial influent containing a mixture of benzene, toluene, and xylene (BTX), followed by using the enrichment culture to degrade the individual BTX substrates under a particular salinity, which ranged 0-50 g l(-1) in batch mode. Then, the measured concentrations of biomass and residual substrate versus time were analyzed with the microbial kinetics; moreover, the obtained microbial kinetic constants under various salinities were modeled using noncompetitive inhibition kinetics. For the three substrates the observed bacterial yields appeared to be decreased from 0.51-0.74 to 0.20-0.22 mg mg(-1) and the maximum specific rate of substrate utilization, q, declined from 0.25-0.42 to 0.07-0.11 h(-1), as the salinity increased from 0 to 50 NaCl g l(-1). The NaCl acted as noncompetitive inhibitor, where the modeling inhibitions of the coefficients, K ( T(S)), were 22.7-29.7 g l(-1) for substrate degradation and K ( T(mu)), 13.0-19.0 g l(-1), for biomass formation. The calculated ratios for the bacterial maintenance rate, m (S), to q, further indicated that the percentage energy spent on maintenance increased from 19-24 to 86-91% as salinity level increased from 0 to 50 g l(-1). These results revealed that the bacterial growth was more inhibited than substrate degradation by the BTX oxidizers under the tested salinity levels. The findings from this study demonstrate the potential of applying NaCl salt to control excessive biomass formation in biotrickling filters.
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Effects of CO2 Enrichment on Growth and Development of Impatiens hawkeri
Zhang, Fan-Fan; Wang, Yan-Li; Huang, Zhi-Zhe; Zhu, Xiao-Chen; Zhang, Feng-Jiao; Chen, Fa-Di; Fang, Wei-Min; Teng, Nian-Jun
2012-01-01
The effects of CO2 enrichment on growth and development of Impatiens hawkeri, an important greenhouse flower, were investigated for the purpose of providing scientific basis for CO2 enrichment to this species in greenhouse. The plants were grown in CO2-controlled growth chambers with 380 (the control) and 760 (CO2 enrichment) μmol·mol−1, respectively. The changes in morphology, physiology, biochemistry, and leaf ultrastructure of Impatiens were examined. Results showed that CO2 enrichment increased flower number and relative leaf area compared with the control. In addition, CO2 enrichment significantly enhanced photosynthetic rate, contents of soluble sugars and starch, activities of peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX), but reduced chlorophyll content and malondialdehyde (MDA) content. Furthermore, significant changes in chloroplast ultrastructure were observed at CO2 enrichment: an increased number of starch grains with an expanded size, and an increased ratio of stroma thylakoid to grana thylakoid. These results suggest that CO2 enrichment had positive effects on Impatiens, that is, it can improve the visual value, promote growth and development, and enhance antioxidant capacity. PMID:22536147
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Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar
2013-12-15
The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Díez-León, María; Bowman, Jeff; Bursian, Steve; Filion, Hélène; Galicia, David; Kanefsky, Jeannette; Napolitano, Angelo; Palme, Rupert; Schulte-Hostedde, Albrecht; Scribner, Kim; Mason, Georgia
2013-01-01
Wild carnivores in zoos, conservation breeding centres, and farms commonly live in relatively small, unstimulating enclosures. Under these captive conditions, in a range of species including giant pandas, black-footed ferrets, and European mink, male reproductive abilities are often poor. Such problems have long been hypothesized to be caused by these animals' housing conditions. We show for the first time that rearing under welfare-improving (i.e., highly valued and stress-reducing) environmental enrichments enhances male carnivores' copulatory performance: in mate choice competitions, enriched male American mink (Neovison vison) mated more often than non-enriched males. We screened for several potential mediators of this effect. First was physiological stress and its impact on reproductive physiology; second, stress-mediated changes in morphology and variables related to immunocompetence that could influence male attractiveness; and third, behavioural changes likely to affect social competence, particularly autistic-like excessive routine and repetition ('perseveration') as is reflected in the stereotypies common in captive animals. Consistent with physiological stress, excreted steroid metabolites revealed that non-enriched males had higher cortisol levels and lower androgen levels than enriched conspecifics. Their os penises (bacula) also tended to be less developed. Consistent with reduced attractiveness, non-enriched males were lighter, with comparatively small spleens and a trend to greater fluctuating asymmetry. Consistent with impaired social competence, non-enriched males performed more stereotypic behaviour (e.g., pacing) in their home cages. Of all these effects, the only significant predictor of copulation number was stereotypy (a trend suggesting that low bodyweights may also be influential): highly stereotypic males gained the fewest copulations. The neurophysiological changes underlying stereotypy thus handicap males sexually. We hypothesise that
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Environmentally Enriched Male Mink Gain More Copulations than Stereotypic, Barren-Reared Competitors
Díez-León, María; Bowman, Jeff; Bursian, Steve; Filion, Hélène; Galicia, David; Kanefsky, Jeannette; Napolitano, Angelo; Palme, Rupert; Schulte-Hostedde, Albrecht; Scribner, Kim; Mason, Georgia
2013-01-01
Wild carnivores in zoos, conservation breeding centres, and farms commonly live in relatively small, unstimulating enclosures. Under these captive conditions, in a range of species including giant pandas, black-footed ferrets, and European mink, male reproductive abilities are often poor. Such problems have long been hypothesized to be caused by these animals' housing conditions. We show for the first time that rearing under welfare-improving (i.e., highly valued and stress-reducing) environmental enrichments enhances male carnivores' copulatory performance: in mate choice competitions, enriched male American mink (Neovison vison) mated more often than non-enriched males. We screened for several potential mediators of this effect. First was physiological stress and its impact on reproductive physiology; second, stress-mediated changes in morphology and variables related to immunocompetence that could influence male attractiveness; and third, behavioural changes likely to affect social competence, particularly autistic-like excessive routine and repetition (‘perseveration’) as is reflected in the stereotypies common in captive animals. Consistent with physiological stress, excreted steroid metabolites revealed that non-enriched males had higher cortisol levels and lower androgen levels than enriched conspecifics. Their os penises (bacula) also tended to be less developed. Consistent with reduced attractiveness, non-enriched males were lighter, with comparatively small spleens and a trend to greater fluctuating asymmetry. Consistent with impaired social competence, non-enriched males performed more stereotypic behaviour (e.g., pacing) in their home cages. Of all these effects, the only significant predictor of copulation number was stereotypy (a trend suggesting that low bodyweights may also be influential): highly stereotypic males gained the fewest copulations. The neurophysiological changes underlying stereotypy thus handicap males sexually. We hypothesise
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Shirai, Yumiko; Okugawa, Yoshinaga; Hishida, Asahi; Ogawa, Aki; Okamoto, Kyoko; Shintani, Miki; Morimoto, Yuki; Nishikawa, Ryutaro; Yokoe, Takeshi; Tanaka, Koji; Urata, Hisashi; Toiyama, Yuji; Inoue, Yasuhiro; Tanaka, Motoyoshi; Mohri, Yasuhiko; Goel, Ajay; Kusunoki, Masato; McMillan, Donald C; Miki, Chikao
2017-07-06
Despite recent advances in chemotherapy for gastrointestinal cancer, a crucial factor related to poor prognosis is reduced tolerance to chemotherapy induced by cancer cachexia. Fish oil (FO)-derived eicosapentaenoic acid (EPA) modulates inflammation in patients with various malignancies; however, the impact of FO-enriched nutrition as a combined modality therapy on clinical outcomes remains controversial. We systemically analysed chronological changes in biochemical and physiological status using bioelectrical impedance analysis in 128 gastrointestinal cancer patients provided with or without FO-enriched nutrition during chemotherapy. Furthermore, we evaluated the clinical significance of FO-enriched nutrition and clarified appropriate patient groups that receive prognostic benefits from FO-enriched nutrition during treatment of gastrointestinal cancer. The control group showed significant up-regulation of serum CRP) levels and no significant difference in both skeletal muscle mass and lean body mass. In contrast, the FO-enriched nutrition group showed no changes in serum CRP concentration and significantly increased skeletal muscle mass and lean body mass over time. Furthermore, high CRP levels significantly correlated with reduced tolerance to chemotherapy, and FO-enriched nutrition improved chemotherapy tolerance and prognosis, particularly in gastrointestinal cancer patients with a modified Glasgow prognostic score (mGPS) of 1 or 2. We conclude that FO-enriched nutrition may improve the prognosis of patients with cancer cachexia and systemic inflammation (i.e., those with a mGPS of 1 or 2).
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Nelson, Craig E; Goldberg, Stuart J; Wegley Kelly, Linda; Haas, Andreas F; Smith, Jennifer E; Rohwer, Forest; Carlson, Craig A
2013-01-01
Increasing algal cover on tropical reefs worldwide may be maintained through feedbacks whereby algae outcompete coral by altering microbial activity. We hypothesized that algae and coral release compositionally distinct exudates that differentially alter bacterioplankton growth and community structure. We collected exudates from the dominant hermatypic coral holobiont Porites spp. and three dominant macroalgae (one each Ochrophyta, Rhodophyta and Chlorophyta) from reefs of Mo'orea, French Polynesia. We characterized exudates by measuring dissolved organic carbon (DOC) and fractional dissolved combined neutral sugars (DCNSs) and subsequently tracked bacterioplankton responses to each exudate over 48 h, assessing cellular growth, DOC/DCNS utilization and changes in taxonomic composition (via 16S rRNA amplicon pyrosequencing). Fleshy macroalgal exudates were enriched in the DCNS components fucose (Ochrophyta) and galactose (Rhodophyta); coral and calcareous algal exudates were enriched in total DCNS but in the same component proportions as ambient seawater. Rates of bacterioplankton growth and DOC utilization were significantly higher in algal exudate treatments than in coral exudate and control incubations with each community selectively removing different DCNS components. Coral exudates engendered the smallest shift in overall bacterioplankton community structure, maintained high diversity and enriched taxa from Alphaproteobacteria lineages containing cultured representatives with relatively few virulence factors (VFs) (Hyphomonadaceae and Erythrobacteraceae). In contrast, macroalgal exudates selected for less diverse communities heavily enriched in copiotrophic Gammaproteobacteria lineages containing cultured pathogens with increased VFs (Vibrionaceae and Pseudoalteromonadaceae). Our results demonstrate that algal exudates are enriched in DCNS components, foster rapid growth of bacterioplankton and select for bacterial populations with more potential VFs than
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Lee, Sun Hee; Kim, Jae Hee; Chung, Chung-Wook; Kim, Do Young; Rhee, Young Ha
2018-04-01
Analysis of mixed microbial populations responsible for the production of medium-chain-length polyhydroxyalkanoates (MCL-PHAs) under periodic substrate feeding in a sequencing batch reactor (SBR) was conducted. Regardless of activated sludge samples and the different MCL alkanoic acids used as the sole external carbon substrate, denaturing gradient gel electrophoresis analysis indicated that Pseudomonas aeruginosa was the dominant bacterium enriched during the SBR process. Several P. aeruginosa strains were isolated from the enriched activated sludge samples. The isolates were subdivided into two groups, one that produced only MCL-PHAs and another that produced both MCL- and short-chain-length PHAs. The SBR periodic feeding experiments with five representative MCL-PHA-producing Pseudomonas species revealed that P. aeruginosa has an advantage over other species that enables it to become dominant in the bacterial community.
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Disturbance opens recruitment sites for bacterial colonization in activated sludge.
Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E
2016-01-01
Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Dallaire, Jamie A; Meagher, Rebecca K; Díez-León, María; Garner, Joseph P; Mason, Georgia J
2011-10-31
We analysed the relationship between abnormal repetitive behaviour (ARB), the presence/absence of environmental enrichment, and two types of behavioural disinhibition in farmed American mink, Neovison vison. The first type, recurrent perseveration, the inappropriate repetition of already completed responses, was assessed using three indices of excessive response repetition and patterning in a bias-corrected serial two-choice guessing task. The second type, disinhibition of prepotent responses to reward cues, a form of impulsivity, was tested in a locomotive detour task adapted from primate reaching tasks: subjects were required to walk around, rather than directly into, a transparent barrier behind which food was visible. In older adult females, recurrent perseveration positively predicted pre-feeding abnormal repetitive locomotion (ARL) in Non-enriched housing. High-ARL subjects also performed repeated (same-choice) responses more rapidly than low-ARL animals, even when statistically controlling for alternated (different-choice) response latency. Mink performed much less ARL following transfer to Enriched housing, but there was no corresponding change in recurrent perseveration. Thus, elevated recurrent perseveration is not sufficient for frequent ARL; and while captive environments do determine ARL frequency, in mink, they do not necessarily do so by modifying levels of perseveration. Disinhibition of prepotent responses to reward cues, meanwhile, did not predict ARL. In a separate sample of differentially housed young adults, neither type of behavioural disinhibition predicted ARL, and again, whether or not housing was enriched did not affect behavioural disinhibition despite affecting ARL. Thus, the relationship between recurrent perseveration and ARB may only develop with age; longitudinal studies are now required for confirmation. Copyright © 2011 Elsevier B.V. All rights reserved.
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Enrichment of intergalactic matter.
NASA Technical Reports Server (NTRS)
Silk, J.; Siluk, R. S.
1972-01-01
The primordial gas out of which the Galaxy condensed may have been significantly enriched in heavy elements. A specific mechanism of enrichment is described, in which quasi-stellar sources eject enriched matter into the intergalactic medium. This matter is recycled through successive generations of these sources, and is progressively enriched. The enriched intergalactic matter is accreted by the protogalaxy and we find, for rates of mass ejection by quasi-stellar sources equal to about one solar mass per year in heavy elements, that this mechanism can account for the heavy-element abundances in the oldest Population II stars. Expressions are given for the degree of enrichment of the intergalactic gas as a function of redshift, and we show that our hypothesis implies that the present density of intergalactic gas must be at least a factor 3 larger than the mean density in galaxies at the present epoch.
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Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China
Wu, Yucheng; Tan, Liangcheng; Liu, Wuxing; Wang, Baozhan; Wang, Jianjun; Cai, Yanjun; Lin, Xiangui
2015-01-01
Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments. PMID:25870592
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Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China.
Wu, Yucheng; Tan, Liangcheng; Liu, Wuxing; Wang, Baozhan; Wang, Jianjun; Cai, Yanjun; Lin, Xiangui
2015-01-01
Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments.
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Effect of a cocoa flavonoid-enriched diet on experimental autoimmune arthritis.
Ramos-Romero, Sara; Pérez-Cano, Francisco J; Pérez-Berezo, Teresa; Castellote, Cristina; Franch, Angels; Castell, Margarida
2012-02-01
Previously we established that a cocoa-enriched diet in young rats reduces specific antibody production and the T helper (Th) lymphocyte proportion in lymphoid tissues. The aim of the present study was to ascertain the modulatory ability of a cocoa flavonoid-enriched diet on collagen-induced arthritis (CIA), which is mediated by anti-collagen autoantibody response and Th lymphocyte activation. Female Louvain (LOU) rats were fed with a cocoa-enriched diet, beginning 2 weeks before CIA induction. Hind-paw swelling and serum cytokine and anti-collagen antibody concentrations were determined. Anti-collagen antibody-secreting cell counts and lymphocyte subset proportions were established in inguinal lymph nodes (ILN). Reactive oxygen species (ROS), nitric oxide (NO) and TNFα produced by peritoneal macrophages were determined. Although arthritic cocoa-fed rats showed a similar hind-paw swelling time course as the arthritic animals fed a standard diet, the cocoa intake was able to decrease specific IgG2a, IgG2b and IgG2c titres. Moreover, cocoa intake in CIA rats reduced ROS production, TNFα and NO release from peritoneal macrophages, and decreased the Th:cytotoxic T cell ratio in ILN. In conclusion, a cocoa flavonoid-enriched diet in LOU rats with CIA produced no effect on hind-paw swelling but was able to modulate the specific antibody response and also the Th lymphocyte proportion, as well as the synthesis of pro-inflammatory mediators from peritoneal macrophages. Therefore, a cocoa-enriched diet could be a good adjuvant therapy in disorders with oxidative stress or autoimmune pathogenesis.
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Golubkina, N A; Mazo, V K; Gmoshinskiĭ, I V; Zorin, S N; Tambiev, A Kh; Kirikova, N N
2000-01-01
The main events caused by anaphilaxis in selenium haemostasis in rats include significant increase of selenium excretion with urine (6.36 +/- 1.18 nM Se/18 h., n = 10, compared with 1.72 +/- 0.38 nM Se/18 h., n = 10) and decrease of selenium plasma/selenium erythrocytes ratio from 0.939 to 0.791. Reduced glutathione (G-SH) administration led to 1.5-fold decrease of plasma selenium level and 1.3-fold increase of selenium concentration in intestinal walls of sensitized rats (r = -0.720, P < 0.001). Chromatographic separation of plasma proteins showed that intragastric intubation of G-SH to sensibilized rats significantly decreased the protein P content and did not influence the concentration of Se-GSHPx, thus indicating the local selenium acceptor role of G-SH. G-SH administration did not influence the intestinal permeability in sensitised rats while use of complex additive: G-SH and selenium enriched spirulina--normalized the latter parameter and the ratio of protein P/Se-GSHPx in plasma.
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Antibiotics for treating bacterial vaginosis in pregnancy.
Brocklehurst, Peter; Gordon, Adrienne; Heatley, Emer; Milan, Stephen J
2013-01-31
Bacterial vaginosis is an imbalance of the normal vaginal flora with an overgrowth of anaerobic bacteria and a lack of the normal lactobacillary flora. Women may have symptoms of a characteristic vaginal discharge but are often asymptomatic. Bacterial vaginosis during pregnancy has been associated with poor perinatal outcomes and, in particular, preterm birth (PTB). Identification and treatment may reduce the risk of PTB and its consequences. To assess the effects of antibiotic treatment of bacterial vaginosis in pregnancy. We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (31 May 2012), searched cited references from retrieved articles and reviewed abstracts, letters to the editor and editorials. Randomised trials comparing antibiotic treatment with placebo or no treatment, or comparing two or more antibiotic regimens in pregnant women with bacterial vaginosis or intermediate vaginal flora whether symptomatic or asymptomatic and detected through screening. Two review authors independently assessed trials for inclusion, trial quality and extracted data. We contacted study authors for additional information. We included 21 trials of good quality, involving 7847 women diagnosed with bacterial vaginosis or intermediate vaginal flora.Antibiotic therapy was shown to be effective at eradicating bacterial vaginosis during pregnancy (average risk ratio (RR) 0.42; 95% confidence interval (CI) 0.31 to 0.56; 10 trials, 4403 women; random-effects, T² = 0.19, I² = 91%). Antibiotic treatment also reduced the risk of late miscarriage (RR 0.20; 95% CI 0.05 to 0.76; two trials, 1270 women, fixed-effect, I² = 0%).Treatment did not reduce the risk of PTB before 37 weeks (average RR 0.88; 95% CI 0.71 to 1.09; 13 trials, 6491 women; random-effects, T² = 0.06, I² = 48%), or the risk of preterm prelabour rupture of membranes (RR 0.74; 95% CI 0.30 to 1.84; two trials, 493 women). It did increase the risk of side-effects sufficient to stop or change treatment
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Oprenyeszk, Frederic; Sanchez, Christelle; Dubuc, Jean-Emile; Maquet, Véronique; Henrist, Catherine; Compère, Philippe; Henrotin, Yves
2015-01-01
This in vitro study investigated the metabolism of human osteoarthritic (OA) chondrocytes encapsulated in a spherical matrix enriched of chitosan. Human OA chondrocytes were encapsulated and cultured for 28 days either in chitosan-alginate beads or in alginate beads. The beads were formed by slowly passing dropwise either the chitosan 0.6%–alginate 1.2% or the alginate 1.2% solution through a syringe into a 102 mM CaCl2 solution. Beads were analyzed histologically after 28 days. Interleukin (IL)-6 and -8, prostaglandin (PG) E2, matrix metalloproteinases (MMPs), hyaluronan and aggrecan were quantified directly in the culture supernatant by specific ELISA and nitric oxide (NO) by using a colorimetric method based on the Griess reaction. Hematoxylin and eosin staining showed that chitosan was homogeneously distributed through the matrix and was in direct contact with chondrocytes. The production of IL-6, IL-8 and MMP-3 by chondrocytes significantly decreased in chitosan-alginate beads compared to alginate beads. PGE2 and NO decreased also significantly but only during the first three days of culture. Hyaluronan and aggrecan production tended to increase in chitosan-alginate beads after 28 days of culture. Chitosan-alginate beads reduced the production of inflammatory and catabolic mediators by OA chondrocytes and tended to stimulate the synthesis of cartilage matrix components. These particular effects indicate that chitosan-alginate beads are an interesting scaffold for chondrocytes encapsulation before transplantation to repair cartilage defects. PMID:26020773
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Colin, Y; Nicolitch, O; Turpault, M-P; Uroz, S
2017-03-01
Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil
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Colin, Y.; Nicolitch, O.; Turpault, M.-P.
2016-01-01
ABSTRACT Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering
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Effects of environmental enrichment on behaviour, physiology and performance of pigs: A review.
Mkwanazi, Mbusiseni Vusumuzi; Ncobela, Cyprial Ndumiso; Kanengoni, Arnold Tapera; Chimonyo, Michael
2017-06-26
The aim of this paper is to critically analyse and synthesise existing knowledge concerning the use of environmental enrichment and its effect on behaviour, physiology and performance of pigs housed in intensive production systems. The objective is also to provide clarity as to what constitute successful enrichment and recommend on when and how enrichment should be used. Environmental enrichment is usually understood as an attempt to improve animal welfare and to lesser extent, performance. Common enrichment objects used are straw bedding, suspended rope and wood shavings, toys, rubber tubing, coloured plastic keys, table tennis balls, chains and strings. These substrates need to be chewable, deformable, destructible and ingestible. For enrichment to be successful four goals are the prerequisite. Firstly, enrichment should increase the number and range of normal behaviours (2) prevent the phenomenon of anomalous behaviours or reduce their frequency (3) increase positive use of the environment such as space and (4) increase the ability of the animals to deal with behavioural and physiological challenges. The performance, behaviour and physiology of pigs in enriched environments is similar or in some cases slightly better when compared with barren environments. In studies where there was no improvement, it should be born in mind that enriching the environment may not always be practical and yield positive results due to factors such as type of enrichment substrates, duration of provision and type of enrichment used. The review also identifies possible areas which still need further research, especially in understanding the role of enrichment, novelty, breed differences and other enrichment alternatives.
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Ghugare, G S; Nair, A; Nimkande, V; Sarode, P; Rangari, P; Khairnar, K
2017-02-01
To develop a method for the isolation and enrichment of bacteriophages selectively against specific bacteria coupled with a membrane filtration technique. Rapid isolation and concentration of host-specific bacteriophages was achieved by exposure of the sample suspected to contain bacteriophages to a specific host immobilized on a 0·45 μm membrane in a membrane filtration unit. The principle behind this method is the exploitation of host-specific interaction of bacteriophages with their host and maximizing this interaction using a classic membrane filtration method. This provides a chance for each bacteriophage in the sample to interact with the specific host on the membrane filter fitted with a vacuum pump. Specific bacteriophages of the host are retained on the membrane along with its host cells due to the effect of adsorption and these adsorbed bacteriophages (along with their hosts) on the filter disc are then amplified and enriched in regular nutritive broth tryptose soya broth by incubation. With the help of the plaque assay method, host-specific phages of various bacterial species were isolated, segregated and enriched. The phage concentration method coupled with membrane filtration immobilization of host bacteria was able to isolate and enrich the host-specific bacteriophages by several fold using a lower quantity of an environmental water sample, or other phage suspensions. Enrichment of phages from single plaques was also achieved. The isolation and detection of host-specific bacteriophages from a low density bacteriophage water sample in a single step by the use of a simple and basic microbiological technique can be achieved. Enrichment of phages from low phage titre suspensions is also achieved very effectively. © 2016 The Society for Applied Microbiology.
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Yoshimura, Emerson H; Santos, Nadine W; Machado, Erica; Agustinho, Bruna C; Pereira, Lucelia M; de Aguiar, Sílvia C; Sá-Nakanishi, Anacharis B; Mareze-da-Costa, Cecília E; Zeoula, Lucia M
2018-01-01
The increasing incidence of diabetes mellitus is becoming a serious threat to human health in various parts of the world. Studies with dairy products have shown a potential beneficial effect against diabetes. This experiment evaluated the supplementation of milk naturally enriched with polyunsaturated fatty acids (PUFA) and polyphenols in rats with streptozotocin-induced diabetes. Forty male 28-day-old Wistar rats were distributed in four experimental treatments of diabetic animals (streptozotocin induction) and a normal group (non-induced). Experimental treatments were: control (water), whole common milk (COM-M), milk enriched with PUFA (PUFA-M), milk enriched with PUFA and polyphenols (PUFA/P-M) through a special diet offered to dairy cows. Milk supplementation at a dose 5 mL/kg body weight was performed for 77 days, 42 days before and 35 days after diabetes induction. The COM-M supplementation increased brown fat deposits, reduced post-induction glucose levels, reduced blood fructosamine levels, and improved glucose tolerance. Milk enriched with PUFA reduced final fasting glucose, LDL levels, and improved blood antioxidant capacity. Milk enriched with PUFA and polyphenols promoted an increase in gastrocnemius muscle mass, and a reduction in mesenteric fat and LDL levels. Milk intake, with an emphasis on milk enriched with PUFA and polyphenols, attenuated the metabolic disorders of streptozotocin-induced diabetes in rats.
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Mumford, Adam C.; Barringer, Julia L.; Reilly, Pamela A.; Eberl, Dennis D.; Blum, Alex E.; Young, Lily Y.
2015-01-01
Release of arsenic (As) from sedimentary rocks has resulted in contamination of groundwater in aquifers of the New Jersey Piedmont Physiographic Province, USA; the contamination also may affect the quality of the region's streamwater to which groundwater discharges. Biogeochemical mechanisms involved in the release process were investigated in the streambeds of Six Mile Run and Pike Run, tributaries to the Millstone River in the Piedmont. At Six Mile Run, streambed pore water and shallow groundwater were low or depleted in oxygen, and contained As at concentrations greater than 20μg/L. At Pike Run, oxidizing conditions were present in the streambed, and the As concentration in pore water was 2.1μg/L. The 16S rRNA gene and the As(V) respiratory reductase gene, arrA, were amplified from DNA extracted from streambed pore water at both sites and analyzed, revealing that distinct bacterial communities that corresponded to the redox conditions were present at each site. Anaerobic enrichment cultures were inoculated with pore water from gaining reaches of the streams with acetate and As(V). As(V) was reduced by microbes to As(III) in enrichments with Six Mile Run pore water and groundwater, whereas no reduction occurred in enrichments with Pike Run pore water. Cloning and sequencing of the arrA gene indicated 8 unique operational taxonomic units (OTUs) at Six Mile Run and 11 unique OTUs at Pike Run, which may be representative of the arsenite oxidase gene arxA. Low-oxygen conditions at Six Mile Run have favored microbial As reduction and release, whereas release was inhibited by oxidizing conditions at Pike Run.
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Petrova, Olga E.; Garcia-Alcalde, Fernando; Zampaloni, Claudia; Sauer, Karin
2017-01-01
Global transcriptomic analysis via RNA-seq is often hampered by the high abundance of ribosomal (r)RNA in bacterial cells. To remove rRNA and enrich coding sequences, subtractive hybridization procedures have become the approach of choice prior to RNA-seq, with their efficiency varying in a manner dependent on sample type and composition. Yet, despite an increasing number of RNA-seq studies, comparative evaluation of bacterial rRNA depletion methods has remained limited. Moreover, no such study has utilized RNA derived from bacterial biofilms, which have potentially higher rRNA:mRNA ratios and higher rRNA carryover during RNA-seq analysis. Presently, we evaluated the efficiency of three subtractive hybridization-based kits in depleting rRNA from samples derived from biofilm, as well as planktonic cells of the opportunistic human pathogen Pseudomonas aeruginosa. Our results indicated different rRNA removal efficiency for the three procedures, with the Ribo-Zero kit yielding the highest degree of rRNA depletion, which translated into enhanced enrichment of non-rRNA transcripts and increased depth of RNA-seq coverage. The results indicated that, in addition to improving RNA-seq sensitivity, efficient rRNA removal enhanced detection of low abundance transcripts via qPCR. Finally, we demonstrate that the Ribo-Zero kit also exhibited the highest efficiency when P. aeruginosa/Staphylococcus aureus co-culture RNA samples were tested. PMID:28117413
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He, Zhanfei; Cai, Chen; Shen, Lidong; Lou, Liping; Zheng, Ping; Xu, Xinhua; Hu, Baolan
2015-01-01
Nitrite-dependent anaerobic methane oxidation (n-damo) is a newly discovered biological process that couples anaerobic oxidation of methane (AOM) to nitrite reduction. In this study, three different inocula, methanogenic sludge, paddy soil, and freshwater sediment were used to enrich n-damo bacteria in three sequencing batch reactors (SBRs), and three n-damo enrichment cultures, C1, C2 and C3, were obtained, respectively. After 500 days of incubation, Methylomirabilis oxyfera-like bacteria and n-damo activities were observed in cultures C1, C2, and C3, and the specific activities were 0.8 ± 0.1, 1.4 ± 0.1, and 1.0 ± 0.1 μmol CH4 h(-1) g(-1) VSS, respectively. The copy numbers of 16S rRNA genes from cultures C1, C2, and C3 were 5.0 ± 0.4 × 10(8), 6.1 ± 0.1 × 10(9), and 1.0 ± 0.2 × 10(9) copies g(-1) dry weight, respectively. The results indicated that paddy soil is an excellent inoculum for n-damo bacterial enrichment. This work expanded the alternative source of n-damo inoculum and benefited the further research of n-damo process.
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NASA Astrophysics Data System (ADS)
Sanyasi, Sridhar; Majhi, Rakesh Kumar; Kumar, Satish; Mishra, Mitali; Ghosh, Arnab; Suar, Mrutyunjay; Satyam, Parlapalli Venkata; Mohapatra, Harapriya; Goswami, Chandan; Goswami, Luna
2016-04-01
Development of effective anti-microbial therapeutics has been hindered by the emergence of bacterial strains with multi-drug resistance and biofilm formation capabilities. In this article, we report an efficient green synthesis of silver nanoparticle (AgNP) by in situ reduction and capping with a semi-synthetic polysaccharide-based biopolymer (carboxymethyl tamarind polysaccharide). The CMT-capped AgNPs were characterized by UV, DLS, FE-SEM, EDX and HR-TEM. These AgNPs have average particle size of ~20-40 nm, and show long time stability, indicated by their unchanged SPR and Zeta-potential values. These AgNPs inhibit growth and biofilm formation of both Gram positive (B. subtilis) and Gram negative (E. coli and Salmonella typhimurium) bacterial strains even at concentrations much lower than the minimum inhibitory concentration (MIC) breakpoints of antibiotics, but show reduced or no cytotoxicity against mammalian cells. These AgNPs alter expression and positioning of bacterial cytoskeletal proteins FtsZ and FtsA. CMT-capped AgNPs can effectively block growth of several clinical isolates and MDR strains representing different genera and resistant towards multiple antibiotics belonging to different classes. We propose that the CMT-capped AgNPs can have potential bio-medical application against multi-drug-resistant microbes with minimal cytotoxicity towards mammalian cells.
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Sanyasi, Sridhar; Majhi, Rakesh Kumar; Kumar, Satish; Mishra, Mitali; Ghosh, Arnab; Suar, Mrutyunjay; Satyam, Parlapalli Venkata; Mohapatra, Harapriya; Goswami, Chandan; Goswami, Luna
2016-01-01
Development of effective anti-microbial therapeutics has been hindered by the emergence of bacterial strains with multi-drug resistance and biofilm formation capabilities. In this article, we report an efficient green synthesis of silver nanoparticle (AgNP) by in situ reduction and capping with a semi-synthetic polysaccharide-based biopolymer (carboxymethyl tamarind polysaccharide). The CMT-capped AgNPs were characterized by UV, DLS, FE-SEM, EDX and HR-TEM. These AgNPs have average particle size of ~20–40 nm, and show long time stability, indicated by their unchanged SPR and Zeta-potential values. These AgNPs inhibit growth and biofilm formation of both Gram positive (B. subtilis) and Gram negative (E. coli and Salmonella typhimurium) bacterial strains even at concentrations much lower than the minimum inhibitory concentration (MIC) breakpoints of antibiotics, but show reduced or no cytotoxicity against mammalian cells. These AgNPs alter expression and positioning of bacterial cytoskeletal proteins FtsZ and FtsA. CMT-capped AgNPs can effectively block growth of several clinical isolates and MDR strains representing different genera and resistant towards multiple antibiotics belonging to different classes. We propose that the CMT-capped AgNPs can have potential bio-medical application against multi-drug-resistant microbes with minimal cytotoxicity towards mammalian cells. PMID:27125749
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-06-10
.... 10-899-02-ML-BD01] In the Matter of Areva Enrichment Services, LLC (Eagle Rock Enrichment Facility... gas centrifuge uranium enrichment facility--denoted as the Eagle Rock Enrichment Facility (EREF)--in... Information for Contention Preparation; In the Matter of Areva Enrichment Services, LLC (Eagle Rock Enrichment...
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Future challenges in the elimination of bacterial meningitis.
Bottomley, Matthew J; Serruto, Davide; Sáfadi, Marco Aurélio Palazzi; Klugman, Keith P
2012-05-30
Despite the widespread implementation of several effective vaccines over the past few decades, bacterial meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis and Group B Streptococcus (GBS) still results in unacceptably high levels of human mortality and morbidity. A residual disease burden due to bacterial meningitis is also apparent due to a number of persistent or emerging pathogens, including Mycobacterium tuberculosis, Escherichia coli, Staphylococcus aureus, Salmonella spp. and Streptococcus suis. Here, we review the current status of bacterial meningitis caused by these pathogens, highlighting how past and present vaccination programs have attempted to counter these pathogens. We discuss how improved pathogen surveillance, implementation of current vaccines, and development of novel vaccines may be expected to further reduce bacterial meningitis and related diseases in the future. Copyright © 2011 Elsevier Ltd. All rights reserved.
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Acute bacterial meningitis in adults.
McGill, Fiona; Heyderman, Robert S; Panagiotou, Stavros; Tunkel, Allan R; Solomon, Tom
2016-12-17
Over the past several decades, the incidence of bacterial meningitis in children has decreased but there remains a significant burden of disease in adults, with a mortality of up to 30%. Although the pathogenesis of bacterial meningitis is not completely understood, knowledge of bacterial invasion and entry into the CNS is improving. Clinical features alone cannot determine whether meningitis is present and analysis of cerebrospinal fluid is essential for diagnosis. Newer technologies, such as multiplex PCR, and novel diagnostic platforms that incorporate proteomics and genetic sequencing, might help provide a quicker and more accurate diagnosis. Even with appropriate antimicrobial therapy, mortality is high and so attention has focused on adjunctive therapies; adjunctive corticosteroids are beneficial in certain circumstances. Any further improvements in outcome are likely to come from either modulation of the host response or novel approaches to therapy, rather than new antibiotics. Ultimately, the best hope to reduce the disease burden is with broadly protective vaccines. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Santos, Nadine W; Yoshimura, Emerson H; Mareze-Costa, Cecília E; Machado, Erica; Agustinho, Bruna C; Pereira, Lucelia M; Brito, Márcia N; Brito, Nilton A; Zeoula, Lucia M
2017-01-01
This study investigated whether intake of cow milk, naturally enriched with polyunsaturated fatty acids (PUFA, omega-3) and polyphenols (from propolis extract and vitamin E), from manipulation of cow's diet, would result in positive metabolic effects in rats from weaning until adulthood. Male Wistar rats were fed a standard chow diet or a hypercaloric diet (metabolically disturbed rats, obese) which was supplemented with either whole common milk, milk enriched with PUFA (PUFA-M) or milk enriched with PUFA and polyphenols (PUFA/P-M), at 5mL/kg body weight,having water as control. Whole milk supplementation increased initial weight gain and reduced gain in the adulthood of rats. Intake of common milk reduced cholesterol levels in non-obese rats and reduced insulin resistance in obese rats. PUFA-milk showed a decreasing effect on plasma triacylglycerol and VLDL concentrations, increasing plasma HDL concentration and reducing adipocyte size of non-obese rats, but no effect was observed in obese rats. PUFA/P-milk in obese rats resulted in greater deposition of muscle mass and mesenteric fat, with a tendency to lower LDL levels, and resulted a visceral fat accumulation in non-obese rats. Thus, whole common milk and PUFA-rich milk have shown to be beneficial in a normal metabolic condition, whereas common milk and milk enriched with PUFA and polyphenols improve metabolic effects of obesity.
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Yousefshahi, Fardin; Azimpour, Khashayar; Boroumand, Mohammad Ali; Najafi, Mahdi; Barkhordari, Khosro; Vaezi, Mitra; Rouhipour, Nahid
2013-01-01
Background: Central venous (CV) catheters play an essential role in the management of critically ill patients in the Intensive Care Unit (ICU). CV lines are, however, allied to catheter-associated blood stream infections. Bacterial colonization of CV lines is deemed the main cause of catheter-associated infection. The purpose of our study was to compare bacterial colony counts in the catheter site before CV line insertion in two groups of post-cardiac surgery patients: a group receiving Sanosil (an antiseptic agent composed of H2O2 and silver) and a control group. Methods: This interventional prospective double-blinded clinical trial recruited the patients in three post-cardiac surgery ICUs of a heart center. The participants were divided into interventional (113 patients) and control (136 patients) groups. Sanosil was added to the routine preparation procedure (Chlorhexidine bath one day before and scrub with Povidone-Iodine just before the CV line insertion). After the removal of the CV lines, the catheters tips were sent for culture and evaluation of colony counts. Results: Catheter colonization occurred in 55 (22.1%) patients: 26 (23%) patients in the Sanosil group and 29 (21.3%) in the control group; there was no significant statistical difference between the two groups (p value = 0.75, RR = 1.05, 95% CI: 0.76–1.45). The most common organism having colonized in the cultures of the catheter tips was staphylococcus epidermis: 20 cases in the control group and 16 cases in the intervention group. Conclusion: Catheter colonization frequently occurs in post-cardiac surgery patients. However, our results did not indicate the effectiveness of adding Sanosil to the routine preparation procedure with respect to reducing catheter bacterial colonization. PMID:23967028
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Pati, Rashmirekha; Mehta, Ranjit Kumar; Mohanty, Soumitra; Padhi, Avinash; Sengupta, Mitali; Vaseeharan, Baskarlingam; Goswami, Chandan; Sonawane, Avinash
2014-08-01
Here we studied immunological and antibacterial mechanisms of zinc oxide nanoparticles (ZnO-NPs) against human pathogens. ZnO-NPs showed more activity against Staphylococcus aureus and least against Mycobacterium bovis-BCG. However, BCG killing was significantly increased in synergy with antituberculous-drug rifampicin. Antibacterial mechanistic studies showed that ZnO-NPs disrupt bacterial cell membrane integrity, reduce cell surface hydrophobicity and down-regulate the transcription of oxidative stress-resistance genes in bacteria. ZnO-NP treatment also augmented the intracellular bacterial killing by inducing reactive oxygen species production and co-localization with Mycobacterium smegmatis-GFP in macrophages. Moreover, ZnO-NPs disrupted biofilm formation and inhibited hemolysis by hemolysin toxin producing S. aureus. Intradermal administration of ZnO-NPs significantly reduced the skin infection, bacterial load and inflammation in mice, and also improved infected skin architecture. We envision that this study offers novel insights into antimicrobial actions of ZnO-NPs and also demonstrates ZnO-NPs as a novel class of topical anti-infective agent for the treatment of skin infections. This in-depth study demonstrates properties of ZnO nanoparticles in infection prevention and treatment in several skin infection models, dissecting the potential mechanisms of action of these nanoparticles and paving the way to human applications. Copyright © 2014 Elsevier Inc. All rights reserved.
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Zagólski, Olaf; Stręk, Paweł; Kasprowicz, Andrzej; Białecka, Anna
2015-01-01
Background Polyvalent bacterial lysate (PBL) is an oral immunostimulating vaccine consisting of bacterial standardized lysates obtained by lysis of different strains of bacteria. Autovaccines are individually prepared based on the results of smears obtained from the patient. Both types of vaccine can be used to treat an ongoing chronic infection. This study sought to determine which method is more effective against nasal colonization by potential respiratory tract pathogens. Material/Methods We enrolled 150 patients with aerobic Gram stain culture and count results indicating bacterial colonization of the nose and/or throat by potential pathogens. The participants were randomly assigned to each of the following groups: 1. administration of PBL, 2. administration of autovaccine, and 3. no intervention (controls). Results Reduction of the bacterial count in Streptococcus pneumoniae-colonized participants was significant after the autovaccine (p<0.001) and PBL (p<0.01). Reduction of the bacterial count of other β-hemolytic streptococcal strains after treatment with the autovaccine was significant (p<0.01) and was non-significant after PBL. In Haemophilus influenzae colonization, significant reduction in the bacterial count was noted in the PBL group (p<0.01). Methicillin-resistant Staphylococcus aureus colonization did not respond to either treatment. Conclusions The autovaccine is more effective than PBL for reducing bacterial count of Streptococcus pneumoniae and β-hemolytic streptococci, while PBL was more effective against Haemophilus influenzae colonization. PMID:26434686
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Kuehn, Joanna S; Gorden, Patrick J; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J; Wang, Chong; Phillips, Gregory J
2013-01-01
Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1-V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease.
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Environmental enrichment delays pup-induced maternal behavior in rats.
Mann, Phyllis E; Gervais, Kristen J
2011-05-01
Adult, virgin rats do not spontaneously display maternal behavior when exposed to foster pups. However, continuous daily exposure of the female to foster pups for about 5-7 days can induce a set of maternal behaviors similar to those shown by postpartum dams. Induction latencies depend upon a number of factors, including the stress and anxiety levels of the female. The goal of this study was to attempt to mitigate the likely stressfulness of being singly housed during testing by enriching the rat's home cage environment and to determine if the concomitant environmental change would alter the latency to express maternal behavior. In addition, the effect of varying the number of test pups used for testing was examined. Two groups of virgin Sprague-Dawley rats were first tested on the elevated plus maze after 1 week of exposure to either control (standard housing) or enriched conditions. One week later, maternal behavior testing began using one or three pups. Upon completion of maternal behavior testing, plasma corticosterone concentrations were determined following a mild stressor. The data indicate that enrichment tends to increase anxiety-like behaviors in the elevated plus maze. In addition, enrichment delayed the onset of maternal behavior irrespective of the number of test pups. There were no effects of environmental enrichment on plasma corticosterone levels following exposure to a stressor. These results indicate that what is considered a modestly enriched environment delays the expression of pup-oriented responses and does not apparently reduce stress or improve performance on all behavioral tasks. Copyright © 2011 Wiley Periodicals, Inc.
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Zhou, Lei; Li, Kai-Ping; Mbadinga, Serge Maurice; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong
2012-08-01
Despite the knowledge on anaerobic degradation of hydrocarbons and signature metabolites in the oil reservoirs, little is known about the functioning microbes and the related biochemical pathways involved, especially about the methanogenic communities. In the present study, a methanogenic consortium enriched from high-temperature oil reservoir production water and incubated at 55 °C with a mixture of long chain n-alkanes (C(15)-C(20)) as the sole carbon and energy sources was characterized. Biodegradation of n-alkanes was observed as methane production in the alkanes-amended methanogenic enrichment reached 141.47 μmol above the controls after 749 days of incubation, corresponding to 17 % of the theoretical total. GC-MS analysis confirmed the presence of putative downstream metabolites probably from the anaerobic biodegradation of n-alkanes and indicating an incomplete conversion of the n-alkanes to methane. Enrichment cultures taken at different incubation times were subjected to microbial community analysis. Both 16S rRNA gene clone libraries and DGGE profiles showed that alkanes-degrading community was dynamic during incubation. The dominant bacterial species in the enrichment cultures were affiliated with Firmicutes members clustering with thermophilic syntrophic bacteria of the genera Moorella sp. and Gelria sp. Other represented within the bacterial community were members of the Leptospiraceae, Thermodesulfobiaceae, Thermotogaceae, Chloroflexi, Bacteroidetes and Candidate Division OP1. The archaeal community was predominantly represented by members of the phyla Crenarchaeota and Euryarchaeota. Corresponding sequences within the Euryarchaeota were associated with methanogens clustering with orders Methanomicrobiales, Methanosarcinales and Methanobacteriales. On the other hand, PCR amplification for detection of functional genes encoding the alkylsuccinate synthase α-subunit (assA) was positive in the enrichment cultures. Moreover, the appearance of a new ass
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Lopes, M; Leite, F L; Valente, B S; Heres, T; Dai Prá, M A; Xavier, E G; Roll, V F B
2015-09-01
Although the use of quicklime (CaO) and tarping are common handling practices aimed at the reuse of litter in the Brazilian poultry industry, few scientific studies have proven the effectiveness of these methods in reducing the pathogenic microbial load during fallowing. The objective of this study was to evaluate the following litter treatments: T1 no treatment (control), T2 quicklime (300 g m(-2)), T3 tarping, T4 tarping+quicklime (300 g m(-2)). The litter samples were collected on day zero and on the sixth and twelfth days after the start of fallowing. The use of quicklime alone or quicklime+tarping was more effective (P<0.05) in reducing bacteria when compared to litter tarping. Except for the control group, all treatments resulted in a more than 84% reduction in the count of colony-forming units (CFUs) at the end of fallowing. It is concluded that the use of quicklime alone in practical terms is the most indicated treatment for the reduction of the bacterial load of poultry litter. © 2015 Poultry Science Association Inc.
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Bulgari, Daniela; Casati, Paola; Brusetti, Lorenzo; Quaglino, Fabio; Brasca, Milena; Daffonchio, Daniele; Bianco, Piero Attilio
2009-08-01
Diversity of bacterial endophytes associated with grapevine leaf tissues was analyzed by cultivation and cultivation-independent methods. In order to identify bacterial endophytes directly from metagenome, a protocol for bacteria enrichment and DNA extraction was optimized. Sequence analysis of 16S rRNA gene libraries underscored five diverse Operational Taxonomic Units (OTUs), showing best sequence matches with gamma-Proteobacteria, family Enterobacteriaceae, with a dominance of the genus Pantoea. Bacteria isolation through cultivation revealed the presence of six OTUs, showing best sequence matches with Actinobacteria, genus Curtobacterium, and with Firmicutes genera Bacillus and Enterococcus. Length Heterogeneity-PCR (LH-PCR) electrophoretic peaks from single bacterial clones were used to setup a database representing the bacterial endophytes identified in association with grapevine tissues. Analysis of healthy and phytoplasma-infected grapevine plants showed that LH-PCR could be a useful complementary tool for examining the diversity of bacterial endophytes especially for diversity survey on a large number of samples.
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Beckstrom, A C; Cleman, P E; Cassis-Ghavami, F L; Kamitsuka, M D
2013-12-01
To determine the bacterial contamination rate of the parent's cell phone and the effectiveness of anti-microbial gel in reducing transmission of bacteria from cell phone to hands. Cross-sectional study of cultures from the cell phone and hands before and after applying anti-microbial gel (n=50). All cell phones demonstrated bacterial contamination. Ninety percent had the same bacteria on the cell phone and their cleaned hands. Twenty two percent had no growth on their hands after applying anti-microbial gel after they had the same bacteria on the cell phone and hands. Ninety-two percent of parents were aware that cell phones carried bacteria, but only 38% cleaned their cell phones at least weekly. Bacterial contamination of cell phones may serve as vectors for nosocomial infection in the neonatal intensive care unit. Bacteria transmitted from cell phone to hands may not be eliminated using anti-microbial gel. Development of hand hygiene and cell phone cleaning guidelines are needed regarding bedside cell phone use.
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Sheridan, Peter P.; Miteva, Vanya I.; Brenchley, Jean E.
2003-01-01
The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at −9°C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 × 107 cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at −2°C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years. PMID:12676695
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Corticosteroids for acute bacterial meningitis.
Brouwer, Matthijs C; McIntyre, Peter; Prasad, Kameshwar; van de Beek, Diederik
2013-06-04
In experimental studies, the outcome of bacterial meningitis has been related to the severity of inflammation in the subarachnoid space. Corticosteroids reduce this inflammatory response. To examine the effect of adjuvant corticosteroid therapy versus placebo on mortality, hearing loss and neurological sequelae in people of all ages with acute bacterial meningitis. We searched CENTRAL 2012, Issue 12, MEDLINE (1966 to January week 2, 2013), EMBASE (1974 to January 2013), Web of Science (2010 to January 2013), CINAHL (2010 to January 2013) and LILACS (2010 to January 2013). Randomised controlled trials (RCTs) of corticosteroids for acute bacterial meningitis. We scored RCTs for methodological quality. We collected outcomes and adverse effects. We performed subgroup analyses for children and adults, causative organisms, low-income versus high-income countries, time of steroid administration and study quality. Twenty-five studies involving 4121 participants were included. Corticosteroids were associated with a non-significant reduction in mortality (17.8% versus 19.9%; risk ratio (RR) 0.90, 95% confidence interval (CI) 0.80 to 1.01, P = 0.07). A similar non-significant reduction in mortality was observed in adults receiving corticosteroids (RR 0.74, 95% CI 0.53 to 1.05, P = 0.09). Corticosteroids were associated with lower rates of severe hearing loss (RR 0.67, 95% CI 0.51 to 0.88), any hearing loss (RR 0.74, 95% CI 0.63 to 0.87) and neurological sequelae (RR 0.83, 95% CI 0.69 to 1.00).Subgroup analyses for causative organisms showed that corticosteroids reduced mortality in Streptococcus pneumoniae (S. pneumoniae) meningitis (RR 0.84, 95% CI 0.72 to 0.98), but not in Haemophilus influenzae (H. influenzae) orNeisseria meningitidis (N. meningitidis) meningitis. Corticosteroids reduced severe hearing loss in children with H. influenzae meningitis (RR 0.34, 95% CI 0.20 to 0.59) but not in children with meningitis due to non-Haemophilus species.In high-income countries
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Genetics and breeding of bacterial leaf spot resistance
USDA-ARS?s Scientific Manuscript database
Bacterial leaf spot (BLS) caused by the pathogen Xanthomonas campestris pv. vitians (Xcv) is a globally important disease of whole head and baby leaf lettuce that reduces crop yield and quality. Host resistance is the most feasible method to reduce disease losses. Screening Lactuca accessions has id...
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Roh, Yul; Liu, Shi V; Li, Guangshan; Huang, Heshu; Phelps, Tommy J; Zhou, Jizhong
2002-12-01
Five bacterial strains were isolated from anaerobic enrichment cultures that had originated from inoculations with samples collected from the deep subsurface environments of the millions-of-years-old, geologically and hydrologically isolated Piceance Basin in Colorado. Small-subunit rRNA gene-based analyses indicated that all of these bacteria were closely related to Thermoanaerobacter ethanolicus, with similarities of 99.4 to 99.5%. Three isolates (X513, X514, and X561) from the five bacterial strains were used to examine physiological characteristics. These thermophilic bacteria were able to use acetate, glucose, hydrogen, lactate, pyruvate, succinate, and xylose as electron donors while reducing Fe(III), cobalt(III), chromium(VI), manganese(IV), and uranium(VI) at 60 degrees C. One of the isolates (X514) was also able to utilize hydrogen as an electron donor for Fe(III) reduction. These bacteria exhibited diverse mineral precipitation capabilities, including the formation of magnetite (Fe(3)O(4)), siderite (FeCO(3)), rhodochrosite (MnCO(3)), and uraninite (UO(2)). The gas composition of the incubation headspace and the ionic composition of the incubation medium exerted profound influences on the types of minerals formed. The susceptibility of the thermophilic Fe(III)-reducing cultures to metabolic inhibitors specific for ferric reductase, hydrogenase, and electron transport indicated that iron reduction by these bacteria is an enzymatic process.
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Technology Enriched Schools: Nine Case Studies with Reflections.
ERIC Educational Resources Information Center
Collis, Betty, Ed.; Carleer, Gerrit, Ed.
Technology enriched school projects are initiatives in real school settings that try to reduce or remove problems and constraints that hamper the effective use of computers in the schools. These projects are based, not on technology, but on educational need and vision. They examine the atmosphere and functioning of a school that uses technology…
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Wang, Cheng; Zeng, Jian; Li, Yin; Yang, Guangxiao; He, Guangyuan
2014-01-01
Carotenoid content is a primary determinant of wheat nutritional value and affects its end-use quality. Wheat grains contain very low carotenoid levels and trace amounts of provitamin A content. In order to enrich the carotenoid content in wheat grains, the bacterial phytoene synthase gene (CrtB) and carotene desaturase gene (CrtI) were transformed into the common wheat cultivar Bobwhite. Expression of CrtB or CrtI alone slightly increased the carotenoid content in the grains of transgenic wheat, while co-expression of both genes resulted in a darker red/yellow grain phenotype, accompanied by a total carotenoid content increase of approximately 8-fold achieving 4.76 μg g–1 of seed dry weight, a β-carotene increase of 65-fold to 3.21 μg g–1 of seed dry weight, and a provitamin A content (sum of α-carotene, β-carotene, and β-cryptoxanthin) increase of 76-fold to 3.82 μg g–1 of seed dry weight. The high provitamin A content in the transgenic wheat was stably inherited over four generations. Quantitative PCR analysis revealed that enhancement of provitamin A content in transgenic wheat was also a result of the highly coordinated regulation of endogenous carotenoid biosynthetic genes, suggesting a metabolic feedback regulation in the wheat carotenoid biosynthetic pathway. These transgenic wheat lines are not only valuable for breeding wheat varieties with nutritional benefits for human health but also for understanding the mechanism regulating carotenoid biosynthesis in wheat endosperm. PMID:24692648
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Wang, Cheng; Zeng, Jian; Li, Yin; Hu, Wei; Chen, Ling; Miao, Yingjie; Deng, Pengyi; Yuan, Cuihong; Ma, Cheng; Chen, Xi; Zang, Mingli; Wang, Qiong; Li, Kexiu; Chang, Junli; Wang, Yuesheng; Yang, Guangxiao; He, Guangyuan
2014-06-01
Carotenoid content is a primary determinant of wheat nutritional value and affects its end-use quality. Wheat grains contain very low carotenoid levels and trace amounts of provitamin A content. In order to enrich the carotenoid content in wheat grains, the bacterial phytoene synthase gene (CrtB) and carotene desaturase gene (CrtI) were transformed into the common wheat cultivar Bobwhite. Expression of CrtB or CrtI alone slightly increased the carotenoid content in the grains of transgenic wheat, while co-expression of both genes resulted in a darker red/yellow grain phenotype, accompanied by a total carotenoid content increase of approximately 8-fold achieving 4.76 μg g(-1) of seed dry weight, a β-carotene increase of 65-fold to 3.21 μg g(-1) of seed dry weight, and a provitamin A content (sum of α-carotene, β-carotene, and β-cryptoxanthin) increase of 76-fold to 3.82 μg g(-1) of seed dry weight. The high provitamin A content in the transgenic wheat was stably inherited over four generations. Quantitative PCR analysis revealed that enhancement of provitamin A content in transgenic wheat was also a result of the highly coordinated regulation of endogenous carotenoid biosynthetic genes, suggesting a metabolic feedback regulation in the wheat carotenoid biosynthetic pathway. These transgenic wheat lines are not only valuable for breeding wheat varieties with nutritional benefits for human health but also for understanding the mechanism regulating carotenoid biosynthesis in wheat endosperm. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.
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Wu, Jiajia; Liu, Huaiqun; Wang, Peng; Zhang, Dun; Sun, Yan; Li, Ee
2017-09-01
Sulfate-reducing bacteria (SRB) were found to be capable of tolerating a certain amount of oxygen (O 2 ), but how they affect oxygen reduction reaction (ORR) has not been clear. The present work investigated the impact of SRB on ORR in 3.5 wt% sodium chloride solution with the cyclic voltammetry method. The addition of SRB culture solution hampered both the reduction of O 2 to superoxide (O 2 ·- ) and hydrogen peroxide (H 2 O 2 ) to water (H 2 O), and the influence of SRB metabolites was much larger than that of bacterial cells. Sulfide and extracellular polymeric substances (EPS), typical inorganic and organic metabolic products, had great impact on ORR. Sulfide played an important role in the decrease of cathodic current for H 2 O 2 reduction due to its hydrolysis and chemical reaction activity with H 2 O 2 . EPS were sticky, easy to adsorb on the electrode surface and abundant in functional groups, which hindered the transformation of O 2 into O 2 ·- and favored the reduction of H 2 O 2 to H 2 O.
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Mammalian DNA enriched for replication origins is enriched for snap-back sequences.
Zannis-Hadjopoulos, M; Kaufmann, G; Martin, R G
1984-11-15
Using the instability of replication loops as a method for the isolation of double-stranded nascent DNA, extruded DNA enriched for replication origins was obtained and denatured. Snap-back DNA, single-stranded DNA with inverted repeats (palindromic sequences), reassociates rapidly into stem-loop structures with zero-order kinetics when conditions are changed from denaturing to renaturing, and can be assayed by chromatography on hydroxyapatite. Origin-enriched nascent DNA strands from mouse, rat and monkey cells growing either synchronously or asynchronously were purified and assayed for the presence of snap-back sequences. The results show that origin-enriched DNA is also enriched for snap-back sequences, implying that some origins for mammalian DNA replication contain or lie near palindromic sequences.
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16. VIEW OF THE ENRICHED URANIUM RECOVERY SYSTEM. ENRICHED URANIUM ...
16. VIEW OF THE ENRICHED URANIUM RECOVERY SYSTEM. ENRICHED URANIUM RECOVERY PROCESSED RELATIVELY PURE MATERIALS AND SOLUTIONS AND SOLID RESIDUES WITH RELATIVELY LOW URANIUM CONTENT. URANIUM RECOVERY INVOLVED BOTH SLOW AND FAST PROCESSES. (4/4/66) - Rocky Flats Plant, General Manufacturing, Support, Records-Central Computing, Southern portion of Plant, Golden, Jefferson County, CO
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Antimicrobial Nanoplexes meet Model Bacterial Membranes: the key role of Cardiolipin
NASA Astrophysics Data System (ADS)
Marín-Menéndez, Alejandro; Montis, Costanza; Díaz-Calvo, Teresa; Carta, Davide; Hatzixanthis, Kostas; Morris, Christopher J.; McArthur, Michael; Berti, Debora
2017-01-01
Antimicrobial resistance to traditional antibiotics is a crucial challenge of medical research. Oligonucleotide therapeutics, such as antisense or Transcription Factor Decoys (TFDs), have the potential to circumvent current resistance mechanisms by acting on novel targets. However, their full translation into clinical application requires efficient delivery strategies and fundamental comprehension of their interaction with target bacterial cells. To address these points, we employed a novel cationic bolaamphiphile that binds TFDs with high affinity to form self-assembled complexes (nanoplexes). Confocal microscopy revealed that nanoplexes efficiently transfect bacterial cells, consistently with biological efficacy on animal models. To understand the factors affecting the delivery process, liposomes with varying compositions, taken as model synthetic bilayers, were challenged with nanoplexes and investigated with Scattering and Fluorescence techniques. Thanks to the combination of results on bacteria and synthetic membrane models we demonstrate for the first time that the prokaryotic-enriched anionic lipid Cardiolipin (CL) plays a key-role in the TFDs delivery to bacteria. Moreover, we can hypothesize an overall TFD delivery mechanism, where bacterial membrane reorganization with permeability increase and release of the TFD from the nanoplexes are the main factors. These results will be of great benefit to boost the development of oligonucleotides-based antimicrobials of superior efficacy.
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Ottesen, Andrea; Ramachandran, Padmini; Reed, Elizabeth; White, James R; Hasan, Nur; Subramanian, Poorani; Ryan, Gina; Jarvis, Karen; Grim, Christopher; Daquiqan, Ninalynn; Hanes, Darcy; Allard, Marc; Colwell, Rita; Brown, Eric; Chen, Yi
2016-11-16
Microbiota that co-enrich during efforts to recover pathogens from foodborne outbreaks interfere with efficient detection and recovery. Here, dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA). Enrichment cultures were analyzed using DNA extraction and sequencing from samples taken every 4 h throughout 48 h of enrichment. Resphera Insight and CosmosID analysis tools were employed for high-resolution profiling of 16S rRNA amplicons and whole genome shotgun data, respectively. During enrichment, other bacterial taxa were identified, including Anoxybacillus, Geobacillus, Serratia, Pseudomonas, Erwinia, and Streptococcus spp. Surprisingly, incidence of L. monocytogenes was proportionally greater at hour 0 than when tested 4, 8, and 12 h later with all three enrichment schemes. The corresponding increase in Anoxybacillus and Geobacillus spp.indicated these taxa co-enriched in competition with L. monocytogenes during early enrichment hours. L. monocytogenes became dominant after 24 h in all three enrichments. DNA sequences obtained from shotgun metagenomic data of Listeria monocytogenes at 48 h were assembled to produce a consensus draft genome which appeared to have a similar tracking utility to pure culture isolates of L. monocytogenes. All three methods performed equally well for enrichment of Listeria monocytogenes. The observation of potential competitive exclusion of L. mono by Anoxybacillus and Geobacillus in early enrichment hours provided novel information that may be used to further optimize enrichment formulations. Application of Resphera Insight for high-resolution analysis of 16S amplicon sequences accurately identified L. monocytogenes
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Copper (II) Removal In Anaerobic Continuous Column Reactor System By Using Sulfate Reducing Bacteria
NASA Astrophysics Data System (ADS)
Bilgin, A.; Jaffe, P. R.
2017-12-01
Copper is an essential element for the synthesis of the number of electrons carrying proteins and the enzymes. However, it has a high level of toxicity. In this study; it is aimed to treat copper heavy metal in anaerobic environment by using anaerobic continuous column reactor. Sulfate reducing bacteria culture was obtained in anaerobic medium using enrichment culture method. The column reactor experiments were carried out with bacterial culture obtained from soil by culture enrichment method. The system is operated with continuous feeding and as parallel. In the first rector, only sand was used as packing material. The first column reactor was only fed with the bacteria nutrient media. The same solution was passed through the second reactor, and copper solution removal was investigated by continuously feeding 15-600 mg/L of copper solution at the feeding inlet in the second reactor. When the experiment was carried out by adding the 10 mg/L of initial copper concentration, copper removal in the rate of 45-75% was obtained. In order to determine the use of carbon source during copper removal of mixed bacterial cultures in anaerobic conditions, total organic carbon TOC analysis was used to calculate the change in carbon content, and it was calculated to be between 28% and 75%. When the amount of sulphate is examined, it was observed that it changed between 28-46%. During the copper removal, the amounts of sulphate and carbon moles were equalized and more sulfate was added by changing the nutrient media in order to determine the consumption of sulphate or carbon. Accordingly, when the concentration of added sulphate is increased, it is calculated that between 35-57% of sulphate is spent. In this system, copper concentration of up to 15-600 mg / L were studied.
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Transgenerational effects of environmental enrichment on repetitive motor behavior development.
Bechard, Allison R; Lewis, Mark H
2016-07-01
The favorable consequences of environmental enrichment (EE) on brain and behavior development are well documented. Much less is known, however, about transgenerational benefits of EE on non-enriched offspring. We explored whether transgenerational effects of EE might extend to the development of repetitive motor behaviors in deer mice. Repetitive motor behaviors are invariant patterns of movement that, across species, can be reduced by EE. We found that EE not only attenuated the development of repetitive behavior in dams, but also in their non-enriched offspring. Moreover, maternal behavior did not seem to mediate the transgenerational effect we found, although repetitive behavior was affected by reproductive experience. These data support a beneficial transgenerational effect of EE on repetitive behavior development and suggest a novel benefit of reproductive experience. Copyright © 2016 Elsevier B.V. All rights reserved.
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Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine
Bokulich, Nicholas A.; Joseph, C. M. Lucy; Allen, Greg; Benson, Andrew K.; Mills, David A.
2012-01-01
While wine fermentation has long been known to involve complex microbial communities, the composition and role of bacteria other than a select set of lactic acid bacteria (LAB) has often been assumed either negligible or detrimental. This study served as a pilot study for using barcoded amplicon next-generation sequencing to profile bacterial community structure in wines and grape musts, comparing the taxonomic depth achieved by sequencing two different domains of prokaryotic 16S rDNA (V4 and V5). This study was designed to serve two goals: 1) to empirically determine the most taxonomically informative 16S rDNA target region for barcoded amplicon sequencing of wine, comparing V4 and V5 domains of bacterial 16S rDNA to terminal restriction fragment length polymorphism (TRFLP) of LAB communities; and 2) to explore the bacterial communities of wine fermentation to better understand the biodiversity of wine at a depth previously unattainable using other techniques. Analysis of amplicons from the V4 and V5 provided similar views of the bacterial communities of botrytized wine fermentations, revealing a broad diversity of low-abundance taxa not traditionally associated with wine, as well as atypical LAB communities initially detected by TRFLP. The V4 domain was determined as the more suitable read for wine ecology studies, as it provided greater taxonomic depth for profiling LAB communities. In addition, targeted enrichment was used to isolate two species of Alphaproteobacteria from a finished fermentation. Significant differences in diversity between inoculated and uninoculated samples suggest that Saccharomyces inoculation exerts selective pressure on bacterial diversity in these fermentations, most notably suppressing abundance of acetic acid bacteria. These results determine the bacterial diversity of botrytized wines to be far higher than previously realized, providing further insight into the fermentation dynamics of these wines, and demonstrate the utility of next
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Laser and gas centrifuge enrichment
NASA Astrophysics Data System (ADS)
Heinonen, Olli
2014-05-01
Principles of uranium isotope enrichment using various laser and gas centrifuge techniques are briefly discussed. Examples on production of high enriched uranium are given. Concerns regarding the possibility of using low end technologies to produce weapons grade uranium are explained. Based on current assessments commercial enrichment services are able to cover the global needs of enriched uranium in the foreseeable future.
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The bacterial community of entomophilic nematodes and host beetles.
Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L
2016-05-01
Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment. © 2016 John Wiley & Sons Ltd.
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Houdijk, A P; Nijveldt, R J; van Leeuwen, P A
1999-01-01
Recently we have shown that glutamine-enriched enteral nutrition in trauma patients reduced the occurrence of pneumonia, bacteremia, and sepsis. In that study, no clear explanation for these results was found except for lower tumor necrosis factor (TNF)-soluble receptors, suggesting immunomodulation. Here we present data on the course of endocrine and metabolic plasma mediators that were analyzed to provide more insight into the working mechanism of glutamine. Endocrine and metabolic mediators were measured in plasma samples taken on admission (day 0) and on days 1, 2, 3, 7, and 10. Glucose, prealbumin, albumin, alanine, C-reactive protein, alpha1-antitrypsin, complement factors, cortisol, glucagon, insulin, and growth hormone were assessed by standard techniques. The rate of feeding, demography, and injury severity did not differ between the glutamine and control group. There was a sustained hyperglycemic response in both groups. Insulin levels rose in the second phase of the period of observation. A moderate cortisol and glucagon response was seen in both groups. There was no alteration in growth hormone levels in either group. C-reactive protein, alpha1-antitrypsin, and complement factors showed similar increases in both groups but levels remained in the normal range. The course of alanine, albumin, and prealbumin also showed no difference between the groups. Glutamine-enriched enteral nutrition had no influence on the endocrine and metabolic response in trauma patients. Therefore, the reduction in infectious morbidity seen in glutamine-supplemented trauma patients is most likely not explained by a modulation of the humoral stress response and its metabolic consequences.
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Chronic nitrate enrichment decreases severity and induces protection against an infectious disease.
Smallbone, Willow; Cable, Jo; Maceda-Veiga, Alberto
2016-05-01
Excessive fertilisation is one of the most pernicious forms of global change resulting in eutrophication. It has major implications for disease control and the conservation of biodiversity. Yet, the direct link between nutrient enrichment and disease remains largely unexplored. Here, we present the first experimental evidence that chronic nitrate enrichment decreases severity and induces protection against an infectious disease. Specifically, this study shows that nitrate concentrations ranging between 50 and 250mgNO3(-)/l reduce Gyrodactylus turnbulli infection intensity in two populations of Trinidadian guppies Poecilia reticulata, and that the highest nitrate concentration can even clean the parasites from the fish. This added to the fact that host nitrate pre-exposure altered the fish epidermal structure and reduced parasite intensity, suggests that nitrate protected the host against the disease. Nitrate treatments also caused fish mortality. As we used ecologically-relevant nitrate concentrations, and guppies are top-consumers widely used for mosquito bio-control in tropical and often nutrient-enriched waters, our results can have major ecological and social implications. In conclusion, this study advocates reducing nitrate level including the legislative threshold to protect the aquatic biota, even though this may control an ectoparasitic disease. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Novel division level bacterial diversity in a Yellowstone hot spring.
Hugenholtz, P; Pitulle, C; Hershberger, K L; Pace, N R
1998-01-01
A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal diversity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609-1613, 1994). Small-subunit rRNA genes (rDNA) were amplified directly from OP sediment DNA by PCR with universally conserved or Bacteria-specific rDNA primers and cloned. Unique rDNA types among > 300 clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (> or = 98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial divisions (main phyla; kingdoms); 30% were unaffiliated with recognized bacterial divisions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, division level lineages termed candidate divisions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen-oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio and Thermodesulfobacterium, or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing delta-Proteobacteria. The occurrence of such organisms is consistent with the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of amplified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These
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NASA Astrophysics Data System (ADS)
Wu, Yucheng; Zeng, Jun; Zhu, Qinghe; Zhang, Zhenfa; Lin, Xiangui
2017-01-01
Acidification and pollution are two major threats to agricultural ecosystems; however, microbial community responses to co-existed soil acidification and pollution remain less explored. In this study, arable soils of broad pH (4.26-8.43) and polycyclic aromatic hydrocarbon (PAH) gradients (0.18-20.68 mg kg-1) were collected from vegetable farmlands. Bacterial community characteristics including abundance, diversity and composition were revealed by quantitative PCR and high-throughput sequencing. The bacterial 16S rRNA gene copies significantly correlated with soil carbon and nitrogen contents, suggesting the control of nutrients accessibility on bacterial abundance. The bacterial diversity was strongly related to soil pH, with higher diversity in neutral samples and lower in acidic samples. Soil pH was also identified by an ordination analysis as important factor shaping bacterial community composition. The relative abundances of some dominant phyla varied along the pH gradient, and the enrichment of a few phylotypes suggested their adaptation to low pH condition. In contrast, at the current pollution level, PAH showed marginal effects on soil bacterial community. Overall, these findings suggest pH was the primary determinant of bacterial community in these arable soils, indicative of a more substantial influence of acidification than PAH pollution on bacteria driven ecological processes.
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Metallization of bacterial cellulose for electrical and electronic device manufacture
Evans, Barbara R [Oak Ridge, TN; O'Neill, Hugh M [Knoxville, TN; Jansen, Valerie Malyvanh [Memphis, TN; Woodward, Jonathan [Knoxville, TN
2011-06-07
A method for the deposition of metals in bacterial cellulose and for the employment of the metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The method for impregnating bacterial cellulose with a metal comprises placing a bacterial cellulose matrix in a solution of a metal salt such that the metal salt is reduced to metallic form and the metal precipitates in or on the matrix. The method for the construction of a fuel cell comprises placing a hydrated bacterial cellulose support structure in a solution of a metal salt such that the metal precipitates in or on the support structure, inserting contact wires into two pieces of the metal impregnated support structure, placing the two pieces of metal impregnated support structure on opposite sides of a layer of hydrated bacterial cellulose, and dehydrating the three layer structure to create a fuel cell.
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Metallization of bacterial cellulose for electrical and electronic device manufacture
Evans, Barbara R [Oak Ridge, TN; O'Neill, Hugh M [Knoxville, TN; Jansen, Valerie Malyvanh [Memphis, TN; Woodward, Jonathan [Knoxville, TN
2010-09-28
A method for the deposition of metals in bacterial cellulose and for the employment of the metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The method for impregnating bacterial cellulose with a metal comprises placing a bacterial cellulose matrix in a solution of a metal salt such that the metal salt is reduced to metallic form and the metal precipitates in or on the matrix. The method for the construction of a fuel cell comprises placing a hydrated bacterial cellulose support structure in a solution of a metal salt such that the metal precipitates in or on the support structure, inserting contact wires into two pieces of the metal impregnated support structure, placing the two pieces of metal impregnated support structure on opposite sides of a layer of hydrated bacterial cellulose, and dehydrating the three layer structure to create a fuel cell.
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Mainardi, Marco; Di Garbo, Angelo; Caleo, Matteo; Berardi, Nicoletta; Sale, Alessandro; Maffei, Lamberto
2013-01-01
Brain aging is characterized by global changes which are thought to underlie age-related cognitive decline. These include variations in brain activity and the progressive increase in the concentration of soluble amyloid-β (Aβ) oligomers, directly impairing synaptic function and plasticity even in the absence of any neurodegenerative disorder. Considering the high social impact of the decline in brain performance associated to aging, there is an urgent need to better understand how it can be prevented or contrasted. Lifestyle components, such as social interaction, motor exercise and cognitive activity, are thought to modulate brain physiology and its susceptibility to age-related pathologies. However, the precise functional and molecular factors that respond to environmental stimuli and might mediate their protective action again pathological aging still need to be clearly identified. To address this issue, we exploited environmental enrichment (EE), a reliable model for studying the effect of experience on the brain based on the enhancement of cognitive, social and motor experience, in aged wild-type mice. We analyzed the functional consequences of EE on aged brain physiology by performing in vivo local field potential (LFP) recordings with chronic implants. In addition, we also investigated changes induced by EE on molecular markers of neural plasticity and on the levels of soluble Aβ oligomers. We report that EE induced profound changes in the activity of the primary visual and auditory cortices and in their functional interaction. At the molecular level, EE enhanced plasticity by an upward shift of the cortical excitation/inhibition balance. In addition, EE reduced brain Aβ oligomers and increased synthesis of the Aβ-degrading enzyme neprilysin. Our findings strengthen the potential of EE procedures as a non-invasive paradigm for counteracting brain aging processes. PMID:24478697
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Mainardi, Marco; Di Garbo, Angelo; Caleo, Matteo; Berardi, Nicoletta; Sale, Alessandro; Maffei, Lamberto
2014-01-01
Brain aging is characterized by global changes which are thought to underlie age-related cognitive decline. These include variations in brain activity and the progressive increase in the concentration of soluble amyloid-β (Aβ) oligomers, directly impairing synaptic function and plasticity even in the absence of any neurodegenerative disorder. Considering the high social impact of the decline in brain performance associated to aging, there is an urgent need to better understand how it can be prevented or contrasted. Lifestyle components, such as social interaction, motor exercise and cognitive activity, are thought to modulate brain physiology and its susceptibility to age-related pathologies. However, the precise functional and molecular factors that respond to environmental stimuli and might mediate their protective action again pathological aging still need to be clearly identified. To address this issue, we exploited environmental enrichment (EE), a reliable model for studying the effect of experience on the brain based on the enhancement of cognitive, social and motor experience, in aged wild-type mice. We analyzed the functional consequences of EE on aged brain physiology by performing in vivo local field potential (LFP) recordings with chronic implants. In addition, we also investigated changes induced by EE on molecular markers of neural plasticity and on the levels of soluble Aβ oligomers. We report that EE induced profound changes in the activity of the primary visual and auditory cortices and in their functional interaction. At the molecular level, EE enhanced plasticity by an upward shift of the cortical excitation/inhibition balance. In addition, EE reduced brain Aβ oligomers and increased synthesis of the Aβ-degrading enzyme neprilysin. Our findings strengthen the potential of EE procedures as a non-invasive paradigm for counteracting brain aging processes.
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Zrafi-Nouira, Ines; Guermazi, Sonda; Chouari, Rakia; Safi, Nimer M D; Pelletier, Eric; Bakhrouf, Amina; Saidane-Mosbahi, Dalila; Sghir, Abdelghani
2009-07-01
The indigenous microbiota of polluted coastal seawater in Tunisia was enriched by increasing the concentration of zarzatine crude oil. The resulting adapted microbiota was incubated with zarzatine crude oil as the only carbon and energy source. Crude oil biodegradation capacity and bacterial population dynamics of the microbiota were evaluated every week for 28 days (day 7, day 14, day 21, and day 28). Results show that the percentage of petroleum degradation was 23.9, 32.1, 65.3, and 77.8%, respectively. At day 28, non-aromatic and aromatic hydrocarbon degradation rates reached 92.6 and 68.7%, respectively. Bacterial composition of the adapted microflora was analysed by 16S rRNA gene cloning and sequencing, using total genomic DNA extracted from the adapted microflora at days 0, 7, 14, 21, and 28. Five clone libraries were constructed and a total of 430 sequences were generated and grouped into OTUs using the ARB software package. Phylogenetic analysis of the adapted microbiota shows the presence of four phylogenetic groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Diversity indices show a clear decrease in bacterial diversity of the adapted microflora according to the incubation time. The Proteobacteria are the most predominant (>80%) at day 7, day 14 and day 21 but not at day 28 for which the microbiota was reduced to only one OTU affiliated with the genus Kocuria of the Actinobacteria. This study shows that the degradation of zarzatine crude oil components depends on the activity of a specialized and dynamic seawater consortium composed of different phylogenetic taxa depending on the substrate complexity.
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Kimer, Nina; Pedersen, Julie S; Tavenier, Juliette; Christensen, Jeffrey E; Busk, Troels M; Hobolth, Lise; Krag, Aleksander; Al-Soud, Waleed Abu; Mortensen, Martin S; Sørensen, Søren J; Møller, Søren; Bendtsen, Flemming
2018-01-01
Decompensated cirrhosis is characterized by disturbed hemodynamics, immune dysfunction, and high risk of infections. Translocation of viable bacteria and bacterial products from the gut to the blood is considered a key driver in this process. Intestinal decontamination with rifaximin may reduce bacterial translocation (BT) and decrease inflammation. A randomized, placebo-controlled trial investigated the effects of rifaximin on inflammation and BT in decompensated cirrhosis. Fifty-four out-patients with cirrhosis and ascites were randomized, mean age 56 years (± 8.4), and model for end-stage liver disease score 12 (± 3.9). Patients received rifaximin 550-mg BD (n = 36) or placebo BD (n = 18). Blood and fecal (n = 15) sampling were conducted at baseline and after 4 weeks. Bacterial DNA in blood was determined by real-time qPCR 16S rRNA gene quantification. Bacterial composition in feces was analyzed by 16S rRNA gene sequencing. Circulating markers of inflammation, including tumor necrosis factor alpha, interleukins 6, 10, and 18, stromal cell-derived factor 1-α, transforming growth factor β-1, and high sensitivity C-reactive protein, were unaltered by rifaximin treatment. Rifaximin altered abundance of bacterial taxa in blood marginally, only a decrease in Pseudomonadales was observed. In feces, rifaximin decreased bacterial richness, but effect on particular species was not observed. Subgroup analyses on patients with severely disturbed hemodynamics (n = 34) or activated lipopolysaccharide binding protein (n = 37) revealed no effect of rifaximin. Four weeks of treatment with rifaximin had no impact on the inflammatory state and only minor effects on BT and intestinal bacterial composition in stable, decompensated cirrhosis (NCT01769040). © 2017 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.
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New potentials for conventional aircraft when powered by hydrogen-enriched gasoline
NASA Technical Reports Server (NTRS)
Menard, W. A.; Moynihan, P. I.; Rupe, J. H.
1976-01-01
Hydrogen enrichment for aircraft piston engines is studied. The feasibility is examined of inflight injection of hydrogen in general aviation aircraft engines to reduce fuel consumption and to lower emission levels. Results are summarized.
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Responses of soil Collembola to long-term atmospheric CO2 enrichment in a mature temperate forest.
Xu, Guo-Liang; Fu, Sheng-Lei; Schleppi, Patrick; Li, Mai-He
2013-02-01
Responses of Collembola to 7 years of CO(2) enrichment (550 ppm) in a Swiss free-air CO(2) enrichment (FACE) experiment in a forest with 80- to 120-year-old trees were investigated in this study. Contrary to our expectations, increased CO(2) caused a significant decrease in Collembola numbers, including a significant decrease in euedaphic Collembola. Increased CO(2), however, did not affect community group richness. Collembola biomass was not significantly changed by CO(2) enrichment, regardless of whether it was considered in terms of the total community, life-strategy groups, or individual species (with an exception of Mesaphorura krausbaueri). The reason for this is that CO(2) enrichment caused a general increase in individual body size, which compensated for reduced abundances. The results are consistent with the idea that the rhizosphere is important for soil fauna, and the combination of reduced fine root growth and increased soil moisture might trigger a reduction in Collembola abundance. Copyright © 2012 Elsevier Ltd. All rights reserved.
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Luo, Gang; Angelidaki, Irini
2014-09-01
The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier
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The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes.
Hu, Yongfei; Yang, Xi; Li, Jing; Lv, Na; Liu, Fei; Wu, Jun; Lin, Ivan Y C; Wu, Na; Weimer, Bart C; Gao, George F; Liu, Yulan; Zhu, Baoli
2016-11-15
Horizontally acquired antibiotic resistance genes (ARGs) in bacteria are highly mobile and have been ranked as principal risk resistance determinants. However, the transfer network of the mobile resistome and the forces driving mobile ARG transfer are largely unknown. Here, we present the whole profile of the mobile resistome in 23,425 bacterial genomes and explore the effects of phylogeny and ecology on the recent transfer (≥99% nucleotide identity) of mobile ARGs. We found that mobile ARGs are mainly present in four bacterial phyla and are significantly enriched in Proteobacteria The recent mobile ARG transfer network, which comprises 703 bacterial species and 16,859 species pairs, is shaped by the bacterial phylogeny, while an ecological barrier also exists, especially when interrogating bacteria colonizing different human body sites. Phylogeny is still a driving force for the transfer of mobile ARGs between farm animals and the human gut, and, interestingly, the mobile ARGs that are shared between the human and animal gut microbiomes are also harbored by diverse human pathogens. Taking these results together, we suggest that phylogeny and ecology are complementary in shaping the bacterial mobile resistome and exert synergistic effects on the development of antibiotic resistance in human pathogens. The development of antibiotic resistance threatens our modern medical achievements. The dissemination of antibiotic resistance can be largely attributed to the transfer of bacterial mobile antibiotic resistance genes (ARGs). Revealing the transfer network of these genes in bacteria and the forces driving the gene flow is of great importance for controlling and predicting the emergence of antibiotic resistance in the clinic. Here, by analyzing tens of thousands of bacterial genomes and millions of human and animal gut bacterial genes, we reveal that the transfer of mobile ARGs is mainly controlled by bacterial phylogeny but under ecological constraints. We also found
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The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes
Hu, Yongfei; Yang, Xi; Li, Jing; Lv, Na; Liu, Fei; Wu, Jun; Lin, Ivan Y. C.; Wu, Na; Gao, George F.
2016-01-01
ABSTRACT Horizontally acquired antibiotic resistance genes (ARGs) in bacteria are highly mobile and have been ranked as principal risk resistance determinants. However, the transfer network of the mobile resistome and the forces driving mobile ARG transfer are largely unknown. Here, we present the whole profile of the mobile resistome in 23,425 bacterial genomes and explore the effects of phylogeny and ecology on the recent transfer (≥99% nucleotide identity) of mobile ARGs. We found that mobile ARGs are mainly present in four bacterial phyla and are significantly enriched in Proteobacteria. The recent mobile ARG transfer network, which comprises 703 bacterial species and 16,859 species pairs, is shaped by the bacterial phylogeny, while an ecological barrier also exists, especially when interrogating bacteria colonizing different human body sites. Phylogeny is still a driving force for the transfer of mobile ARGs between farm animals and the human gut, and, interestingly, the mobile ARGs that are shared between the human and animal gut microbiomes are also harbored by diverse human pathogens. Taking these results together, we suggest that phylogeny and ecology are complementary in shaping the bacterial mobile resistome and exert synergistic effects on the development of antibiotic resistance in human pathogens. IMPORTANCE The development of antibiotic resistance threatens our modern medical achievements. The dissemination of antibiotic resistance can be largely attributed to the transfer of bacterial mobile antibiotic resistance genes (ARGs). Revealing the transfer network of these genes in bacteria and the forces driving the gene flow is of great importance for controlling and predicting the emergence of antibiotic resistance in the clinic. Here, by analyzing tens of thousands of bacterial genomes and millions of human and animal gut bacterial genes, we reveal that the transfer of mobile ARGs is mainly controlled by bacterial phylogeny but under ecological
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Environmental Enrichment Duration Differentially Affects Behavior and Neuroplasticity in Adult Mice.
Leger, Marianne; Paizanis, Eleni; Dzahini, Kwamivi; Quiedeville, Anne; Bouet, Valentine; Cassel, Jean-Christophe; Freret, Thomas; Schumann-Bard, Pascale; Boulouard, Michel
2015-11-01
Environmental enrichment is a powerful way to stimulate brain and behavioral plasticity. However the required exposure duration to reach such changes has not been substantially analyzed. We aimed to assess the time-course of appearance of the beneficial effects of enriched environment. Thus, different behavioral tests and neurobiological parameters (such as neurogenesis, brain monoamines levels, and stress-related hormones) were concomitantly realized after different durations of enriched environment (24 h, 1, 3, or 5 weeks). While short enrichment exposure (24 h) was sufficient to improve object recognition memory performances, a 3-week exposure was required to improve aversive stimulus-based memory performances and to reduce anxiety-like behavior; effects that were not observed with longer duration. The onset of behavioral changes after a 3-week exposure might be supported by higher serotonin levels in the frontal cortex, but seems independent of neurogenesis phenomenon. Additionally, the benefit of 3-week exposure on memory was not observed 3 weeks after cessation of enrichment. Thus, the 3-week exposure appears as an optimal duration in order to induce the most significant behavioral effects and to assess the underlying mechanisms. Altogether, these results suggest that the duration of exposure is a keystone of the beneficial behavioral and neurobiological effects of environmental enrichment. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Spatial organization shapes the turnover of a bacterial transcriptome
Moffitt, Jeffrey R; Pandey, Shristi; Boettiger, Alistair N; Wang, Siyuan; Zhuang, Xiaowei
2016-01-01
Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Time-resolved RNA-sequencing revealed that degradation rates of inner-membrane-protein mRNAs are on average greater that those of the other mRNAs and that this selective destabilization of inner-membrane-protein mRNAs is abolished by dissociating the RNA degradosome from the membrane. Together, these results demonstrate that the bacterial transcriptome is spatially organized and suggest that this organization shapes the post-transcriptional dynamics of mRNAs. DOI: http://dx.doi.org/10.7554/eLife.13065.001 PMID:27198188
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Kozlowsky-Suzuki, B; Bozelli, R L
2002-11-01
Non-treated sewage disposal is one of the main impacts to which Imboassica Lagoon has been subjected. The aim of this study was to evaluate the effect of a potential increase in the artificial enrichment on the environmental conditions and zooplankton of this system. To this end, an experimental study was conducted in mesocosms where nutrients were added daily. Bacterial numbers, chlorophyll-a, and picoplanktonic cyanobacteria densities showed an increase with the availability of nutrients. Bacterio- and phytoplankton seemed to be regulated by the rotifers Brachionus rotundiformis and Hexarthra brandorffi.
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Radiological analysis of plutonium glass batches with natural/enriched boron
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rainisch, R.
2000-06-22
The disposition of surplus plutonium inventories by the US Department of Energy (DOE) includes the immobilization of certain plutonium materials in a borosilicate glass matrix, also referred to as vitrification. This paper addresses source terms of plutonium masses immobilized in a borosilicate glass matrix where the glass components include both natural boron and enriched boron. The calculated source terms pertain to neutron and gamma source strength (particles per second), and source spectrum changes. The calculated source terms corresponding to natural boron and enriched boron are compared to determine the benefits (decrease in radiation source terms) for to the use ofmore » enriched boron. The analysis of plutonium glass source terms shows that a large component of the neutron source terms is due to (a, n) reactions. The Americium-241 and plutonium present in the glass emit alpha particles (a). These alpha particles interact with low-Z nuclides like B-11, B-10, and O-17 in the glass to produce neutrons. The low-Z nuclides are referred to as target particles. The reference glass contains 9.4 wt percent B{sub 2}O{sub 3}. Boron-11 was found to strongly support the (a, n) reactions in the glass matrix. B-11 has a natural abundance of over 80 percent. The (a, n) reaction rates for B-10 are lower than for B-11 and the analysis shows that the plutonium glass neutron source terms can be reduced by artificially enriching natural boron with B-10. The natural abundance of B-10 is 19.9 percent. Boron enriched to 96-wt percent B-10 or above can be obtained commercially. Since lower source terms imply lower dose rates to radiation workers handling the plutonium glass materials, it is important to know the achievable decrease in source terms as a result of boron enrichment. Plutonium materials are normally handled in glove boxes with shielded glass windows and the work entails both extremity and whole-body exposures. Lowering the source terms of the plutonium batches will
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Jean-Gilles Beaubrun, Junia; Flamer, Marie-Laure; Addy, Nicole; Ewing, Laura; Gopinath, Gopal; Jarvis, Karen; Grim, Chris; Hanes, Darcy E
2016-08-01
Phenolic compounds associated with essential oils of spices and herbs possess a variety of antioxidant and antimicrobial properties that interfere with Salmonella detection from fresh and dried products. Finding a compound to neutralize the effect of these antimicrobial compounds, while allowing Salmonella growth during pre-enrichment, is a crucial step in both traditional pathogen isolation and molecular detection from these foods. This study evaluated the effectiveness of corn oil as a component of the pre-enrichment broth to counteract antimicrobial compounds properties and increase the recovery of Salmonella from spices. Oregano samples artificially contaminated with Salmonella enterica were pre-enriched in modified Buffered Peptone Water (mBPW) supplemented with and without 2% (vol/vol) corn oil respectively. Samples were incubated overnight at 37 °C. The results showed that recovery of Salmonella from oregano samples was increased by ≥50% when pre-enriched with corn oil. Serovars were confirmed using a PCR serotyping method. In addition, shot-gun metagenomics analyses demonstrated bacterial diversity and the effect of corn oil on the relative prevalence of Salmonella in the oregano samples. Modifying pre-enrichment broths with corn oil improved the detection and isolation of Salmonella from oregano, and may provide an alternative method for pathogen detection in dried food matrices such as spices. Published by Elsevier Ltd.
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Kuehn, Joanna S.; Gorden, Patrick J.; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J.; Wang, Chong; Phillips, Gregory J.
2013-01-01
Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1–V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease. PMID:23634219
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Selective enrichment of a methanol-utilizing consortium using pulp & paper mill waste streams
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gregory R. Mockos; William A. Smith; Frank J. Loge
Efficient utilization of carbon inputs is critical to the economic viability of the current forest products sector. Input carbon losses occur in various locations within a pulp mill, including losses as volatile organics and wastewater . Opportunities exist to capture this carbon in the form of value-added products such as biodegradable polymers. Waste activated sludge from a pulp mill wastewater facility was enriched for 80 days for a methanol-utilizing consortium with the goal of using this consortium to produce biopolymers from methanol-rich pulp mill waste streams. Five enrichment conditions were utilized: three high-methanol streams from the kraft mill foul condensatemore » system, one methanol-amended stream from the mill wastewater plant, and one methanol-only enrichment. Enrichment reactors were operated aerobically in sequencing batch mode at neutral pH and 25°C with a hydraulic residence time and a solids retention time of four days. Non-enriched waste activated sludge did not consume methanol or reduce chemical oxygen demand. With enrichment, however, the chemical oxygen demand reduction over 24 hour feed/decant cycles ranged from 79 to 89 %, and methanol concentrations dropped below method detection limits. Neither the non-enriched waste activated sludge nor any of the enrichment cultures accumulated polyhydroxyalkanoates (PHAs) under conditions of nitrogen sufficiency. Similarly, the non-enriched waste activated sludge did not accumulate PHAs under nitrogen limited conditions. By contrast, enriched cultures accumulated PHAs to nearly 14% on a dry weight basis under nitrogen limited conditions. This indicates that selectively-enriched pulp mill waste activated sludge can serve as an inoculum for PHA production from methanol-rich pulp mill effluents.« less
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Eichorst, Stephanie A.
2012-01-01
Many bacteria and fungi are known to degrade cellulose in culture, but their combined response to cellulose in different soils is unknown. Replicate soil microcosms amended with [13C]cellulose were used to identify bacterial and fungal communities responsive to cellulose in five geographically and edaphically different soils. The diversity and composition of the cellulose-responsive communities were assessed by DNA-stable isotope probing combined with Sanger sequencing of small-subunit and large-subunit rRNA genes for the bacterial and fungal communities, respectively. In each soil, the 13C-enriched, cellulose-responsive communities were of distinct composition compared to the original soil community or 12C-nonenriched communities. The composition of cellulose-responsive taxa, as identified by sequence operational taxonomic unit (OTU) similarity, differed in each soil. When OTUs were grouped at the bacterial order level, we found that members of the Burkholderiales, Caulobacteriales, Rhizobiales, Sphingobacteriales, Xanthomonadales, and the subdivision 1 Acidobacteria were prevalent in the 13C-enriched DNA in at least three of the soils. The cellulose-responsive fungi were identified as members of the Trichocladium, Chaetomium, Dactylaria, and Arthrobotrys genera, along with two novel Ascomycota clusters, unique to one soil. Although similarities were identified in higher-level taxa among some soils, the composition of cellulose-responsive bacteria and fungi was generally unique to a certain soil type, suggesting a strong potential influence of multiple edaphic factors in shaping the community. PMID:22287013
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The paradox of enrichment in phytoplankton by induced competitive interactions
Tubay, Jerrold M.; Ito, Hiromu; Uehara, Takashi; Kakishima, Satoshi; Morita, Satoru; Togashi, Tatsuya; Tainaka, Kei-ichi; Niraula, Mohan P.; Casareto, Beatriz E.; Suzuki, Yoshimi; Yoshimura, Jin
2013-01-01
The biodiversity loss of phytoplankton with eutrophication has been reported in many aquatic ecosystems, e.g., water pollution and red tides. This phenomenon seems similar, but different from the paradox of enrichment via trophic interactions, e.g., predator-prey systems. We here propose the paradox of enrichment by induced competitive interactions using multiple contact process (a lattice Lotka-Volterra competition model). Simulation results demonstrate how eutrophication invokes more competitions in a competitive ecosystem resulting in the loss of phytoplankton diversity in ecological time. The paradox is enhanced under local interactions, indicating that the limited dispersal of phytoplankton reduces interspecific competition greatly. Thus, the paradox of enrichment appears when eutrophication destroys an ecosystem either by elevated interspecific competition within a trophic level and/or destabilization by trophic interactions. Unless eutrophication due to human activities is ceased, the world's aquatic ecosystems will be at risk. PMID:24089056
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Investigating the feasibility of stem cell enrichment mediated by immobilized selectins.
Charles, Nichola; Liesveld, Jane L; King, Michael R
2007-01-01
Hematopoietic stem cell therapy is used to treat both malignant and non-malignant diseases, and enrichment of the hematopoietic stem and progenitor cells (HSPCs) has the potential to reduce the likelihood of graft vs host disease or relapse, potentially fatal complications associated with the therapy. Current commercial HSPC isolation technologies rely solely on the CD34 surface marker, and while they have proven to be invaluable, they can be time-consuming with variable recoveries reported. We propose that selectin-mediated enrichment could prove to be a quick and effective method for recovering HSPCs from adult bone marrow (ABM) on the basis of differences in rolling velocities and independently of CD34 expression. Purified CD34+ ABM cells and the unselected CD34- ABM cells were perfused over immobilized P-, E-, and L-selectin-IgG at physiologic wall shear stresses, and rolling velocities and cell retention data were collected. CD34+ ABM cells generally exhibited lower rolling velocities and higher retention than the unselected CD34- ABM cells on all three selectins. For initial CD34+ ABM cell concentrations ranging from 1% to 5%, we predict an increase in purity ranging from 5.2% to 36.1%, depending on the selectin used. Additionally, selectin-mediated cell enrichment is not limited to subsets of cells with inherent differences in rolling velocities. CD34+ KG1a cells and CD34- HL60 cells exhibited nearly identical rolling velocities on immobilized P-selectin-IgG over the entire range of shear stresses studied. However, when anti-CD34 antibody was co-immobilized with the P-selectin-IgG, the rolling velocity of the CD34+ KG1a cells was significantly reduced, making selectin-mediated cell enrichment a feasible option. Optimal cell enrichment in immobilized selectin surfaces can be achieved within 10 min, much faster than most current commercially available systems.
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Impact of Environmental Enrichment Devices on NTP In Vivo Studies
Churchill, Sheba R.; Morgan, Daniel L.; Kissling, Grace E.; Travlos, Gregory S.; King-Herbert, Angela P.
2015-01-01
The goal of this study was to determine whether the use of nesting material or polycarbonate shelters, as enrichment devices would have an impact on endpoints commonly measured during the conduct of the National Toxicology Program (NTP) 13-week studies. The study design was consistent with the NTP 13-week toxicity studies. Harlan Sprague Dawley (HSD) rats and their offspring, and B6C3F1/N mice were assigned to control (unenriched) and enriched experimental groups. Body weight, food and water consumption, behavioral observations, fecal content, clinical pathology, gross pathology, organ weights, and histopathology were evaluated. Enriched male mice and male and female rats exhibited decreased feed intake without a subsequent decrease in body weight; this may have been the result of the nesting material reducing the effect of cold stress thereby allowing for more efficient use of feed. There were statistical differences in some hematological parameters, however these were not considered physiologically relevant since all values were within the normal range. Gross pathology and histopathological findings were background changes and were not considered enrichment-related. Nesting material and shelters were used frequently and consistently and allowed animals to display species typical behavior. There was no significant impact on commonly measured endpoints in HSD rats and B6C3F1/N mice given enrichment devices. PMID:26873679
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Hemovigilance monitoring of platelet septic reactions with effective bacterial protection systems.
Benjamin, Richard J; Braschler, Thomas; Weingand, Tina; Corash, Laurence M
2017-12-01
Delayed, large-volume bacterial culture and amotosalen/ultraviolet-A light pathogen reduction are effective at reducing the risk of bacterial proliferation in platelet concentrates (PCs). Hemovigilance programs continue to receive reports of suspected septic transfusion reactions, most with low imputability. Here, we compile national hemovigilance data to determine the relative efficacy of these interventions. Annual reports from the United Kingdom, France, Switzerland, and Belgium were reviewed between 2005 and 2016 to assess the risk of bacterial contamination and septic reactions. Approximately 1.65 million delayed, large-volume bacterial culture-screened PCs in the United Kingdom and 2.3 million amotosalen/ultraviolet-A-treated PCs worldwide were issued with no reported septic fatalities. One definite, one possible, and 12 undetermined/indeterminate septic reactions and eight contaminated "near misses" were reported with delayed, large-volume bacterial cultures between 2011 and 2016, for a lower false-negative culture rate than that in the previous 5 years (5.4 vs. 16.3 per million: odds ratio, 3.0; 95% confidence interval, 1.4-6.5). Together, the Belgian, Swiss, and French hemovigilance programs documented zero probable or definite/certain septic reactions with 609,290 amotosalen/ultraviolet-A-treated PCs (<1.6 per million). The rates were significantly lower than those reported with concurrently transfused, nonpathogen-reduced PCs in Belgium (<4.4 vs. 35.6 per million: odds ratio, 8.1; 95% confidence interval,1.1-353.3) and with historic septic reaction rates in Switzerland (<6.0 vs. 82.9 per million: odds ratio, 13.9; 95% confidence interval, 2.1-589.2), and the rates tended to be lower than those from concurrently transfused, nonpathogen-reduced PCs in France (<4.7 vs. 19.0 per million: odds ratio, 4.1; 95% confidence interval, 0.7-164.3). Pathogen reduction and bacterial culture both reduced the incidence of septic reactions, although under-reporting and
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Justice, N. B.; Sczesnak, A.; Hazen, T. C.; ...
2017-08-04
A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Justice, N. B.; Sczesnak, A.; Hazen, T. C.
A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection
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Gill, Bradley C; Shoskes, Daniel A
2016-02-01
The review provides the infectious disease community with a urologic perspective on bacterial prostatitis. Specifically, the article briefly reviews the categorization of prostatitis by type and provides a distillation of new findings published on bacterial prostatitis over the past year. It also highlights key points from the established literature. Cross-sectional prostate imaging is becoming more common and may lead to more incidental diagnoses of acute bacterial prostatitis. As drug resistance remains problematic in this condition, the reemergence of older antibiotics such as fosfomycin, has proven beneficial. With regard to chronic bacterial prostatitis, no clear clinical risk factors emerged in a large epidemiological study. However, bacterial biofilm formation has been associated with more severe cases. Surgery has a limited role in bacterial prostatitis and should be reserved for draining of a prostatic abscess or the removal of infected prostatic stones. Prostatitis remains a common and bothersome clinical condition. Antibiotic therapy remains the basis of treatment for both acute and chronic bacterial prostatitis. Further research into improving prostatitis treatment is indicated.
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Saalfield, Samantha L; Bostick, Benjamin C
2009-12-01
Biologically mediated redox processes have been shown to affect the mobility of iron oxide-bound arsenic in reducing aquifers. This work investigates how dissimilatory sulfate reduction and secondary iron reduction affect sulfur, iron, and arsenic speciation. Incubation experiments were conducted with As(III/V)-bearing ferrihydrite in carbonate-buffered artificial groundwater enriched with lactate (10 mM) and sulfate (0.08-10 mM) and inoculated with Desulfovibrio vulgaris (ATCC 7757, formerly D. desulfuricans), which reduces sulfate but not iron or arsenic. Sulfidization of ferrihydrite led to formation of magnetite, elemental sulfur, and trace iron sulfides. Observed reaction rates imply that the majority of sulfide is recycled to sulfate, promoting microbial sulfate reduction in low-sulfate systems. Despite dramatic changes in Fe and S speciation, and minimal formation of Fe or As sulfides, most As remained in the solid phase. Arsenic was not solubilized in As(V)-loaded incubations, which experienced slow As reduction by sulfide, whereas As(III)-loaded incubations showed limited and transient As release associated with iron remineralization. This suggests that As(III) production is critical to As release under reducing conditions, with sulfate reduction alone unlikely to release As. These data also suggest that bacterial reduction of As(V) is necessary for As sequestration in sulfides, even where sulfate reduction is active.
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Augustin, Jean-Christophe; Kalmokoff, Martin; Ells, Timothy; Favret, Sandra; Desreumaux, Jennifer; Decourseulles Brasseur, Emilie; Gnanou Besse, Nathalie
2016-12-01
A stochastic model describing the growth of Listeria monocytogenes during enrichment in half Fraser was developed for the purpose of estimating the effects of modifications to the first enrichment step of the EN ISO 11290-1 detection method. Information pertaining to the variability of growth rates, physiological state of the cell, and the behavior of individual cells contaminating the food were obtained from previously published studies. We used this model to investigate the impact of pooling enrichment broths (wet pooling) on the performance of the standard method. For validation of the model, the numbers of L. monocytogenes occurring in 88 naturally contaminated foods following pre-enrichment were compared to model-simulated microbial counts. The model was then used to perform simulations representative of the natural contamination observed for smoked salmon in the European baseline survey of 2010-2011. The model-estimated L. monocytogenes levels following individual enrichment or following the pooling of five broths where only one would be contaminated were compared. The model indicated a 10% loss of method sensitivity resulting from wet pooling. The model also predicted a 5% decrease in the sensitivity of the method when the duration of the enrichment was reduced from 24 to 22 h. Copyright © 2016 Elsevier Ltd. All rights reserved.
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NASA Technical Reports Server (NTRS)
2004-01-01
Data shows that elevated sialidase in bacterial vaginosis patients correlates to premature births in women. Bacterial sialidase also plays a significant role in the unusual colonization of Pseudomonas aeruginosa in cystic fibrosis patients. Crystals of Salmonella sialidase have been reproduced and are used for studying the inhibitor-enzyme complexes. These inhibitors may also be used to inhibit a trans-sialidase of Trypanosome cruzi, a very similar enzyme to bacterial sialidase, therefore preventing T. cruzi infection, the causitive agent of Chagas' disease. The Center for Macromolecular Crystallography suggests that inhibitors of bacterial sialidases can be used as prophylactic drugs to prevent bacterial infections in these critical cases.
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Prevalence of gastrointestinal bacterial pathogens in a population of zoo animals.
Stirling, J; Griffith, M; Blair, I; Cormican, M; Dooley, J S G; Goldsmith, C E; Glover, S G; Loughrey, A; Lowery, C J; Matsuda, M; McClurg, R; McCorry, K; McDowell, D; McMahon, A; Cherie Millar, B; Nagano, Y; Rao, J R; Rooney, P J; Smyth, M; Snelling, W J; Xu, J; Moore, J E
2008-04-01
Faecal prevalence of gastrointestinal bacterial pathogens, including Campylobacter, Escherichia coli O157:H7, Salmonella, Shigella, Yersinia, as well as Arcobacter, were examined in 317 faecal specimens from 44 animal species in Belfast Zoological Gardens, during July-September 2006. Thermophilic campylobacters including Campylobacter jejuni, Campylobacter coli and Campylobacter lari, were the most frequently isolated pathogens, where members of this genus were isolated from 11 animal species (11 of 44; 25%). Yersinia spp. were isolated from seven animal species (seven of 44; 15.9%) and included, Yersinia enterocolitica (five of seven isolates; 71.4%) and one isolate each of Yersinia frederiksenii and Yersinia kristensenii. Only one isolate of Salmonella was obtained throughout the entire study, which was an isolate of Salmonella dublin (O 1,9,12: H g, p), originating from tiger faeces after enrichment. None of the animal species found in public contact areas of the zoo were positive for any gastrointestinal bacterial pathogens. Also, water from the lake in the centre of the grounds, was examined for the same bacterial pathogens and was found to contain C. jejuni. This study is the first report on the isolation of a number of important bacterial pathogens from a variety of novel host species, C. jejuni from the red kangaroo (Macropus rufus), C. lari from a maned wolf (Chrysocyon brachyurus), Y. kristensenii from a vicugna (Vicugna vicugna) and Y. enterocolitica from a maned wolf and red panda (Ailurus fulgens). In conclusion, this study demonstrated that the faeces of animals in public contact areas of the zoo were not positive for the bacterial gastrointestinal pathogens examined. This is reassuring for the public health of visitors, particularly children, who enjoy this educational and recreational resource.
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Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations
Chopyk, Jessica; Allard, Sarah; Nasko, Daniel J.; Bui, Anthony; Mongodin, Emmanuel F.; Sapkota, Amy R.
2018-01-01
Agricultural ponds have a great potential as a means of capture and storage of water for irrigation. However, pond topography (small size, shallow depth) leaves them susceptible to environmental, agricultural, and anthropogenic exposures that may influence microbial dynamics. Therefore, the aim of this project was to characterize the bacterial and viral communities of pond water in the Mid-Atlantic United States with a focus on the late season (October–December), where decreasing temperature and nutrient levels can affect the composition of microbial communities. Ten liters of freshwater from an agricultural pond were sampled monthly, and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, and the bacterial communities were characterized using 16S rRNA gene sequencing. The remaining filtrate was chemically concentrated for viruses, DNA-extracted, and shotgun sequenced. Bacterial community profiling showed significant fluctuations over the sampling period, corresponding to changes in the condition of the pond freshwater (e.g., pH, nutrient load). In addition, there were significant differences in the alpha-diversity and core bacterial operational taxonomic units (OTUs) between water fractions filtered through different pore sizes. The viral fraction was dominated by tailed bacteriophage of the order Caudovirales, largely those of the Siphoviridae family. Moreover, while present, genes involved in virulence/antimicrobial resistance were not enriched within the viral fraction during the study period. Instead, the viral functional profile was dominated by phage associated proteins, as well as those related to nucleotide production. Overall, these data suggest that agricultural pond water harbors a diverse core of bacterial and bacteriophage species whose abundance and composition are influenced by environmental variables characteristic of pond topology and the late season. PMID:29740420
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Singh, Madhu; Singh, Dileep Kumar
2014-01-30
Three bacterial strains identified as Klebsiella sp. M3, Achromobacter sp. M6 and Rhodococcus sp. M2 were isolated by soil enrichment with endosulfan followed by shake flask enrichment technique. They were efficiently degrading endosulfan in the NSM (non sulfur medium) broth. Degradation of endosulfan was faster with the cell free extract of bacterial cells grown in the sulfur deficient medium (NSM) supplemented with endosulfan than that of nutrient rich medium (Luria Bertani). In the cell free extract of NSM supplemented with endosulfan as sole sulfur source, a unique band was visualized on SDS-PAGE but not with magnesium sulfate as the sole sulfur source in NSM and LB with endosulfan. Expression of a unique polypeptide band was speculated to be induced by endosulfan under sulfur starved condition. These unique polypeptide bands were identified as OmpK35 protein, sulfate binding protein and outer membrane porin protein, respectively, in Klebsiella sp. M3, Achromobacter sp. M6 and Rhodococcus sp. M2. Endosulfan showed dose dependent negative effect on total RNA yield of bacterial strains in nutrient rich medium. Absence of plasmid DNA indicated the presence of endosulfan metabolizing gene on genomic DNA. Copyright © 2013 Elsevier B.V. All rights reserved.
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Kamke, Janine; Soni, Priya; Li, Yang; Ganesh, Siva; Kelly, William J; Leahy, Sinead C; Shi, Weibing; Froula, Jeff; Rubin, Edward M; Attwood, Graeme T
2017-08-08
Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH 4 /kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep. KEGG genes enriched in high methane yield sheep were reassembled from raw reads and existing contigs and analysed by MEGAN to predict their phylogenetic origin. Protein coding sequences from Succinivibrio dextrinosolvens strains were analysed using Effective DB to predict bacterial type III secreted proteins. The effect of S. dextrinosolvens strain H5 growth on methane formation by rumen methanogens was explored using co-cultures. Detailed analysis of the rumen microbiomes of high methane yield sheep shows that gene and transcript abundances of bacterial type III secretion system genes are positively correlated with methane yield in sheep. Most of the bacterial type III secretion system genes could not be assigned to a particular bacterial group, but several genes were affiliated with the genus Succinivibrio, and searches of bacterial genome sequences found that strains of S. dextrinosolvens were part of a small group of rumen bacteria that encode this type of secretion system. In co-culture experiments, S. dextrinosolvens strain H5 showed a growth-enhancing effect on a methanogen belonging to the order Methanomassiliicoccales, and inhibition of a representative of the Methanobrevibacter gottschalkii clade. This is the first report of bacterial type III secretion system genes being associated with high
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Quantitative proteomic analysis of bacterial enzymes released in cheese during ripening.
Jardin, Julien; Mollé, Daniel; Piot, Michel; Lortal, Sylvie; Gagnaire, Valérie
2012-04-02
Due to increasingly available bacterial genomes in databases, proteomic tools have recently been used to screen proteins expressed by micro-organisms in food in order to better understand their metabolism in situ. While the main objective is the systematic identification of proteins, the next step will be to bridge the gap between identification and quantification of these proteins. For that purpose, a new mass spectrometry-based approach was applied, using isobaric tagging reagent for quantitative proteomic analysis (iTRAQ), which are amine specific and yield labelled peptides identical in mass. Experimental Swiss-type cheeses were manufactured from microfiltered milk using Streptococcus thermophilus ITG ST20 and Lactobacillus helveticus ITG LH1 as lactic acid starters. At three ripening times (7, 20 and 69 days), cheese aqueous phases were extracted and enriched in bacterial proteins by fractionation. Each sample, standardised in protein amount prior to proteomic analyses, was: i) analysed by 2D-electrophoresis for qualitative analysis and ii) submitted to trypsinolysis, and labelled with specific iTRAQ tag, one per ripening time. The three labelled samples were mixed together and analysed by nano-LC coupled on-line with ESI-QTOF mass spectrometer. Thirty proteins, both from bacterial or bovine origin, were identified and efficiently quantified. The free bacterial proteins detected were enzymes from the central carbon metabolism as well as stress proteins. Depending on the protein considered, the quantity of these proteins in the cheese aqueous extract increased from 2.5 to 20 fold in concentration from day 7 to day 69 of ripening. Copyright © 2012 Elsevier B.V. All rights reserved.
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Palladium-bacterial cellulose membranes for fuel cells.
Evans, Barbara R; O'Neill, Hugh M; Malyvanh, Valerie P; Lee, Ida; Woodward, Jonathan
2003-07-01
Bacterial cellulose is a versatile renewable biomaterial that can be used as a hydrophilic matrix for the incorporation of metals into thin, flexible, thermally stable membranes. In contrast to plant cellulose, we found it catalyzed the deposition of metals within its structure to generate a finely divided homogeneous catalyst layer. Experimental data suggested that bacterial cellulose possessed reducing groups capable of initiating the precipitation of palladium, gold, and silver from aqueous solution. Since the bacterial cellulose contained water equivalent to at least 200 times the dry weight of the cellulose, it was dried to a thin membranous structure suitable for the construction of membrane electrode assemblies (MEAs). Results of our study with palladium-cellulose showed that it was capable of catalyzing the generation of hydrogen when incubated with sodium dithionite and generated an electrical current from hydrogen in an MEA containing native cellulose as the polyelectrolyte membrane (PEM). Advantages of using native and metallized bacterial cellulose membranes in an MEA over other PEMs such as Nafion 117 include its higher thermal stability to 130 degrees C and lower gas crossover.
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Effect of disopyramide on bacterial diversity in drinking water
NASA Astrophysics Data System (ADS)
Wu, Qing; Zhao, Xiaofei; Tian, Qi; Wang, Lei; Zhao, Xinhua
2018-02-01
Disopyramide was detected in drinking water by LC-MS/MS and the microbial diversity was investigated by PCR and high-throughput sequencing. The results showed that bacteria community structure in drinking water changed a lot when added different concentrations of disopyramide. The results of Shannon index showed that the total number and abundance of bacterial community species in drinking water samples decreased significantly after the addition of disopyramide. However, the number and abundance of community structure did not change with the concentration of disopyramide. Disopyramide inhibits the activity of bacterial community in drinking water and also can reduce the bacterial community diversity in drinking water.
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Li, Ki Angel; Lund, Emilie Torp; Voigt, Jörg-Peter W
2016-01-01
The early postnatal period is a sensitive period in rodents as behavioural systems are developing and maturing during this time. However, relatively little information is available about the impact of environmental enrichment on offspring behaviour if enrichment is implemented only during this period. Here, environmental enrichment was provided from postnatal day 1 until weaning. On post-natal day 9, maternal behaviour and nonmaternal behaviour of the dam was observed. Nursing time in the enriched group was reduced but dams showed more non-maternal appetitive behaviours. Offspring were exposed to either the open field or the elevated plus maze (EPM) after weaning. In the open field, rats from the enriched group approached the more aversive inner zone of the open field later than control rats. Offspring from the enriched group made fewer entries into the inner zone and spent less time in this part of the arena. Enrichment had no impact on behaviour in the EPM. The present study provides evidence that postnatal enrichment can interfere with maternal behaviour in rats and can possibly lead to increased anxiety in the offspring. The findings suggest that enrichment procedures can have potentially unintended effects, interfering with the development of emotional behaviours in rats. Copyright © 2015 Elsevier B.V. All rights reserved.
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Heaney, Jennifer L J; Phillips, Anna C; Carroll, Douglas; Drayson, Mark T
2015-12-01
Bacterial infections in the elderly are common and associated with high morbidity and mortality, with pneumonia the second commonest cause of death. Reductions in antibodies against specific bacterial antigens in saliva and serum could contribute to infection risk in older adults, although they have yet to be examined in relation to age. IgG, IgA and IgM antibody levels in paired saliva and serum samples were measured against 12 pneumococcal, 4 meningococcal and haemophilus polysaccharide antigens and diphtheria and tetanus toxoids in healthy younger (n = 28, 21-34 years) and older (n = 44, 60-80 years) adults. Older adults had lower antibody concentrations in saliva than young adults, with the most striking differences observed for salivary antibody secretion rates. In serum, older adults registered lower concentrations for only a minority of antibodies. Young adults who had previously received a polysaccharide pneumococcal vaccination (PPV23) had higher levels of anti-pneumococcal antibodies in serum and in saliva. Only minor differences were observed in antibody levels between older adults who had/had not received PPV23, and there was no evidence of memory in saliva. Age differences were much greater in salivary antibodies than in serum; older adults had reduced salivary secretion rates of antibodies across bacterial antigens. This decline in local immunity may contribute to increased infection risk in the elderly. The poor memory from pneumococcal vaccination in serum and saliva suggests that PPV23 may be ineffective in older adults for both systemic and local protection. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Effects of exercise and enrichment on behaviour in CD-1 mice.
Aujnarain, Amiirah B; Luo, Owen D; Taylor, Natalie; Lai, Jonathan K Y; Foster, Jane A
2018-04-16
A host of scholarly work has characterized the positive effects of exercise and environmental enrichment on behaviour and cognition in animal studies. The purpose of this study was to investigate the uptake and longitudinal impact of exercise and enrichment on the behavioural phenotype of male and female CD-1 mice. CD-1 mice housed in standard (STD) or exercise and enrichment (EE) conditions post-weaning were tested in the 3-chamber sociability test, open field, and elevated plus maze and exercise activity was monitored throughout the enrichment protocol. Male and female EE mice both showed reduced anxiety and activity in the open field and elevated plus maze relative to sex-matched STD mice. EE altered social behaviours in a sex-specific fashion, with only female EE mice showing increased social preference relative to female STD mice and a preference for social novelty only present in male EE mice. This sexual dimorphism was not observed to be a product of exercise uptake, as CD-1 mice of both sexes demonstrated a consistent trend of wheel rotation frequencies. These findings suggest the importance of considering variables such as sex and strain on experimental design variables in future work on environmental enrichment. Copyright © 2018 Elsevier B.V. All rights reserved.
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Kumar, B; Han, L-F; Wassenaar, L I; Klaus, P M; Kainz, G G; Hillegonds, D; Brummer, D; Ahmad, M; Belachew, D L; Araguás, L; Aggarwal, P
2016-12-01
Tritium ( 3 H) in natural waters is a powerful tracer of hydrological processes, but its low concentrations require electrolytic enrichment before precise measurements can be made with a liquid scintillation counter. Here, we describe a newly developed, compact tritium enrichment unit which can be used to enrich up to 2L of a water sample. This allows a high enrichment factor (>100) for measuring low 3 H contents of <0.05TU. The TEU uses a small cell (250mL) with automated re-filling and a CO 2 bubbling technique to neutralize the high alkalinity of enriched samples. The enriched residual sample is retrieved from the cell under vacuum by cryogenic distillation at -20°C and the tritium enrichment factor for each sample is accurately determined by measuring pre- and post- enrichment 2 H concentrations with laser spectrometry. Copyright © 2016. Published by Elsevier Ltd.
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Snoeyenbos-West, O.L.; Nevin, K.P.; Anderson, R.T.; Lovely, D.R.
2000-01-01
Engineered stimulation of Fe(III) has been proposed as a strategy to enhance the immobilization of radioactive and toxic metals in metal-contaminated subsurface environments. Therefore, laboratory and field studies were conducted to determine which microbial populations would respond to stimulation of Fe(III) reduction in the sediments of sandy aquifers. In laboratory studies, the addition of either various organic electron donors or electron shuttle compounds stimulated Fe(III) reduction and resulted in Geobacter sequences becoming important constituents of the Bacterial 16S rDNA sequences that could be detected with PCR amplification and denaturing gradient gel electrophoresis (DGGE). Quantification of Geobacteraceae sequences with a PCR most-probable-number technique indicated that the extent to which numbers of Geobacter increased was related to the degree of stimulation of Fe(III) reduction. Geothrix species were also enriched in some instances, but were orders of magnitude less numerous than Geobacter species. Shewanella species were not detected, even when organic compounds known to be electron donors for Shewanella species were used to stimulate Fe(III) reduction in the sediments. Geobacter species were also enriched in two field experiments in which Fe(III) reduction was stimulated with the addition of benzoate or aromatic hydrocarbons. The apparent growth of Geobacter species concurrent with increased Fe(III) reduction suggests that Geobacter species were responsible for much of the Fe(III) reduction in all of the stimulation approaches evaluated in three geographically distinct aquifers. Therefore, strategies for subsurface remediation that involve enhancing the activity of indigenous Fe(III)-reducing populations in aquifers should consider the physiological properties of Geobacter species in their treatment design.
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Eizaguirre, I; Aldámiz, L; Aldazábal, P; García, N; Asensio, A B; Bachiller, P; García Arenzana, J M; Sanjurjo, P; Pérez Nanclares, G
2002-01-01
Alterations in the antioxidant system (AS) has been observed during total parenteral nutrition (TPN). Light exposure or changes in the composition of TPN may affect this deleterious effect. On the other hand, bacterial translocation (BT) is frequent under TPN and may be related to AS. The aim of the study was to determine the adverse effect of standard and glutamine-enriched (GE) TPN, with or without light exposure, on the AS, and its relationship to BT. Forty-nine adult Wistar rats underwent central venous cannulation and were randomly assigned to one of five groups: Sham (n = 16): chow and water ad libitum and saline i.v. TPN (n = 10): had standard TPN. TPN(-) (n = 8): standard TPN without light-exposure. GTPN (n = 8): GE TPN. GTPN(-) (n = 7): GE TPN without light exposure. After 10 days, glutation reduced (GSH) was determined in liver and kidney. Mesenteric lymph nodes, peripheral and portal blood samples were cultured for BT. Comparing to Sham rats, TPN groups had statistically significant lower GSH levels, but there were no differences between standard or GE groups nor with or without light exposure groups. Sham animals had 12% BT. Significantly higher BT (p < 0.05) was found in TPN rats: 70% in TPN group, 88% in TPN(-) group, 86% in GTPN(-) animals and only 50% in GTPN group (p = 0.06 vs TPN group). To conclude: 1. TPN reduces antioxidant capacity and induces BT. 2. Glutamine supplementation or light protection do not improve tissue antioxidant capacity under TPN. 3. Glutamine supplementation tends to reduce BT only in the presence of light. 4. Absence of light exposure does not improve BT TPN-related.
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Linking soil bacterial biodiversity and soil carbon stability.
Mau, Rebecca L; Liu, Cindy M; Aziz, Maliha; Schwartz, Egbert; Dijkstra, Paul; Marks, Jane C; Price, Lance B; Keim, Paul; Hungate, Bruce A
2015-06-01
Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.
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31 CFR 540.316 - Uranium enrichment.
Code of Federal Regulations, 2013 CFR
2013-07-01
... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process of...
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31 CFR 540.316 - Uranium enrichment.
Code of Federal Regulations, 2014 CFR
2014-07-01
... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process of...
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31 CFR 540.316 - Uranium enrichment.
Code of Federal Regulations, 2011 CFR
2011-07-01
... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process of...
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31 CFR 540.316 - Uranium enrichment.
Code of Federal Regulations, 2012 CFR
2012-07-01
... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process of...
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A short and valid measure of work-family enrichment.
Kacmar, K Michele; Crawford, Wayne S; Carlson, Dawn S; Ferguson, Merideth; Whitten, Dwayne
2014-01-01
The stream of research concerning work-family enrichment has generated a significant body of research because it plays an important role in occupational health (Masuda, McNall, Allen, & Nicklin, 2012). work-family enrichment has been defined as "the extent to which experiences in one role improve the quality of life in the other role" (Greenhaus & Powell, 2006, p. 73). Within work-family enrichment, there are two directions: work to family and family to work. Carlson, Kacmar, Wayne, and Grzywacz (2006) developed an 18-item scale to measure this construct. Although the scale has been shown to be both reliable and valid, it also requires work-family researchers to include a proportionally large number of items to capture this construct in a study. The goal of the current study was to isolate a subset of the items in this measure that produces results similar to the full version thereby providing a more streamlined scale for researchers. Using a five-sample study that follows the scale reduction procedures offered by Stanton, Sinar, Balzer, and Smith (2002), we provide evidence that scales containing only three items for each direction of enrichment produce results equivalent to the full scale with respect to reliability and discriminant, convergent, and predictive validity. Reducing the original scale by two thirds, without losing explanatory power, allows scholars to measure enrichment in the work and family domains more efficiently, which should help minimize survey time, lower refusal rates, and generate less missing data. PsycINFO Database Record (c) 2014 APA, all rights reserved.
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Carbendazim induces a temporary change in soil bacterial community structure.
Wang, Xiuguo; Song, Min; Gao, Chunming; Dong, Bin; Zhang, Qun; Fang, Hua; Yu, Yunlong
2009-01-01
The effect of carbendazim applications on the diversity and structure of a soil bacterial community was studied under field conditions using temperature gradient gel electrophoresis (TGGE) and partial sequence analysis of PCR-amplified 16S rRNA gene. After four successive introductions of carbendazim at a level of 0.94 kg active ingredient (a.i.)/ha, the genetic diversity (expressed as Shannon index, H') decreased from 1.43 in the control to 1.29 in treated soil. This harmful effect seems to increase with the concentration of carbendazim. The value of H' in the soil treated with carbendazim at 4.70 kg a.i./ha was reduced to 1.05 (P < or = 0.05). The structure of soil bacterial community was also affected after four repeated applications of carbendazim at levels of 0.94, 1.88 and 4.70 kg a.i./ha, as seen in the relative intensities of the individual band. However, the bacterial community in carbendazim-treated soil recovered to that in the control 360 d after the first treatment. The results indicated that repeated applications of carbendazim could reduce soil microbial diversity and alter the bacterial community structure temporarily.
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Pawar, Kiran D; Dar, Mudasir A; Rajput, Bharati P; Kulkarni, Girish J
2015-02-01
The cellulolytic bacterial community structure in gastrointestinal (GI) tract of Achatina fulica was studied using culture-independent and -dependent methods by enrichment in carboxymethyl cellulose (CMC). Culture-dependent method indicated that GI tract of snail was dominated by Enterobacteriaceae members. When tested for cellulase activities, all isolates obtained by culture-dependent method showed both or either of CMCase or avicelase activity. Isolate identified as Citrobacter freundii showed highest CMCase and medium avicelase activity. Sequencing of clones from the 16S rRNA gene clone library identified ten operational taxonomic units (OTUs), which were affiliated to Enterobacteriaceae of phylum Gammaproteobacteria. Of these ten OTUs, eight OTUs closely matched with Enterobacter and Klebsiella genera. The most abundant OTU allied to Klebsiella oxytoca accounted for 70 % of the total sequences. The members of Klebsiella and Enterobacter were observed by both methods indicating their dominance among the cellulolytic bacterial community in the GI tract of the snail.
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McDowell, Ian C; Nikapitiya, Chamilani; Aguiar, Derek; Lane, Christopher E; Istrail, Sorin; Gomez-Chiarri, Marta
2014-01-01
The American oyster Crassostrea virginica, an ecologically and economically important estuarine organism, can suffer high mortalities in areas in the Northeast United States due to Roseovarius Oyster Disease (ROD), caused by the gram-negative bacterial pathogen Roseovarius crassostreae. The goals of this research were to provide insights into: 1) the responses of American oysters to R. crassostreae, and 2) potential mechanisms of resistance or susceptibility to ROD. The responses of oysters to bacterial challenge were characterized by exposing oysters from ROD-resistant and susceptible families to R. crassostreae, followed by high-throughput sequencing of cDNA samples from various timepoints after disease challenge. Sequence data was assembled into a reference transcriptome and analyzed through differential gene expression and functional enrichment to uncover genes and processes potentially involved in responses to ROD in the American oyster. While susceptible oysters experienced constant levels of mortality when challenged with R. crassostreae, resistant oysters showed levels of mortality similar to non-challenged oysters. Oysters exposed to R. crassostreae showed differential expression of transcripts involved in immune recognition, signaling, protease inhibition, detoxification, and apoptosis. Transcripts involved in metabolism were enriched in susceptible oysters, suggesting that bacterial infection places a large metabolic demand on these oysters. Transcripts differentially expressed in resistant oysters in response to infection included the immune modulators IL-17 and arginase, as well as several genes involved in extracellular matrix remodeling. The identification of potential genes and processes responsible for defense against R. crassostreae in the American oyster provides insights into potential mechanisms of disease resistance.
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McDowell, Ian C.; Nikapitiya, Chamilani; Aguiar, Derek; Lane, Christopher E.; Istrail, Sorin; Gomez-Chiarri, Marta
2014-01-01
The American oyster Crassostrea virginica, an ecologically and economically important estuarine organism, can suffer high mortalities in areas in the Northeast United States due to Roseovarius Oyster Disease (ROD), caused by the gram-negative bacterial pathogen Roseovarius crassostreae. The goals of this research were to provide insights into: 1) the responses of American oysters to R. crassostreae, and 2) potential mechanisms of resistance or susceptibility to ROD. The responses of oysters to bacterial challenge were characterized by exposing oysters from ROD-resistant and susceptible families to R. crassostreae, followed by high-throughput sequencing of cDNA samples from various timepoints after disease challenge. Sequence data was assembled into a reference transcriptome and analyzed through differential gene expression and functional enrichment to uncover genes and processes potentially involved in responses to ROD in the American oyster. While susceptible oysters experienced constant levels of mortality when challenged with R. crassostreae, resistant oysters showed levels of mortality similar to non-challenged oysters. Oysters exposed to R. crassostreae showed differential expression of transcripts involved in immune recognition, signaling, protease inhibition, detoxification, and apoptosis. Transcripts involved in metabolism were enriched in susceptible oysters, suggesting that bacterial infection places a large metabolic demand on these oysters. Transcripts differentially expressed in resistant oysters in response to infection included the immune modulators IL-17 and arginase, as well as several genes involved in extracellular matrix remodeling. The identification of potential genes and processes responsible for defense against R. crassostreae in the American oyster provides insights into potential mechanisms of disease resistance. PMID:25122115
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Di Gregorio, Simona; Siracusa, Giovanna; Becarelli, Simone; Mariotti, Lorenzo; Gentini, Alessandro; Lorenzi, Roberto
2016-06-01
Seven hydrocarbonoclastic new bacterial isolates were isolated from dredged sediments of a river estuary in Italy. The sediments were contaminated by shipyard activities since decades, mainly ascribable to the exploitation of diesel oil as the fuel for recreational and commercial navigation of watercrafts. The bacterial isolates were able to utilize diesel oil as sole carbon source. Their metabolic capacities were evaluated by GC-MS analysis, with reference to the depletion of both the normal and branched alkanes, the nC18 fatty acid methyl ester and the unresolved complex mixture of organic compounds. They were taxonomically identified as different species of Stenotrophomonas and Pseudomonas spp. by the combination of amplified ribosomal DNA restriction analysis (ARDRA) and repetitive sequence-based PCR (REP-PCR) analysis. The metabolic activities of interest were analyzed both in relation to the single bacterial strains and to the combination of the latter as a multibacterial species system. After 6 days of incubation in mineral medium with diesel oil as sole carbon source, the Stenotrophomonas sp. M1 strain depleted 43-46 % of Cn-alkane from C28 up to C30, 70 % of the nC18 fatty acid methyl ester and the 46 % of the unresolved complex mixture of organic compounds. On the other hand, the Pseudomonas sp. NM1 strain depleted the 76 % of the nC18 fatty acid methyl ester, the 50 % of the unresolved complex mixture of organic compounds. The bacterial multispecies system was able to completely deplete Cn-alkane from C28 up to C30 and to deplete the 95 % of the unresolved complex mixture of organic compounds. The isolates, either as single strains and as a bacterial multispecies system, were proposed as candidates for bioaugmentation in bio-based processes for the decontamination of dredged sediments.
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Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS
Tominski, Claudia; Kappler, Andreas; Behrens, Sebastian
2016-01-01
Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458–1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochrome c system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochrome c and multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration. PMID:26896135
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Wu, Yucheng; Zeng, Jun; Zhu, Qinghe; Zhang, Zhenfa; Lin, Xiangui
2017-01-01
Acidification and pollution are two major threats to agricultural ecosystems; however, microbial community responses to co-existed soil acidification and pollution remain less explored. In this study, arable soils of broad pH (4.26–8.43) and polycyclic aromatic hydrocarbon (PAH) gradients (0.18–20.68 mg kg−1) were collected from vegetable farmlands. Bacterial community characteristics including abundance, diversity and composition were revealed by quantitative PCR and high-throughput sequencing. The bacterial 16S rRNA gene copies significantly correlated with soil carbon and nitrogen contents, suggesting the control of nutrients accessibility on bacterial abundance. The bacterial diversity was strongly related to soil pH, with higher diversity in neutral samples and lower in acidic samples. Soil pH was also identified by an ordination analysis as important factor shaping bacterial community composition. The relative abundances of some dominant phyla varied along the pH gradient, and the enrichment of a few phylotypes suggested their adaptation to low pH condition. In contrast, at the current pollution level, PAH showed marginal effects on soil bacterial community. Overall, these findings suggest pH was the primary determinant of bacterial community in these arable soils, indicative of a more substantial influence of acidification than PAH pollution on bacteria driven ecological processes. PMID:28051171
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Uhlik, Ondrej; Musilova, Lucie; Ridl, Jakub; Hroudova, Miluse; Vlcek, Cestmir; Koubek, Jiri; Holeckova, Marcela; Mackova, Martina; Macek, Tomas
2013-10-01
The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites
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Acute Bacterial Prostatitis: Diagnosis and Management.
Coker, Timothy J; Dierfeldt, Daniel M
2016-01-15
Acute bacterial prostatitis is an acute infection of the prostate gland that causes pelvic pain and urinary tract symptoms, such as dysuria, urinary frequency, and urinary retention, and may lead to systemic symptoms, such as fevers, chills, nausea, emesis, and malaise. Although the true incidence is unknown, acute bacterial prostatitis is estimated to comprise approximately 10% of all cases of prostatitis. Most acute bacterial prostatitis infections are community acquired, but some occur after transurethral manipulation procedures, such as urethral catheterization and cystoscopy, or after transrectal prostate biopsy. The physical examination should include abdominal, genital, and digital rectal examination to assess for a tender, enlarged, or boggy prostate. Diagnosis is predominantly made based on history and physical examination, but may be aided by urinalysis. Urine cultures should be obtained in all patients who are suspected of having acute bacterial prostatitis to determine the responsible bacteria and its antibiotic sensitivity pattern. Additional laboratory studies can be obtained based on risk factors and severity of illness. Radiography is typically unnecessary. Most patients can be treated as outpatients with oral antibiotics and supportive measures. Hospitalization and broad-spectrum intravenous antibiotics should be considered in patients who are systemically ill, unable to voluntarily urinate, unable to tolerate oral intake, or have risk factors for antibiotic resistance. Typical antibiotic regimens include ceftriaxone and doxycycline, ciprofloxacin, and piperacillin/tazobactam. The risk of nosocomial bacterial prostatitis can be reduced by using antibiotics, such as ciprofloxacin, before transrectal prostate biopsy.
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[Clinical, epidemiological and microbiological aspects of Mobiluncus sp. in bacterial vaginosis].
Menolascina, A; Nieves, B; Velazco, E; Rivero, N; Calderas, Z
1999-05-01
In this paper, our goal was to determine the optimal isolation conditions, biochemical characterization, and preservation of species of the genus Mobiluncus, associated with bacterial vaginosis in patients attending the family planning clinic. Also, we tried to relate its presence with demographic variables and criteria used in the clinical diagnosis of bacterial diagnosis. The specimen from the posterior fornix were collected and transported to the laboratory in a Stuart medium, one at room temperature and the other at 4 degrees C. These samples were inoculated in anaerobic culture media. Of a total of 92 patients studied, 61 (66.3%) were normal, 28 (30.4%) bacterial vaginosis, and 3 (3.3%) had intermediate vaginosis. There was statistically significant relationship only with intrauterine device use (p = 0.00499). The presence of curved rod, using Gram's method, was significantly related with pH (p = 0.00000) positive amines test (p = 0.00000), and the presence of clue cells (p = 0.00000). Mobiluncus was observed in 23 samples (82%), and the majority (15) using RLK agar (cold enrichment technique). With conventional techniques, we identified 12 strains as Mobiluncus curtisii and 3 strains as Mobiluncus mulieris. The strains of Mobiluncus sp. grew better from litmus milk conserved at -30 degrees C. Isolating Mobiluncus sp. is fairly easy, if the right media and the techniques are used.
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Use of Natural Antimicrobial Peptides and Bacterial Biopolymers for Cultured Pearl Production
Simon-Colin, Christelle; Gueguen, Yannick; Bachere, Evelyne; Kouzayha, Achraf; Saulnier, Denis; Gayet, Nicolas; Guezennec, Jean
2015-01-01
Cultured pearls are the product of grafting and rearing of Pinctada margaritifera pearl oysters in their natural environment. Nucleus rejections and oyster mortality appear to result from bacterial infections or from an inappropriate grafting practice. To reduce the impact of bacterial infections, synthetic antibiotics have been applied during the grafting practice. However, the use of such antibiotics presents a number of problems associated with their incomplete biodegradability, limited efficacy in some cases, and an increased risk of selecting for antimicrobial resistant bacteria. We investigated the application of a marine antimicrobial peptide, tachyplesin, which is present in the Japanese horseshoe crab Tachypleus tridentatus, in combination with two marine bacterial exopolymers as alternative treatment agents. In field studies, the combination treatment resulted in a significant reduction in graft failures vs. untreated controls. The combination of tachyplesin (73 mg/L) with two bacterial exopolysaccharides (0.5% w/w) acting as filming agents, reduces graft-associated bacterial contamination. The survival data were similar to that reported for antibiotic treatments. These data suggest that non-antibiotic treatments of pearl oysters may provide an effective means of improving oyster survival following grafting procedures. PMID:26110895
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Kumar, Amit; Thotakura, Pragna Lakshmi; Tiwary, Basant Kumar; Krishna, Ramadas
2016-05-12
Fusobacterium nucleatum, a well studied bacterium in periodontal diseases, appendicitis, gingivitis, osteomyelitis and pregnancy complications has recently gained attention due to its association with colorectal cancer (CRC) progression. Treatment with berberine was shown to reverse F. nucleatum-induced CRC progression in mice by balancing the growth of opportunistic pathogens in tumor microenvironment. Intestinal microbiota imbalance and the infections caused by F. nucleatum might be regulated by therapeutic intervention. Hence, we aimed to predict drug target proteins in F. nucleatum, through subtractive genomics approach and host-pathogen protein-protein interactions (HP-PPIs). We also carried out enrichment analysis of host interacting partners to hypothesize the possible mechanisms involved in CRC progression due to F. nucleatum. In subtractive genomics approach, the essential, virulence and resistance related proteins were retrieved from RefSeq proteome of F. nucleatum by searching against Database of Essential Genes (DEG), Virulence Factor Database (VFDB) and Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) tool respectively. A subsequent hierarchical screening to identify non-human homologous, metabolic pathway-independent/pathway-specific and druggable proteins resulted in eight pathway-independent and 27 pathway-specific druggable targets. Co-aggregation of F. nucleatum with host induces proinflammatory gene expression thereby potentiates tumorigenesis. Hence, proteins from IBDsite, a database for inflammatory bowel disease (IBD) research and those involved in colorectal adenocarcinoma as interpreted from The Cancer Genome Atlas (TCGA) were retrieved to predict drug targets based on HP-PPIs with F. nucleatum proteome. Prediction of HP-PPIs exhibited 186 interactions contributed by 103 host and 76 bacterial proteins. Bacterial interacting partners were accounted as putative targets. And enrichment analysis of host interacting partners showed statistically
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21 CFR 137.165 - Enriched flour.
Code of Federal Regulations, 2011 CFR
2011-04-01
... 21 Food and Drugs 2 2011-04-01 2011-04-01 false Enriched flour. 137.165 Section 137.165 Food and... Related Products § 137.165 Enriched flour. Enriched flour conforms to the definition and standard of.... Enriched flour may be acidified with monocalcium phosphate within the limits prescribed by § 137.175 for...
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21 CFR 137.165 - Enriched flour.
Code of Federal Regulations, 2012 CFR
2012-04-01
... 21 Food and Drugs 2 2012-04-01 2012-04-01 false Enriched flour. 137.165 Section 137.165 Food and... Related Products § 137.165 Enriched flour. Enriched flour conforms to the definition and standard of.... Enriched flour may be acidified with monocalcium phosphate within the limits prescribed by § 137.175 for...
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21 CFR 137.165 - Enriched flour.
Code of Federal Regulations, 2014 CFR
2014-04-01
... 21 Food and Drugs 2 2014-04-01 2014-04-01 false Enriched flour. 137.165 Section 137.165 Food and... Related Products § 137.165 Enriched flour. Enriched flour conforms to the definition and standard of.... Enriched flour may be acidified with monocalcium phosphate within the limits prescribed by § 137.175 for...
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21 CFR 137.165 - Enriched flour.
Code of Federal Regulations, 2013 CFR
2013-04-01
... 21 Food and Drugs 2 2013-04-01 2013-04-01 false Enriched flour. 137.165 Section 137.165 Food and... Related Products § 137.165 Enriched flour. Enriched flour conforms to the definition and standard of.... Enriched flour may be acidified with monocalcium phosphate within the limits prescribed by § 137.175 for...
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NASA Astrophysics Data System (ADS)
Favalli, A.; Lombardi, M.; MacArthur, D. W.; McCluskey, C.; Moss, C. E.; Paffett, M. T.; Ianakiev, K. D.
2018-01-01
Improving the quality of safeguards measurements at Gas Centrifuge Enrichment Plants while reducing the inspection effort is an important objective given the number of existing and new plants that need to be safeguarded. A useful tool in many safeguards approaches is the on-line monitoring of enrichment in process pipes. One requirement of such a monitor is a simple, reliable and precise passive measurement of the 186-keV line from 235U. The other information required is the amount of gas in the pipe, which can be obtained by a transmission or pressure measurement. We describe our research to develop such a passive measurement system. Unfortunately, a complication arises in the interpretation of the gamma measurements, from the contribution of uranium deposits on the wall of the pipe to the 186-keV peak. A multi-detector approach to address this complication is presented where two measurements, one with signal primarily from gas and one with signal primarily from deposits, are performed simultaneously with different detectors and geometries. This allows a correction to be made to the 186-keV peak for the contribution from the deposit. We present the design of the multi-detector system and the results of the experimental calibration of the proof-of-principle prototype built at LANL.
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Urinary tract infections and bacterial prostatitis in men.
Wagenlehner, Florian M E; Weidner, Wolfgang; Pilatz, Adrian; Naber, Kurt G
2014-02-01
The purpose of this review is to highlight advances in research on urinary tract infections (UTIs) and bacterial prostatitis in men in the preceding year. The antiseptic properties of the prostate secretions might be an important factor for prevention of recurrency. Risk factors for UTI in men include prostate enlargement and urological interventions, such as transrectal prostate biopsy. Preventive treatment of prostate enlargement has been demonstrated to reduce frequency of UTI. Ensuing infections after prostate biopsy, such as UTI and bacterial prostatitis, are increasing due to increasing rates of fluoroquinolone resistance. The increasing global antibiotic resistance also significantly affects management of UTI in men, and therefore calls for alternative strategies.Apart from prevention of complicating factors leading to UTI, a more thorough understanding of the pathophysiology may play a more important role in the future, to define new targets for treatment. Interesting results that might interfere with the intracellular mucosal bacterial load in the bladder wall have been found in the last years. UTI in men and bacterial prostatitis are currently underrepresented in the medical literature. Increasing antibacterial resistance calls for novel strategies in the prevention and management of UTI and bacterial prostatitis in men.
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Contribution of Progranulin to Protective Lung Immunity During Bacterial Pneumonia.
Zou, Shan; Luo, Qin; Song, Zhixin; Zhang, Liping; Xia, Yun; Xu, Huajian; Xiang, Yu; Yin, Yibing; Cao, Ju
2017-06-01
Progranulin (PGRN) is an important immunomodulatory factor in a variety of inflammatory diseases. However, its role in pulmonary immunity against bacterial infection remains unknown. Pneumonia was induced in PGRN-deficient and normal wild-type mice using Pseudomonas aeruginosa or Staphylococcus aureus, and we assessed the effects of PGRN on survival, bacterial burden, cytokine and chemokine production, and pulmonary leukocyte recruitment after bacterial pneumonia. Patients with community-acquired pneumonia displayed elevated PGRN levels. Likewise, mice with Gram-negative and Gram-positive pneumonia had increased PGRN production in the lung and circulation. Progranulin deficiency led to increased bacterial growth and dissemination accompanied by enhanced lung injury and mortality in bacterial pneumonia, which was associated with impaired recruitment of macrophages and neutrophils in the lung. The reduced number of pulmonary macrophages and neutrophils observed in PGRN-deficient mice was related to a reduction of CCL2 and CXCL1 in the lungs after bacterial pneumonia. Importantly, therapeutic administration of PGRN improved mortality in severe bacterial pneumonia. This study supports a novel role for PGRN in pulmonary immunity and suggests that treatment with PGRN may be a viable therapy for bacterial pneumonia. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.
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Spontaneous bacterial peritonitis
Koulaouzidis, Anastasios; Bhat, Shivaram; Saeed, Athar A
2009-01-01
Since its initial description in 1964, research has transformed spontaneous bacterial peritonitis (SBP) from a feared disease (with reported mortality of 90%) to a treatable complication of decompensated cirrhosis, albeit with steady prevalence and a high recurrence rate. Bacterial translocation, the key mechanism in the pathogenesis of SBP, is only possible because of the concurrent failure of defensive mechanisms in cirrhosis. Variants of SBP should be treated. Leucocyte esterase reagent strips have managed to shorten the ‘tap-to-shot’ time, while future studies should look into their combined use with ascitic fluid pH. Third generation cephalosporins are the antibiotic of choice because they have a number of advantages. Renal dysfunction has been shown to be an independent predictor of mortality in patients with SBP. Albumin is felt to reduce the risk of renal impairment by improving effective intravascular volume, and by helping to bind pro-inflammatory molecules. Following a single episode of SBP, patients should have long-term antibiotic prophylaxis and be considered for liver transplantation. PMID:19266595
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Smalla, K.; Wieland, G.; Buchner, A.; Zock, A.; Parzy, J.; Kaiser, S.; Roskot, N.; Heuer, H.; Berg, G.
2001-01-01
The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae, field-grown strawberry (Fragaria ananassa Duch.), oilseed rape (Brassica napus L.), and potato (Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands. PMID:11571180
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Variations and heredity in bacterial colonies
Čepl, Jaroslav; Blahůšková, Anna; Neubauer, Zdeněk; Markoš, Anton
2016-01-01
ABSTRACT Spontaneous variation in appearance was studied in bacterial colonies of Serratia marcescens F morphotype1: (i) A defined array of non-heritable phenotype variations does appear repeatedly; (ii) The presence of colonies of different bacterial species will narrow the variability toward the typical F appearance, as if such an added environmental factor curtailed the capacity of colony morphospace; (iii) Similarly the morphospace becomes reduced by random mutations leading to new, heritable morphotypes—at the same time opening a new array of variations typical for the mutant but not accessible directly from the original F morphospace. Results are discussed in context with biphasic model of early morphogenesis applicable to all multicellular bodies. PMID:28042382
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Jiang, Tieshan; Mandal, Rabindra K.; Wideman, Robert F.; Khatiwara, Anita; Pevzner, Igal; Min Kwon, Young
2015-01-01
Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in