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Sample records for culturable bacterial populations

  1. Optimization of conditions for profiling bacterial populations in food by culture-independent methods.

    PubMed

    Cocolin, Luca; Diez, Ana; Urso, Rosalinda; Rantsiou, Kalliopi; Comi, Giuseppe; Bergmaier, Ingrid; Beimfohr, Claudia

    2007-11-30

    In this study we used culture-independent methods to profile bacterial populations in food products. Denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) were employed in order to identify bacterial species without the need of isolation and biochemical identification. The protocols used to extract the DNA, subsequently subjected to PCR amplification for DGGE, as well as the hybridization procedure for FISH, were optimised. Moreover, an extensive study on the primers and probes to be used for the direct detection and identification of microorganisms commonly found in food, was carried out. Meat and cheese samples, fresh or processed, were subjected to DGGE and FISH analysis and the results obtained highlighted how the processing in food industry is decreasing the bacterial biodiversity. Not only processed cheese or meat but also fermented products were dominated by only one or few species. Lactobacillus sakei, Lactobacillus curvatus and Brochothrix thermosphacta were the main species found in meat products, while in cheese(s) Lactococcus lactis, Streptococcus thermophilus and Leuconostoc spp. were repeatedly detected. The results obtained by the two culture-independent methods used always correlated well.

  2. Bacterial Wound Culture

    MedlinePlus

    ... and services. Advertising & Sponsorship: Policy | Opportunities Bacterial Wound Culture Share this page: Was this page helpful? Also known as: Aerobic Wound Culture; Anaerobic Wound Culture Formal name: Culture, wound Related ...

  3. Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting.

    PubMed

    Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

    2008-04-01

    A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment

  4. The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations

    PubMed Central

    2014-01-01

    Background Bacterial habitats, such as soil and the gut, are structured at the micrometer scale. Important aspects of microbial life in such spatial ecosystems are migration and colonization. Here we explore the colonization of a structured ecosystem by two neutrally labeled strains of Escherichia coli. Using time-lapse microscopy we studied the colonization of one-dimensional arrays of habitat patches linked by connectors, which were invaded by the two E. coli strains from opposite sides. Results The two strains colonize a habitat from opposite sides by a series of traveling waves followed by an expansion front. When population waves collide, they branch into a continuing traveling wave, a reflected wave and a stationary population. When the two strains invade the landscape from opposite sides, they remain segregated in space and often one population will displace the other from most of the habitat. However, when the strains are co-cultured before entering the habitats, they colonize the habitat together and do not separate spatially. Using physically separated, but diffusionally coupled, habitats we show that colonization waves and expansion fronts interact trough diffusible molecules, and not by direct competition for space. Furthermore, we found that colonization outcome is influenced by a culture’s history, as the culture with the longest doubling time in bulk conditions tends to take over the largest fraction of the habitat. Finally, we observed that population distributions in parallel habitats located on the same device and inoculated with cells from the same overnight culture are significantly more similar to each other than to patterns in identical habitats located on different devices inoculated with cells from different overnight cultures, even tough all cultures were started from the same −80°C frozen stock. Conclusions We found that the colonization of spatially structure habitats by two interacting populations can lead to the formation of

  5. Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

    PubMed Central

    Ryall, Ben; Eydallin, Gustavo

    2012-01-01

    Summary: Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior. PMID:22933562

  6. Response of the rumen archaeal and bacterial populations to anti-methanogenic organosulphur compounds in continuous-culture fermenters.

    PubMed

    Martínez-Fernández, Gonzalo; Abecia, Leticia; Martín-García, A Ignacio; Ramos-Morales, Eva; Denman, Stuart E; Newbold, Charles J; Molina-Alcaide, Eduarda; Yáñez-Ruiz, David R

    2015-08-01

    Study of the efficacy of methanogenesis inhibitors in the rumen has given inconsistent results, mainly due to poorly understood effects on the key microbial groups involved in pathways for methane (CH4) synthesis. The experiment described in this report was designed to assess the effect of propyl propane thiosulfinate (PTS), diallyl disulfide (DDS) and bromochloromethane (BCM) on rumen fermentation, methane production and microbial populations in continuous culture fermenters. No effects on total volatile fatty acids (VFA) were observed with PTS or DDS, but VFA were decreased with BCM. Amylase activity increased with BCM as compared with the other treatments. A decrease in methane production was observed with PTS (48%) and BCM (94%) as compared with control values. The concentration of methanogenic archaea decreased with BCM from day 4 onward and with PTS on days 4 and 8. Pyrosequencing analysis revealed that PTS and BCM decreased the relative abundance of Methanomicrobiales and increased that of Methanobrevibacter and Methanosphaera. The total concentration of bacteria was not modified by any treatment, although treatment with BCM increased the relative abundance of Prevotella and decreased that of Ruminococcus. These results suggest that the inhibition of methane production in the rumen by PTS and BCM is associated with a shift in archaeal biodiversity and changes in the bacterial community with BCM.

  7. The reductive dechlorination of 2,3,4,5-tetrachlorobiphenyl in three different sediment cultures: evidence for the involvement of phylogenetically similar Dehalococcoides-like bacterial populations.

    PubMed

    Yan, Tao; LaPara, Timothy M; Novak, Paige J

    2006-02-01

    Anaerobic cultures capable of reductively dechlorinating 2,3,4,5-tetrachlorobiphenyl (CB) were enriched from three different sediments, one estuarine, one marine and one riverine. Two different electron donors were used in enrichments with the estuarine sediment (elemental iron or a mixture of fatty acids). The removal of doubly flanked meta and para chlorines to form 2,3,5-CB and 2,4,5-CB was observed in all cultures. Bacterial community analysis of PCR-amplified 16S rRNA gene fragments revealed different communities in these cultures, with the exception of one common population that showed a high phylogentic relatedness to Dehalococcoides species. No Dehalococcoides-like populations were ever detected in control cultures to which no PCBs were added. In addition, the dynamics of this Dehalococcoides-like population were strongly correlated with dechlorination. Subcultures of the estuarine sediment culture demonstrated that the Dehalococcoides-like population disappeared when dechlorination was inhibited with 2-bromoethanesulfonate or when 2,3,4,5-CB had been consumed. These results provide evidence that Dehalococcoides-like populations were involved in the removal of doubly flanked chlorines from 2,3,4,5-CB. Furthermore, the successful enrichment of these populations from geographically distant and geochemically distinct environments indicates the widespread presence of these PCB-dechlorinating, Dehalococcoides-like organisms.

  8. Bacterial computing with engineered populations.

    PubMed

    Amos, Martyn; Axmann, Ilka Maria; Blüthgen, Nils; de la Cruz, Fernando; Jaramillo, Alfonso; Rodriguez-Paton, Alfonso; Simmel, Friedrich

    2015-07-28

    We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell-cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research.

  9. HRT dependent performance and bacterial community population of granular hydrogen-producing mixed cultures fed with galactose.

    PubMed

    Kumar, Gopalakrishnan; Sivagurunathan, Periyasamy; Park, Jeong-Hoon; Park, Jong-Hun; Park, Hee-Deung; Yoon, Jeong-Jun; Kim, Sang-Hyoun

    2016-04-01

    The effects of hydraulic retention times (HRTs-6, 3 and 2 h) on H2 production, operational stability and bacterial population response in a continuously stirred tank reactor (CSTR) were evaluated using galactose. A peak hydrogen production rate (HPR) of 25.9 L H2/L-d was obtained at a 3 h HRT with an organic loading rate (OLR) of 120 g/L-d, while the maximum hydrogen yield (HY) of 2.21 mol H2/mol galactose was obtained at a 6 h HRT (60 g galactose/L-d). Butyrate was dominant and the lactate concentration increased as HRT decreased, which significantly affected the HY. Biomass concentration (VSS) decreased from 16 to 3g/L at a 2 h HRT, leading to failure. A 3 h HRT supported the favorable growth of Clostridium species, as indicated by an increase in their populations from 25.4% to 27%, while significantly reducing Bacilli populations from 61.6% to 54.2%, indicating that this was the optimal condition.

  10. Bacterial population autowave patterns: spontaneous symmetry bursting

    NASA Astrophysics Data System (ADS)

    Medvinsky, A. B.; Tsyganov, M. A.; Karpov, V. A.; Kresteva, I. B.; Shakhbazian, V. Yu.; Ivanitsky, G. R.

    1994-12-01

    Bacteria are known to form autowave patterns (population waves) like those formed by propagating nerve impulses, phase transitions, concentration waves in the Belousov-Zhabotinsky reaction, etc. The formation of bacterial waves is due to the ability of bacteria to drift (through chemotaxis) into the regions with higher attractant concentration. As a result, in contrast to other types of autowaves, bacterial population waves have not only a diffusion component of a bacterial flow but a chemotaxis flow as well. We present the experimental results of the study of spontaneous symmetry loss of bacterial autowave patterns. We show that this phenomenon can be simulated with a simple cellular automata model, and symmetry bursting depends on the parameters characterizing chemotactic sensitivity and motility of the cells forming the population wave. In the experiments in vivo we show that the distortion of a bacterial wave shape can be initiated by bacterial density fluctuations in the parent population that the bacterial waves flake off from.

  11. Bacterial Populations Associated with Smokeless Tobacco Products

    PubMed Central

    Han, Jing; Sanad, Yasser M.; Deck, Joanna; Sutherland, John B.; Li, Zhong; Walters, Matthew J.; Duran, Norma; Holman, Matthew R.

    2016-01-01

    ABSTRACT There are an estimated 8 million users of smokeless tobacco products (STPs) in the United States, and yet limited data on microbial populations within these products exist. To better understand the potential microbiological risks associated with STP use, a study was conducted to provide a baseline microbiological profile of STPs. A total of 90 samples, representing 15 common STPs, were purchased in metropolitan areas in Little Rock, AR, and Washington, DC, in November 2012, March 2013, and July 2013. Bacterial populations were evaluated using culture, pyrosequencing, and denaturing gradient gel electrophoresis (DGGE). Moist-snuff products exhibited higher levels of bacteria (average of 1.05 × 106 CFU/g STP) and diversity of bacterial populations than snus (average of 8.33 × 101 CFU/g STP) and some chewing tobacco products (average of 2.54 × 105 CFU/g STP). The most common species identified by culturing were Bacillus pumilus, B. licheniformis, B. safensis, and B. subtilis, followed by members of the genera Oceanobacillus, Staphylococcus, and Tetragenococcus. Pyrosequencing analyses of the 16S rRNA genes identified the genera Tetragenococcus, Carnobacterium, Lactobacillus, Geobacillus, Bacillus, and Staphylococcus as the predominant taxa. Several species identified are of possible concern due to their potential to cause opportunistic infections and reported abilities to reduce nitrates to nitrites, which may be an important step in the formation of carcinogenic tobacco-specific N′-nitrosamines. This report provides a microbiological baseline to help fill knowledge gaps associated with microbiological risks of STPs and to inform potential regulations regarding manufacture and testing of STPs. IMPORTANCE It is estimated that there 8 million users of smokeless tobacco products (STPs) in the United States; however, there are limited data on microbial populations that exist within these products. The current study was undertaken to better understand the

  12. Differential resistance of drinking water bacterial populations to monochloramine disinfection.

    PubMed

    Chiao, Tzu-Hsin; Clancy, Tara M; Pinto, Ameet; Xi, Chuanwu; Raskin, Lutgarde

    2014-04-01

    The impact of monochloramine disinfection on the complex bacterial community structure in drinking water systems was investigated using culture-dependent and culture-independent methods. Changes in viable bacterial diversity were monitored using culture-independent methods that distinguish between live and dead cells based on membrane integrity, providing a highly conservative measure of viability. Samples were collected from lab-scale and full-scale drinking water filters exposed to monochloramine for a range of contact times. Culture-independent detection of live cells was based on propidium monoazide (PMA) treatment to selectively remove DNA from membrane-compromised cells. Quantitative PCR (qPCR) and pyrosequencing of 16S rRNA genes was used to quantify the DNA of live bacteria and characterize the bacterial communities, respectively. The inactivation rate determined by the culture-independent PMA-qPCR method (1.5-log removal at 664 mg·min/L) was lower than the inactivation rate measured by the culture-based methods (4-log removal at 66 mg·min/L). Moreover, drastic changes in the live bacterial community structure were detected during monochloramine disinfection using PMA-pyrosequencing, while the community structure appeared to remain stable when pyrosequencing was performed on samples that were not subject to PMA treatment. Genera that increased in relative abundance during monochloramine treatment include Legionella, Escherichia, and Geobacter in the lab-scale system and Mycobacterium, Sphingomonas, and Coxiella in the full-scale system. These results demonstrate that bacterial populations in drinking water exhibit differential resistance to monochloramine, and that the disinfection process selects for resistant bacterial populations.

  13. Bacterial community associated with Pfiesteria-like dinoflagellate cultures.

    PubMed

    Alavi, M; Miller, T; Erlandson, K; Schneider, R; Belas, R

    2001-06-01

    Dinoflagellates (Eukaryota; Alveolata; Dinophyceae) are single-cell eukaryotic microorganisms implicated in many toxic outbreaks in the marine and estuarine environment. Co-existing with dinoflagellate communities are bacterial assemblages that undergo changes in species composition, compete for nutrients and produce bioactive compounds, including toxins. As part of an investigation to understand the role of the bacteria in dinoflagellate physiology and toxigenesis, we have characterized the bacterial community associated with laboratory cultures of four 'Pfiesteria-like' dinoflagellates isolated from 1997 fish killing events in Chesapeake Bay. A polymerase chain reaction with oligonucleotide primers specific to prokaryotic 16S rDNA gene sequences was used to characterize the total bacterial population, including culturable and non-culturable species, as well as possible endosymbiotic bacteria. The results indicate a diverse group of over 30 bacteria species co-existing in the dinoflagellate cultures. The broad phylogenetic types of dinoflagellate-associated bacteria were generally similar, although not identical, to those bacterial types found in association with other harmful algal species. Dinoflagellates were made axenic, and the culturable bacteria were added back to determine the contribution of the bacteria to dinoflagellate growth. Confocal scanning laser fluorescence microscopy with 16S rDNA probes was used to demonstrate a physical association of a subset of the bacteria and the dinoflagellate cells. These data point to a key component in the bacterial community being species in the marine alpha-proteobacteria group, most closely associated with the alpha-3 or SAR83 cluster.

  14. Dynamic control and quantification of bacterial population dynamics in droplets.

    PubMed

    Huang, Shuqiang; Srimani, Jaydeep K; Lee, Anna J; Zhang, Ying; Lopatkin, Allison J; Leong, Kam W; You, Lingchong

    2015-08-01

    Culturing and measuring bacterial population dynamics are critical to develop insights into gene regulation or bacterial physiology. Traditional methods, based on bulk culture to obtain such quantification, have the limitations of higher cost/volume of reagents, non-amendable to small size of population and more laborious manipulation. To this end, droplet-based microfluidics represents a promising alternative that is cost-effective and high-throughput. However, difficulties in manipulating the droplet environment and monitoring encapsulated bacterial population for long-term experiments limit its utilization. To overcome these limitations, we used an electrode-free injection technology to modulate the chemical environment in droplets. This ability is critical for precise control of bacterial dynamics in droplets. Moreover, we developed a trapping device for long-term monitoring of population dynamics in individual droplets for at least 240 h. We demonstrated the utility of this new microfluidic system by quantifying population dynamics of natural and engineered bacteria. Our approach can further improve the analysis for systems and synthetic biology in terms of manipulability and high temporal resolution.

  15. Dynamic control and quantification of bacterial population dynamics in droplets

    PubMed Central

    Huang, Shuqiang; Srimani, Jaydeep K.; Lee, Anna J.; Zhang, Ying; Lopatkin, Allison J.; Leong, Kam W.; You, Lingchong

    2015-01-01

    Culturing and measuring bacterial population dynamics are critical to develop insights into gene regulation or bacterial physiology. Traditional methods, based on bulk culture to obtain such quantification, have the limitations of higher cost/volume of reagents, non-amendable to small size of population and more laborious manipulation. To this end, droplet-based microfluidics represents a promising alternative that is cost-effective and high-throughput. However, difficulties in manipulating the droplet environment and monitoring encapsulated bacterial population for long-term experiments limit its utilization. To overcome these limitations, we used an electrode-free injection technology to modulate the chemical environment in droplets. This ability is critical for precise control of bacterial dynamics in droplets. Moreover, we developed a trapping device for long-term monitoring of population dynamics in individual droplets for at least 240 h. We demonstrated the utility of this new microfluidic system by quantifying population dynamics of natural and engineered bacteria. Our approach can further improve the analysis for systems and synthetic biology in terms of manipulability and high temporal resolution. PMID:26005763

  16. Population bottlenecks promote cooperation in bacterial biofilms.

    PubMed

    Brockhurst, Michael A

    2007-07-25

    Population bottlenecks are assumed to play a key role in the maintenance of social traits in microbes. Ecological parameters such as colonisation or disturbances can favour cooperation through causing population bottlenecks that enhance genetic structuring (relatedness). However, the size of the population bottleneck is likely to play a crucial role in determining the success of cooperation. Relatedness is likely to increase with decreasing bottleneck size thus favouring the evolution of cooperation. I used an experimental evolution approach to test this prediction with biofilm formation by the bacterium Pseudomonas fluorescens as the cooperative trait. Replicate populations were exposed to disturbance events every four days under one of six population bottleneck treatments (from 10(3) to 10(8) bacterial cells). In line with predictions, the frequency of evolved cheats within the populations increased with increasing bottleneck size. This result highlights the importance of ecologically mediated population bottlenecks in the maintenance of social traits in microbes.

  17. Population dynamics on heterogeneous bacterial substrates

    NASA Astrophysics Data System (ADS)

    Mobius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2012-02-01

    How species invade new territories and how these range expansions influence the population's genotypes are important questions in the field of population genetics. The majority of work addressing these questions focuses on homogeneous environments. Much less is known about the population dynamics and population genetics when the environmental conditions are heterogeneous in space. To better understand range expansions in two-dimensional heterogeneous environments, we employ a system of bacteria and bacteriophage, the viruses of bacteria. Thereby, the bacteria constitute the environment in which a population of bacteriophages expands. The spread of phage constitutes itself in lysis of bacteria and thus formation of clear regions on bacterial lawns, called plaques. We study the population dynamics and genetics of the expanding page for various patterns of environments.

  18. Scanning electron microscopy studies of bacterial cultures

    NASA Astrophysics Data System (ADS)

    Swinger, Tracy; Blust, Brittni; Calabrese, Joseph; Tzolov, Marian

    2012-02-01

    Scanning electron microscopy is a powerful tool to study the morphology of bacteria. We have used conventional scanning electron microscope to follow the modification of the bacterial morphology over the course of the bacterial growth cycle. The bacteria were fixed in vapors of Glutaraldehyde and ruthenium oxide applied in sequence. A gold film of about 5 nm was deposited on top of the samples to avoid charging and to enhance the contrast. We have selected two types of bacteria Alcaligenes faecalis and Kocuria rhizophila. Their development was carefully monitored and samples were taken for imaging in equal time intervals during their cultivation. These studies are supporting our efforts to develop an optical method for identification of the Gram-type of bacterial cultures.

  19. Adenoid bacterial colonization in a paediatric population.

    PubMed

    Subtil, João; Rodrigues, João Carlos; Reis, Lúcia; Freitas, Luís; Filipe, Joana; Santos, Alberto; Macor, Carlos; Duarte, Aida; Jordao, Luisa

    2017-04-01

    Adenoids play a key role in both respiratory and ear infection in children. It has also been shown that adenoidectomy improves these symptoms in this population. The main goal of the present study was to evaluate adenoid bacterial colonization and document a possible relation with infectious respiratory disease. A prospective observational study was designed to evaluate the proposed hypothesis in a paediatric population submitted to adenoidectomy by either infectious or non-infectious indications and compare these two cohorts. A total of 62 patients with ages ranging from 1 to 12 years old were enrolled in the study. Adenoid surface, adenoid core and middle meatus microbiota were compared. A close association between adenoid colonization and nasal infection was found, supporting that adenoids may function as bacterial reservoir for upper airway infection. The obtained results also contribute to explain the success of adenoidectomy in patients with infectious indications.

  20. Bacterial Population Genetics in a Forensic Context

    SciTech Connect

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations augmented by phylogenetic representations

  1. Survival Probability of Beneficial Mutations in Bacterial Batch Culture

    PubMed Central

    Wahl, Lindi M.; Zhu, Anna Dai

    2015-01-01

    The survival of rare beneficial mutations can be extremely sensitive to the organism’s life history and the trait affected by the mutation. Given the tremendous impact of bacteria in batch culture as a model system for the study of adaptation, it is important to understand the survival probability of beneficial mutations in these populations. Here we develop a life-history model for bacterial populations in batch culture and predict the survival of mutations that increase fitness through their effects on specific traits: lag time, fission time, viability, and the timing of stationary phase. We find that if beneficial mutations are present in the founding population at the beginning of culture growth, mutations that reduce the mortality of daughter cells are the most likely to survive drift. In contrast, of mutations that occur de novo during growth, those that delay the onset of stationary phase are the most likely to survive. Our model predicts that approximately fivefold population growth between bottlenecks will optimize the occurrence and survival of beneficial mutations of all four types. This prediction is relatively insensitive to other model parameters, such as the lag time, fission time, or mortality rate of the population. We further estimate that bottlenecks that are more severe than this optimal prediction substantially reduce the occurrence and survival of adaptive mutations. PMID:25758382

  2. Survival probability of beneficial mutations in bacterial batch culture.

    PubMed

    Wahl, Lindi M; Zhu, Anna Dai

    2015-05-01

    The survival of rare beneficial mutations can be extremely sensitive to the organism's life history and the trait affected by the mutation. Given the tremendous impact of bacteria in batch culture as a model system for the study of adaptation, it is important to understand the survival probability of beneficial mutations in these populations. Here we develop a life-history model for bacterial populations in batch culture and predict the survival of mutations that increase fitness through their effects on specific traits: lag time, fission time, viability, and the timing of stationary phase. We find that if beneficial mutations are present in the founding population at the beginning of culture growth, mutations that reduce the mortality of daughter cells are the most likely to survive drift. In contrast, of mutations that occur de novo during growth, those that delay the onset of stationary phase are the most likely to survive. Our model predicts that approximately fivefold population growth between bottlenecks will optimize the occurrence and survival of beneficial mutations of all four types. This prediction is relatively insensitive to other model parameters, such as the lag time, fission time, or mortality rate of the population. We further estimate that bottlenecks that are more severe than this optimal prediction substantially reduce the occurrence and survival of adaptive mutations.

  3. Pecorino Crotonese cheese: study of bacterial population and flavour compounds.

    PubMed

    Randazzo, C L; Pitino, I; Ribbera, A; Caggia, C

    2010-05-01

    The diversity and dynamics of the dominant bacterial population during the manufacture and the ripening of two artisanal Pecorino Crotonese cheeses, provided by different farms, were investigated by the combination of culture-dependent and -independent approaches. Three hundred and thirty-three strains were isolated from selective culture media, clustered using Restriction Fragment Length Polymorphism and were identified by 16S rRNA gene sequencing. The results indicate a decrease in biodiversity during ripening, revealing the presence of Lactococcus lactis and Streptococcus thermophilus species in the curd and in aged cheese samples and the occurrence of several lactobacilli throughout cheese ripening, with the dominance of Lactobacillus rhamnosus species. Bacterial dynamics determined by Denaturant Gradient Gel Electrophoresis provided a more precise description of the distribution of bacteria, highlighting differences in the bacterial community among cheese samples, and allowed to detect Lactobacillus plantarum, Lactobacillus buchneri and Leuconostoc mesenteroides species, which were not isolated. Moreover, the concentration of flavour compounds produced throughout cheese ripening was investigated and related to lactic acid bacteria presence. Fifty-seven compounds were identified in the volatile fraction of Pecorino Crotonese cheeses by Gas Chromatography-Mass Spectrometry. Esters, alcohols and free fatty acids were the most abundant compounds, while aldehydes and hydrocarbons were present at low levels.

  4. Antarctic ice core samples: culturable bacterial diversity.

    PubMed

    Shivaji, Sisinthy; Begum, Zareena; Shiva Nageswara Rao, Singireesu Soma; Vishnu Vardhan Reddy, Puram V; Manasa, Poorna; Sailaja, Buddi; Prathiba, Mambatta S; Thamban, Meloth; Krishnan, Kottekkatu P; Singh, Shiv M; Srinivas, Tanuku N R

    2013-01-01

    Culturable bacterial abundance at 11 different depths of a 50.26 m ice core from the Tallaksenvarden Nunatak, Antarctica, varied from 0.02 to 5.8 × 10(3) CFU ml(-1) of the melt water. A total of 138 bacterial strains were recovered from the 11 different depths of the ice core. Based on 16S rRNA gene sequence analyses, the 138 isolates could be categorized into 25 phylotypes belonging to phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. All isolates had 16S rRNA sequences similar to previously determined sequences (97.2-100%). No correlation was observed in the distribution of the isolates at the various depths either at the phylum, genus or species level. The 25 phylotypes varied in growth temperature range, tolerance to NaCl, growth pH range and ability to produce eight different extracellular enzymes at either 4 or 18 °C. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a significant proportion of the total fatty acid composition.

  5. Dynamics of genome rearrangement in bacterial populations.

    PubMed

    Darling, Aaron E; Miklós, István; Ragan, Mark A

    2008-07-18

    characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes.

  6. Which games are growing bacterial populations playing?

    PubMed Central

    Li, Xiang-Yi; Pietschke, Cleo; Fraune, Sebastian; Altrock, Philipp M.; Bosch, Thomas C. G.; Traulsen, Arne

    2015-01-01

    Microbial communities display complex population dynamics, both in frequency and absolute density. Evolutionary game theory provides a natural approach to analyse and model this complexity by studying the detailed interactions among players, including competition and conflict, cooperation and coexistence. Classic evolutionary game theory models typically assume constant population size, which often does not hold for microbial populations. Here, we explicitly take into account population growth with frequency-dependent growth parameters, as observed in our experimental system. We study the in vitro population dynamics of the two commensal bacteria (Curvibacter sp. (AEP1.3) and Duganella sp. (C1.2)) that synergistically protect the metazoan host Hydra vulgaris (AEP) from fungal infection. The frequency-dependent, nonlinear growth rates observed in our experiments indicate that the interactions among bacteria in co-culture are beyond the simple case of direct competition or, equivalently, pairwise games. This is in agreement with the synergistic effect of anti-fungal activity observed in vivo. Our analysis provides new insight into the minimal degree of complexity needed to appropriately understand and predict coexistence or extinction events in this kind of microbial community dynamics. Our approach extends the understanding of microbial communities and points to novel experiments. PMID:26236827

  7. Persistence of antibiotic resistance in bacterial populations.

    PubMed

    Andersson, Dan I; Hughes, Diarmaid

    2011-09-01

    Unfortunately for mankind, it is very likely that the antibiotic resistance problem we have generated during the last 60 years due to the extensive use and misuse of antibiotics is here to stay for the foreseeable future. This view is based on theoretical arguments, mathematical modeling, experiments and clinical interventions, suggesting that even if we could reduce antibiotic use, resistant clones would remain persistent and only slowly (if at all) be outcompeted by their susceptible relatives. In this review, we discuss the multitude of mechanisms and processes that are involved in causing the persistence of chromosomal and plasmid-borne resistance determinants and how we might use them to our advantage to increase the likelihood of reversing the problem. Of particular interest is the recent demonstration that a very low antibiotic concentration can be enriching for resistant bacteria and the implication that antibiotic release into the environment could contribute to the selection for resistance. Several mechanisms are contributing to the stability of antibiotic resistance in bacterial populations and even if antibiotic use is reduced it is likely that most resistance mechanisms will persist for considerable times.

  8. Gardnerella vaginalis population dynamics in bacterial vaginosis.

    PubMed

    Hilbert, D W; Schuyler, J A; Adelson, M E; Mordechai, E; Sobel, J D; Gygax, S E

    2017-02-14

    Bacterial vaginosis (BV) is the leading cause of vaginal discharge and is associated with the facultative Gram-variable bacterium Gardnerella vaginalis, whose population structure consists of four clades. Our goal was to determine if these clades differ with regard to abundance during BV. We performed a short-term longitudinal study of BV. Patients were evaluated according to the Amsel criteria and Nugent scoring at initial diagnosis, immediately after treatment and at a 40- to 45-day follow-up visit. G. vaginalis clade abundance was determined by quantitative real-time polymerase chain reactions (qPCRs). Among all specimens, the abundance of clades 1 and 4 were higher than that of clades 2 and 3 (P < 0.001). In general, the abundance of each clade increased with the degree of vaginal dysbiosis, as determined by the Nugent score and was greater in women with Amsel 4 compared with those with Amsel 0. Only clade 1 abundance was greater when Amsel 0 or 1 specimens were compared with Amsel 2 or 3 specimens (P < 0.01). Following antimicrobial treatment, abundance of clades 1 (P < 0.001) and 4 (P < 0.05) decreased regardless of the clinical and microbiological outcome, whereas clade 2 only decreased in women who had a sustained treatment response for 40-45 days (P < 0.01). Recurrent BV was characterized by post-treatment increases of clade 1 and 2 (P < 0.01). Clades 1 and 4 predominate in vaginal specimens. Clade abundance differs with regard to the Nugent score, the Amsel criteria, and response to therapy and BV recurrence.

  9. Optimal control methods for controlling bacterial populations with persister dynamics

    NASA Astrophysics Data System (ADS)

    Cogan, N. G.

    2016-06-01

    Bacterial tolerance to antibiotics is a well-known phenomena; however, only recent studies of bacterial biofilms have shown how multifaceted tolerance really is. By joining into a structured community and offering shared protection and gene transfer, bacterial populations can protect themselves genotypically, phenotypically and physically. In this study, we collect a line of research that focuses on phenotypic (or plastic) tolerance. The dynamics of persister formation are becoming better understood, even though there are major questions that remain. The thrust of our results indicate that even without detailed description of the biological mechanisms, theoretical studies can offer strategies that can eradicate bacterial populations with existing drugs.

  10. Molecular population genetic analysis of emerged bacterial pathogens: selected insights.

    PubMed Central

    Musser, J. M.

    1996-01-01

    Research in bacterial population genetics has increased in the last 10 years. Population genetic theory and tools and related strategies have been used to investigate bacterial pathogens that have contributed to recent episodes of temporal variation in disease frequency and severity. A common theme demonstrated by these analyses is that distinct bacterial clones are responsible for disease outbreaks and increases in infection frequency. Many of these clones are characterized by unique combinations of virulence genes or alleles of virulence genes. Because substantial interclonal variance exists in relative virulence, molecular population genetic studies have led to the concept that the unit of bacterial pathogenicity is the clone or cell line. Continued new insights into host parasite interactions at the molecular level will be achieved by combining clonal analysis of bacterial pathogens with large-scale comparative sequencing of virulence genes. PMID:8903193

  11. Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes

    PubMed Central

    Buck, Moritz; Nilsson, Louise K. J.; Brunius, Carl; Dabiré, Roch K.; Hopkins, Richard; Terenius, Olle

    2016-01-01

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world. PMID:26960555

  12. Raw Cow Milk Bacterial Population Shifts Attributable to Refrigeration

    PubMed Central

    Lafarge, Véronique; Ogier, Jean-Claude; Girard, Victoria; Maladen, Véronique; Leveau, Jean-Yves; Gruss, Alexandra; Delacroix-Buchet, Agnès

    2004-01-01

    We monitored the dynamic changes in the bacterial population in milk associated with refrigeration. Direct analyses of DNA by using temporal temperature gel electrophoresis (TTGE) and denaturing gradient gel electrophoresis (DGGE) allowed us to make accurate species assignments for bacteria with low-GC-content (low-GC%) (<55%) and medium- or high-GC% (>55%) genomes, respectively. We examined raw milk samples before and after 24-h conservation at 4°C. Bacterial identification was facilitated by comparison with an extensive bacterial reference database (∼150 species) that we established with DNA fragments of pure bacterial strains. Cloning and sequencing of fragments missing from the database were used to achieve complete species identification. Considerable evolution of bacterial populations occurred during conservation at 4°C. TTGE and DGGE are shown to be a powerful tool for identifying the main bacterial species of the raw milk samples and for monitoring changes in bacterial populations during conservation at 4°C. The emergence of psychrotrophic bacteria such as Listeria spp. or Aeromonas hydrophila is demonstrated. PMID:15345453

  13. Raw cow milk bacterial population shifts attributable to refrigeration.

    PubMed

    Lafarge, Véronique; Ogier, Jean-Claude; Girard, Victoria; Maladen, Véronique; Leveau, Jean-Yves; Gruss, Alexandra; Delacroix-Buchet, Agnès

    2004-09-01

    We monitored the dynamic changes in the bacterial population in milk associated with refrigeration. Direct analyses of DNA by using temporal temperature gel electrophoresis (TTGE) and denaturing gradient gel electrophoresis (DGGE) allowed us to make accurate species assignments for bacteria with low-GC-content (low-GC%) (<55%) and medium- or high-GC% (>55%) genomes, respectively. We examined raw milk samples before and after 24-h conservation at 4 degrees C. Bacterial identification was facilitated by comparison with an extensive bacterial reference database ( approximately 150 species) that we established with DNA fragments of pure bacterial strains. Cloning and sequencing of fragments missing from the database were used to achieve complete species identification. Considerable evolution of bacterial populations occurred during conservation at 4 degrees C. TTGE and DGGE are shown to be a powerful tool for identifying the main bacterial species of the raw milk samples and for monitoring changes in bacterial populations during conservation at 4 degrees C. The emergence of psychrotrophic bacteria such as Listeria spp. or Aeromonas hydrophila is demonstrated.

  14. Local environmental pollution strongly influences culturable bacterial aerosols at an urban aquatic superfund site.

    PubMed

    Dueker, M Elias; O'Mullan, Gregory D; Juhl, Andrew R; Weathers, Kathleen C; Uriarte, Maria

    2012-10-16

    In polluted environments, when microbial aerosols originate locally, species composition of the aerosols should reflect the polluted source. To test the connection between local environmental pollution and microbial aerosols near an urban waterfront, we characterized bacterial aerosols at Newtown Creek (NTC), a public waterway and Superfund site in a densely populated area of New York, NY, USA. Culturable bacterial aerosol fallout rate and surface water bacterial concentrations were at least an order of magnitude greater at NTC than at a neighboring, less polluted waterfront and a nonurban coastal site in Maine. The NTC culturable bacterial aerosol community was significantly different in taxonomic structure from previous urban and coastal aerosol studies, particularly in relative abundances of Actinobacteria and Proteobacteria. Twenty-four percent of the operational taxonomic units in the NTC overall (air + water) bacterial isolate library were most similar to bacterial 16S rRNA gene sequences previously described in terrestrial or aquatic environments contaminated with sewage, hydrocarbons, heavy metals, and other industrial waste. This study is the first to examine the community composition and local deposition of bacterial aerosols from an aquatic Superfund site. The findings have important implications for the use of aeration remediation in polluted aquatic environments and suggest a novel pathway of microbial exposure in densely populated urban communities containing contaminated soil and water.

  15. Measurement of Behavioral Evolution in Bacterial Populations

    NASA Astrophysics Data System (ADS)

    Austin, Robert

    2013-03-01

    A curious aspect of bacterial behavior under stress is the induction of filamentation: the anomalous growth of certain bacteria in which cells continue to elongate but do not divide into progeny. We show that E.coli under the influence of the genotoxic antibiotic ciprofloxacin have robust filamentous growth, which provides individual bacteria a mesoscopic niche for evolution until resistant progeny can bud off and propagate. Hence, filamentation is a form of genomic amplification where even a single, isolated bacteria can have access to multiple genomes. We propose a model that predicts that the first arrival time of the normal sized progeny should follow a Gompertz distribution with the mean first arrival time proportional to the elongation rate of filament. These predictions agree with our experimental measurements. Finally, we suggest bacterial filament growth and budding has many similarities to tumor growth and metastasis and can serve as a simpler model to study those complicated processes. Sponsored by the NCI/NIH Physical Sciences Oncology Centers

  16. Sustainability of culture-driven population dynamics.

    PubMed

    Ghirlanda, Stefano; Enquist, Magnus; Perc, Matjaz

    2010-05-01

    We consider models of the interactions between human population dynamics and cultural evolution, asking whether they predict sustainable or unsustainable patterns of growth. Phenomenological models predict either unsustainable population growth or stabilization in the near future. The latter prediction, however, is based on extrapolation of current demographic trends and does not take into account causal processes of demographic and cultural dynamics. Most existing causal models assume (or derive from simplified models of the economy) a positive feedback between cultural evolution and demographic growth, and predict unlimited growth in both culture and population. We augment these models taking into account that: (1) cultural transmission is not perfect, i.e., culture can be lost; (2) culture does not always promote population growth. We show that taking these factors into account can cause radically different model behavior, such as population extinction rather than stability, and extinction rather than growth. We conclude that all models agree that a population capable of maintaining a large amount of culture, including a powerful technology, runs a high risk of being unsustainable. We suggest that future work must address more explicitly both the dynamics of resource consumption and the cultural evolution of beliefs implicated in reproductive behavior (e.g., ideas about the preferred family size) and in resource use (e.g., environmentalist stances).

  17. Dynamics of Sequence -Discrete Bacterial Populations Inferred Using Metagenomes

    SciTech Connect

    Stevens, Sarah; Bendall, Matthew; Kang, Dongwan; Froula, Jeff; Egan, Rob; Chan, Leong-Keat; Tringe, Susannah; McMahon, Katherine; Malmstrom, Rex

    2014-03-14

    From a multi-year metagenomic time series of two dissimilar Wisconsin lakes we have assembled dozens of genomes using a novel approach that bins contigs into distinct genome based on sequence composition, e.g. kmer frequencies, and contig coverage patterns at various times points. Next, we investigated how these genomes, which represent sequence-discrete bacterial populations, evolved over time and used the time series to discover the population dynamics. For example, we explored changes in single nucleotide polymorphism (SNP) frequencies as well as patterns of gene gain and loss in multiple populations. Interestingly, SNP diversity was purged at nearly every genome position in some populations during the course of this study, suggesting these populations may have experienced genome-wide selective sweeps. This represents the first direct, time-resolved observations of periodic selection in natural populations, a key process predicted by the ecotype model of bacterial diversification.

  18. Current and past strategies for bacterial culture in clinical microbiology.

    PubMed

    Lagier, Jean-Christophe; Edouard, Sophie; Pagnier, Isabelle; Mediannikov, Oleg; Drancourt, Michel; Raoult, Didier

    2015-01-01

    A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome.

  19. Current and Past Strategies for Bacterial Culture in Clinical Microbiology

    PubMed Central

    Lagier, Jean-Christophe; Edouard, Sophie; Pagnier, Isabelle; Mediannikov, Oleg; Drancourt, Michel

    2015-01-01

    SUMMARY A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome. PMID:25567228

  20. Bioremediation of MGP soils with mixed fungal and bacterial cultures

    SciTech Connect

    Lee, C.J.B.; Fletcher, M.A.; Avila, O.I.; Munnecke, D.M.; Callanan, J.; Yunker, S.

    1995-12-31

    This culture selection study examines the degradation of polycyclic automatic hydrocarbon (PAH) by a number of brown- and white-rot fungi and bacterial cultures for the treatment of coal tar wastes. Cultures were screened for naphthalene degradation in shake flasks, and selected organisms were then examined for their ability to degrade a mixture of PAHs in aqueous culture. PAH degradation in the presence of the surfactant, TWEEN 80, was examined for some cultures. Many of the organisms were observed to be resistant to greater than 10 mg/L free cyanide. Solid substrate growth conditions were optimized for the selected fungal cultures in preparation for manufactured gas plant (MGP) soil microcosm experiments. The fungi generally produced more biomass under conditions of acidic to neutral pH, incubation at 30 C with 90% moisture saturation, and with granulated corncobs or alfalfa pellets supplied as a lignocellulosic substrate. Of the cultures screened, nine fungal cultures were selected based on their ability to degrade at least 40% of naphthalene, fluorene, or benzo(a)pyrene in 2 weeks or less. A bacterial culture capable of degrading 30 mg/L of naphthalene in 1 week was also selected, and the cultures were examined further in PAH-degradation studies in contaminated soils.

  1. Determining the culturability of the rumen bacterial microbiome

    PubMed Central

    Creevey, Christopher J; Kelly, William J; Henderson, Gemma; Leahy, Sinead C

    2014-01-01

    The goal of the Hungate1000 project is to generate a reference set of rumen microbial genome sequences. Toward this goal we have carried out a meta-analysis using information from culture collections, scientific literature, and the NCBI and RDP databases and linked this with a comparative study of several rumen 16S rRNA gene-based surveys. In this way we have attempted to capture a snapshot of rumen bacterial diversity to examine the culturable fraction of the rumen bacterial microbiome. Our analyses have revealed that for cultured rumen bacteria, there are many genera without a reference genome sequence. Our examination of culture-independent studies highlights that there are few novel but many uncultured taxa within the rumen bacterial microbiome. Taken together these results have allowed us to compile a list of cultured rumen isolates that are representative of abundant, novel and core bacterial species in the rumen. In addition, we have identified taxa, particularly within the phylum Bacteroidetes, where further cultivation efforts are clearly required. This information is being used to guide the isolation efforts and selection of bacteria from the rumen microbiota for sequencing through the Hungate1000. PMID:24986151

  2. Correlated Mutations and Homologous Recombination Within Bacterial Populations.

    PubMed

    Lin, Mingzhi; Kussell, Edo

    2017-02-01

    Inferring the rate of homologous recombination within a bacterial population remains a key challenge in quantifying the basic parameters of bacterial evolution. Due to the high sequence similarity within a clonal population, and unique aspects of bacterial DNA transfer processes, detecting recombination events based on phylogenetic reconstruction is often difficult, and estimating recombination rates using coalescent model-based methods is computationally expensive, and often infeasible for large sequencing data sets. Here, we present an efficient solution by introducing a set of mutational correlation functions computed using pairwise sequence comparison, which characterize various facets of bacterial recombination. We provide analytical expressions for these functions, which precisely recapitulate simulation results of neutral and adapting populations under different coalescent models. We used these to fit correlation functions measured at synonymous substitutions using whole-genome data on Escherichia coli and Streptococcus pneumoniae populations. We calculated and corrected for the effect of sample selection bias, i.e., the uneven sampling of individuals from natural microbial populations that exists in most datasets. Our method is fast and efficient, and does not employ phylogenetic inference or other computationally intensive numerics. By simply fitting analytical forms to measurements from sequence data, we show that recombination rates can be inferred, and the relative ages of different samples can be estimated. Our approach, which is based on population genetic modeling, is broadly applicable to a wide variety of data, and its computational efficiency makes it particularly attractive for use in the analysis of large sequencing datasets.

  3. Selection of bacterial wilt-resistant tomato through tissue culture.

    PubMed

    Toyoda, H; Shimizu, K; Chatani, K; Kita, N; Matsuda, Y; Ouchi, S

    1989-06-01

    Bacterial wilt-resistant plants were obtained using a tomato tissue culture system. A virulent strain ofPseudomonas solanacearum secreted some toxic substances into the culture medium. Leaf explant-derived callus tissues which were resistant to these toxic substances in the culture filtrate were selectedin vitro and regenerated into plants. These plants expressed bacterial wilt resistance at the early infection stage to suppress or delay the growth of the inoculated bacteria. On the other hand, complete resistance was obtained in self-pollinated progeny of regenerants derived from non-selected callus tissues. These plants showed a high resistance when inoculated with this strain, and were also resistant when planted in a field infested with a different strain of the pathogen.

  4. Innovativeness, population size and cumulative cultural evolution.

    PubMed

    Kobayashi, Yutaka; Aoki, Kenichi

    2012-08-01

    Henrich [Henrich, J., 2004. Demography and cultural evolution: how adaptive cultural processes can produce maladaptive losses-the Tasmanian case. Am. Antiquity 69, 197-214] proposed a model designed to show that larger population size facilitates cumulative cultural evolution toward higher skill levels. In this model, each newborn attempts to imitate the most highly skilled individual of the parental generation by directly-biased social learning, but the skill level he/she acquires deviates probabilistically from that of the exemplar (cultural parent). The probability that the skill level of the imitator exceeds that of the exemplar can be regarded as the innovation rate. After reformulating Henrich's model rigorously, we introduce an overlapping-generations analog based on the Moran model and derive an approximate formula for the expected change per generation of the highest skill level in the population. For large population size, our overlapping-generations model predicts a much larger effect of population size than Henrich's discrete-generations model. We then investigate by way of Monte Carlo simulations the case where each newborn chooses as his/her exemplar the most highly skilled individual from among a limited number of acquaintances. When the number of acquaintances is small relative to the population size, we find that a change in the innovation rate contributes more than a proportional change in population size to the cumulative cultural evolution of skill level.

  5. Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils.

    PubMed

    França, Luís; Sannino, Ciro; Turchetti, Benedetta; Buzzini, Pietro; Margesin, Rosa

    2016-11-01

    The effect of altitude and season on abundance and diversity of the culturable heterotrophic bacterial and yeast community was examined at four forest sites in the Italian Alps along an altitude gradient (545-2000 m). Independently of altitude, bacteria isolated at 0 °C (psychrophiles) were less numerous than those recovered at 20 °C. In autumn, psychrophilic bacterial population increased with altitude. The 1194 bacterial strains were primarily affiliated with the classes Alpha-, Beta-, Gammaproteobacteria, Spingobacteriia and Flavobacteriia. Fifty-seven of 112 operational taxonomic units represented potential novel species. Strains isolated at 20 °C had a higher diversity and showed similarities in taxa composition and abundance, regardless of altitude or season, while strains isolated at 0 °C showed differences in community composition at lower and higher altitudes. In contrast to bacteria, yeast diversity was season-dependent: site- and altitude-specific effects on yeast diversity were only detected in spring. Isolation temperature affected the relative proportions of yeast genera. Isolations recovered 719 strains, belonging to the classes Dothideomycetes, Saccharomycetes, Tremellomycetes and Mycrobotryomycetes. The presence of few dominant bacterial OTUs and yeast species indicated a resilient microbial population that is not affected by season or altitude. Soil nutrient contents influenced significantly abundance and diversity of culturable bacteria, but not of culturable yeasts.

  6. Characterization of cellulolytic bacterial cultures grown in different substrates.

    PubMed

    Alshelmani, Mohamed Idris; Loh, Teck Chwen; Foo, Hooi Ling; Lau, Wei Hong; Sazili, Awis Qurni

    2013-01-01

    Nine aerobic cellulolytic bacterial cultures were obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Culture (DSMZ) and the American Type Culture Collection (ATCC). The objectives of this study were to characterize the cellulolytic bacteria and to determine the optimum moisture ratio required for solid state fermentation (SSF) of palm kernel cake (PKC). The bacteria cultures were grown on reconstituted nutrient broth, incubated at 30°C and agitated at 200 rpm. Carboxymethyl cellulase, xylanase, and mannanase activities were determined using different substrates and after SSF of PKC. The SSF was conducted for 4 and 7 days with inoculum size of 10% (v/w) on different PKC concentration-to-moisture ratios: 1 : 0.2, 1 : 0.3, 1 : 0.4, and 1 : 0.5. Results showed that Bacillus amyloliquefaciens 1067 DSMZ, Bacillus megaterium 9885 ATCC, Paenibacillus curdlanolyticus 10248 DSMZ, and Paenibacillus polymyxa 842 ATCC produced higher enzyme activities as compared to other bacterial cultures grown on different substrates. The cultures mentioned above also produced higher enzyme activities when they were incubated under SSF using PKC as a substrate in different PKC-to-moisture ratios after 4 days of incubation, indicating that these cellulolytic bacteria can be used to degrade and improve the nutrient quality of PKC.

  7. Substrate versatility of polyhydroxyalkanoate producing glycerol grown bacterial enrichment culture.

    PubMed

    Moralejo-Gárate, Helena; Kleerebezem, Robbert; Mosquera-Corral, Anuska; Campos, José Luis; Palmeiro-Sánchez, Tania; van Loosdrecht, Mark C M

    2014-12-01

    Waste-based polyhydroxyalkanoate (PHA) production by bacterial enrichments generally follows a three step strategy in which first the wastewater is converted into a volatile fatty acid rich stream that is subsequently used as substrate in a selector and biopolymer production units. In this work, a bacterial community with high biopolymer production capacity was enriched using glycerol, a non-fermented substrate. The substrate versatility and PHA production capacity of this community was studied using glucose, lactate, acetate and xylitol as substrate. Except for xylitol, very high PHA producing capacities were obtained. The PHA accumulation was comparable or even higher than with glycerol as substrate. This is the first study that established a high PHA content (≈70 wt%) with glucose as substrate in a microbial enrichment culture. The results presented in this study support the development of replacing pure culture based PHA production by bacterial enrichment cultures. A process where mixtures of substrates can be easily handled and the acidification step can potentially be avoided is described.

  8. Bacterial populations and the volatilome associated to meat spoilage.

    PubMed

    Casaburi, Annalisa; Piombino, Paola; Nychas, George-John; Villani, Francesco; Ercolini, Danilo

    2015-02-01

    Microbial spoilage of meat is a complex event to which many different bacterial populations can contribute depending on the temperature of storage and packaging conditions. The spoilage can derive from microbial development and consumption of meat nutrients by bacteria with a consequent release of undesired metabolites. The volatile organic compounds (VOCs) that are generated during meat storage can have an olfactory impact and can lead to rejection of the product when their concentration increase significantly as a result of microbial development. The VOCs most commonly identified in meat during storage include alcohols, aldehydes, ketones, fatty acids, esters and sulfur compounds. In this review, the VOCs found in fresh meat during storage in specific conditions are described together with the possible bacterial populations responsible of their production. In addition, on the basis of the data available in the literature, the sensory impact of the VOCs and their dynamics during storage is discussed to highlight their possible contribution to the spoilage of meat.

  9. Detection of Only Viable Bacterial Spores Using a Live/Dead Indicator in Mixed Populations

    NASA Technical Reports Server (NTRS)

    Behar, Alberto E.; Stam, Christina N.; Smiley, Ronald

    2013-01-01

    This method uses a photoaffinity label that recognizes DNA and can be used to distinguish populations of bacterial cells from bacterial spores without the use of heat shocking during conventional culture, and live from dead bacterial spores using molecular-based methods. Biological validation of commercial sterility using traditional and alternative technologies remains challenging. Recovery of viable spores is cumbersome, as the process requires substantial incubation time, and the extended time to results limits the ability to quickly evaluate the efficacy of existing technologies. Nucleic acid amplification approaches such as PCR (polymerase chain reaction) have shown promise for improving time to detection for a wide range of applications. Recent real-time PCR methods are particularly promising, as these methods can be made at least semi-quantitative by correspondence to a standard curve. Nonetheless, PCR-based methods are rarely used for process validation, largely because the DNA from dead bacterial cells is highly stable and hence, DNA-based amplification methods fail to discriminate between live and inactivated microorganisms. Currently, no published method has been shown to effectively distinguish between live and dead bacterial spores. This technology uses a DNA binding photoaffinity label that can be used to distinguish between live and dead bacterial spores with detection limits ranging from 109 to 102 spores/mL. An environmental sample suspected of containing a mixture of live and dead vegetative cells and bacterial endospores is treated with a photoaffinity label. This step will eliminate any vegetative cells (live or dead) and dead endospores present in the sample. To further determine the bacterial spore viability, DNA is extracted from the spores and total population is quantified by real-time PCR. The current NASA standard assay takes 72 hours for results. Part of this procedure requires a heat shock step at 80 degC for 15 minutes before the

  10. Nutrient reduction induced stringent responses promote bacterial quorum-sensing divergence for population fitness

    PubMed Central

    Zhao, Kelei; Zhou, Xikun; Li, Wujiao; Zhang, Xiuyue; Yue, Bisong

    2016-01-01

    Bacteria use a cell-cell communication system termed quorum-sensing (QS) to adjust population size by coordinating the costly but beneficial cooperative behaviors. It has long been suggested that bacterial social conflict for expensive extracellular products may drive QS divergence and cause the “tragedy of the commons”. However, the underlying molecular mechanism of social divergence and its evolutionary consequences for the bacterial ecology still remain largely unknown. By using the model bacterium Pseudomonas aeruginosa PAO1, here we show that nutrient reduction can promote QS divergence for population fitness during evolution but requiring adequate cell density. Mechanically, decreased nutrient supplies can induce RpoS-directed stringent response and enhance the selection pressure on lasR gene, and lasR mutants are evolved in association with the DNA mismatch repair “switch-off”. The lasR mutants have higher relative fitness than QS-intact individuals due to their energy-saving characteristic under nutrient decreased condition. Furthermore an optimal incorporation of lasR mutants is capable of maximizing the fitness of entire population during in vitro culture and the colonization in mouse lung. Consequently, rather than worsen the population health, QS-coordinated social divergence is an elaborate evolutionary strategy that renders the entire bacterial population more fit in tough times. PMID:27713502

  11. Genetic Drift of HIV Populations in Culture

    PubMed Central

    Voronin, Yegor; Holte, Sarah; Overbaugh, Julie; Emerman, Michael

    2009-01-01

    Populations of Human Immunodeficiency Virus type 1 (HIV-1) undergo a surprisingly large amount of genetic drift in infected patients despite very large population sizes, which are predicted to be mostly deterministic. Several models have been proposed to explain this phenomenon, but all of them implicitly assume that the process of virus replication itself does not contribute to genetic drift. We developed an assay to measure the amount of genetic drift for HIV populations replicating in cell culture. The assay relies on creation of HIV populations of known size and measurements of variation in frequency of a neutral allele. Using this assay, we show that HIV undergoes approximately ten times more genetic drift than would be expected from its population size, which we defined as the number of infected cells in the culture. We showed that a large portion of the increase in genetic drift is due to non-synchronous infection of target cells. When infections are synchronized, genetic drift for the virus is only 3-fold higher than expected from its population size. Thus, the stochastic nature of biological processes involved in viral replication contributes to increased genetic drift in HIV populations. We propose that appreciation of these effects will allow better understanding of the evolutionary forces acting on HIV in infected patients. PMID:19300501

  12. Modeling Bacterial Population Growth from Stochastic Single-Cell Dynamics

    PubMed Central

    Molina, Ignacio; Theodoropoulos, Constantinos

    2014-01-01

    A few bacterial cells may be sufficient to produce a food-borne illness outbreak, provided that they are capable of adapting and proliferating on a food matrix. This is why any quantitative health risk assessment policy must incorporate methods to accurately predict the growth of bacterial populations from a small number of pathogens. In this aim, mathematical models have become a powerful tool. Unfortunately, at low cell concentrations, standard deterministic models fail to predict the fate of the population, essentially because the heterogeneity between individuals becomes relevant. In this work, a stochastic differential equation (SDE) model is proposed to describe variability within single-cell growth and division and to simulate population growth from a given initial number of individuals. We provide evidence of the model ability to explain the observed distributions of times to division, including the lag time produced by the adaptation to the environment, by comparing model predictions with experiments from the literature for Escherichia coli, Listeria innocua, and Salmonella enterica. The model is shown to accurately predict experimental growth population dynamics for both small and large microbial populations. The use of stochastic models for the estimation of parameters to successfully fit experimental data is a particularly challenging problem. For instance, if Monte Carlo methods are employed to model the required distributions of times to division, the parameter estimation problem can become numerically intractable. We overcame this limitation by converting the stochastic description to a partial differential equation (backward Kolmogorov) instead, which relates to the distribution of division times. Contrary to previous stochastic formulations based on random parameters, the present model is capable of explaining the variability observed in populations that result from the growth of a small number of initial cells as well as the lack of it compared to

  13. Modeling bacterial population growth from stochastic single-cell dynamics.

    PubMed

    Alonso, Antonio A; Molina, Ignacio; Theodoropoulos, Constantinos

    2014-09-01

    A few bacterial cells may be sufficient to produce a food-borne illness outbreak, provided that they are capable of adapting and proliferating on a food matrix. This is why any quantitative health risk assessment policy must incorporate methods to accurately predict the growth of bacterial populations from a small number of pathogens. In this aim, mathematical models have become a powerful tool. Unfortunately, at low cell concentrations, standard deterministic models fail to predict the fate of the population, essentially because the heterogeneity between individuals becomes relevant. In this work, a stochastic differential equation (SDE) model is proposed to describe variability within single-cell growth and division and to simulate population growth from a given initial number of individuals. We provide evidence of the model ability to explain the observed distributions of times to division, including the lag time produced by the adaptation to the environment, by comparing model predictions with experiments from the literature for Escherichia coli, Listeria innocua, and Salmonella enterica. The model is shown to accurately predict experimental growth population dynamics for both small and large microbial populations. The use of stochastic models for the estimation of parameters to successfully fit experimental data is a particularly challenging problem. For instance, if Monte Carlo methods are employed to model the required distributions of times to division, the parameter estimation problem can become numerically intractable. We overcame this limitation by converting the stochastic description to a partial differential equation (backward Kolmogorov) instead, which relates to the distribution of division times. Contrary to previous stochastic formulations based on random parameters, the present model is capable of explaining the variability observed in populations that result from the growth of a small number of initial cells as well as the lack of it compared to

  14. [Septic arthritis? Gonococcal infection despite negative bacterial cultures].

    PubMed

    Saur, M; Distler, O; Müller, N

    2008-09-10

    Clinical signs of acute arthritis are non-specific. An acute painfull joint with effusion of unknown origin needs to be evaluated by puncture. The analysis of the synovial fluid will enable to divide an arthritis into three categories: crystal induced, rheumatological or septic arthritis. A bacterial infection should always be suspected. Cultures from blood, synovia and Gram stain do not reliably exclude a bacterial infection. If gonococcal, mycobacterial, borrelial and non-gonococcal-infective arthritis under antibiotic therapy is suspected, direct DNA-amplification can be helpful. A disseminated gonococcal infection (DGI) must be suspected on appearance of tenosynovitis, polyarthralgia and skin lesions. The clinical picture, diagnosis and therapy of a case with DGI is discussed.

  15. Bacteriocin-Mediated Competitive Interactions of Bacterial Populations and Communities

    NASA Astrophysics Data System (ADS)

    Riley, Margaret A.

    Explaining the coexistence of competing species is a major challenge in community ecology. In bacterial systems, competition is often driven by the production of bacteriocins; narrow spectrum proteinaceous toxins that serve to kill closely related species providing the producer better access to limited resources. Bacteriocin producers have been shown to competitively exclude sensitive, nonproducing strains. However, the interaction dynamics between bacteriocin producers, each lethal to its competitor, are largely unknown. Several recent studies have revealed some of the complexity of these interactions, employing a suite of in vitro, in vivo, and in silico bacterial model systems. This chapter describes the current state of knowledge regarding the population and community ecology of this potent family of toxins.

  16. Spatio-temporal transitions in the dynamics of bacterial populations

    NASA Astrophysics Data System (ADS)

    Lin, Anna; Lincoln, Bryan; Mann, Bernward; Torres, Gelsy; Kas, Josef; Swinney, Harry

    2001-03-01

    We experimentally investigate the population dynamics of a strain of E. coli bacteria living under spatially inhomogeneous growth conditions. A localized perturbation that moves with a well-defined drift velocity is imposed on the system. A reaction-diffusion model of this situation^1 predicts that an abrupt transition between spatial localization and extinction of the colony occurs for a fixed average growth rate when the drift velocity exceeds a critical value. Also, a transition between localized and delocalized populations is predicted to occur at a fixed drift velocity when the spatially averaged growth rate is varied. We create a spatially localized perturbation with UV light and vary the strength and drift velocity of the perturbation to investigate the existence of the different bacterial population distributions and the transitions between them. Numerical simulations of a 250 mm by 20 mm system guide our experiments. ^1K. A. Dahmen, D. R. Nelson, N. M. Shnerb, Jour. Math. Bio., 41 1 (2000).

  17. Interactions of Botryococcus braunii cultures with bacterial biofilms.

    PubMed

    Rivas, Mariella O; Vargas, Pedro; Riquelme, Carlos E

    2010-10-01

    Unicellular microalgae generally grow in the presence of bacteria, particularly when they are farmed massively. This study analyzes the bacteria associated with mass culture of Botryococcus braunii: both the planktonic bacteria in the water column and those forming biofilms adhered to the surface of the microalgal cells (∼10⁷-10⁸ culturable cells per gram microalgae). Furthermore, we identified the culturable bacteria forming a biofilm in the microalgal cells by 16S rDNA sequencing. At least eight different culturable species of bacteria were detected in the biofilm and were evaluated for the presence of quorum-sensing signals in these bacteria. Few studies have considered the implications of this phenomenon as regards the interaction between bacteria and microalgae. Production of C4-AHL and C6-AHL were detected in two species, Pseudomonas sp. and Rhizobium sp., which are present in the bacterial biofilm associated with B. braunii. This type of signal was not detected in the planktonic bacteria isolated from the water. We also noted that the bacterium, Rhizobium sp., acted as a probiotic bacterium and significantly encouraged the growth of B. braunii. A direct application of these beneficial bacteria associated with B. braunii could be, to use them like inoculants for large-scale microalgal cultures. They could optimize biomass production by enhancing growth, particularly in this microalga that has a low growth rate.

  18. Bacterial population structure of the jute-retting environment.

    PubMed

    Munshi, Tulika K; Chattoo, Bharat B

    2008-08-01

    Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria ( approximately 37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes ( approximately 11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; approximately 9, 7%), Verrucomicrobia ( approximately 6, 5%), Acidobacteria ( approximately 4, 5%), Chlorobiales ( approximately 5, 5%), and Actinobacteria ( approximately 4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the beta-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria ( approximately 47%), Firmicutes ( approximately 22%), CFB group ( approximately 19%), and Actinobacteria ( approximately 13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality.

  19. Community dynamics of a mixed-bacterial culture growing on petroleum hydrocarbons in batch culture.

    PubMed

    Van Hamme, J D; Odumeru, J A; Ward, O P

    2000-05-01

    The effects of various hydrocarbon substrates, and a chemical surfactant capable of enhancing crude-oil biodegradation, on the community structure of a mixed-bacterial inoculum were examined in batch culture. Of 1000 TSA-culturable isolates, 68.6% were identified at the genus level or better by phospholipid fatty acid analysis over 7-day time course experiments. Cultures were exposed to 20 g/L Bow River crude oil with and without 0.625 g/L Igepal CO-630 (a nonylphenol ethoxylate surfactant), 5 g/L saturates, 5 g/L aromatics, or 125 g/L refinery sludge. A group of six genera dominated the cultures: Acinetobacter, Alcaligenes, Ochrobactrum, Pseudomonas/Flavimonas, Stenotrophomonas, and Yersinia. Species from four of the genera were shown to be capable of hydrocarbon degradation, and counts of hydrocarbon degrading and total heterotrophic bacteria over time were nearly identical. Pseudomonas/Flavimonas and Stenotrophomonas normally dominated during the early portions of cultures, although the lag phase of Stenotrophomonas appears to have been increased by surfactant addition. Acinetobacter calcoaceticus was the most frequently isolated microorganism during exposure to the saturate fraction of crude oil. Regardless of substrate, the culture medium supported a greater variety of organisms during the latter portions of cultures. Understanding the community structure and dynamics of mixed bacterial cultures involved in treatment of heterogeneous waste substrates may assist in process development and optimization studies.

  20. Bacterial Nanoscale Cultures for Phenotypic Multiplexed Antibiotic Susceptibility Testing

    PubMed Central

    Weibull, Emilie; Antypas, Haris; Kjäll, Peter; Brauner, Annelie; Andersson-Svahn, Helene

    2014-01-01

    An optimal antimicrobial drug regimen is the key to successful clinical outcomes of bacterial infections. To direct the choice of antibiotic, access to fast and precise antibiotic susceptibility profiling of the infecting bacteria is critical. We have developed a high-throughput nanowell antibiotic susceptibility testing (AST) device for direct, multiplexed analysis. By processing in real time the optical recordings of nanoscale cultures of reference and clinical uropathogenic Escherichia coli strains with a mathematical algorithm, the time point when growth shifts from lag phase to early logarithmic phase (Tlag) was identified for each of the several hundreds of cultures tested. Based on Tlag, the MIC could be defined within 4 h. Heatmap presentation of data from this high-throughput analysis allowed multiple resistance patterns to be differentiated at a glance. With a possibility to enhance multiplexing capacity, this device serves as a high-throughput diagnostic tool that rapidly aids clinicians in prescribing the optimal antibiotic therapy. PMID:24989602

  1. Detection of Blood Culture Bacterial Contamination using Natural Language Processing

    PubMed Central

    Matheny, Michael E.; FitzHenry, Fern; Speroff, Theodore; Hathaway, Jacob; Murff, Harvey J.; Brown, Steven H.; Fielstein, Elliot M.; Dittus, Robert S.; Elkin, Peter L.

    2009-01-01

    Microbiology results are reported in semi-structured formats and have a high content of useful patient information. We developed and validated a hybrid regular expression and natural language processing solution for processing blood culture microbiology reports. Multi-center Veterans Affairs training and testing data sets were randomly extracted and manually reviewed to determine the culture and sensitivity as well as contamination results. The tool was iteratively developed for both outcomes using a training dataset, and then evaluated on the test dataset to determine antibiotic susceptibility data extraction and contamination detection performance. Our algorithm had a sensitivity of 84.8% and a positive predictive value of 96.0% for mapping the antibiotics and bacteria with appropriate sensitivity findings in the test data. The bacterial contamination detection algorithm had a sensitivity of 83.3% and a positive predictive value of 81.8%. PMID:20351890

  2. Dynamics of adaptive immunity against phage in bacterial populations

    NASA Astrophysics Data System (ADS)

    Bradde, Serena; Vucelja, Marija; Tesileanu, Tiberiu; Balasubramanian, Vijay

    The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We propose a population dynamical model where immunity can be both acquired and lost. The model predicts regimes where bacterial and phage populations can co-exist, others where the populations oscillate, and still others where one population is driven to extinction. Our model considers two key parameters: (1) ease of acquisition and (2) spacer effectiveness in conferring immunity. Analytical calculations and numerical simulations show that if spacers differ mainly in ease of acquisition, or if the probability of acquiring them is sufficiently high, bacteria develop a diverse population of spacers. On the other hand, if spacers differ mainly in their effectiveness, their final distribution will be highly peaked, akin to a ``winner-take-all'' scenario, leading to a specialized spacer distribution. Bacteria can interpolate between these limiting behaviors by actively tuning their overall acquisition rate.

  3. Comparative study of normal and sensitive skin aerobic bacterial populations.

    PubMed

    Hillion, Mélanie; Mijouin, Lily; Jaouen, Thomas; Barreau, Magalie; Meunier, Pauline; Lefeuvre, Luc; Lati, Elian; Chevalier, Sylvie; Feuilloley, Marc G J

    2013-12-01

    The purpose of this study was to investigate if the sensitive skin syndrome, a frequent skin disorder characterized by abnormal painful reactions to environmental factors in the absence of visible inflammatory response, could be linked to a modification in the skin bacterial population. A total of 1706 bacterial isolates was collected at the levels of the forehead, cheekbone, inner elbow, and lower area of the scapula on the skin of normal and sensitive skin syndrome-suffering volunteers of both sexes and of different ages. Among these isolates, 21 strains were randomly selected to validate in a first step the Matrix-Assisted Laser Desorption/Ionization (MALDI)-Biotyper process as an efficient identification tool at the group and genus levels, by comparison to API(®) strips and 16S ribosomal RNA gene sequencing identification techniques. In a second step, identification of the skin microbiota isolates by the MALDI-Biotyper tool allowed to pinpoint some differences in terms of bacterial diversity with regard to the collection area, and the volunteer's age and gender. Finally, comparison of the skin microbiota from normal and sensitive skin syndrome-suffering volunteers pointed out gender-related variations but no detectable correlation between a phylum, a genus or a dominant bacterial species and the sensitive skin phenotype. This study reveals that there is no dysbiosis of aerobic cultivable bacteria associated with the sensitive skin syndrome and further demonstrates that the MALDI-Biotyper is a powerful technique that can be efficiently employed to the study of cultivable human skin bacteria. To our knowledge, this is the first study focusing on bacteria in the sensitive skin syndrome. These results are of potential importance for pharmaceutical and cosmetic industries, which are looking for new strategies to treat this multiparametric disorder.

  4. Attached bacterial populations shared by four species of aquatic angiosperms.

    PubMed

    Crump, Byron C; Koch, Evamaria W

    2008-10-01

    Symbiotic relationships between microbes and plants are common and well studied in terrestrial ecosystems, but little is known about such relationships in aquatic environments. We compared the phylogenetic diversities of leaf- and root-attached bacteria from four species of aquatic angiosperms using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of PCR-amplified 16S rRNA genes. Plants were collected from three beds in Chesapeake Bay at sites characterized as freshwater (Vallisneria americana), brackish (Potomogeton perfoliatus and Stuckenia pectinata), and marine (Zostera marina). DGGE analyses showed that bacterial communities were very similar for replicate samples of leaves from canopy-forming plants S. pectinata and P. perfoliatus and less similar for replicate samples of leaves from meadow-forming plants Z. marina and V. americana and of roots of all species. In contrast, bacterial communities differed greatly among plant species and between leaves and roots. DNA sequencing identified 154 bacterial phylotypes, most of which were restricted to single plant species. However, 12 phylotypes were found on more than one plant species, and several of these phylotypes were abundant in clone libraries and represented the darkest bands in DGGE banding patterns. Root-attached phylotypes included relatives of sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Deltaproteobacteria. Leaf-attached phylotypes included relatives of polymer-degrading Bacteroidetes and phototrophic Alphaproteobacteria. Also, leaves and roots of three plant species hosted relatives of methylotrophic Betaproteobacteria belonging to the family Methylophilaceae. These results suggest that aquatic angiosperms host specialized communities of bacteria on their surfaces, including several broadly distributed and potentially mutualistic bacterial populations.

  5. Comparative study of normal and sensitive skin aerobic bacterial populations

    PubMed Central

    Hillion, Mélanie; Mijouin, Lily; Jaouen, Thomas; Barreau, Magalie; Meunier, Pauline; Lefeuvre, Luc; Lati, Elian; Chevalier, Sylvie; Feuilloley, Marc G J

    2013-01-01

    The purpose of this study was to investigate if the sensitive skin syndrome, a frequent skin disorder characterized by abnormal painful reactions to environmental factors in the absence of visible inflammatory response, could be linked to a modification in the skin bacterial population. A total of 1706 bacterial isolates was collected at the levels of the forehead, cheekbone, inner elbow, and lower area of the scapula on the skin of normal and sensitive skin syndrome-suffering volunteers of both sexes and of different ages. Among these isolates, 21 strains were randomly selected to validate in a first step the Matrix-Assisted Laser Desorption/Ionization (MALDI)-Biotyper process as an efficient identification tool at the group and genus levels, by comparison to API® strips and 16S ribosomal RNA gene sequencing identification techniques. In a second step, identification of the skin microbiota isolates by the MALDI-Biotyper tool allowed to pinpoint some differences in terms of bacterial diversity with regard to the collection area, and the volunteer's age and gender. Finally, comparison of the skin microbiota from normal and sensitive skin syndrome-suffering volunteers pointed out gender-related variations but no detectable correlation between a phylum, a genus or a dominant bacterial species and the sensitive skin phenotype. This study reveals that there is no dysbiosis of aerobic cultivable bacteria associated with the sensitive skin syndrome and further demonstrates that the MALDI-Biotyper is a powerful technique that can be efficiently employed to the study of cultivable human skin bacteria. To our knowledge, this is the first study focusing on bacteria in the sensitive skin syndrome. These results are of potential importance for pharmaceutical and cosmetic industries, which are looking for new strategies to treat this multiparametric disorder. PMID:24151137

  6. Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.

    PubMed

    Sun, Christine L; Thomas, Brian C; Barrangou, Rodolphe; Banfield, Jillian F

    2016-04-01

    Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452,686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses.

  7. Diamagnetic levitation enhances growth of liquid bacterial cultures by increasing oxygen availability.

    PubMed

    Dijkstra, Camelia E; Larkin, Oliver J; Anthony, Paul; Davey, Michael R; Eaves, Laurence; Rees, Catherine E D; Hill, Richard J A

    2011-03-06

    Diamagnetic levitation is a technique that uses a strong, spatially varying magnetic field to reproduce aspects of weightlessness, on the Earth. We used a superconducting magnet to levitate growing bacterial cultures for up to 18 h, to determine the effect of diamagnetic levitation on all phases of the bacterial growth cycle. We find that diamagnetic levitation increases the rate of population growth in a liquid culture and reduces the sedimentation rate of the cells. Further experiments and microarray gene analysis show that the increase in growth rate is owing to enhanced oxygen availability. We also demonstrate that the magnetic field that levitates the cells also induces convective stirring in the liquid. We present a simple theoretical model, showing how the paramagnetic force on dissolved oxygen can cause convection during the aerobic phases of bacterial growth. We propose that this convection enhances oxygen availability by transporting oxygen around the liquid culture. Since this process results from the strong magnetic field, it is not present in other weightless environments, e.g. in Earth orbit. Hence, these results are of significance and timely to researchers considering the use of diamagnetic levitation to explore effects of weightlessness on living organisms and on physical phenomena.

  8. Diamagnetic levitation enhances growth of liquid bacterial cultures by increasing oxygen availability

    PubMed Central

    Dijkstra, Camelia E.; Larkin, Oliver J.; Anthony, Paul; Davey, Michael R.; Eaves, Laurence; Rees, Catherine E. D.; Hill, Richard J. A.

    2011-01-01

    Diamagnetic levitation is a technique that uses a strong, spatially varying magnetic field to reproduce aspects of weightlessness, on the Earth. We used a superconducting magnet to levitate growing bacterial cultures for up to 18 h, to determine the effect of diamagnetic levitation on all phases of the bacterial growth cycle. We find that diamagnetic levitation increases the rate of population growth in a liquid culture and reduces the sedimentation rate of the cells. Further experiments and microarray gene analysis show that the increase in growth rate is owing to enhanced oxygen availability. We also demonstrate that the magnetic field that levitates the cells also induces convective stirring in the liquid. We present a simple theoretical model, showing how the paramagnetic force on dissolved oxygen can cause convection during the aerobic phases of bacterial growth. We propose that this convection enhances oxygen availability by transporting oxygen around the liquid culture. Since this process results from the strong magnetic field, it is not present in other weightless environments, e.g. in Earth orbit. Hence, these results are of significance and timely to researchers considering the use of diamagnetic levitation to explore effects of weightlessness on living organisms and on physical phenomena. PMID:20667843

  9. In Vitro Culture of Previously Uncultured Oral Bacterial Phylotypes

    PubMed Central

    Thompson, Hayley; Rybalka, Alexandra; Moazzez, Rebecca; Dewhirst, Floyd E.

    2015-01-01

    Around a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use an in vitro biofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA). In vitro biofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxa Bacteroidetes bacteria HOT 365 and HOT 281, Lachnospiraceae bacteria HOT 100 and HOT 500, and Clostridiales bacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype, Actinomyces sp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected in in vitro-cultivated biofilms. Lachnospiraceae bacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture with Parvimonas micra or Veillonella dispar/parvula after colony hybridization-directed enrichment. The establishment of in vitro biofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture. PMID:26407883

  10. In vitro culture of previously uncultured oral bacterial phylotypes.

    PubMed

    Thompson, Hayley; Rybalka, Alexandra; Moazzez, Rebecca; Dewhirst, Floyd E; Wade, William G

    2015-12-01

    Around a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use an in vitro biofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA). In vitro biofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxa Bacteroidetes bacteria HOT 365 and HOT 281, Lachnospiraceae bacteria HOT 100 and HOT 500, and Clostridiales bacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype, Actinomyces sp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected in in vitro-cultivated biofilms. Lachnospiraceae bacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture with Parvimonas micra or Veillonella dispar/parvula after colony hybridization-directed enrichment. The establishment of in vitro biofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture.

  11. Bacterial community composition in Brazilian Anthrosols and adjacent soils characterized using culturing and molecular identification.

    PubMed

    O'Neill, B; Grossman, J; Tsai, M T; Gomes, J E; Lehmann, J; Peterson, J; Neves, E; Thies, J E

    2009-07-01

    Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared from soil extracts to isolate bacteria unique to the two soil types and then sequenced their 16S rRNA genes to determine their phylogenetic placement. Higher numbers of culturable bacteria, by over two orders of magnitude at the deepest sampling depths, were counted in the Anthrosols. Sequences of bacteria isolated on soil extract media yielded five possible new bacterial families. Also, a higher number of families in the bacteria were represented by isolates from the deeper soil depths in the Anthrosols. Higher bacterial populations and a greater diversity of isolates were found in all of the Anthrosols, to a depth of up to 1 m, compared to adjacent soils located within 50-500 m of their associated Anthrosols. Compared to standard culture media, soil extract media revealed diverse soil microbial populations adapted to the unique biochemistry and physiological ecology of these Anthrosols.

  12. Bacterial Growth in Mixed Cultures on Dissolved Organic Carbon from Humic and Clear Waters

    PubMed Central

    Tranvik, Lars J.; Höfle, Manfred G.

    1987-01-01

    Interactions between bacterial assemblages and dissolved organic carbon (DOC) from different sources were investigated. Mixed batch cultures were set up with water from a humic and a clear-water lake by a 1:20 dilution of the bacterial assemblage (1.0 μm of prefiltered lake water) with natural medium (sterile filtered lake water) in all four possible combinations of the two waters and their bacterial assemblages. Bacterial numbers and biomass, DOC, thymidine incorporation, ATP, and uptake of glucose and phenol were followed in these cultures. Growth curves and exponential growth rates were similar in all cultures, regardless of inoculum or medium. However, bacterial biomass produced was double in cultures based on water from the humic lake. The fraction of DOC consumed by heterotrophic bacteria during growth was in the same range, 15 to 22% of the total DOC pool, in all cultures. Bacterial growth efficiency, calculated from bacterial biomass produced and DOC consumed, was in the order of 20%. Glucose uptake reached a peak during exponential growth in all cultures. Phenol uptake was insignificant in the cultures based on the clear-water medium, but occurred in humic medium cultures after exponential growth. The similarity in the carbon budgets of all cultures indicated that the source of the bacterial assemblage did not have a significant effect on the overall carbon flux. However, fluxes of specific organic compounds differed, as reflected by glucose and phenol uptake, depending on the nature of the DOC and the bacterial assemblage. PMID:16347296

  13. Bacterial finite-size effects for population expansion under flow

    NASA Astrophysics Data System (ADS)

    Toschi, Federico; Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.; Brunsveld, Luc

    2016-11-01

    For organisms living in a liquid ecosystem, flow and flow gradients have a dual role as they transport nutrient while, at the same time, dispersing the individuals. In absence of flow and under homogeneous conditions, the growth of a population towards an empty region is usually described by a reaction-diffusion equation. The effect of fluid flow is not yet well understood and the interplay between transport of individuals and growth opens a wide scenario of possible behaviors. In this work, we study experimentally the dynamics of non-motile E. coli bacteria colonies spreading inside rectangular channels, in PDMS microfluidic devices. By use of a fluorescent microscope we analyze the dynamics of the population density subjected to different co- and counter-flow conditions and shear rates. A simple model incorporating growth, dispersion and drift of finite size beads is able to explain the experimental findings. This indicates that models based on the Fisher-Kolmogorov-Petrovsky-Piscounov equation (FKPP) may have to be supplemented with bacterial finite-size effects in order to be able to accurately reproduce experimental results for population spatial growth.

  14. Population Dynamics of Patients with Bacterial Resistance in Hospital Environment

    PubMed Central

    Qu, Leilei; Pan, Qiuhui; Gao, Xubin; He, Mingfeng

    2016-01-01

    During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1) have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings. PMID:26904150

  15. Population Dynamics of Patients with Bacterial Resistance in Hospital Environment.

    PubMed

    Qu, Leilei; Pan, Qiuhui; Gao, Xubin; He, Mingfeng

    2016-01-01

    During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1) have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings.

  16. Cultural competency and recovery within diverse populations.

    PubMed

    Ida, D J

    2007-01-01

    Recovery for diverse populations with mental health problems includes communities of color, those with limited English proficiency and individuals who are lesbian, gay, bisexual or transgender (LGBT). The process of healing and recovery must take into consideration the critical role of culture and language and look at the individual within the context of an environment that is influenced by racism, sexism, colonization, homophobia, and poverty as well as the stigma and shame associated with having a mental illness. Recovery must assess the impact of isolation brought about by cultural and language barriers and work towards reducing the negative influence it has on the emotional and physical well-being of the person. It is imperative that recovery occur at multiple levels and involves the person in recovery, the service provider, the larger community and the system that establishes policies that often work against those who do not fit the mold of what mainstream society considers being "the norm." Recovery must respect the cultural and language backgrounds of the individual.

  17. Diversity of bacterial population of table olives assessed by PCR-DGGE analysis.

    PubMed

    Randazzo, Cinzia L; Ribbera, Angela; Pitino, Iole; Romeo, Flora V; Caggia, Cinzia

    2012-10-01

    Nocellara Etnea and Geracese table olives are produced according to traditional process, in which lactic acid bacteria (LAB) and yeasts are the dominant microorganisms. With the aim to evaluate the effect of selected starter cultures on dynamics of bacterial population during fermentation and on growth/survival of Listeria spp. artificially inoculated into the olive brine, a polyphasic approach based on the combination of culturing and PCR-DGGE analysis was applied. Plating results showed a different concentration of the major bacterial groups considered among cultivars and the beneficial effect of LAB starters, which clearly inhibited Enterobacteriaceae. Moreover, results indicated that the brine conditions applied did not support the growth/survival of Listeria monocytogenes strain, artificially inoculated, highlighting the importance of selecting right fermentation parameters for assuring microbiological safety of the final products. Comparison of DGGE profile of Nocellara Etnea and Geracese table olives, displayed a great difference among cultivars, revealing a wide biodiversity within Lactobacillus population during Geracese olives fermentation. Based on cloning and sequencing of the most dominant amplicons, the presence, among others, of Lactobacillus paracollinoides and Lactobacillus coryniformis in Geracese table olives was revealed in table olives for the first time.

  18. Polycyclic aromatic hydrocarbon biodegradation by a mixed bacterial culture

    SciTech Connect

    Dreyer, G.; Koenig, J.; Ringpfeil, M.

    1995-12-31

    Biodegradation of polycyclic aromatic hydrocarbons (PAHs), which are a complex mixture of organic compounds, was demonstrated using a bacterial mixed culture selected from a contaminated site by the BIOPRACT GmbH. The investigations were carried out in a laboratory fermenter using emulsified tar oil as the substrate to determine the following: (1) concentration of the single PAH and of the sum of PAHs relative to fermentation time, (2) carbon dioxide (CO{sub 2}) and oxygen (O{sub 2}) content in the outflowing air during fermentation, (3) chemical oxygen demand (COD) of the broth, and (4) toxicity of the broth before and after fermentation according to the bioluminescence test (DIN 38412, part 34/1). The results of this model experiment indicated that the investigated mixed culture is able to effectively metabolize the PAHs contained in tar oil, including the higher condensed compounds such as benzo(a)pyrene. In the first 8 days of fermentation, the PAH sum decreased to below 5% of the starting concentration connected with a five-fold reduction of the toxic effect on Vibrio fischeri. The PAH degradation rate correlated with the rate of COD decrease, the rate of evolving CO{sub 2}, and the consumption of O{sub 2}.

  19. The Molecular Bacterial Load Assay Replaces Solid Culture for Measuring Early Bactericidal Response to Antituberculosis Treatment

    PubMed Central

    Mtafya, Bariki; Phillips, Patrick P. J.; Hoelscher, Michael; Ntinginya, Elias N.; Kohlenberg, Anke; Rachow, Andrea; Rojas-Ponce, Gabriel; McHugh, Timothy D.; Heinrich, Norbert

    2014-01-01

    We evaluated the use of the molecular bacterial load (MBL) assay, for measuring viable Mycobacterium tuberculosis in sputum, in comparison with solid agar and liquid culture. The MBL assay provides early information on the rate of decline in bacterial load and has technical advantages over culture in either form. PMID:24871215

  20. MULTISCALE MODELS OF TAXIS-DRIVEN PATTERNING IN BACTERIAL POPULATIONS

    PubMed Central

    XUE, CHUAN; OTHMER, HANS G.

    2009-01-01

    Spatially-distributed populations of various types of bacteria often display intricate spatial patterns that are thought to result from the cellular response to gradients of nutrients or other attractants. In the past decade a great deal has been learned about signal transduction, metabolism and movement in E. coli and other bacteria, but translating the individual-level behavior into population-level dynamics is still a challenging problem. However, this is a necessary step because it is computationally impractical to use a strictly cell-based model to understand patterning in growing populations, since the total number of cells may reach 1012 - 1014 in some experiments. In the past phenomenological equations such as the Patlak-Keller-Segel equations have been used in modeling the cell movement that is involved in the formation of such patterns, but the question remains as to how the microscopic behavior can be correctly described by a macroscopic equation. Significant progress has been made for bacterial species that employ a “run-and-tumble” strategy of movement, in that macroscopic equations based on simplified schemes for signal transduction and turning behavior have been derived [14, 15]. Here we extend previous work in a number of directions: (i) we allow for time-dependent signals, which extends the applicability of the equations to natural environments, (ii) we use a more general turning rate function that better describes the biological behavior, and (iii) we incorporate the effect of hydrodynamic forces that arise when cells swim in close proximity to a surface. We also develop a new approach to solving the moment equations derived from the transport equation that does not involve closure assumptions. Numerical examples show that the solution of the lowest-order macroscopic equation agrees well with the solution obtained from a Monte Carlo simulation of cell movement under a variety of temporal protocols for the signal. We also apply the method to

  1. Blood Culture Bottle and Standard Culture Bottle Methods for Detection of Bacterial Pathogens in Parapneumonic Pleural Effusion

    PubMed Central

    Charoentunyarak, Surapan; Kananuraks, Sarassawan; Chindaprasirt, Jarin; Limpawattana, Panita; Sawanyawisuth, Kittisak

    2015-01-01

    Background: Bacterial parapneumonic pleural effusions (PPEs) have high morbidity. The accurate identification of pathogens is vital for initiating the appropriate treatment. A previous study suggested that the use of blood culture bottles might improve the bacterial yield in PPEs. Objectives: The aim of this study was to compare the culture positivity rate by the blood culture bottles and the standard culture bottles in bacterial PPEs. Patients and Methods: Patients diagnosed with PPEs at the Khon Kaen Hospital, Khon Kaen, Thailand, which is an endemic area of melioidosis, were enrolled consecutively and prospectively. The study period was from June first, 2012 to December 31st, 2013. The inclusion criteria were adult patients aged > 18 years, with exudative, neutrophilic parapneumonic effusion. Of the pleural fluid samples, 5 mL from all the eligible patients were collected in both blood culture bottles and the standard culture bottles. Patient baseline characteristics, laboratory results, and culture results were collected and analyzed. Results: During the study period, 129 patients met the study criteria. The bacteria-positive rate of pleural fluid culture using the standard culture bottle was 14.0%, whereas the positive rate using blood culture bottles was 24.0% (P < 0.001). Conclusions: The blood culture bottle method is more effective than the standard culture bottle method for the detection of bacterial pathogens in PPE. PMID:26587217

  2. The structure of resting bacterial populations in soil and subsoil permafrost.

    PubMed

    Soina, Vera S; Mulyukin, Andrei L; Demkina, Elena V; Vorobyova, Elena A; El-Registan, Galina I

    2004-01-01

    The structure of individual cells in microbial populations in situ of the Arctic and Antarctic permafrost was studied by scanning and transmission electron microscopy methods and compared with that of cyst-like resting forms generated under special conditions by the non-spore-forming bacteria Arthrobacter and Micrococcus isolated from the permafrost. Electron microscopy examination of microorganisms in situ revealed several types of bacterial cells having no signs of damage, including "dwarf" curved forms similar to nanoforms. Intact bacterial cells in situ and frozen cultures of the permafrost isolates differed from vegetative cells by thickened cell walls, the altered structure of cytoplasm, and the compact nucleoid, and were similar in these features to cyst-like resting forms of non-spore-forming "permafrost" bacterial strains of Arthrobacter and Micrococcus spp. Cyst-like cells, being resistant to adverse external factors, are regarded as being responsible for survival of the non-spore-formers under prolonged exposure to subzero temperatures and can be a target to search for living microorganisms in natural environments both on the Earth and on extraterrestrial bodies.

  3. The Structure of Resting Bacterial Populations in Soil and Subsoil Permafrost

    NASA Astrophysics Data System (ADS)

    Soina, Vera S.; Mulyukin, Andrei L.; Demkina, Elena V.; Vorobyova, Elena A.; El-Registan, Galina I.

    2004-09-01

    The structure of individual cells in microbial populations in situ of the Arctic and Antarctic permafrost was studied by scanning and transmission electron microscopy methods and compared with that of cyst-like resting forms generated under special conditions by the non-sporeforming bacteria Arthrobacter and Micrococcus isolated from the permafrost. Electron microscopy examination of microorganisms in situ revealed several types of bacterial cells having no signs of damage, including "dwarf" curved forms similar to nanoforms. Intact bacterial cells in situ and frozen cultures of the permafrost isolates differed from vegetative cells by thickened cell walls, the altered structure of cytoplasm, and the compact nucleoid, and were similar in these features to cyst-like resting forms of non-spore-forming "permafrost" bacterial strains of Arthrobacter and Micrococcus spp. Cyst-like cells, being resistant to adverse external factors, are regarded as being responsible for survival of the non-spore-formers under prolonged exposure to subzero temperatures and can be a target to search for living microorganisms in natural environments both on the Earth and on extraterrestrial bodies.

  4. Population dynamics of zooxanthellae during a bacterial bleaching event

    NASA Astrophysics Data System (ADS)

    Shenkar, N.; Fine, M.; Kramarsky-Winter, E.; Loya, Y.

    2006-05-01

    Each summer 80-90% of the colonies of Oculina patagonica undergo bleaching off the Mediterranean coast of Israel. To investigate fluctuations through a yearly bleaching cycle, monthly measurements of zooxanthella density, mitotic index and chlorophyll- a concentration were conducted. Results showed (1) a significant negative correlation between sea surface temperature (SST) and zooxanthella density; (2) both significantly lower zooxanthella mitotic index and higher chlorophyll -a per zooxanthella content during the bleaching season compared with the non-bleaching period; (3) prior to bleaching, a lag between the peak of zooxanthella density and chlorophyll- a concentration followed by a similar lag during recovery. Zooxanthella density declined significantly between March and May while chlorophyll- a concentration peaked in April, and then declined. Zooxanthella density increased significantly in November while chlorophyll- a concentration increased significantly in January. We conclude that during bacterial bleaching events, zooxanthellae are severely damaged. However, by the time of the following bleaching event the coral tissues regain their “normal” (pre-bleaching) zooxanthella population density.

  5. Bacterial population structure and dynamics during the development of almond drupes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: To describe the bacterial populations and their dynamics during the development of almond drupes. Methods and Results: We examined 16S rRNA gene libraries derived from the bacterial populations on almond drupes at three stages of development: 1) when the drupes were full sized, but before embr...

  6. MULTISCALE MODELS OF TAXIS-DRIVEN PATTERNING IN BACTERIAL POPULATIONS.

    PubMed

    Xue, Chuan; Othmer, Hans G

    2009-01-01

    Spatially-distributed populations of various types of bacteria often display intricate spatial patterns that are thought to result from the cellular response to gradients of nutrients or other attractants. In the past decade a great deal has been learned about signal transduction, metabolism and movement in E. coli and other bacteria, but translating the individual-level behavior into population-level dynamics is still a challenging problem. However, this is a necessary step because it is computationally impractical to use a strictly cell-based model to understand patterning in growing populations, since the total number of cells may reach 10(12) - 10(14) in some experiments. In the past phenomenological equations such as the Patlak-Keller-Segel equations have been used in modeling the cell movement that is involved in the formation of such patterns, but the question remains as to how the microscopic behavior can be correctly described by a macroscopic equation. Significant progress has been made for bacterial species that employ a "run-and-tumble" strategy of movement, in that macroscopic equations based on simplified schemes for signal transduction and turning behavior have been derived [14, 15]. Here we extend previous work in a number of directions: (i) we allow for time-dependent signals, which extends the applicability of the equations to natural environments, (ii) we use a more general turning rate function that better describes the biological behavior, and (iii) we incorporate the effect of hydrodynamic forces that arise when cells swim in close proximity to a surface. We also develop a new approach to solving the moment equations derived from the transport equation that does not involve closure assumptions. Numerical examples show that the solution of the lowest-order macroscopic equation agrees well with the solution obtained from a Monte Carlo simulation of cell movement under a variety of temporal protocols for the signal. We also apply the method to

  7. Bacterial Profile of Dentine Caries and the Impact of pH on Bacterial Population Diversity

    PubMed Central

    Kianoush, Nima; Adler, Christina J.; Nguyen, Ky-Anh T.; Browne, Gina V.; Simonian, Mary; Hunter, Neil

    2014-01-01

    Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3–V4 region) to compare microbial communities in layers ranging in pH from 4.5–7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies. PMID:24675997

  8. Cultural relevance of physical activity intervention research with underrepresented populations

    PubMed Central

    Conn, Vicki S.; Chan, Keith; Banks, JoAnne; Ruppar, Todd M.; Scharff, Jane

    2015-01-01

    This paper describes cultural relevance in physical activity intervention research with underrepresented populations. Seventy-one extant studies which tested interventions to increase physical activity among underrepresented adults were included. Verbatim descriptions of efforts to enhance cultural relevance of study designs and interventions were extracted and then content analyzed. We found strategies to enhance cultural relevance of interventions as soliciting input from population members, linking intervention content with values, addressing language and literacy challenges, incorporating population media figures, using culturally relevant forms of physical activity, and addressing specific population linked barriers to activity. Methodological approaches included specialized recruitment and study locations, culturally relevant measures, underrepresented personnel, and cost-awareness study procedures to prevent fiscal barriers to participation. Most reported activities were surface matching. Existing research neither compared the effectiveness of cultural relevance approaches to standardized interventions nor addressed economic, education, geographic, or cultural heterogeneity among groups. PMID:25228486

  9. Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2014-12-01

    Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine

  10. Direct detection of various pathogens by loop-mediated isothermal amplification assays on bacterial culture and bacterial colony.

    PubMed

    Yan, Muxia; Li, Weidong; Zhou, Zhenwen; Peng, Hongxia; Luo, Ziyan; Xu, Ling

    2017-01-01

    In this work, loop-mediated isothermal amplification based detection assay using bacterial culture and bacterial colony for various common pathogens direct detection had been established, evaluated and further applied. A total of five species of common pathogens and nine detection targets (tlh, tdh and trh for V. Parahaemolyticus, rfbE, stx1 and stx2 for E. coli, oprI for P. aeruginosa, invA for Salmonella and hylA for L. monocytogenes) were performed on bacterial culture and bacterial colony LAMP. To evaluate and optimize this assay, a total of 116 standard strains were included. Then, for each detected targets, 20 random selected strains were applied. Results were determined through both visual observation of the changed color by naked eye and electrophoresis, which increased the accuracy of survey. The minimum adding quantity of each primer had been confirmed, and the optimal amplification was obtained under 65 °C for 45 min with 25 μl reaction volume. The detection limit of bacterial culture LAMP and PCR assay were determined to be 10(2) and 10(4) or 10(5) CFU/reaction, respectively. No false positive amplification was observed when subjecting the bacterial -LAMP assay to 116 reference strains. This was the first report of colony-LAMP and culture-LAMP assay, which had been demonstrated to be a fast, reliable, cost-effective and simple method on detection of various common pathogens.

  11. Protozoan Grazing, Bacterial Activity, and Mineralization in Two-Stage Continuous Cultures

    PubMed Central

    Bloem, Jaap; Starink, Mathieu; Bär-Gilissen, Marie-José B.; Cappenberg, Thomas E.

    1988-01-01

    In two-stage continuous cultures, at bacterial concentrations, biovolumes, and growth rates similar to values found in Lake Vechten, ingestion rates of heterotrophic nanoflagellates (HNAN) increased from 2.3 bacteria HNAN−1 · h−1 at a growth rate of 0.15 day−1 to 9.2 bacteria · HNAN−1 · h−1 at a growth rate of 0.65 day−1. On a yeast extract medium with a C/N/P ratio of 100:15:1.2 (Redfield ratio), a mixed bacterial population showed a yield of 18% (C/C) and a specific carbon content of 211 fg of C · μm−3. The HNAN carbon content and yield were estimated at 127 fg of C · μm−3 and 47% (C/C). Although P was not growth limiting, HNAN accelerated the mineralization of PO4-P from dissolved organic matter by 600%. The major mechanism of P remineralization appeared to be direct consumption of bacteria by HNAN. N mineralization was performed mainly (70%) by bacteria but was increased 30% by HNAN. HNAN did not enhance the decomposition of the relatively mineral-rich dissolved organic matter. An accelerated decomposition of organic carbon by protozoa may be restricted to mineral-poor substrates and may be explained mainly by protozoan nutrient regeneration. Growth and grazing in the cultures were compared with methods for in situ estimates. Thymidine incorporation by actively growing bacteria yielded an empirical conversion factor of 1.1 × 1018 bacteria per mol of thymidine incorporated into DNA. However, nongrowing bacteria also showed considerable incorporation. Protozoan grazing was found to be accurately measured by uptake of fluorescently labeled bacteria, whereas artificial fluorescent microspheres were not ingested, and selective prokaryotic inhibitors blocked not only bacterial growth but also protozoan grazing. PMID:16347801

  12. Evaluation of postmortem bacterial migration using culturing and real-time quantitative PCR.

    PubMed

    Tuomisto, Sari; Karhunen, Pekka J; Vuento, Risto; Aittoniemi, Janne; Pessi, Tanja

    2013-07-01

    Postmortem bacteriology can be a valuable tool for evaluating deaths due to bacterial infection or for researching the involvement of bacteria in various diseases. In this study, time-dependent postmortem bacterial migration into liver, mesenteric lymph node, pericardial fluid, portal, and peripheral vein was analyzed in 33 autopsy cases by bacterial culturing and real-time quantitative polymerase chain reaction (RT-qPCR). None suffered or died from bacterial infection. According to culturing, pericardial fluid and liver were the most sterile samples up to 5 days postmortem. In these samples, multigrowth and staphylococci were not or rarely detected. RT-qPCR was more sensitive and showed higher bacterial positivity in all samples. Relative amounts of intestinal bacterial DNA (bifidobacteria, bacteroides, enterobacter, clostridia) increased with time. Sterility of blood samples was low during the studied time periods (1-7 days). The best postmortem microbiological sampling sites were pericardial fluid and liver up to 5 days after death.

  13. Development of biological process with pure bacterial cultures for effective bioconversion of sewage treatment plant sludge.

    PubMed

    Alam, Zahangir; Muyibi, Suleyman A; Jamal, Parveen

    2007-02-15

    Forty-six bacterial strains were isolated from nine different sources in four treatment plants namely Indah Water Konsortium (IWK) sewage treatment plant (STP), International Islamic University Malaysia (IIUM) wastewater treatment plant-1,-2 and -3 to evaluate the bioconversion process in terms of efficient biodegradation and bioseparation. The bacterial strains isolated were found to be 52.2% (24 isolates) and 47.8% (22 isolates) in the IWK and IIUM treatment plants, respectively. The results showed that higher microbial population (9-10 x 10(4) cfu/mL) was observed in the secondary clarifier of IWK treatment plant. Among the isolates, 23 isolates were gram-positive bacillus (GPB) and gram-positive cocci (GPC), 19 isolates were gram-negative bacillus (GNB) and gram-negative cocci (GNC), and the rest were undetermined. Gram-negative cocci (GNC) were not found in the isolates from IWK. A total of 15 bacterial strains were selected for effective and efficient sludge bioconversion. All the strains were tested against sludge (1% total suspended solids, TSS) to evaluate the biosolids production (TSS% content), chemical oxygen demand (COD) removal and filtration rate (filterability test). The strain S-1 (IWK1001) showed lower TSS content (0.8% TSS), maximum COD removal (84%) and increased filterability (1.1 min/10 mL of filtrate) of treated sludge followed by the strains S-11, S-14, S-2, S-15, S-13, S-7, S-8, S-4, S-3, S-6, S-12, S-16, S-17 and S-9. The pH values in the fermentation broth were affected by the bacterial cultures and recorded as well. Effective bioconversion was observed during the first three days of sludge treatment.

  14. Mathematical Modelling of Bacterial Populations in Bio-remediation Processes

    NASA Astrophysics Data System (ADS)

    Vasiliadou, Ioanna A.; Vayenas, Dimitris V.; Chrysikopoulos, Constantinos V.

    2011-09-01

    An understanding of bacterial behaviour concerns many field applications, such as the enhancement of water, wastewater and subsurface bio-remediation, the prevention of environmental pollution and the protection of human health. Numerous microorganisms have been identified to be able to degrade chemical pollutants, thus, a variety of bacteria are known that can be used in bio-remediation processes. In this study the development of mathematical models capable of describing bacterial behaviour considered in bio-augmentation plans, such as bacterial growth, consumption of nutrients, removal of pollutants, bacterial transport and attachment in porous media, is presented. The mathematical models may be used as a guide in designing and assessing the conditions under which areas contaminated with pollutants can be better remediated.

  15. Reductive genome evolution at both ends of the bacterial population size spectrum.

    PubMed

    Batut, Bérénice; Knibbe, Carole; Marais, Gabriel; Daubin, Vincent

    2014-12-01

    Bacterial genomes show substantial variations in size. The smallest bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum.

  16. Utilising bacterial communities associated with digested piggery effluent as a primary food source for the batch culture of Moina australiensis.

    PubMed

    Patil, Sayali S; Ward, Andrew J; Kumar, Martin S; Ball, Andrew S

    2010-05-01

    In this study, a cladoceran planktonic invertebrate, Moina australiensis was uniquely cultured in two stage digested piggery wastewater and fed associated piggery wastewater bacteria. The viability of M. australiensis cultured in digested piggery wastewater under closed dark conditions to limit phytoplankton activity was tested by determining suitable effluent total ammonia nitrogen (TAN) concentrations. The highest total M. australiensis biomass production 0.94+/-0.47g and the rate of population increase (r) 0.15+/-0.08 was recorded in the 30mgl(-1) TAN concentration treatment. The lowest 'r' values and decreased biomass production was observed with increasing TAN concentration levels. This study, also focused on profiling and quantification of the associated bacterial populations in the wastewater culture media and within the digestive tract of M. australiensis by denaturing gradient gel electrophoresis (DGGE) and real-time polymerase chain reaction (RT-PCR) which revealed the feeding specificity of M. australiensis towards "gamma-Proteobacteria."

  17. Cultural humility and working with marginalized populations in developing countries.

    PubMed

    Kools, Susan; Chimwaza, Angela; Macha, Swebby

    2015-03-01

    Population health needs in developing countries are great and countries are scaling up health professional education to meet these needs. Marginalized populations, in particular, are vulnerable to poor health and health care. This paper presents a culturally appropriate diversity training program delivered to Global Health Fellows who are educators and leaders in health professions in Malawi and Zambia. The purpose of this interprofessional education experience was to promote culturally competent and humble care for marginalized populations.

  18. Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities.

    PubMed

    Rubbens, Peter; Props, Ruben; Boon, Nico; Waegeman, Willem

    2017-01-01

    Bacterial cells can be characterized in terms of their cell properties using flow cytometry. Flow cytometry is able to deliver multiparametric measurements of up to 50,000 cells per second. However, there has not yet been a thorough survey concerning the identification of the population to which bacterial single cells belong based on flow cytometry data. This paper not only aims to assess the quality of flow cytometry data when measuring bacterial populations, but also suggests an alternative approach for analyzing synthetic microbial communities. We created so-called in silico communities, which allow us to explore the possibilities of bacterial flow cytometry data using supervised machine learning techniques. We can identify single cells with an accuracy >90% for more than half of the communities consisting out of two bacterial populations. In order to assess to what extent an in silico community is representative for its synthetic counterpart, we created so-called abundance gradients, a combination of synthetic (i.e., in vitro) communities containing two bacterial populations in varying abundances. By showing that we are able to retrieve an abundance gradient using a combination of in silico communities and supervised machine learning techniques, we argue that in silico communities form a viable representation for synthetic bacterial communities, opening up new opportunities for the analysis of synthetic communities and bacterial flow cytometry data in general.

  19. On a Mathematical Model with Noncompact Boundary Conditions Describing Bacterial Population

    NASA Astrophysics Data System (ADS)

    Boulanouar, Mohamed

    2013-04-01

    In this work, we are concerned with the well-posedness of a mathematical model describing a maturation-velocity structured bacterial population. Each bacterium is distinguished by its degree of maturity and its maturation velocity. The bacterial mitosis is mathematically described by noncompact boundary conditions. We show that the mathematical model is governed by a positive strongly continuous semigroup.

  20. Grazing activity and ruminal bacterial population associated with frothy bloat in steers grazing winter wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two grazing experiments were designed to elucidate the shifts in rumen bacterial populations (Exp. 1) and grazing activities (Exp. 2) in wheat forage diets between bloated and non-bloated steers. In Exp. 1, the bacterial DNA density was greatest for Ruminococcus flavefaciens, Streptococcus bovis, a...

  1. Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities

    PubMed Central

    Boon, Nico; Waegeman, Willem

    2017-01-01

    Bacterial cells can be characterized in terms of their cell properties using flow cytometry. Flow cytometry is able to deliver multiparametric measurements of up to 50,000 cells per second. However, there has not yet been a thorough survey concerning the identification of the population to which bacterial single cells belong based on flow cytometry data. This paper not only aims to assess the quality of flow cytometry data when measuring bacterial populations, but also suggests an alternative approach for analyzing synthetic microbial communities. We created so-called in silico communities, which allow us to explore the possibilities of bacterial flow cytometry data using supervised machine learning techniques. We can identify single cells with an accuracy >90% for more than half of the communities consisting out of two bacterial populations. In order to assess to what extent an in silico community is representative for its synthetic counterpart, we created so-called abundance gradients, a combination of synthetic (i.e., in vitro) communities containing two bacterial populations in varying abundances. By showing that we are able to retrieve an abundance gradient using a combination of in silico communities and supervised machine learning techniques, we argue that in silico communities form a viable representation for synthetic bacterial communities, opening up new opportunities for the analysis of synthetic communities and bacterial flow cytometry data in general. PMID:28122063

  2. Dissociation of a population of Pectobacterium atrosepticum SCRI1043 in tobacco plants: formation of bacterial emboli and dormant cells.

    PubMed

    Gorshkov, Vladimir; Daminova, Amina; Ageeva, Marina; Petrova, Olga; Gogoleva, Natalya; Tarasova, Nadezhda; Gogolev, Yuri

    2014-05-01

    The population dynamics of Pectobacterium atrosepticum SCRI1043 (Pba) within tobacco plants was monitored from the time of inoculation until after long-term preservation of microorganisms in the remnants of dead plants. We found and characterised peculiar structures that totally occlude xylem vessels, which we have named bacterial emboli. Viable but non-culturable (VBN) Pba cells were identified in the remnants of dead plants, and the conditions for resuscitation of these VBN cells were established. Our investigation shows that dissociation of the integrated bacterial population during plant colonisation forms distinct subpopulations and cell morphotypes, which are likely to perform specific functions that ensure successful completion of the life cycle within the plant.

  3. Design Factors Affect User Experience for Different Cultural Populations

    ERIC Educational Resources Information Center

    Chu, Sauman

    2016-01-01

    With increasing changes in our demographic populations and new immigrants settling in the US, there is an increasing need for visual communications that address the diversity of our populations. This paper draws from the results of the researcher's several past research and teaching projects that worked with different cultural populations. These…

  4. Culturable bacterial microbiota of the stomach of Helicobacter pylori positive and negative gastric disease patients.

    PubMed

    Khosravi, Yalda; Dieye, Yakhya; Poh, Bee Hoon; Ng, Chow Goon; Loke, Mun Fai; Goh, Khean Lee; Vadivelu, Jamuna

    2014-01-01

    Human stomach is the only known natural habitat of Helicobacter pylori (Hp), a major bacterial pathogen that causes different gastroduodenal diseases. Despite this, the impact of Hp on the diversity and the composition of the gastric microbiota has been poorly studied. In this study, we have analyzed the culturable gastric microbiota of 215 Malaysian patients, including 131 Hp positive and 84 Hp negative individuals that were affected by different gastric diseases. Non-Hp bacteria isolated from biopsy samples were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry based biotyping and 16SrRNA sequencing. The presence of Hp did not significantly modify the diversity of the gastric microbiota. However, correlation was observed between the isolation of Streptococci and peptic ulcer disease. In addition, as a first report, Burkholderia pseudomallei was also isolated from the gastric samples of the local population. This study suggested that there may be geographical variations in the diversity of the human gastric microbiome. Geographically linked diversity in the gastric microbiome and possible interactions between Hp and other bacterial species from stomach microbiota in pathogenesis are proposed for further investigations.

  5. Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

    PubMed Central

    Nanda, Arun M.; Thormann, Kai

    2014-01-01

    Bacteriophages and genetic elements, such as prophage-like elements, pathogenicity islands, and phage morons, make up a considerable amount of bacterial genomes. Their transfer and subsequent activity within the host's genetic circuitry have had a significant impact on bacterial evolution. In this review, we consider what underlying mechanisms might cause the spontaneous activity of lysogenic phages in single bacterial cells and how the spontaneous induction of prophages can lead to competitive advantages for and influence the lifestyle of bacterial populations or the virulence of pathogenic strains. PMID:25404701

  6. Aerobic Heterotrophic Bacterial Populations of Sewage and Activated Sludge

    PubMed Central

    Prakasam, T. B. S.; Dondero, N. C.

    1970-01-01

    Two procedures, the confidence interval method and Mountford's index, were tested in analyses of the microbial populations of 11 laboratory activated sludges acclimated to aromatic compounds. The two methods gave somewhat different results but indicated that the populations were quite dissimilar. The activity of seven of the sludges correlated well with the population structure. Some considerations in analysis of microbial population structure are discussed. PMID:5418947

  7. Expansion of Cultured Bacterial Diversity by Large-Scale Dilution-to-Extinction Culturing from a Single Seawater Sample.

    PubMed

    Yang, Seung-Jo; Kang, Ilnam; Cho, Jang-Cheon

    2016-01-01

    High-throughput cultivation (HTC) based on a dilution-to-extinction method has been applied broadly to the cultivation of marine bacterial groups, which has often led to the repeated isolation of abundant lineages such as SAR11 and oligotrophic marine gammaproteobacteria (OMG). In this study, to expand the phylogenetic diversity of HTC isolates, we performed a large-scale HTC with a single surface seawater sample collected from the East Sea, the Western Pacific Ocean. Phylogenetic analyses of the 16S rRNA genes from 847 putative pure cultures demonstrated that some isolates were affiliated with not-yet-cultured clades, including the OPB35 and Puniceicoccaceae marine group of Verrucomicrobia and PS1 of Alphaproteobacteria. In addition, numerous strains were obtained from abundant clades, such as SAR11, marine Roseobacter clade, OMG (e.g., SAR92 and OM60), OM43, and SAR116, thereby increasing the size of available culture resources for representative marine bacterial groups. Comparison between the composition of HTC isolates and the bacterial community structure of the seawater sample used for HTC showed that diverse marine bacterial groups exhibited various growth capabilities under our HTC conditions. The growth response of many bacterial groups, however, was clearly different from that observed with conventional plating methods, as exemplified by numerous isolates of the SAR11 clade and Verrucomicrobia. This study showed that a large number of novel bacterial strains could be obtained by an extensive HTC from even a small number of samples.

  8. Assessment of microbial populations dynamics in a blue cheese by culturing and denaturing gradient gel electrophoresis.

    PubMed

    Alegría, Angel; González, Renata; Díaz, Mario; Mayo, Baltasar

    2011-03-01

    The composition and development of microbial population during the manufacture and ripening of two batches of a blue-veined cheese was examined by culturing and polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) (PCR-DGGE). Nine selective and/or differential media were used to track the cultivable populations of total and indicator microbial groups. For PCR-DGGE, the V3 hyper variable region of the bacterial 16S rRNA gene and the eukaryotic D1 domain of 28S rDNA were amplified with universal primers, specific for prokaryotes and eukaryotes, respectively. Similarities and differences between the results obtained by the culturing and the molecular method were recorded for some populations. Culturing analysis allows minority microbial groups (coliforms, staphylococci) to be monitored, although in this study PCR-DGGE identified a population of Streptococcus thermophilus that went undetected by culturing. These results show that the characterization of the microbial populations interacting and evolving during the cheese-making process is improved by combining culturing and molecular methods.

  9. Characterization of an isoproturon mineralizing bacterial culture enriched from a French agricultural soil.

    PubMed

    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.

  10. Differences in activity profile of bacterial cultures studied by dynamic speckle patterns

    NASA Astrophysics Data System (ADS)

    Ramírez-Miquet, E. E.; Otero, I.; Rodríguez, D.; Darias, J. G.; Combarro, A. M.; Contreras, O. R.

    2013-02-01

    We outline the main differences in the activity profile of bacterial cultures studied by dynamic laser speckle (or biospeckle) patterns. The activity is detected in two sorts of culture mediums. The optical setup and the experimental procedure are presented. The experimentally obtained images are processed by the temporal difference method and a qualitative assessment is made with the time history of speckle patterns of the sample. The main differences are studied after changing the culture medium composition. We conclude that the EC medium is suitable to detect the E. coli bacterial presence in early hours and that Mueller Hinton agar delays some additional hours to make possible the assessment of bacteria in time.

  11. Most of the Dominant Members of Amphibian Skin Bacterial Communities Can Be Readily Cultured

    PubMed Central

    Becker, Matthew H.; Hughey, Myra C.; Swartwout, Meredith C.; Jensen, Roderick V.; Belden, Lisa K.

    2015-01-01

    Currently, it is estimated that only 0.001% to 15% of bacteria in any given system can be cultured by use of commonly used techniques and media, yet culturing is critically important for investigations of bacterial function. Despite this situation, few studies have attempted to link culture-dependent and culture-independent data for a single system to better understand which members of the microbial community are readily cultured. In amphibians, some cutaneous bacterial symbionts can inhibit establishment and growth of the fungal pathogen Batrachochytrium dendrobatidis, and thus there is great interest in using these symbionts as probiotics for the conservation of amphibians threatened by B. dendrobatidis. The present study examined the portion of the culture-independent bacterial community (based on Illumina amplicon sequencing of the 16S rRNA gene) that was cultured with R2A low-nutrient agar and whether the cultured bacteria represented rare or dominant members of the community in the following four amphibian species: bullfrogs (Lithobates catesbeianus), eastern newts (Notophthalmus viridescens), spring peepers (Pseudacris crucifer), and American toads (Anaxyrus americanus). To determine which percentage of the community was cultured, we clustered Illumina sequences at 97% similarity, using the culture sequences as a reference database. For each amphibian species, we cultured, on average, 0.59% to 1.12% of each individual's bacterial community. However, the average percentage of bacteria that were culturable for each amphibian species was higher, with averages ranging from 2.81% to 7.47%. Furthermore, most of the dominant operational taxonomic units (OTUs), families, and phyla were represented in our cultures. These results open up new research avenues for understanding the functional roles of these dominant bacteria in host health. PMID:26162880

  12. Instability in bacterial populations and the curvature tensor

    NASA Astrophysics Data System (ADS)

    Melgarejo, Augusto; Langoni, Laura; Ruscitti, Claudia

    2016-09-01

    In the geometry associated with equilibrium thermodynamics the scalar curvature Rs is a measure of the volume of correlation, and therefore the singularities of Rs indicates the system instabilities. We explore the use of a similar approach to study instabilities in non-equilibrium systems and we choose as a test example, a colony of bacteria. In this regard we follow the proposal made by Obata et al. of using the curvature tensor for studying system instabilities. Bacterial colonies are often found in nature in concentrated biofilms, or other colony types, which can grow into spectacular patterns visible under the microscope. For instance, it is known that a decrease of bacterial motility with density can promote separation into bulk phases of two coexisting densities; this is opposed to the logistic law for birth and death that allows only a single uniform density to be stable. Although this homogeneous configuration is stable in the absence of bacterial interactions, without logistic growth, a density-dependent swim speed v(ρ) leads to phase separation via a spinodal instability. Thus we relate the singularities in the curvature tensor R to the spinodal instability, that is the appearance of regions of different densities of bacteria.

  13. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence.

    PubMed

    Avitia, Morena; Escalante, Ana E; Rebollar, Eria A; Moreno-Letelier, Alejandra; Eguiarte, Luis E; Souza, Valeria

    2014-01-01

    Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes.

  14. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence

    PubMed Central

    Avitia, Morena; Escalante, Ana E.; Rebollar, Eria A.; Moreno-Letelier, Alejandra; Eguiarte, Luis E.

    2014-01-01

    Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes. PMID:25548732

  15. Maintenance of Bacterial Cultures on Anhydrous Silica Gel

    ERIC Educational Resources Information Center

    Lennox, John E.

    1977-01-01

    Suspensions of 20 different cultures were grown on appropriate media, then pipetted into sterile anhydrous silica gel. Silica gel cultures after incubation and refrigerated storage were tested for viability. Results showed little mutation, low replication, low contamination, minimal expenses, and survival up to two years. (CS)

  16. Teaching Multi-Cultural Populations: Five Heritages.

    ERIC Educational Resources Information Center

    Stone, James C., Ed.; DeNevi, Donald P., Ed.

    This book is an attempt to help fill the tremendous gap that presently exists between teachers' will to become more skillful with multicultural student populations and the as-yet short supply of the quality materials they urgently need in order to do so. Its organizing principle is that, inasmuch as America is an immense living laboratory for…

  17. Population structure and cultural geography of a folktale in Europe.

    PubMed

    Ross, Robert M; Greenhill, Simon J; Atkinson, Quentin D

    2013-04-07

    Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture.

  18. Populations of Stored Product Mite Tyrophagus putrescentiae Differ in Their Bacterial Communities

    PubMed Central

    Erban, Tomas; Klimov, Pavel B.; Smrz, Jaroslav; Phillips, Thomas W.; Nesvorna, Marta; Kopecky, Jan; Hubert, Jan

    2016-01-01

    Background: Tyrophagus putrescentiae colonizes different human-related habitats and feeds on various post-harvest foods. The microbiota acquired by these mites can influence the nutritional plasticity in different populations. We compared the bacterial communities of five populations of T. putrescentiae and one mixed population of T. putrescentiae and T. fanetzhangorum collected from different habitats. Material: The bacterial communities of the six mite populations from different habitats and diets were compared by Sanger sequencing of cloned 16S rRNA obtained from amplification with universal eubacterial primers and using bacterial taxon-specific primers on the samples of adults/juveniles or eggs. Microscopic techniques were used to localize bacteria in food boli and mite bodies. The morphological determination of the mite populations was confirmed by analyses of CO1 and ITS fragment genes. Results: The following symbiotic bacteria were found in compared mite populations: Wolbachia (two populations), Cardinium (five populations), Bartonella-like (five populations), Blattabacterium-like symbiont (three populations), and Solitalea-like (six populations). From 35 identified OTUs97, only Solitalea was identified in all populations. The next most frequent and abundant sequences were Bacillus, Moraxella, Staphylococcus, Kocuria, and Microbacterium. We suggest that some bacterial species may occasionally be ingested with food. The bacteriocytes were observed in some individuals in all mite populations. Bacteria were not visualized in food boli by staining, but bacteria were found by histological means in ovaria of Wolbachia-infested populations. Conclusion: The presence of Blattabacterium-like, Cardinium, Wolbachia, and Solitalea-like in the eggs of T. putrescentiae indicates mother to offspring (vertical) transmission. Results of this study indicate that diet and habitats influence not only the ingested bacteria but also the symbiotic bacteria of T. putrescentiae. PMID

  19. Evaluating the effect of intraoperative peritoneal lavage on bacterial culture in dogs with suspected septic peritonitis.

    PubMed

    Swayne, Seanna L; Brisson, Brigitte; Weese, J Scott; Sears, William

    2012-09-01

    This pilot study describes the effect of intraoperative peritoneal lavage (IOPL) on bacterial counts and outcome in clinical cases of septic peritonitis. Intraoperative samples were cultured before and after IOPL. Thirty-three dogs with presumed septic peritonitis on the basis of cytology were managed surgically during the study period. Positive pre-lavage bacterial cultures were found in 14 cases, 13 of which were a result of intestinal leakage. The post-lavage cultures showed fewer isolates in 9 cases and in 1 case became negative. The number of dogs with a decrease in the concentration of bacteria cultured from pre-lavage to post-lavage samples was not statistically significant. There was no significant effect of the change in pre- to post-lavage culture, single versus multiple types of bacteria, selection of an appropriate empiric antimicrobial on survival or the need for subsequent surgery.

  20. Bacterial oxidation of dibromomethane and methyl bromide in natural waters and enrichment cultures

    USGS Publications Warehouse

    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.

  1. Effect of antibiotics on the bacterial population of the rabbit caecum.

    PubMed

    Abecia, Leticia; Fondevila, Manuel; Balcells, Joaquim; Edwards, Joan E; Newbold, C James; McEwan, Neil R

    2007-07-01

    The effect feeding antibiotics has on the bacterial population of the rabbit caecum was investigated. No changes in total volatile fatty acid production or total bacterial counts were observed compared with nonantibiotic treated controls. However, treatment with chlortetracycline resulted in an increase of propionate at the apparent cost of butyrate (P<0.05). Denaturing gradient gel electrophoresis analysis indicated that the two antibiotics that inhibit protein synthesis (chlortetracycline and tiamulin) exerted the most similar changes on the bacterial population structure, decreasing the diversity of the profiles. Sequence analysis of DNA from excised denaturing gradient gel electrophoresis bands was carried out. The majority of the sequences observed were most similar to bacterial sequences previously described in other gut environments, with 11% being most similar to those previously reported from the rabbit, and 95% of the sequences having 95% or greater identity to sequences already in GenBank.

  2. Bacteriophages may bias outcome of bacterial enrichment cultures.

    PubMed

    Muniesa, Maite; Blanch, Anicet R; Lucena, Francisco; Jofre, Juan

    2005-08-01

    Enrichment cultures are widely used for the isolation of bacteria in clinical, biotechnological, and environmental studies. However, competition, relative growth rates, or inhibitory effects may alter the outcome of enrichment cultures, causing the phenomenon known as enrichment bias. Bacteriophages are a major component in many microbial systems, and it abounds in natural settings. This abundance means that bacteriophages are likely to be present in many laboratory enrichment cultures. Our hypothesis was that bacteriophages present in the sample might bias the enriched subpopulation, since it can infect and lyse the target bacteria during the enrichment step once the bacteria reach a given density. Here we show that the presence of bacteriophages in Salmonella and Shigella enrichment cultures produced a significant reduction (more than 1 log unit) in the number of these bacteria compared with samples in which bacteriophages had been reduced by filtration through 0.45-microm non-protein-binding membranes. Furthermore, our data indicate that the Salmonella biotypes isolated after the enrichment culture change if bacteriophages are present, thus distorting the results of the analysis.

  3. Anammox bacterial populations in deep marine hypersaline gradient systems.

    PubMed

    Borin, Sara; Mapelli, Francesca; Rolli, Eleonora; Song, Bongkeun; Tobias, Craig; Schmid, Markus C; De Lange, Gert J; Reichart, Gert J; Schouten, Stefan; Jetten, Mike; Daffonchio, Daniele

    2013-03-01

    To extend the knowledge of anaerobic ammonium oxidation (anammox) habitats, bacterial communities were examined in two hypersaline sulphidic basins in Eastern Mediterranean Sea. The 2 m thick seawater-brine haloclines of the deep anoxic hypersaline basins Bannock and L'Atalante were sampled in intervals of 10 cm with increasing salinity. (15)N isotope pairing incubation experiments showed the production of (29)N2 and (30)N2 gases in the chemoclines, ranging from 6.0 to 9.2 % salinity of the L'Atalante basin. Potential anammox rates ranged from 2.52 to 49.65 nmol N2 L(-1) day(-1) while denitrification was a major N2 production pathway, accounting for more than 85.5 % of total N2 production. Anammox-related 16S rRNA genes were detected along the L'Atalante and Bannock haloclines up to 24 % salinity, and the amplification of the hydrazine synthase genes (hzsA) further confirmed the presence of anammox bacteria in Bannock. Fluorescence in situ hybridisation and sequence analysis of 16S rRNA genes identified representatives of the marine anammox genus 'Candidatus Scalindua' and putatively new operational taxonomic units closely affiliated to sequences retrieved in marine environments that have documented anammox activity. 'Scalindua brodae' like sequences constituted up to 84.4 % of the sequences retrieved from Bannock. The anammox community in L'Atalante was different than in Bannock and was stratified according to salinity increase. This study putatively extends anammox bacterial habitats to extremely saline sulphidic ecosystems.

  4. Bacterial populations growth under co- and counter-flow condition

    NASA Astrophysics Data System (ADS)

    Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.; Toschi, Federico

    2014-11-01

    For organisms living in a liquid ecosystem, flow and flow gradients play a major role on the population level: the flow has a dual role as it transports the nutrient while dispersing the individuals. In absence of flow and under homogeneous conditions, the growth of a population towards an empty region is usually described by a reaction diffusion equation. The solution predicts the expansion as a wave front (Fisher wave) proceeding at constant speed, till the carrying capacity is reached everywhere. The effect of fluid flow, however, is not well understood and the interplay between transport of individuals and nutrient opens a wide scenario of possible behaviors. In this work, we experimentally observe non-motile E. coli bacteria spreading inside rectangular channels in a PDMS microfluidic device. By use of a fluorescent microscope we analyze the dynamics of the population density subjected to different co- and counter-flow conditions and shear rates.

  5. Distributed Classifier Based on Genetically Engineered Bacterial Cell Cultures

    PubMed Central

    2015-01-01

    We describe a conceptual design of a distributed classifier formed by a population of genetically engineered microbial cells. The central idea is to create a complex classifier from a population of weak or simple classifiers. We create a master population of cells with randomized synthetic biosensor circuits that have a broad range of sensitivities toward chemical signals of interest that form the input vectors subject to classification. The randomized sensitivities are achieved by constructing a library of synthetic gene circuits with randomized control sequences (e.g., ribosome-binding sites) in the front element. The training procedure consists in reshaping of the master population in such a way that it collectively responds to the “positive” patterns of input signals by producing above-threshold output (e.g., fluorescent signal), and below-threshold output in case of the “negative” patterns. The population reshaping is achieved by presenting sequential examples and pruning the population using either graded selection/counterselection or by fluorescence-activated cell sorting (FACS). We demonstrate the feasibility of experimental implementation of such system computationally using a realistic model of the synthetic sensing gene circuits. PMID:25349924

  6. Evaluation of Bacterial & Fungal Culture Practices in School Classrooms

    ERIC Educational Resources Information Center

    Weese, J. Scott

    2009-01-01

    A wide range of activities may be undertaken in elementary and secondary school science laboratories as part of regular curricular activities or optional classroom activities, including science fair projects. Among these is the culturing of microorganisms such as bacteria or fungi. There are various potential educational opportunities associated…

  7. Development of a novel in vitro co-culture system for studying host response to native bacterial antigens.

    PubMed

    Mason, K M; Bigley, N J; Fink, P S

    1998-02-01

    We have developed a novel co-culture system in which murine splenocytes are cultured with live bacteria in the presence of a bacteriostatic antibiotic. Superantigens, like staphylococcal enterotoxin B (SEB) are important factors in bacterial pathogenicity. Research has shown that superantigens affect numerous immune cell types, either directly or indirectly, yet their involvement in pathogenic mechanisms remains poorly defined. In these studies, we utilize the co-culture system to study how superantigen pretreatment affects interferon-gamma (IFN-gamma) production by splenocytes co-cultured with gram-positive bacteria. Streptococcus mutans, S. sanguis and Bacillus subtilis were tested for susceptibility to a panel of antibiotics. Spectinomycin was found to maintain a bacteriostatic state of approximately 10(5) bacteria ml(-1) at optimal concentrations for each bacterial strain. Co-culturing splenocytes with bacteria did not affect splenocyte viability and cultured splenocytes responded to mitogenic stimulation as expected. Two days after SEB pretreatment, isolated splenocytes cultured with either Streptococcus species produced 10-15 times more IFN-gamma than splenocytes from sham-injected controls; however, no differences in CD4+ or CD8+ T cell populations appeared in cultures with or without bacteria. Splenocytes isolated four days after SEB treatment did not produce significant amounts of IFN-gamma in co-culture. Co-cultures containing live bacteria produced four times more IFN-gamma than cultures containing heat-killed bacteria. Splenocytes depleted of natural killer (NK) cells prior to SEB treatment produced 25% less IFN-gamma after 20 h co-culturing with S. mutans. T lymphocytes were identified to be the major producer of IFN-gamma at this time point by intracellular cytokine staining. Apparently SEB exposure primes a response to live bacteria and the response is evident two days after initial exposure. The in vitro co-culture system allows us to observe host

  8. Bacterial Programmed Cell Death as a Population Phenomenon

    DTIC Science & Technology

    2013-06-11

    Moving in for the kil:Activation of an endoribonuclease toxin by quorum sensing peptide, Molecular Cell, (03 2011): . doi: 06/11/2013 11.00...shown that E. coli mazEF-mediated cell death is a population phenomenon requiring the E. coli quorum sensing factor EDF (Extracellular Death Factor... quorum - sensing factor required for mazEF-mediated cell death in Escherichia coli. Science 318: 652-655. 7) Kolodkin-Gal I, Engelberg-Kulka, H (2008

  9. Molecular Ecology of Bacterial Population in Environmental Hazardous Chemical Control

    DTIC Science & Technology

    1993-01-14

    Pseudomonas putida F1 to measure toluene driven co-metabolic oxidation of TCE. (2) Demonstration of a new pathway for aerobic biodegradation of DDT...mediated by Alcaligenes eutrophus strain A5 previously shown competent for biodegradation of chlorobiphenyl congeners. (3) Confirmation that...the dynamics in microbial population density and activity during environmental biodegradation processes. Metabolism of PAHs. Pseudomonas £luorescens 5RL

  10. Bacterial Diversity in a Nonsaline Alkaline Environment: Heterotrophic Aerobic Populations

    PubMed Central

    Tiago, Igor; Chung, Ana Paula; Veríssimo, António

    2004-01-01

    Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)2-enriched, extremely diluted groundwater with pH 11.4. One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods. To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis. Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates. Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species Dietzia natrolimnae (32% of the isolates), to Frigoribacterium/Clavibacter lineages (29% of the isolates), and to the type strain of Microbacterium kitamiense (20% of the isolates). Other isolates were phylogenetically related to strains of the genera Agrococcus, Leifsonia, Kytococcus, Janibacter, Kocuria, Rothia, Nesterenkonia, Citrococcus, Micrococcus, Actinomyces, Rhodococcus, Bacillus, and Staphylococcus. Only five isolates were gram negative: one was related to the Sphingobacteria lineage and the other four were related to the α-Proteobacteria lineage. Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11. PMID:15574939

  11. Population size does not explain past changes in cultural complexity

    PubMed Central

    Vaesen, Krist; Collard, Mark; Cosgrove, Richard; Roebroeks, Wil

    2016-01-01

    Demography is increasingly being invoked to account for features of the archaeological record, such as the technological conservatism of the Lower and Middle Pleistocene, the Middle to Upper Paleolithic transition, and cultural loss in Holocene Tasmania. Such explanations are commonly justified in relation to population dynamic models developed by Henrich [Henrich J (2004) Am Antiq 69:197–214] and Powell et al. [Powell A, et al. (2009) Science 324(5932):1298–1301], which appear to demonstrate that population size is the crucial determinant of cultural complexity. Here, we show that these models fail in two important respects. First, they only support a relationship between demography and culture in implausible conditions. Second, their predictions conflict with the available archaeological and ethnographic evidence. We conclude that new theoretical and empirical research is required to identify the factors that drove the changes in cultural complexity that are documented by the archaeological record. PMID:27044082

  12. Comparison between Flow Cytometry and Traditional Culture Methods for Efficacy Assessment of Six Disinfectant Agents against Nosocomial Bacterial Species

    PubMed Central

    Massicotte, Richard; Mafu, Akier A.; Ahmad, Darakhshan; Deshaies, Francis; Pichette, Gilbert; Belhumeur, Pierre

    2017-01-01

    The present study was undertaken to compare the use of flow cytometry (FCM) and traditional culture methods for efficacy assessment of six disinfectants used in Quebec hospitals including: two quaternary ammonium-based, two activated hydrogen peroxide-based, one phenol-based, and one sodium hypochlorite-based. Four nosocomial bacterial species, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Vancomycin-resistant Enterococci faecalis, were exposed to minimum lethal concentrations (MLCs) and sublethal concentrations (1/2 MLCs) of disinfectants under study. The results showed a strong correlation between the two techniques for the presence of dead and live cell populations, as well as, evidence of injured populations with the FCM. The only exception was observed with sodium hypochlorite at higher concentrations where fluorescence was diminished and underestimating dead cell population. The results also showed that FCM can replace traditional microbiological methods to study disinfectant efficacy on bacteria. Furthermore, FCM profiles for E. coli and E. faecalis cells exposed to sublethal concentrations exhibited distinct populations of injured cells, opening a new aspect for future research and investigation to elucidate the role of injured, cultural/noncuturable/resuscitable cell populations in infection control. PMID:28217115

  13. Interactions of bacterial and amoebal populations in soil microcosms with fluctuating moisture content.

    PubMed

    Bryant, R J; Woods, L E; Coleman, D C; Fairbanks, B C; McClellan, J F; Cole, C V

    1982-04-01

    Sterilized soil samples (20 g of soil per 50-ml flask), amended with 600 mug of glucose-carbon and 60 mug of NH(4)-N . g of dry soil, were inoculated with bacteria (Pseudomonas paucimobilis) alone or with bacteria and amoebae (Acanthamoeba polyphaga). We used wet-dry treatments, which involved air drying the samples to a moisture content of approximately 2% and remoistening the samples three times during the 83-day experiment. Control treatments were kept moist. In the absence of amoebae, bacterial populations were reduced by the first drying to about 60% of the moist control populations, but the third drying had no such effect. With amoebae present, bacterial numbers were not significantly affected by the dryings. Amoebal grazing reduced bacterial populations to 20 to 25% of the ungrazed bacterial populations in both moisture treatments. Encystment was an efficient survival mechanism for amoebae subjected to wet-dry cycles. The amoebal population was entirely encysted in dry soil, but the total number of amoebae was not affected by the three dryings. Growth efficiencies for amoebae feeding on bacteria were 0.33 and 0.39 for wet-dry and constantly moist treatments, respectively, results that compared well with those previously reported for Acanthamoeba spp.

  14. Interactions of Bacterial and Amoebal Populations in Soil Microcosms with Fluctuating Moisture Content

    PubMed Central

    Bryant, R. J.; Woods, L. E.; Coleman, D. C.; Fairbanks, B. C.; McClellan, J. F.; Cole, C. V.

    1982-01-01

    Sterilized soil samples (20 g of soil per 50-ml flask), amended with 600 μg of glucose-carbon and 60 μg of NH4-N · g of dry soil−1, were inoculated with bacteria (Pseudomonas paucimobilis) alone or with bacteria and amoebae (Acanthamoeba polyphaga). We used wet-dry treatments, which involved air drying the samples to a moisture content of approximately 2% and remoistening the samples three times during the 83-day experiment. Control treatments were kept moist. In the absence of amoebae, bacterial populations were reduced by the first drying to about 60% of the moist control populations, but the third drying had no such effect. With amoebae present, bacterial numbers were not significantly affected by the dryings. Amoebal grazing reduced bacterial populations to 20 to 25% of the ungrazed bacterial populations in both moisture treatments. Encystment was an efficient survival mechanism for amoebae subjected to wet-dry cycles. The amoebal population was entirely encysted in dry soil, but the total number of amoebae was not affected by the three dryings. Growth efficiencies for amoebae feeding on bacteria were 0.33 and 0.39 for wet-dry and constantly moist treatments, respectively, results that compared well with those previously reported for Acanthamoeba spp. PMID:16345984

  15. Broad diversity and newly cultured bacterial isolates from enrichment of pig feces on complex polysaccharides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One of the fascinating functions of the mammalian intestinal microbiota is the fermentation of plant cell wall components. We used 8 week continuous culture enrichments of pig feces with cellulose and xylan/pectin to isolated bacteria from this community. A total of 575 bacterial isolates were class...

  16. Population-based surveillance for bacterial meningitis in the Dominican Republic: implications for control by vaccination.

    PubMed

    Gomez, E; Peguero, M; Sanchez, J; Castellanos, P L; Feris, J; Peña, C; Brudzinski-LaClaire, L; Levine, O S

    2000-12-01

    Quantifying the local burden of disease is an important step towards the introduction of new vaccines, such as Haemophilus influenzae type b (Hib) conjugate vaccine. We adapted a generic protocol developed by the World Health Organization for population-based surveillance of bacterial meningitis. All hospitals that admit paediatric patients with meningitis in the National District, Dominican Republic were included in the system and standard laboratory methods were used. The system identified 111 cases of confirmed bacterial meningitis. Hib was the leading cause of bacterial meningitis, followed by group B streptococcus, S. pneumoniae, and N. meningitidis. Unlike hospital-based case series, this population-based system was able to calculate incidence rates. The incidence of Hib meningitis was 13 cases per 100,000 children < 5 years old. The data from this study were used by the Ministry of Health to support the introduction of routine Hib vaccination and will be used to monitor its effectiveness.

  17. Population-based surveillance for bacterial meningitis in the Dominican Republic: implications for control by vaccination.

    PubMed Central

    Gomez, E.; Peguero, M.; Sanchez, J.; Castellanos, P. L.; Feris, J.; Peña, C.; Brudzinski-LaClaire, L.; Levine, O. S.

    2000-01-01

    Quantifying the local burden of disease is an important step towards the introduction of new vaccines, such as Haemophilus influenzae type b (Hib) conjugate vaccine. We adapted a generic protocol developed by the World Health Organization for population-based surveillance of bacterial meningitis. All hospitals that admit paediatric patients with meningitis in the National District, Dominican Republic were included in the system and standard laboratory methods were used. The system identified 111 cases of confirmed bacterial meningitis. Hib was the leading cause of bacterial meningitis, followed by group B streptococcus, S. pneumoniae, and N. meningitidis. Unlike hospital-based case series, this population-based system was able to calculate incidence rates. The incidence of Hib meningitis was 13 cases per 100,000 children < 5 years old. The data from this study were used by the Ministry of Health to support the introduction of routine Hib vaccination and will be used to monitor its effectiveness. PMID:11218205

  18. Population pharmacokinetics of ceftaroline in patients with acute bacterial skin and skin structure infections or community-acquired bacterial pneumonia.

    PubMed

    Van Wart, Scott A; Forrest, Alan; Khariton, Tatiana; Rubino, Christopher M; Bhavnani, Sujata M; Reynolds, Daniel K; Riccobene, Todd; Ambrose, Paul G

    2013-11-01

    Ceftaroline, the active form of ceftaroline fosamil, is a broad-spectrum cephalosporin antibiotic. A population pharmacokinetic (PPK) model for ceftaroline was developed in NONMEM® using data from 185 healthy subjects and 92 patients with acute bacterial skin and skin structure infection (ABSSSI). Data from 128 patients with community-acquired bacterial pneumonia (CABP) were used for external model validation. Healthy subjects received 50-2,000 mg ceftaroline fosamil via intravenous (IV) infusion over 1 hour or intramuscular (IM) injection q12h or q24h. ABSSSI and CABP patients received 600 mg of ceftaroline fosamil IV over 1 hour q12h. A three-compartment model with zero-order IV or parallel first-order IM input and first-order elimination described ceftaroline fosamil PK. A two-compartment model with first-order conversion of prodrug to ceftaroline and parallel linear and saturable elimination described ceftaroline PK. Creatinine clearance was the primary determinant of ceftaroline exposure. Good agreement between the observed data and both population (r(2)  = 0.93) and individual post-hoc (r(2)  = 0.98) predictions suggests the PPK model can adequately approximate ceftaroline PK using covariate information. Such a PPK model can evaluate dose adjustments for patients with renal impairment and generate ceftaroline exposures for use in pharmacokinetic-pharmacodynamic assessments of efficacy in patients with ABSSSI or CABP.

  19. Population policies and cultural values: a Mexican editorial.

    PubMed

    1978-01-01

    A new population policy for Mexico, based on the need to regulate demographic growth, should be developed without damaging the cultural values of the Mexican people. The role of cultural values in the identification of demographic problems, formulation of population policies, and implementation of programs, was studied in Mexico under sponsorship of the U.N. Population Fund. Population policies should be understood as a creative response to problems that life poses. Problems, policies, and national programs often originate with the elite or the middle class and are imposed with little respect for the real sense of the popular culture of the lower classes. It is an error to identify the traditional or folk values with a pronatalist attitude, because pronatalist attitudes can change when the people comprehend that birth control will aid in their fight for survival. The improvement of life for the Mexican peasant, proletarian and subproletarian is related to the modification of reproductive and migratory behavior. It is therefore an error to depict the new population policies as an interest of the upper classes and the imperialist countries. Population programs should be conceived and implemented by taking into account the values and aspirations of the popular majority.

  20. Comparative modifications in bacterial gill-endosymbiotic populations of the two bivalves Codakia orbiculata and Lucina pensylvanica during bacterial loss and reacquisition.

    PubMed

    Elisabeth, Nathalie H; Caro, Audrey; Césaire, Thierry; Mansot, Jean-Louis; Escalas, Arthur; Sylvestre, Marie-Noëlle; Jean-Louis, Patrick; Gros, Olivier

    2014-09-01

    Until now, the culture of sulphur-oxidizing bacterial symbionts associated with marine invertebrates remains impossible. Therefore, few studies focused on symbiont's physiology under stress conditions. In this study, we carried out a comparative experiment based on two different species of lucinid bivalves (Codakia orbiculata and Lucina pensylvanica) under comparable stress factors. The bivalves were starved for 6 months in sulphide-free filtered seawater. For C. orbiculata only, starved individuals were then put back to the field, in natural sediment. We used in situ hybridization, flow cytometry and X-ray fluorescence to characterize the symbiont population hosted in the gills of both species. In L. pensylvanica, no decrease in symbiont abundance was observed throughout the starvation experiment, whereas elemental sulphur slowly decreased to zero after 3 months of starvation. Conversely, in C. orbiculata, symbiont abundance within bacteriocytes decreased rapidly and sulphur from symbionts disappeared during the first weeks of the experiment. The modifications of the cellular characteristics (SSC--relative cell size and FL1--genomic content) of the symbiotic populations along starvation were not comparable between species. Return to the sediment of starved C. orbiculata individuals led to a rapid (2-4 weeks) recovery of symbiotic cellular characteristics, comparable with unstressed symbionts. These results suggest that endosymbiotic population regulation is host-species-dependent in lucinids.

  1. Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?

    PubMed Central

    Apprill, Amy; Robbins, Jooke; Eren, A. Murat; Pack, Adam A.; Reveillaud, Julie; Mattila, David; Moore, Michael; Niemeyer, Misty; Moore, Kathleen M. T.; Mincer, Tracy J.

    2014-01-01

    Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly

  2. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

    PubMed

    Apprill, Amy; Robbins, Jooke; Eren, A Murat; Pack, Adam A; Reveillaud, Julie; Mattila, David; Moore, Michael; Niemeyer, Misty; Moore, Kathleen M T; Mincer, Tracy J

    2014-01-01

    Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve

  3. Bacterial populations on the surfaces of organic and conventionally grown almond drupes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: To compare the bacterial populations on organically and conventionally grown almond drupes before and after hull split. Methods and Results: We constructed 16S rRNA gene libraries containing approximately 3,000 sequences each from the bacteria from organically and conventionally grown drupes b...

  4. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    PubMed

    Gorochowski, Thomas E; Matyjaszkiewicz, Antoni; Todd, Thomas; Oak, Neeraj; Kowalska, Kira; Reid, Stephen; Tsaneva-Atanasova, Krasimira T; Savery, Nigel J; Grierson, Claire S; di Bernardo, Mario

    2012-01-01

    Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

  5. Bacterial community analysis in chlorpyrifos enrichment cultures via DGGE and use of bacterial consortium for CP biodegradation.

    PubMed

    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.

  6. Vision Marker-Based In Situ Examination of Bacterial Growth in Liquid Culture Media

    PubMed Central

    Kim, Kyukwang; Choi, Duckyu; Lim, Hwijoon; Kim, Hyeongkeun; Jeon, Jessie S.

    2016-01-01

    The detection of bacterial growth in liquid media is an essential process in determining antibiotic susceptibility or the level of bacterial presence for clinical or research purposes. We have developed a system, which enables simplified and automated detection using a camera and a striped pattern marker. The quantification of bacterial growth is possible as the bacterial growth in the culturing vessel blurs the marker image, which is placed on the back of the vessel, and the blurring results in a decrease in the high-frequency spectrum region of the marker image. The experiment results show that the FFT (fast Fourier transform)-based growth detection method is robust to the variations in the type of bacterial carrier and vessels ranging from the culture tubes to the microfluidic devices. Moreover, the automated incubator and image acquisition system are developed to be used as a comprehensive in situ detection system. We expect that this result can be applied in the automation of biological experiments, such as the Antibiotics Susceptibility Test or toxicity measurement. Furthermore, the simple framework of the proposed growth measurement method may be further utilized as an effective and convenient method for building point-of-care devices for developing countries. PMID:27999349

  7. Effects of space flight and mixing on bacterial growth in low volume cultures

    NASA Technical Reports Server (NTRS)

    Kacena, M. A.; Manfredi, B.; Todd, P.

    1999-01-01

    Previous investigations have shown that liquid suspension bacterial cultures grow to higher cell concentrations in spaceflight than on Earth. None of these studies included ground-control experiments designed to evaluate the fluid effects potentially responsible for the reported increases. Therefore, the emphasis of this research was to both confirm differences in final cell concentration between 1g and microgravity cultures, and to examine the effects of mixing as a partial explanation for this difference. Flight experiments were performed in the Fluid Processing Apparatus (FPA), aboard Space Shuttle Missions STS-63 and STS-69, with simultaneous 1g static and agitated controls. Additional static 1g, agitated, and clino-rotated controls were performed in 9-ml culture tubes. This research revealed that both E. coli and B. subtilis samples cultured in space flight grew to higher final cell densities (120-345% increase) than simultaneous static 1g controls. The final cell concentration of E. coli cells cultured under agitation was 43% higher than in static 1g cultures and was 102% higher with clino-rotation. However, for B. subtilis cultures grown while being agitated on a shaker or clino-rotated, the final cell concentrations were nearly identical to those of the simultaneous static 1g controls. Therefore, these data suggest that the unique fluid quiescence in the microgravity environment (lack of sedimentation, creating unique transfer of nutrients and waste products), was responsible for the enhanced bacterial proliferation reported in this and other studies.

  8. Rubber-Degrading Enzyme from a Bacterial Culture

    PubMed Central

    Tsuchii, Akio; Takeda, Kiyoshi

    1990-01-01

    Rubber-degrading activity was found in the extracellular culture medium of Xanthomonas sp. strain 35Y which was grown on natural rubber latex. Natural rubber in the latex state was degraded by the crude enzyme, and two fractions were separately observed by gel permeation chromatography of the reaction products. One fraction was of higher molecular weight (HMW) with a very wide MW distribution from 103 to 105, and the other fraction was of lower molecular weight (LMW) with a MW of a few hundred. 1H-nuclear magnetic resonance spectra of the partially purified fractions were those expected of cis-1,4-polyisoprene mixtures with the structure OHC-CH2-(-CH2-C(-CH3) = CH-CH2-)n-CH2-C(=O)-CH3, with average values of n of about 113 and 2 for HMW and LMW fractions, respectively. The LMW fraction consisted mostly of one component in gas-liquid chromatography as well as in gel permeation chromatography, and the main component was identified as 12-oxo-4,8-dimethyl trideca-4,8-diene-1-al (acetonyl diprenyl acetoaldehyde, AlP2At) by 13C-nuclear magnetic resonance and gas chromatography-mass spectra. Not only the latices of natural and synthetic isoprene rubber, but also some kinds of low-MW polyisoprene compounds of cis-1,4 type, were degraded by the crude enzyme. The rubber-degrading reaction was found to be at least partly oxygenase catalyzed from the incorporation of 18O into AlP2At under an 18O2 atmosphere. PMID:16348100

  9. Simplified Protocol for Carba NP Test for Enhanced Detection of Carbapenemase Producers Directly from Bacterial Cultures

    PubMed Central

    Pasteran, Fernando; Tijet, Nathalie; Melano, Roberto G.

    2015-01-01

    We compared carbapenemase detection among 266 Gram-negative bacilli (161 carbapenemase producers) using the Carba NP tests issued by the CLSI (CNPt-CLSI) and a novel protocol (CNPt-direct) designed for carbapenemase detection direct from bacterial cultures (instead of bacterial extracts required by the CLSI tests). The specificities were comparable (100%), but the CNPt-direct was more sensitive (98% versus 84%). The CNPt-direct was easier to perform due to the direct use of colonies and offered a more robust detection of carbapenemase producers. PMID:26424841

  10. Simplified Protocol for Carba NP Test for Enhanced Detection of Carbapenemase Producers Directly from Bacterial Cultures.

    PubMed

    Pasteran, Fernando; Tijet, Nathalie; Melano, Roberto G; Corso, Alejandra

    2015-12-01

    We compared carbapenemase detection among 266 Gram-negative bacilli (161 carbapenemase producers) using the Carba NP tests issued by the CLSI (CNPt-CLSI) and a novel protocol (CNPt-direct) designed for carbapenemase detection direct from bacterial cultures (instead of bacterial extracts required by the CLSI tests). The specificities were comparable (100%), but the CNPt-direct was more sensitive (98% versus 84%). The CNPt-direct was easier to perform due to the direct use of colonies and offered a more robust detection of carbapenemase producers.

  11. Culture-independent analysis of the soil bacterial assemblage at the Great Salt Plains of Oklahoma

    PubMed Central

    Caton, Ingrid R.; Schneegurt, Mark A.

    2013-01-01

    The Great Salt Plains (GSP) of Oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly NaCl. Previous work described GSP bacterial assemblages through the phylogenetic and phenetic characterization of 105 isolates from 46 phylotypes. The current report describes the same bacterial assemblages through culture-independent 16S rRNA gene clone libraries. Although from similar hypersaline mud flats, the bacterial libraries from two sites, WP3 and WP6, were quite different. The WP3 library was dominated by cyanobacteria, mainly Cyanothece and Euhalothece. The WP6 library was rich in anaerobic sulfur-cycle organisms, including abundant Desulfuromonas. This pattern likely reflects differences in abiotic factors, such as frequency of flooding and hydrologic push. While more than 100 OTUs were identified, the assemblages were not as diverse, based on Shannon indexes, as bacterial communities from oligohaline soils. Since natural inland hypersaline soils are relatively unstudied, it was not clear what kind of bacteria would be present. The bacterial assemblage is predominantly genera typically found in hypersaline systems, although some were relatives of microbes common in oligohaline and marine environments. The bacterial clones did not reflect wide functional diversity, beyond phototrophs, sulfur metabolizers, and numerous heterotrophs. PMID:21953014

  12. Antioxidant treatments counteract the non-culturability of bacterial endophytes isolated from legume nodules.

    PubMed

    Muresu, Rosella; Tondello, Alessandra; Polone, Elisa; Sulas, Leonardo; Baldan, Barbara; Squartini, Andrea

    2013-06-01

    In many wild legumes, attempts to cultivate nodule bacteria fail. We hypothesized that the limited culturability could be related to injury from oxidative stress caused by disruption of plant tissues during isolation. To test that, we isolated bacteria from nodules of Hedysarum spinosissimum and Tetragonolobus purpureus using buffers supplemented with scavenging systems to prevent damage from reactive oxygen species (ROS). Treatments included the following: antioxidants (glutathione, ascorbate, EDTA) or enzymes (catalase, peroxidase, superoxide dismutase), tested either as modified squashing buffers or added in plates. Some combinations yielded dramatic increases of culturability. Different endophytes were found, including additional Rhizobiaceae that were not the primary symbiont and were unable to nodulate. Their H2O2 tolerance in broth culture showed differences consistent with the unequal culturability observed. In wild legumes species, ROS generation during extraction appears to be a major factor limiting microbiota isolation, and protocols presented here significantly improve the recovery of culturable bacterial endophytes from plants.

  13. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes

    PubMed Central

    Colman, Daniel R.; Jay, Zackary J.; Inskeep, William P.; Jennings, Ryan deM.; Maas, Kendra R.; Rusch, Douglas B.; Takacs-Vesbach, Cristina D.

    2016-01-01

    Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous “streamer” communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name “Pyropristinus”). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the “Pyropristinus” and Calescamantes populations showed that these organisms appear to be chemoorganoheterotrophs and have the genomic potential for aerobic respiration and oxidative phosphorylation via archaeal-like V-type, and bacterial F-type ATPases, respectively. A survey of similar phylotypes (>97% nt identity) within 16S rRNA gene datasets suggest that the newly described organisms are restricted to terrestrial thermal springs ranging from 70 to 90°C and pH values of ~7–9. The characterization of these lineages is important for understanding the diversity of deeply-branching bacterial phyla, and their functional role in high-temperature circumneutral “streamer” communities. PMID:27014227

  14. Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine

    PubMed Central

    Stephens, W. Zac; Wiles, Travis J.; Martinez, Emily S.; Jemielita, Matthew; Burns, Adam R.; Parthasarathy, Raghuveer; Bohannan, Brendan J. M.

    2015-01-01

    ABSTRACT The zebrafish, Danio rerio, is a powerful model for studying bacterial colonization of the vertebrate intestine, but the genes required by commensal bacteria to colonize the zebrafish gut have not yet been interrogated on a genome-wide level. Here we apply a high-throughput transposon mutagenesis screen to Aeromonas veronii Hm21 and Vibrio sp. strain ZWU0020 during their colonization of the zebrafish intestine alone and in competition with each other, as well as in different colonization orders. We use these transposon-tagged libraries to track bacterial population sizes in different colonization regimes and to identify gene functions required during these processes. We show that intraspecific, but not interspecific, competition with a previously established bacterial population greatly reduces the ability of these two bacterial species to colonize. Further, using a simple binomial sampling model, we show that under conditions of interspecific competition, genes required for colonization cannot be identified because of the population bottleneck experienced by the second colonizer. When bacteria colonize the intestine alone or at the same time as the other species, we find shared suites of functional requirements for colonization by the two species, including a prominent role for chemotaxis and motility, regardless of the presence of another species. PMID:26507229

  15. [Use of transport medium in sputum bacterial culture examination of lower airway infection].

    PubMed

    Muraki, Masato; Kitaguchi, Sayako; Ichihashi, Hideo; Tsuji, Fumio; Ohmori, Takashi; Haraguchi, Ryuta; Tohda, Yuji

    2006-06-01

    Our medical institution does not have a bacterial culture facility, requiring outsourcing of bacterial culture tests. Due to the time elapsed from the time of specimen collection to culturing, the identification of causative bacteria in respiratory tract infections tends to be difficult. We therefore used transport medium for sputum bacteria examinations. Expectorated purulent or purulent-mucous sputum specimens were collected from 32 patients with lower respiratory tract infection. We divided each of the sputum specimens into the two treatment groups: transport medium (Seedswab gamma2) ndar and stad disinfection container. Paired samples prepared from each patient were sent out for bacterial culture together. The time elapsed from collection to delivery to the lab were as follows: day 0 (same day, n = 14 patients), day 1 (n = 15), day 2 (n = 2), and day 3 (n = 1). The identified causative bacteria were Streptococcus pneumoniae (n = 6 patients), Haemophilus influenzae (n =5), Pseudomonas aeruginosa (n = 4), Staphylococcus aureus (n = 2), Moraxella catarrhalis (n = 2), Klebsiella pneumoniae (n = 1), and Streptococcus agalactiae (n = 1). Samples prepared by each of the two methods gave similar results. The utility of transport medium for examination of general bacteria for lower airway infection from sputum samples was not demonstrated. The rate of detection of bacteria decreased, when the transport of samples was delayed. Therefore, we need to send the sputum specimens as quickly as possible.

  16. Oil removal from petroleum sludge using bacterial culture with molasses substrate at temperature variation

    NASA Astrophysics Data System (ADS)

    Ni'matuzahroh, Puspitasari, Alvin Oktaviana; Pratiwi, Intan Ayu; Fatimah, Sumarsih, Sri; Surtiningsih, Tini; Salamun

    2016-03-01

    The study aims to reveal the potency of biosurfactant-producing bacterial culture with molasses as substrate growth in releasing oil from the petroleum sludge at temperature variations. Bacteria used consisted of (Acinetobacter sp. P2(1), Pseudomonas putida T1(8), Bacillus subtilis 3KP and Micrococcus sp. L II 61). The treatments were tested at 40°C, 50°C and 60 °C for 7 days of incubation. Synthetic surfactant (Tween 20) was used as a positive control and molasses as a negative control. Release of petroleum hydrocarbons from oil sludge was expressed in percentage of oil removal from oil sludge (%). Data were analyzed statistically using the Analysis of Variance (α = 0.05) and continued with Games-Howell test. The kinds of bacterial cultures, incubation temperature and combination of both affected the percentage of oil removal. The abilities of Bacillus subtilis 3KP and Micrococcus sp. LII 61cultures in oil removal from oil sludge at the temperature exposure of 60°C were higher than Tween 20. Both of bacterial cultures grown on molasses can be proposed as a replacement for synthetic surfactant to clean up the accumulation of oil sludge in a bottom of oil refinery tank.

  17. Trends of Bacterial Keratitis Culture Isolates in Jerusalem; a 13- Years Analysis

    PubMed Central

    Politis, Michael; Wajnsztajn, Denise; Rosin, Boris; Block, Colin; Solomon, Abraham

    2016-01-01

    Purpose To describe the trends in pathogens and antibacterial resistance of corneal culture isolates in infectious keratitis during a period of 13 years at Hadassah-Hebrew University Medical Center. Methods A Retrospective analysis of bacterial corneal isolates was performed during the months of January 2002 to December 2014 at Hadassah Hebrew University Medical Center. Demographics, microbiological data and antibiotic resistance and sensitivity were collected. Results A total of 943 corneal isolates were analyzed during a 13 year period. A total of 415 positive bacterial cultures and 37 positive fungal cultures were recovered, representing 48% of the total cultures. The Annual incidence was 34.78 ± 6.54 cases. The most common isolate was coagulase-negative staphylococcus (32%), which had a significant decrease in trend throughout the study period (APC = -8.1, p = 0.002). Methicillin-resistant Staphylococcus aureus (MRSA) appears to have a decrease trend (APC = -31.2, P = 0.5). There was an increase in the resistance trend of coagulase-negative staphylococci to penicillin (APC = 5.0, P = <0.001). None of the pathogens had developed any resistance to Vancomycin. (P = 0.88). Conclusions Coagulase negative staphylococci were the predominant bacteria isolated from patients with keratitis. There was no significant change in the annual incidence of cases of bacterial keratitis seen over the past 13 years. Keratitis caused by MRSA appeared to decrease in contrast to the reported literature. PMID:27893743

  18. Preparation of a blood culture pellet for rapid bacterial identification and antibiotic susceptibility testing.

    PubMed

    Croxatto, Antony; Prod'hom, Guy; Durussel, Christian; Greub, Gilbert

    2014-10-15

    Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a rapid identification of the infectious agent to guide optimal antibiotic treatment. The analysis of Gram stains from positive blood culture can be rapidly conducted and already significantly impact the antibiotic regimen. However, the accurate identification of the infectious agent is still required to establish the optimal targeted treatment. We present here a simple and fast bacterial pellet preparation from a positive blood culture that can be used as a sample for several essential downstream applications such as identification by MALDI-TOF MS, antibiotic susceptibility testing (AST) by disc diffusion assay or automated AST systems and by automated PCR-based diagnostic testing. The performance of these different identification and AST systems applied directly on the blood culture bacterial pellets is very similar to the performance normally obtained from isolated colonies grown on agar plates. Compared to conventional approaches, the rapid acquisition of a bacterial pellet significantly reduces the time to report both identification and AST. Thus, following blood culture positivity, identification by MALDI-TOF can be reported within less than 1 hr whereas results of AST by automated AST systems or disc diffusion assays within 8 to 18 hr, respectively. Similarly, the results of a rapid PCR-based assay can be communicated to the clinicians less than 2 hr following the report of a bacteremia. Together, these results demonstrate that the rapid preparation of a blood culture bacterial pellet has a significant impact on the identification and AST turnaround time and thus on the successful outcome of patients suffering from bloodstream infections.

  19. Preparation of a Blood Culture Pellet for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

    PubMed Central

    Croxatto, Antony; Prod'hom, Guy; Durussel, Christian; Greub, Gilbert

    2014-01-01

    Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a rapid identification of the infectious agent to guide optimal antibiotic treatment. The analysis of Gram stains from positive blood culture can be rapidly conducted and already significantly impact the antibiotic regimen. However, the accurate identification of the infectious agent is still required to establish the optimal targeted treatment. We present here a simple and fast bacterial pellet preparation from a positive blood culture that can be used as a sample for several essential downstream applications such as identification by MALDI-TOF MS, antibiotic susceptibility testing (AST) by disc diffusion assay or automated AST systems and by automated PCR-based diagnostic testing. The performance of these different identification and AST systems applied directly on the blood culture bacterial pellets is very similar to the performance normally obtained from isolated colonies grown on agar plates. Compared to conventional approaches, the rapid acquisition of a bacterial pellet significantly reduces the time to report both identification and AST. Thus, following blood culture positivity, identification by MALDI-TOF can be reported within less than 1 hr whereas results of AST by automated AST systems or disc diffusion assays within 8 to 18 hr, respectively. Similarly, the results of a rapid PCR-based assay can be communicated to the clinicians less than 2 hr following the report of a bacteremia. Together, these results demonstrate that the rapid preparation of a blood culture bacterial pellet has a significant impact on the identification and AST turnaround time and thus on the successful outcome of patients suffering from bloodstream infections. PMID:25350577

  20. Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections.

    PubMed

    Karslake, Jason; Maltas, Jeff; Brumm, Peter; Wood, Kevin B

    2016-10-01

    The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments.

  1. Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections

    PubMed Central

    Maltas, Jeff; Brumm, Peter; Wood, Kevin B.

    2016-01-01

    The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments. PMID:27764095

  2. Biodegradation of crude oil by a defined co-culture of indigenous bacterial consortium and exogenous Bacillus subtilis.

    PubMed

    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.

  3. Population size vs. social connectedness - A gene-culture coevolutionary approach to cumulative cultural evolution.

    PubMed

    Kobayashi, Yutaka; Ohtsuki, Hisashi; Wakano, Joe Y

    2016-10-01

    It has long been debated if population size is a crucial determinant of the level of culture. While empirical results are mixed, recent theoretical studies suggest that social connectedness between people may be a more important factor than the size of the entire population. These models, however, do not take into account evolutionary responses of learning strategies determining the mode of transmission and innovation and are hence not suitable for predicting the long-term implications of parameters of interest. In the present paper, to address this issue, we provide a gene-culture coevolution model, in which the microscopic learning process of each individual is explicitly described as a continuous-time stochastic process and time allocation to social and individual learning is allowed to evolve. We have found that social connectedness has a larger impact on the equilibrium level of culture than population size especially when connectedness is weak and population size is large. This result, combined with those of previous culture-only models, points to the importance of studying separate effects of population size and internal social structure to better understand spatiotemporal variation in the level of culture.

  4. Influence of combined pollution of antimony and arsenic on culturable soil microbial populations and enzyme activities.

    PubMed

    Wang, Qiongshan; He, Mengchang; Wang, Ying

    2011-01-01

    The effects of both combined and single pollution of antimony (Sb) and arsenic (As) in different concentrations on culturable soil microbial populations and enzyme activities were studied under laboratory conditions. Joint effects of both Sb and As were different from that of Sb or As alone. The inhibition rate of culturable soil microbial populations under Sb and As pollution followed the order: bacterial > fungi > actinomycetes. There existed antagonistic inhibiting effect on urease and acid phophatase and synergistic inhibiting effect on protease under the combined pollution of Sb (III) and As (III). Only urease appeared to be the most sensitive indicator under Sb (V) and As (V) pollution, and there existed antagonistic inhibiting effect on acid phophatase and synergistic inhibiting effect on urease and protease under Sb (V) and As (V) combined pollution at most time. In this study, we also confirmed that the trivalent states of Sb and As were more toxic to all the microbes tested and more inhibitory on microbial enzyme activities then their pentavalent counterparts. The results also suggest that not only the application rate of the two metalloids but also the chemical form of metalloids should be considered while assessing the effect of metalloid on culturable microbial populations and enzyme activities. Urease and acid phosphatase can be used as potential biomarkers to evaluate the intensity of Sb (III) and As (III) stress.

  5. Bacterial flora and antimicrobial resistance in raw frozen cultured seafood imported to Denmark.

    PubMed

    Noor Uddin, Gazi M; Larsen, Marianne Halberg; Guardabassi, Luca; Dalsgaard, Anders

    2013-03-01

    Intensified aquaculture includes the use of antimicrobials for disease control. In contrast to the situation in livestock, Escherichia coli and enterococci are not part of the normal gastrointestinal flora of fish and shrimp and therefore not suitable indicators of antimicrobial resistance in seafood. In this study, the diversity and phenotypic characteristics of the bacterial flora in raw frozen cultured and wild-caught shrimp and fish were evaluated to identify potential indicators of antimicrobial resistance. The bacterial flora cultured on various agar media at different temperatures yielded total viable counts of 4.0 × 10(4) to 3.0 × 10(5) CFU g(-1). Bacterial diversity was indicated by 16S rRNA sequence analysis of 84 isolates representing different colony types; 24 genera and 51 species were identified. Pseudomonas spp. (23% of isolates), Psychrobacter spp. (17%), Serratia spp. (13%), Exiguobacterium spp. (7%), Staphylococcus spp. (6%), and Micrococcus spp. (6%) dominated. Disk susceptibility testing of 39 bacterial isolates to 11 antimicrobials revealed resistance to ampicillin, amoxicillin-clavulanic acid, erythromycin, and third generation cephalosporins. Resistance to third generation cephalosporins was found in Pseudomonas, a genus naturally resistant to most β-lactam antibiotics, and in Staphylococcus hominis. Half of the isolates were susceptible to all antimicrobials tested. Results indicate that identification of a single bacterial resistance indicator naturally present in seafood at point of harvest is unlikely. The bacterial flora found likely represents a processing rather than a raw fish flora because of repeated exposure of raw material to water during processing. Methods and appropriate indicators, such as quantitative PCR of resistance genes, are needed to determine how antimicrobials used in aquaculture affect resistance of bacteria in retailed products.

  6. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

    DOE PAGES

    Bendall, Matthew L.; Stevens, Sarah L.R.; Chan, Leong-Keat; ...

    2016-01-08

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Using a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of genemore » gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. Furthermore, these patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model’ of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Finally, evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.« less

  7. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

    PubMed Central

    Bendall, Matthew L; Stevens, Sarah LR; Chan, Leong-Keat; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Froula, Jeff; Kang, Dongwan; Tringe, Susannah G; Bertilsson, Stefan; Moran, Mary A; Shade, Ashley; Newton, Ryan J; McMahon, Katherine D; Malmstrom, Rex R

    2016-01-01

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment. PMID:26744812

  8. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

    SciTech Connect

    Bendall, Matthew L.; Stevens, Sarah L.R.; Chan, Leong-Keat; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Froula, Jeff; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary A.; Shade, Ashley; Newton, Ryan J.; McMahon, Katherine D.; Malmstrom, Rex R.

    2016-01-08

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Using a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. Furthermore, these patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model’ of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Finally, evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.

  9. Culture-dependent and -independent molecular analysis of the bacterial community within uranium ore.

    PubMed

    Islam, Ekramul; Sar, Pinaki

    2011-08-01

    The bacterial community structure within a uranium ore was investigated using culture-dependent and -independent clone library analysis and denaturing gradient gel electrophoresis of 16S rRNA genes. The major aerobic heterotrophic bacteria were isolated and identified, and their resistance to uranium and other heavy metals was characterized. Together with near neutral pH, moderate organic carbon content, elevated U and other heavy metals (V, Ni, Mn, Cu, etc.), the ore showed high microbial counts and phylotype richness. The bacterial community mainly consisted of uncultured Proteobacteria, with the predominance of γ - over β - and α -subdivisions, along with Actinobacteria and Firmicutes. A phylogenetic study revealed that nearly one-third of the community was affiliated to as yet uncultured and unidentified bacteria having a closer relationship to Pseudomonas. Lineages of Burkholderiaceae and Moraxellaceae were relatively more abundant in the total community, while genera affiliated to Xanthomonadaceae and Microbacteriaceae and Exiguobacterium were detected in the culturable fraction. More than 50% of the bacterial isolates affiliated to Stenotrophomonas, Microbacterium, Acinetobacter, Pseudomonas and Enterobacter showed resistance to uranium and other heavy metals. The study showed for the first time that uranium ore harbors major bacterial groups related to organisms having a wide range of environmentally significant functional attributes, and the most abundant members are possibly new groups/taxa. These findings provide new insights into U-ore geomicrobiology that could be useful in biohydrometallurgy and bioremediation applications.

  10. Comparative dynamics of adherent and nonadherent bacterial populations on maize leaves.

    PubMed

    Beattie, Gwyn A; Marcell, Lise M

    2002-09-01

    ABSTRACT The dynamics of the adherent and nonadherent populations of three bacterial species on maize leaves were examined to identify the extent to which bacteria adhere to leaves and the importance of this adhesion to leaf colonization. Pantoea agglomerans strain BRT98, Clavibacter michiganensis subsp. nebraskensis strain GH2390, and Pseudomonas syringae pv. syringae strain HS191R all rapidly adhered to maize leaves following inoculation, but differed in the percentage of cells that adhered to the leaves. Immediately following inoculation, the percentage of adherent cells was highest for the saprophyte P. agglomerans (8 to 10%) and was much lower for the pathogens C. michiganensis subsp. nebras-kensis and P. syringae pv. syringae (2 to 3 and <1%, respectively), although the results for P. syringae pv. syringae HS191R were based on only one experiment. In the 4 days following inoculation, the percentage of the P. agglomerans populations that adhered to the leaves increased to approximately 70%. Similarly, the percentage of C. michiganensis subsp. nebraskensis and P. syringae pv. syringae cells that resisted removal steadily increased in the days following inoculation, although these increases probably reflected both adherence and localization to endophytic sites. Based on differences in the percentage of cells adhering to several cuticular wax mutants of maize, the rapid adherence of C. michiganensis subsp. nebraskensis cells to maize leaves was influenced by the cuticular wax properties, while the rapid adherence of P. agglomerans was not. Finally, bacterial adherence to leaves was advantageous to P. agglomerans survival and growth on leaves based on the finding that the nonadherent populations of the P. agglomerans strain decreased significantly more than did the adherent populations in the 24 h following inoculation, and increased much less than did the adherent populations over the next 3 days. Similar results with the C. michiganensis subsp. nebraskensis and

  11. Use of Natural Antimicrobial Peptides and Bacterial Biopolymers for Cultured Pearl Production.

    PubMed

    Simon-Colin, Christelle; Gueguen, Yannick; Bachere, Evelyne; Kouzayha, Achraf; Saulnier, Denis; Gayet, Nicolas; Guezennec, Jean

    2015-06-11

    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.

  12. Use of Natural Antimicrobial Peptides and Bacterial Biopolymers for Cultured Pearl Production

    PubMed Central

    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

  13. Changes in bacterial population of gastrointestinal tract of weaned pigs fed with different additives.

    PubMed

    Roca, Mercè; Nofrarías, Miquel; Majó, Natàlia; Pérez de Rozas, Ana María; Segalés, Joaquim; Castillo, Marisol; Martín-Orúe, Susana María; Espinal, Anna; Pujols, Joan; Badiola, Ignacio

    2014-01-01

    This study aimed to provide novel insights into the gastrointestinal microbial diversity from different gastrointestinal locations in weaning piglets using PCR-restriction fragment length polymorphism (PCR-RFLP). Additionally, the effect of different feed additives was analyzed. Thirty-two piglets were fed with four different diets: a control group and three enriched diets, with avilamycin, sodium butyrate, and a plant extract mixture. Digesta samples were collected from eight different gastrointestinal segments of each animal and the bacterial population was analysed by a PCR-RFLP technique that uses 16S rDNA gene sequences. Bacterial diversity was assessed by calculating the number of bands and the Shannon-Weaver index. Dendrograms were constructed to estimate the similarity of bacterial populations. A higher bacterial diversity was detected in large intestine compared to small intestine. Among diets, the most relevant microbial diversity differences were found between sodium butyrate and plant extract mixture. Proximal jejunum, ileum, and proximal colon were identified as those segments that could be representative of microbial diversity in pig gut. Results indicate that PCR-RFLP technique allowed detecting modifications on the gastrointestinal microbial ecology in pigs fed with different additives, such as increased biodiversity by sodium butyrate in feed.

  14. Changes in Bacterial Population of Gastrointestinal Tract of Weaned Pigs Fed with Different Additives

    PubMed Central

    Roca, Mercè; Nofrarías, Miquel; Majó, Natàlia; Pérez de Rozas, Ana María; Castillo, Marisol; Martín-Orúe, Susana María; Espinal, Anna; Pujols, Joan; Badiola, Ignacio

    2014-01-01

    This study aimed to provide novel insights into the gastrointestinal microbial diversity from different gastrointestinal locations in weaning piglets using PCR-restriction fragment length polymorphism (PCR-RFLP). Additionally, the effect of different feed additives was analyzed. Thirty-two piglets were fed with four different diets: a control group and three enriched diets, with avilamycin, sodium butyrate, and a plant extract mixture. Digesta samples were collected from eight different gastrointestinal segments of each animal and the bacterial population was analysed by a PCR-RFLP technique that uses 16S rDNA gene sequences. Bacterial diversity was assessed by calculating the number of bands and the Shannon-Weaver index. Dendrograms were constructed to estimate the similarity of bacterial populations. A higher bacterial diversity was detected in large intestine compared to small intestine. Among diets, the most relevant microbial diversity differences were found between sodium butyrate and plant extract mixture. Proximal jejunum, ileum, and proximal colon were identified as those segments that could be representative of microbial diversity in pig gut. Results indicate that PCR-RFLP technique allowed detecting modifications on the gastrointestinal microbial ecology in pigs fed with different additives, such as increased biodiversity by sodium butyrate in feed. PMID:24575403

  15. Marinobacter Dominates the Bacterial Community of the Ostreococcus tauri Phycosphere in Culture

    PubMed Central

    Lupette, Josselin; Lami, Raphaël; Krasovec, Marc; Grimsley, Nigel; Moreau, Hervé; Piganeau, Gwenaël; Sanchez-Ferandin, Sophie

    2016-01-01

    Microalgal–bacterial interactions are commonly found in marine environments and are well known in diatom cultures maintained in laboratory. These interactions also exert strong effects on bacterial and algal diversity in the oceans. Small green eukaryote algae of the class Mamiellophyceae (Chlorophyta) are ubiquitous and some species, such as Ostreococcus spp., are particularly important in Mediterranean coastal lagoons, and are observed as dominant species during phytoplankton blooms in open sea. Despite this, little is known about the diversity of bacteria that might facilitate or hinder O. tauri growth. We show, using rDNA 16S sequences, that the bacterial community found in O. tauri RCC4221 laboratory cultures is dominated by γ-proteobacteria from the Marinobacter genus, regardless of the growth phase of O. tauri RCC4221, the photoperiod used, or the nutrient conditions (limited in nitrogen or phosphorous) tested. Several strains of Marinobacter algicola were detected, all closely related to strains found in association with taxonomically distinct organisms, particularly with dinoflagellates and coccolithophorids. These sequences were more distantly related to M. adhaerens, M. aquaeoli and bacteria usually associated to euglenoids. This is the first time, to our knowledge, that distinct Marinobacter strains have been found to be associated with a green alga in culture. PMID:27656176

  16. Exploiting bacterial peptide display technology to engineer biomaterials for neural stem cell culture.

    PubMed

    Little, Lauren E; Dane, Karen Y; Daugherty, Patrick S; Healy, Kevin E; Schaffer, David V

    2011-02-01

    Stem cells are often cultured on substrates that present extracellular matrix (ECM) proteins; however, the heterogeneous and poorly defined nature of ECM proteins presents challenges both for basic biological investigation of cell-matrix investigations and translational applications of stem cells. Therefore, fully synthetic, defined materials conjugated with bioactive ligands, such as adhesive peptides, are preferable for stem cell biology and engineering. However, identifying novel ligands that engage cellular receptors can be challenging, and we have thus developed a high throughput approach to identify new adhesive ligands. We selected an unbiased bacterial peptide display library for the ability to bind adult neural stem cells (NSCs), and 44 bacterial clones expressing peptides were identified and found to bind to NSCs with high avidity. Of these clones, four contained RGD motifs commonly found in integrin binding domains, and three exhibited homology to ECM proteins. Three peptide clones were chosen for further analysis, and their synthetic analogs were adsorbed on tissue culture polystyrene (TCPS) or grafted onto an interpenetrating polymer network (IPN) for cell culture. These three peptides were found to support neural stem cell self-renewal in defined medium as well as multi-lineage differentiation. Therefore, bacterial peptide display offers unique advantages to isolate bioactive peptides from large, unbiased libraries for applications in biomaterials engineering.

  17. A population memetics approach to cultural evolution in chaffinch song: meme diversity within populations.

    PubMed

    Lynch, A; Baker, A J

    1993-04-01

    We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, Canaries) and neighboring continental regions (Morocco, Iberia) by employing a population memetics approach. To quantify variability within populations, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The frequency distribution of memes within populations generally fit a neutral model in which there is an equilibrium between mutation, migration, and drift, which suggests that memes are functionally equivalent. The diversity of memes of single syllables is significantly greater in the Azores compared to all other regions, consistent with higher population densities of chaffinches there. On the other hand, memes of two to five syllables have greater diversity in Atlantic island and Moroccan populations compared to their Iberian counterparts. This higher diversity emanates from a looser syntax and increased recombination in songs, presumably because of relaxed selection for distinctive songs in these peripheral and depauperate avifaunas. We urge comparative population memetic studies of other species of songbirds and predict that they will lead to a formulation of a general theory for the cultural evolution of bird song analogous to population genetics theory for biological traits.

  18. Measuring the Rate of Conjugal Plasmid Transfer and Phage Infection in a Bacterial Population Using Quantitative PCR

    NASA Astrophysics Data System (ADS)

    Wan, Zhenmao; Goddard, Noel

    2012-02-01

    Horizontal gene transfer between species is an important mechanism for bacterial genome evolution. In Escherichia coli, conjugation is the transfer from a donor(F^+) to a recipient(F^-) cell through cell-to-cell contact. We demonstrate a novel qPCR method for quantifying the transfer kinetics of the F plasmid in a population by enumerating the relative abundance of genetic loci unique to the plasmid and the chromosome. This approach allows us to query the plasmid transfer rate without the need for selective culturing with unprecedented single locus resolution. It also allows us to investigate the inhibition of conjugation in the presence of filamentous bacteriophages M13. Experimental data is then compared with numerical simulation using a mass action, resource limited model.

  19. Bacterial Communities Differ among Drosophila melanogaster Populations and Affect Host Resistance against Parasitoids

    PubMed Central

    Dini-Andreote, Francisco; Falcao Salles, Joana

    2016-01-01

    In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population background effects, we characterized the bacterial communities in larvae of six genetically differentiated and geographically distant D. melanogaster lines collected from natural populations across Europe. The diet for these six lines had been identical for ca. 50 generations, thus any differences in the composition of the microbiome originates from the host populations. We also investigated whether induced shifts in the microbiome—in this case by controlled antibiotic administration—alters the hosts’ resistance to parasitism. Our data revealed a clear signature of population background on the diversity and composition of D. melanogaster microbiome that differed across lines, even after hosts had been maintained at the same diet and laboratory conditions for over 4 years. In particular, the number of bacterial OTUs per line ranged from 8 to 39 OTUs. Each line harboured 2 to 28 unique OTUs, and OTUs that were highly abundant in some lines were entirely missing in others. Moreover, we found that the response to antibiotic treatment differed among the lines and significantly altered the host resistance to the parasitoid Asobara tabida in one of the six lines. Wolbachia, a widespread intracellular endosymbiont associated with parasitoid resistance, was lacking in this line, suggesting that other components of the Drosophila microbiome caused a change in host resistance. Collectively, our results revealed that lines that originate from different population backgrounds show significant differences in the established Drosophila microbiome, outpacing the long-term effect of diet. Perturbations on these naturally assembled microbiomes to some degree influenced the hosts

  20. Bacterial Community in Ancient Siberian Permafrost as Characterized by Culture and Culture-Independent Methods

    NASA Astrophysics Data System (ADS)

    Vishnivetskaya, Tatiana A.; Petrova, Maya A.; Urbance, John; Ponder, Monica; Moyer, Craig L.; Gilichinsky, David A.; Tiedje, James M.

    2006-06-01

    The microbial composition of ancient permafrost sediments from the Kolyma lowland of Northeast Eurasia was examined through culture and culture-independent approaches. These sediments have been continuously frozen for 5,000 to 2-3 million years. A total of 265 Bacteria 16S rRNA gene sequences were amplified from the permafrost total-community genomic DNA and screened by amplified ribosomal 16S rRNA restriction analysis. Members of three major lineages were found: gamma-Proteobacteria (mostly Xanthomonadaceae), Actinobacteria, and Firmicutes. We also determined partial 16S rRNA gene sequences of 49 isolates from a collection of 462 aerobes isolated from these sediments. The bacteria included Actinomycetales (Arthrobacter and Microbacteriaceae); followed by the Firmicutes (Exiguobacterium and Planomicrobium); the Bacteroidetes (Flavobacterium); the gamma-Proteobacteria (Psychrobacter); and the alpha-Proteobacteria (Sphingomonas). Both culture and culture-independent approaches showed the presence of high and low G+C Gram-positive bacteria and gamma-Proteobacteria. Some of the 16S rRNA gene sequences of environmental clones matched those of Arthrobacter isolates. Two-thirds of the isolates grew at -2.5°C, indicating that they are psychroactive, and all are closely related to phylogenetic groups with strains from other cold environments, mostly commonly from Antarctica. The culturable and non-culturable microorganisms found in the terrestrial permafrost provide a prototype for possible life on the cryogenic planets of the Solar System.

  1. Flow cytometric determination of bacterial populations in bottled natural mineral waters

    NASA Astrophysics Data System (ADS)

    Beisker, Wolfgang; Meier, H.

    1998-04-01

    In order to enhance the quality and safety of bottled natural mineral waters, new methodologies besides classical bacteriology have been evaluated. Multi laser flow cytometry has been used to identify bacterial populations based on their DNA content, physiological activity and phylogeny from in situ hybridization with rRNA targeted DNA probes. Due to the low content of organic material in these waters, the bacterial population are under conditions (low ribosome content, low activity, etc.) which makes it hard to detect them flow cytometrically. The numbers of bacteria are in the range between 1000 and 100,000 per ml (for uncarbonated waters). Filtration techniques to enrich the bacterial population have been developed in combination with specific staining and hybridization protocols. First results on some selected brands show, that most bacteria belong to the beta subclass of proteobacteria. If the DNA containing cells (DAPI staining) are counted as 100%, 84% could be stained with a eubacteria probe. From these 84% 68% belong to the beta subclass, 8.2% to the alpha and 0.3% to the gamma subclass of roteobacteria. 8.5% could be identified as cytophaga flexibacter. By optimizing DNA staining with cyanine dyes and enhancing the sensitivity of light scatter detection, the detection limit could be considerably lowered.

  2. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

    PubMed Central

    Kumar, Nitin; Lad, Ganesh; Giuntini, Elisa; Kaye, Maria E.; Udomwong, Piyachat; Shamsani, N. Jannah; Young, J. Peter W.; Bailly, Xavier

    2015-01-01

    Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny. PMID:25589577

  3. Chromosome painting in silico in a bacterial species reveals fine population structure.

    PubMed

    Yahara, Koji; Furuta, Yoshikazu; Oshima, Kenshiro; Yoshida, Masaru; Azuma, Takeshi; Hattori, Masahira; Uchiyama, Ikuo; Kobayashi, Ichizo

    2013-06-01

    Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify population structure have limitations in analyzing haplotypes and recombination across the genome. Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome sequences. This method detects the genome-wide transfer of DNA sequence chunks through homologous recombination. Here, we apply it to the frequently recombining bacterial species Helicobacter pylori that has infected Homo sapiens since their birth in Africa and shows wide phylogeographic divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa, Japan, that we recently sequenced. The newer method revealed a finer population structure than revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic network analysis of the core genome. Novel subgroups were found in Europe, Amerind, and East Asia groups. Examination of genetic flux showed some singleton strains to be hybrids of subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of Asia. We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale.

  4. Gene Expression Variability Underlies Adaptive Resistance in Phenotypically Heterogeneous Bacterial Populations.

    PubMed

    Erickson, Keesha E; Otoupal, Peter B; Chatterjee, Anushree

    2015-11-13

    The root cause of the antibiotic resistance crisis is the ability of bacteria to evolve resistance to a multitude of antibiotics and other environmental toxins. The regulation of adaptation is difficult to pinpoint due to extensive phenotypic heterogeneity arising during evolution. Here, we investigate the mechanisms underlying general bacterial adaptation by evolving wild-type Escherichia coli populations to dissimilar chemical toxins. We demonstrate the presence of extensive inter- and intrapopulation phenotypic heterogeneity across adapted populations in multiple traits, including minimum inhibitory concentration, growth rate, and lag time. To search for a common response across the heterogeneous adapted populations, we measured gene expression in three stress-response networks: the mar regulon, the general stress response, and the SOS response. While few genes were differentially expressed, clustering revealed that interpopulation gene expression variability in adapted populations was distinct from that of unadapted populations. Notably, we observed both increases and decreases in gene expression variability upon adaptation. Sequencing select genes revealed that the observed gene expression trends are not necessarily attributable to genetic changes. To further explore the connection between gene expression variability and adaptation, we propagated single-gene knockout and CRISPR (clustered regularly interspaced short palindromic repeats) interference strains and quantified impact on adaptation to antibiotics. We identified significant correlations that suggest genes with low expression variability have greater impact on adaptation. This study provides evidence that gene expression variability can be used as an indicator of bacterial adaptive resistance, even in the face of the pervasive phenotypic heterogeneity underlying adaptation.

  5. Biodegradation of munitions compounds by a sulfate reducing bacterial enrichment culture

    SciTech Connect

    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 incomplete 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.

  6. Bacterial cellulose production by Gluconacetobacter xylinus by employing alternative culture media.

    PubMed

    Jozala, Angela Faustino; Pértile, Renata Aparecida Nedel; dos Santos, Carolina Alves; de Carvalho Santos-Ebinuma, Valéria; Seckler, Marcelo Martins; Gama, Francisco Miguel; Pessoa, Adalberto

    2015-02-01

    Bacterial cellulose (BC) is used in different fields as a biological material due to its unique properties. Despite there being many BC applications, there still remain many problems associated with bioprocess technology, such as increasing productivity and decreasing production cost. New technologies that use waste from the food industry as raw materials for culture media promote economic advantages because they reduce environmental pollution and stimulate new research for science sustainability. For this reason, BC production requires optimized conditions to increase its application. The main objective of this study was to evaluate BC production by Gluconacetobacter xylinus using industry waste, namely, rotten fruits and milk whey, as culture media. Furthermore, the structure of BC produced at different conditions was also determined. The culture media employed in this study were composed of rotten fruit collected from the disposal of free markets, milk whey from a local industrial disposal, and their combination, and Hestrin and Schramm media was used as standard culture media. Although all culture media studied produced BC, the highest BC yield-60 mg/mL-was achieved with the rotten fruit culture. Thus, the results showed that rotten fruit can be used for BC production. This culture media can be considered as a profitable alternative to generate high-value products. In addition, it combines environmental concern with sustainable processes that can promote also the reduction of production cost.

  7. Bacterial degradation of synthetic and kraft lignin by axenic and mixed culture and their metabolic products.

    PubMed

    Chandra, Ram; Bharagava, Ram Naresh

    2013-11-01

    Pulp paper mill effluent has high pollution load due to presence of lignin and its derivatives as major colouring and polluting constituents. In this study, two lignin degrading bacteria IITRL1 and IITRSU7 were isolated and identified as Citrobacter freundii (FJ581026) and Citrobacter sp. (FJ581023), respectively. In degradation study by axenic and mixed culture, mixed bacterial culture was found more effective compared to axenic culture as it decolourized 85 and 62% of synthetic and kraft lignin whereas in axenic conditions, bacterium IITRL1 and IITRSU7 decolourized 61 and 64% synthetic and 49 and 54% kraft lignin, respectively. Further, the mixed bacterial culture also showed the removal of 71, 58% TOC; 78, 53% AOX; 70, 58% COD and 74, 58% lignin from synthetic and kraft lignin, respectively. The ligninolytic enzyme was characterized as manganese peroxidase by SDS-PAGE yielding a single band of 43 KDa. The HPLC analysis of degraded samples showed reduction as well as shifting of peaks compared to control indicating the degradation as well as transformation of compounds. Further, in GC-MS analysis of synthetic and kraft lignin degraded samples, hexadecanoic acid was found as recalcitrant compounds while 2,4,6-trichloro-phenol, 2,3,4,5-tetrachloro-phenol and pentachloro-phenol were detected as new metabolites.

  8. Biodegradation of Palm Kernel Cake by Cellulolytic and Hemicellulolytic Bacterial Cultures through Solid State Fermentation

    PubMed Central

    Alshelmani, Mohamed Idris; Loh, Teck Chwen; Foo, Hooi Ling; Lau, Wei Hong; Sazili, Awis Qurni

    2014-01-01

    Four cellulolytic and hemicellulolytic bacterial cultures were purchased from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Culture (DSMZ) and the American Type Culture Collection (ATCC). Two experiments were conducted; the objective of the first experiment was to determine the optimum time period required for solid state fermentation (SSF) of palm kernel cake (PKC), whereas the objective of the second experiment was to investigate the effect of combinations of these cellulolytic and hemicellulolytic bacteria on the nutritive quality of the PKC. In the first experiment, the SSF was lasted for 12 days with inoculum size of 10% (v/w) on different PKC to moisture ratios. In the second experiment, fifteen combinations were created among the four microbes with one untreated PKC as a control. The SSF lasted for 9 days, and the samples were autoclaved, dried, and analyzed for proximate analysis. Results showed that bacterial cultures produced high enzymes activities at the 4th day of SSF, whereas their abilities to produce enzymes tended to be decreased to reach zero at the 8th day of SSF. Findings in the second experiment showed that hemicellulose and cellulose was significantly (P < 0.05) decreased, whereas the amount of reducing sugars were significantly (P < 0.05) increased in the fermented PKC (FPKC) compared with untreated PKC. PMID:25019097

  9. The importance of the viable but non-culturable state in human bacterial pathogens

    PubMed Central

    Li, Laam; Mendis, Nilmini; Trigui, Hana; Oliver, James D.; Faucher, Sebastien P.

    2014-01-01

    Many bacterial species have been found to exist in a viable but non-culturable (VBNC) state since its discovery in 1982. VBNC cells are characterized by a loss of culturability on routine agar, which impairs their detection by conventional plate count techniques. This leads to an underestimation of total viable cells in environmental or clinical samples, and thus poses a risk to public health. In this review, we present recent findings on the VBNC state of human bacterial pathogens. The characteristics of VBNC cells, including the similarities and differences to viable, culturable cells and dead cells, and different detection methods are discussed. Exposure to various stresses can induce the VBNC state, and VBNC cells may be resuscitated back to culturable cells under suitable stimuli. The conditions that trigger the induction of the VBNC state and resuscitation from it are summarized and the mechanisms underlying these two processes are discussed. Last but not least, the significance of VBNC cells and their potential influence on human health are also reviewed. PMID:24917854

  10. The Cultural Mind: Environmental Decision Making and Cultural Modeling within and across Populations

    ERIC Educational Resources Information Center

    Atran, Scott; Medin, Douglas L.; Ross, Norbert O.

    2005-01-01

    This article describes cross-cultural research on the relation between how people conceptualize nature and how they act in it. Mental models of nature differ dramatically among populations living in the same area and engaged in similar activities. This has novel implications for environmental decision making and management, including commons…

  11. Bacterial siderophores efficiently provide iron to iron-starved tomato plants in hydroponics culture.

    PubMed

    Radzki, W; Gutierrez Mañero, F J; Algar, E; Lucas García, J A; García-Villaraco, A; Ramos Solano, B

    2013-09-01

    Iron is one of the essential elements for a proper plant development. Providing plants with an accessible form of iron is crucial when it is scant or unavailable in soils. Chemical chelates are the only current alternative and are highly stable in soils, therefore, posing a threat to drinking water. The aim of this investigation was to quantify siderophores produced by two bacterial strains and to determine if these bacterial siderophores would palliate chlorotic symptoms of iron-starved tomato plants. For this purpose, siderophore production in MM9 medium by two selected bacterial strains was quantified, and the best was used for biological assay. Bacterial culture media free of bacteria (S) and with bacterial cells (BS), both supplemented with Fe were delivered to 12-week-old plants grown under iron starvation in hydroponic conditions; controls with full Hoagland solution, iron-free Hoagland solution and water were also conducted. Treatments were applied twice along the experiment, with a week in between. At harvest, plant yield, chlorophyll content and nutritional status in leaves were measured. Both the bacterial siderophore treatments significantly increased plant yield, chlorophyll and iron content over the positive controls with full Hoagland solution, indicating that siderophores are effective in providing Fe to the plant, either with or without the presence of bacteria. In summary, siderophores from strain Chryseobacterium C138 are effective in supplying Fe to iron-starved tomato plants by the roots, either with or without the presence of bacteria. Based on the amount of siderophores produced, an effective and economically feasible organic Fe chelator could be developed.

  12. Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics

    PubMed Central

    2014-01-01

    Background The liver is the first line of defence against continuously occurring influx of microbial-derived products and bacteria from the gut. Intestinal bacteria have been implicated in the pathogenesis of alcoholic liver cirrhosis. Escape of intestinal bacteria into the ascites is involved in the pathogenesis of spontaneous bacterial peritonitis, which is a common complication of liver cirrhosis. The association between faecal bacterial populations and alcoholic liver cirrhosis has not been resolved. Methods Relative ratios of major commensal bacterial communities (Bacteroides spp., Bifidobacterium spp., Clostridium leptum group, Enterobactericaea and Lactobacillus spp.) were determined in faecal samples from post mortem examinations performed on 42 males, including cirrhotic alcoholics (n = 13), non-cirrhotic alcoholics (n = 15), non-alcoholic controls (n = 14) and in 7 healthy male volunteers using real-time quantitative PCR (RT-qPCR). Translocation of bacteria into liver in the autopsy cases and into the ascites of 12 volunteers with liver cirrhosis was also studied with RT-qPCR. CD14 immunostaining was performed for the autopsy liver samples. Results Relative ratios of faecal bacteria in autopsy controls were comparable to those of healthy volunteers. Cirrhotics had in median 27 times more bacterial DNA of Enterobactericaea in faeces compared to the healthy volunteers (p = 0.011). Enterobactericaea were also the most common bacteria translocated into cirrhotic liver, although there were no statistically significant differences between the study groups. Of the ascites samples from the volunteers with liver cirrhosis, 50% contained bacterial DNA from Enterobactericaea, Clostridium leptum group or Lactobacillus spp.. The total bacterial DNA in autopsy liver was associated with the percentage of CD14 expression (p = 0.045). CD14 expression percentage in cirrhotics was significantly higher than in the autopsy controls (p = 0

  13. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens

    PubMed Central

    WILSON, BENJAMIN A.; GARUD, NANDITA R.; FEDER, ALISON F.; ASSAF, ZOE J.; PENNINGS, PLEUNI S.

    2016-01-01

    Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance. PMID:26578204

  14. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.

    PubMed

    Wilson, Benjamin A; Garud, Nandita R; Feder, Alison F; Assaf, Zoe J; Pennings, Pleuni S

    2016-01-01

    Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.

  15. Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate–Methane Transition Zone

    PubMed Central

    Mills, Heath J.; Reese, Brandi Kiel; Shepard, Alicia K.; Riedinger, Natascha; Dowd, Scot E.; Morono, Yuki; Inagaki, Fumio

    2012-01-01

    A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate–methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques. PMID:22485111

  16. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    SciTech Connect

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  17. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    SciTech Connect

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

    2014-06-18

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

  18. Identifying currents in the gene pool for bacterial populations using an integrative approach.

    PubMed

    Tang, Jing; Hanage, William P; Fraser, Christophe; Corander, Jukka

    2009-08-01

    The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html.

  19. Influence of oyster culture on biogeochemistry and bacterial community structure at the sediment-water interface.

    PubMed

    Azandégbé, Afi; Poly, Franck; Andrieux-Loyer, Françoise; Kérouel, Roger; Philippon, Xavier; Nicolas, Jean-Louis

    2012-10-01

    Bacterial community structure and some biogeochemical parameters were studied in the sediment of two Pacific oyster farming sites, Aber Benoît (AB) and Rivière d'Auray (RA) in Brittany (France), to examine the ecological impact of oysters and to evaluate the emission of sulfide and ammonia from sediment. At AB, the organic matter accumulated in the sediment beneath the oyster tables was rapidly mineralized, with strong fluxes of ammonia and sulfide that reached 1014 and 215 μmol m(-2) h(-1), respectively, in June 2007. At RA, the fluxes were about half as strong on average and better distributed through the year. The ammonia and sulfide concentrations in the overlying water never reached levels that would be toxic to oysters in either site, nor did hypoxia occur. Total culturable bacteria (TCB) varied greatly according to the temperature: from 1.6 × 10(4) to 9.4 × 10(7) cell g(-1) sediment. Inversely, the bacterial community structure remained surprising stable through the seasons, marginally influenced by the presence of oysters and by temperature. Bacterial communities appeared to be characteristic of the sites, with only one common phylotype, Vibrio aestuarianus, a potential oyster pathogen. These data refine the hypothesis of seawater toxicity to oysters because of ammonia and sulfide fluxes and show that the measured environmental factors had only a weak influence on bacterial community structure.

  20. On the relationship between traditional culture and population in China.

    PubMed

    Yang, Y

    1994-01-01

    The Chinese agricultural base of production and livelihood has ensured the maintenance of traditional culture. Chinese lifestyles have changed little. Population might be developed economically, but traditional practices are likely to remain. Social and cultural conditions still determine the chosen number and gender of children. High fertility in rural agricultural society is related to a desire for greater wealth, for balancing the mortality rate, and for building security in old age. Traditional Chinese thinking promoted early marriage and childbearing. The desire for more children was really a desire for more sons. The desire for sons traditionally was so strong that men kept concubines in order to have more sons. Traditional society between 1949 and 1989 produced population reproduction that increased from 400 million to 800 million. Traditional society is based on the literati, farmers, workers or craftsmen, and business people. Society's strength was measured in Chinese tradition by the amount of food produced or the greater population involved in agriculture. During the Ming and Qing dynasties and periods of famine and natural disaster, government provided farmers with land, seeds, oxen and praise. Conversely, businessmen and crafts persons were taxed as a means of restricting their growth, and children's education was restricted. Literati held the highest status. Officials held a preferential rank over farming. An exemplary goal was to become an official and a farmer. The number of literati was small and it was difficult to gain access to these professions. Traditional culture reflected the importance of staying in one place; the only mass migrations historically were ones due to survival needs in times of war and during the Tang Dynasty and the Song Dynasty. Feudal rulers restricted travel, but families and clans were the strong binding force that kept migration limited. Clans also restricted occupational choices and inheritance. Traditional isolated and

  1. Increasing cell culture population doublings for long-term growth of finite life span human cell cultures

    DOEpatents

    Stampfer, Martha R; Garbe, James C

    2015-02-24

    Cell culture media formulations for culturing human epithelial cells are herein described. Also described are methods of increasing population doublings in a cell culture of finite life span human epithelial cells and prolonging the life span of human cell cultures. Using the cell culture media disclosed alone and in combination with addition to the cell culture of a compound associated with anti-stress activity achieves extended growth of pre-stasis cells and increased population doublings and life span in human epithelial cell cultures.

  2. Increasing cell culture population doublings for long-term growth of finite life span human cell cultures

    SciTech Connect

    Stampfer, Martha R.; Garbe, James C.

    2016-06-28

    Cell culture media formulations for culturing human epithelial cells are herein described. Also described are methods of increasing population doublings in a cell culture of finite life span human epithelial cells and prolonging the life span of human cell cultures. Using the cell culture media disclosed alone and in combination with addition to the cell culture of a compound associated with anti-stress activity achieves extended growth of pre-stasis cells and increased population doublings and life span in human epithelial cell cultures.

  3. Metabolites from the Fungal Endophyte Aspergillus austroafricanus in Axenic Culture and in Fungal-Bacterial Mixed Cultures.

    PubMed

    Ebrahim, Weaam; El-Neketi, Mona; Lewald, Laura-Isabell; Orfali, Raha S; Lin, Wenhan; Rehberg, Nidja; Kalscheuer, Rainer; Daletos, Georgios; Proksch, Peter

    2016-04-22

    The endophytic fungus Aspergillus austroafricanus isolated from leaves of the aquatic plant Eichhornia crassipes was fermented axenically on solid rice medium as well as in mixed cultures with Bacillus subtilis or with Streptomyces lividans. Chromatographic analysis of EtOAc extract of axenic cultures afforded two new metabolites, namely, the xanthone dimer austradixanthone (1) and the sesquiterpene (+)-austrosene (2), along with five known compounds (3-7). Austradixanthone (1) represents the first highly oxygenated heterodimeric xanthone derivative. When A. austroafricanus was grown in mixed cultures with B. subtilis or with S. lividans, several diphenyl ethers (8-11) including the new austramide (8) were induced up to 29-fold. The structures of new compounds were unambiguously elucidated using 1D- and 2D-NMR spectroscopy, HRESIMS, and chemical derivatization. Compound 7 exhibited weak cytotoxicity against the murine lymphoma L5178Y cell line (EC50 is 12.6 μM). In addition, compounds 9 and 10, which were enhanced in mixed fungal/bacterial cultures, proved to be active against Staphylococcus aureus (ATCC 700699) with minimal inhibitory concentrations (MICs) of 25 μM each (6.6 μg/mL), whereas compound 11 revealed moderate antibacterial activity against B. subtilis 168 trpC2 with an MIC value of 34.8 μM (8 μg/mL).

  4. Mineralization of the s-triazine ring of atrazine by stable bacterial mixed cultures.

    PubMed Central

    Mandelbaum, R T; Wackett, L P; Allan, D L

    1993-01-01

    Enrichment cultures containing atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) at a concentration of 100 ppm (0.46 mM) as a sole nitrogen source were obtained from soils exposed to repeated spills of atrazine, alachlor, and metolachlor. Bacterial growth occurred concomitantly with formation of metabolites from atrazine and subsequent biosynthesis of protein. When ring-labeled [14C]atrazine was used, 80% or more of the s-triazine ring carbon atoms were liberated as 14CO2. Hydroxyatrazine may be an intermediate in the atrazine mineralization pathway. More than 200 pure cultures isolated from the enrichment cultures failed to utilize atrazine as a nitrogen source. Mixing pure cultures restored atrazine-mineralizing activity. Repeated transfer of the mixed cultures led to increased rates of atrazine metabolism. The rate of atrazine degradation, even at the elevated concentrations used, far exceeded the rates previously reported in soils, waters, and mixed and pure cultures of bacteria. PMID:8328795

  5. Comparison of culture-dependent and -independent methods for bacterial community monitoring during Montasio cheese manufacturing.

    PubMed

    Carraro, Lisa; Maifreni, Michela; Bartolomeoli, Ingrid; Martino, Maria Elena; Novelli, Enrico; Frigo, Francesca; Marino, Marilena; Cardazzo, Barbara

    2011-04-01

    The microbial community in milk is of great importance in the manufacture of traditional cheeses produced using raw milk and natural cultures. During milk curdling and cheese ripening, complex interactions occur in the microbial community, and accurate identification of the microorganisms involved provides essential information for understanding their role in these processes and in flavor production. Recent improvements in molecular biological methods have led to their application to food matrices, and thereby opened new perspectives for the study of microbial communities in fermented foods. In this study, a description of microbial community composition during the manufacture and ripening of Montasio cheese was provided. A combined approach using culture-dependent and -independent methods was applied. Culture-dependent identification was compared with 16S clone libraries sequencing data obtained from both DNA and reverse-transcribed RNA (cDNA) amplification and real-time quantitative PCR (qPCR) assays developed to detect and quantify specific bacterial species/genera (Streptococcus thermophilus, Lactobacillus casei, Pediococcus pentosaceus, Enterococcus spp., Pseudomonas spp.). S. thermophilus was the predominant LAB species throughout the entire ripening period of Montasio cheese. The culture-independent method demonstrates the relevant presence of Pseudomonas spp. and Lactococcus piscium at the beginning of ripening. The culture-dependent approach and the two culture-independent approaches produced complementary information, together generating a general view of cheese microbial ecology.

  6. Sulfolane degradation by mixed cultures and a bacterial isolate identified as a Variovorax sp.

    PubMed

    Greene, E A; Beatty, P H; Fedorak, P M

    2000-01-01

    Sulfolane (tetrahydrothiophene-1,1-dioxide) is used in the Sulfinol process for natural gas sweetening. At many sour-gas processing plants spills, landfills and leakage from unlined surface storage ponds have contaminated groundwaters with sulfolane. Due to its high water solubility and mobility in aquifers, sulfolane poses a risk for off-site contamination. This study investigated the aerobic biodegradation of sulfolane by two mixed microbial enrichment cultures and by three bacterial isolates. Sulfolane served as the sole C, S and energy source for these cultures. In the two mixed cultures, 60% and 80% of the sulfolane C was recovered as CO2, whereas in cultures of the three isolates only 40-42% of the substrate C was recovered as CO,. In the mixed cultures, 81% and 97% of the sulfolane S was converted to sulfate, and in the pure isolates, 55-90% of the substrate S was converted to sulfate. Thus, the mixed cultures were capable of greater mineralization than the pure isolates. One isolate, strain WP1, was identified using a combination of 16S rRNA gene sequencing, physiological traits and cell morphology. WP1 was determined to be most similar to Varioivorax paradoxus.

  7. Influence of Molecular Noise on the Growth of Single Cells and Bacterial Populations

    PubMed Central

    Schmidt, Mischa; Creutziger, Martin; Lenz, Peter

    2012-01-01

    During the last decades experimental studies have revealed that single cells of a growing bacterial population are significantly exposed to molecular noise. Important sources for noise are low levels of metabolites and enzymes that cause significant statistical variations in the outcome of biochemical reactions. In this way molecular noise affects biological processes such as nutrient uptake, chemotactic tumbling behavior, or gene expression of genetically identical cells. These processes give rise to significant cell-to-cell variations of many directly observable quantities such as protein levels, cell sizes or individual doubling times. In this study we theoretically explore if there are evolutionary benefits of noise for a growing population of bacteria. We analyze different situations where noise is either suppressed or where it affects single cell behavior. We consider two specific examples that have been experimentally observed in wild-type Escherichia coli cells: (i) the precision of division site placement (at which molecular noise is highly suppressed) and (ii) the occurrence of noise-induced phenotypic variations in fluctuating environments. Surprisingly, our analysis reveals that in these specific situations both regulatory schemes [i.e. suppression of noise in example (i) and allowance of noise in example (ii)] do not lead to an increased growth rate of the population. Assuming that the observed regulatory schemes are indeed caused by the presence of noise our findings indicate that the evolutionary benefits of noise are more subtle than a simple growth advantage for a bacterial population in nutrient rich conditions. PMID:22238678

  8. Changes in equine hindgut bacterial populations during oligofructose-induced laminitis.

    PubMed

    Milinovich, G J; Trott, D J; Burrell, P C; van Eps, A W; Thoefner, M B; Blackall, L L; Al Jassim, R A M; Morton, J M; Pollitt, C C

    2006-05-01

    In the horse, carbohydrate overload is thought to play an integral role in the onset of laminitis by drastically altering the profile of bacterial populations in the hindgut. The objectives of this study were to develop and validate microbial ecology methods to monitor changes in bacterial populations throughout the course of experimentally induced laminitis and to identify the predominant oligofructose-utilizing organisms. Laminitis was induced in five horses by administration of oligofructose. Faecal specimens were collected at 8 h intervals from 72 h before to 72 h after the administration of oligofructose. Hindgut microbiota able to utilize oligofructose were enumerated throughout the course of the experiment using habitat-simulating medium. Isolates were collected and representatives identified by 16S rRNA gene sequencing. The majority of these isolates collected belonged to the genus Streptococcus, 91% of which were identified as being most closely related to Streptococcus infantarius ssp. coli. Furthermore, S. infantarius ssp. coli was the predominant oligofructose-utilizing organism isolated before the onset of lameness. Fluorescence in situ hybridization probes developed to specifically target the isolated Streptococcus spp. demonstrated marked population increases between 8 and 16 h post oligofructose administration. This was followed by a rapid population decline which corresponded with a sharp decline in faecal pH and subsequently lameness at 24-32 h post oligofructose administration. This research suggests that streptococci within the Streptococcus bovis/equinus complex may be involved in the series of events which precede the onset of laminitis in the horse.

  9. Nonselective Bottlenecks Control the Divergence and Diversification of Phase-Variable Bacterial Populations

    PubMed Central

    Aidley, Jack; Rajopadhye, Shweta; Akinyemi, Nwanekka M.; Lango-Scholey, Lea

    2017-01-01

    ABSTRACT   Phase variation occurs in many pathogenic and commensal bacteria and is a major generator of genetic variability. A putative advantage of phase variation is to counter reductions in variability imposed by nonselective bottlenecks during transmission. Genomes of Campylobacter jejuni, a widespread food-borne pathogen, contain multiple phase-variable loci whose rapid, stochastic variation is generated by hypermutable simple sequence repeat tracts. These loci can occupy a vast number of combinatorial expression states (phasotypes) enabling populations to rapidly access phenotypic diversity. The imposition of nonselective bottlenecks can perturb the relative frequencies of phasotypes, changing both within-population diversity and divergence from the initial population. Using both in vitro testing of C. jejuni populations and a simple stochastic simulation of phasotype change, we observed that single-cell bottlenecks produce output populations of low diversity but with bimodal patterns of either high or low divergence. Conversely, large bottlenecks allow divergence only by accumulation of diversity, while interpolation between these extremes is observed in intermediary bottlenecks. These patterns are sensitive to the genetic diversity of initial populations but stable over a range of mutation rates and number of loci. The qualitative similarities of experimental and in silico modeling indicate that the observed patterns are robust and applicable to other systems where localized hypermutation is a defining feature. We conclude that while phase variation will maintain bacterial population diversity in the face of intermediate bottlenecks, narrow transmission-associated bottlenecks could produce host-to-host variation in bacterial phenotypes and hence stochastic variation in colonization and disease outcomes. PMID:28377533

  10. Molecular Detection of Culture-Confirmed Bacterial Bloodstream Infections with Limited Enrichment Time

    PubMed Central

    Moore, Miranda S.; McCann, Chase D.

    2013-01-01

    Conventional blood culturing using automated instrumentation with phenotypic identification requires a significant amount of time to generate results. This study investigated the speed and accuracy of results generated using PCR and pyrosequencing compared to the time required to obtain Gram stain results and final culture identification for cases of culture-confirmed bloodstream infections. Research and physician-ordered blood cultures were drawn concurrently. Aliquots of the incubating research blood culture fluid were removed hourly between 5 and 8 h, at 24 h, and again at 5 days. DNA was extracted from these 6 time point aliquots and analyzed by PCR and pyrosequencing for bacterial rRNA gene targets. These results were then compared to those of the physician-ordered blood culture. PCR and pyrosequencing accurately identified 92% of all culture-confirmed cases after a mean enrichment time of 5.8 ± 2.9 h. When the time needed to complete sample processing was included for PCR and pyrosequencing protocols, the molecular approach yielded results in 11.8 ± 2.9 h compared to means of 27.9 ± 13.6 h to obtain the Gram stain results and 81.6 ± 24.0 h to generate the final culture-based identification. The molecular approach enabled accurate detection of most bacteria present in incubating blood culture bottles on average about 16 h sooner than Gram stain results became available and approximately 3 days sooner than the phenotypic identification was entered in the Laboratory Information System. If implemented, this more rapid molecular approach could minimize the number of doses of unnecessary or ineffective antibiotics administered to patients. PMID:23985915

  11. Elucidation of the tidal influence on bacterial populations in a monsoon influenced estuary through simultaneous observations.

    PubMed

    Khandeparker, Lidita; Eswaran, Ranjith; Gardade, Laxman; Kuchi, Nishanth; Mapari, Kaushal; Naik, Sneha D; Anil, Arga Chandrashekar

    2017-01-01

    The influence of tides on bacterial populations in a monsoon influenced tropical estuary was assessed through fine resolution sampling (1 to 3 h) during spring and neap tides from mouth to the freshwater end at four stations during pre-monsoon, monsoon and post-monsoon seasons. Higher abundance of total bacterial count (TBC) in surface water near the river mouth, compared to the upstream, during pre-monsoon was followed by an opposite scenario during the monsoon When seasonally compared, it was during the post-monsoon season when TBC in surface water was highest, with simultaneous decrease in their count in the river sediment. The total viable bacterial count (TVC) was influenced by the depth-wise stratification of salinity, which varied with tidal fluctuation, usually high and low during the neap and spring tides respectively. The abundance of both the autochthonous Vibrio spp. and allochthonous coliform bacteria was influenced by the concentrations of dissolved nutrients and suspended particulate matter (SPM). It is concluded that depending on the interplay of riverine discharge and tidal amplitude, sediment re-suspension mediated increase in SPM significantly regulates bacteria populations in the estuarine water, urging the need of systematic regular monitoring for better prediction of related hazards, including those associated with the rise in pathogenic Vibrio spp. in the changing climatic scenarios.

  12. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations.

    PubMed

    Fridman, Ofer; Goldberg, Amir; Ronin, Irine; Shoresh, Noam; Balaban, Nathalie Q

    2014-09-18

    The great therapeutic achievements of antibiotics have been dramatically undercut by the evolution of bacterial strategies that overcome antibiotic stress. These strategies fall into two classes. 'Resistance' makes it possible for a microorganism to grow in the constant presence of the antibiotic, provided that the concentration of the antibiotic is not too high. 'Tolerance' allows a microorganism to survive antibiotic treatment, even at high antibiotic concentrations, as long as the duration of the treatment is limited. Although both resistance and tolerance are important reasons for the failure of antibiotic treatments, the evolution of resistance is much better understood than that of tolerance. Here we followed the evolution of bacterial populations under intermittent exposure to the high concentrations of antibiotics used in the clinic and characterized the evolved strains in terms of both resistance and tolerance. We found that all strains adapted by specific genetic mutations, which became fixed in the evolved populations. By monitoring the phenotypic changes at the population and single-cell levels, we found that the first adaptive change to antibiotic stress was the development of tolerance through a major adjustment in the single-cell lag-time distribution, without a change in resistance. Strikingly, we found that the lag time of bacteria before regrowth was optimized to match the duration of the antibiotic-exposure interval. Whole genome sequencing of the evolved strains and restoration of the wild-type alleles allowed us to identify target genes involved in this antibiotic-driven phenotype: 'tolerance by lag' (tbl). Better understanding of lag-time evolution as a key determinant of the survival of bacterial populations under high antibiotic concentrations could lead to new approaches to impeding the evolution of antibiotic resistance.

  13. Measuring the Level of Agreement Between Cloacal Gram's Stains and Bacterial Cultures in Hispaniolan Amazon Parrots ( Amazona ventralis ).

    PubMed

    Evans, Erika E; Mitchell, Mark A; Whittington, Julia K; Roy, Alma; Tully, Thomas N

    2014-12-01

    Cloacal or fecal Gram's stains and bacterial cultures are routinely performed during avian physical examinations to assess the microbial flora of the gastrointestinal tract. Although cloacal or fecal Gram's stains and bacterial cultures are considered routine diagnostic procedures, the level of agreement between the individual tests has not been determined. To investigate the level of agreement between results from Gram's stain and bacterial culture when used to assess cloacal or fecal samples from psittacine birds, samples were taken from 21 clinically healthy Hispaniolan Amazon parrots ( Amazona ventralis ) and tested by Gram's stain cytology and bacterial culture. Most bacteria (97.2%) identified by Gram's stain were gram positive. However, gram-negative organisms were identified in 7 of 21 (33.3%; 95% confidence interval: 13.3%-53.3%) birds. Escherichia coli was the only gram-negative organism identified on culture. Agreement between results of Gram's stain and culture was fair (weighted κ = 0.27). The results of this study suggest that Gram's stains and bacterial culture may need to be performed with a parallel testing strategy to limit the likelihood of misclassifying the microbial flora of psittacine patients.

  14. Degradation and total mineralization of monohalogenated biphenyls in natural sediment and mixed bacterial culture.

    PubMed Central

    Kong, H L; Sayler, G S

    1983-01-01

    Mixed bacterial cultures obtained from polychlorinated biphenyl-contaminated river sediments are capable of degrading monohalogenated biphenyls under simulated natural conditions. Culture conditions include river water as supportive medium and mixed bacterial cultures obtained from river sediments. Degradation occurs when the substrates are supplied as the sole carbon source or when added together with glucose. The degradation rates of 2-, 3-, and 4-chlorobiphenyl, at 30 micrograms ml-1, were 1.1, 1.6, and 2.0 micrograms ml-1 day-1, respectively. Monobrominated biphenyls, including 2-, 3-, and 4-bromobiphenyl, were degraded at rates of 2.3, 4.2, and 1.4 micrograms ml-1 day-1, respectively. Metabolites, including halogenated benzoates, were detected by high-performance liquid chromatography and mass spectrometry. By using chlorophenyl ring-labeled monochlorobiphenyls as substrates, total mineralization (defined as CO2 production from the chlorophenyl ring) was observed for 4-chlorobiphenyl but not for 2-chlorobiphenyl. Rates of total mineralization of 4-chlorobiphenyl (at 39 to 385 micrograms ml-1 levels) were dependent on substrate concentration, whereas variation of cell number in the range of 10(5) to 10(7) cells ml-1 had no significant effects. Simulated sunlight enhanced the rate of mineralization by ca. 400%. PMID:6639021

  15. Daily variations in pathogenic bacterial populations in a monsoon influenced tropical environment.

    PubMed

    Khandeparker, Lidita; Anil, Arga Chandrashekar; Naik, Sneha D; Gaonkar, Chetan C

    2015-07-15

    Changing climatic conditions have influenced the monsoon pattern in recent years. Variations in bacterial population in one such tropical environment were observed everyday over two years and point out intra and inter annual changes driven by the intensity of rainfall. Vibrio spp. were abundant during the monsoon and so were faecal coliforms. Vibrio alginolyticus were negatively influenced by nitrate, whereas, silicate and rainfall positively influenced Vibrio parahaemolyticus numbers. It is also known that pathogenic bacteria are associated with the plankton. Changes in the abundance of plankton, which are governed mainly by environmental changes, could be responsible for variation in pathogenic bacterial abundance during monsoon, other than the land runoff due to precipitation and influx of fresh water.

  16. Horizontal Gene Transfer and the Evolution of Bacterial and Archaeal Population Structure

    PubMed Central

    Alm, Eric J.; Hanage, William P.

    2013-01-01

    Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity. PMID:23332119

  17. Bacterial diversity in a contaminated Alpine glacier as determined by culture-based and molecular approaches.

    PubMed

    Cappa, Fabrizio; Suciu, Nicoleta; Trevisan, Marco; Ferrari, Susanna; Puglisi, Edoardo; Cocconcelli, Pier Sandro

    2014-11-01

    Glaciers are important ecosystems, hosting bacterial communities that are adapted to cold conditions and scarcity of available nutrients. Several works focused on the composition of bacterial communities in glaciers and on the long-range atmospheric deposition of pollutants in glaciers, but it is not clear yet if ski resorts can represent a source of point pollution in near-by glaciers, and if these pollutants can influence the residing bacterial communities. To test these hypotheses, 12 samples were analyzed in Madaccio Glacier, in a 3200 ma.s.l. from two areas, one undisturbed and one close to a summer ski resort that is active since the 1930s. Chemical analyses found concentrations up to 43 ng L(-1) for PCBs and up to 168 μg L(-1) for PAHs in the contaminated area: these values are significantly higher than the ones found in undisturbed glaciers because of long-range atmospheric deposition events, and can be explained as being related to the near-by ski resort activities. Isolation of strains on rich medium plates and PCR-DGGE analyses followed by sequencing of bands allowed the identification of a bacterial community with phylogenetic patterns close to other glacier environments, with Proteobacteria and Actinobacteria the mostly abundant phyla, with Acidobacteria, Firmicutes and Cyanobacteria also represented in the culture-independent analyses. A number of isolates were identified by molecular and biochemical methods as phylogenetic related to known xenobiotic-degrading strains: glaciers subjected to chemical contamination can be important reservoirs of bacterial strains with potential applications in bioremediation.

  18. Identification and characterization of metabolic properties of bacterial populations recovered from arsenic contaminated ground water of North East India (Assam).

    PubMed

    Ghosh, Soma; Sar, Pinaki

    2013-12-01

    Diversity of culturable bacterial populations within the Arsenic (As) contaminated groundwater of North Eastern state (Assam) of India is studied. From nine As contaminated samples 89 bacterial strains are isolated. 16S rRNA gene sequence analysis reveals predominance of Brevundimonas (35%) and Acidovorax (23%) along with Acinetobacter (10%), Pseudomonas (9%) and relatively less abundant (<5%) Undibacterium, Herbaspirillum, Rhodococcus, Staphylococcus, Bosea, Bacillus, Ralstonia, Caulobacter and Rhizobiales members. High As(III) resistance (MTC 10-50 mM) is observed for the isolates obtained from As(III) enrichment, particularly for 3 isolates of genus Brevundimonas (MTC 50 mM). In contrast, high resistance to As(V) (MTC as high as 550 mM) is present as a ubiquitous property, irrespective of isolates' enrichment condition. Bacterial genera affiliated to other groups showed relatively lower degree of As resistance [MTCs of 15-20 mM As(III) and 250-350 mM As(V)]. As(V) reductase activity is detected in strains with high As(V) as well as As(III) resistance. A strong correlation could be established among isolates capable of reductase activity and siderophore production as well as As(III) tolerance. A large number of isolates (nearly 50%) is capable of anaerobic respiration using alternate inorganic electron acceptors [As(V), Se(VI), Fe(III), [NO(3)(2), SO(4)(2), S(2)O(3)(2). Ability to utilize different carbon sources ranging from C2-C6 compounds along with some complex sugars is also observed. Particularly, a number of strains is found to possess ability to grow chemolithotrophically using As(III) as the electron donor. The study reports for the first time the identity and metabolic abilities of bacteria in As contaminated ground water of North East India, useful to elucidate the microbial role in influencing mobilization of As in the region.

  19. Bacterial Population in Intestines of the Black Tiger Shrimp (Penaeus monodon) under Different Growth Stages

    PubMed Central

    Rungrassamee, Wanilada; Klanchui, Amornpan; Chaiyapechara, Sage; Maibunkaew, Sawarot; Tangphatsornruang, Sithichoke; Jiravanichpaisal, Pikul; Karoonuthaisiri, Nitsara

    2013-01-01

    Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon), bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15), 1- (J1), 2- (J2), and 3-month-old (J3) juveniles) using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE) approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases) were obtained, which were categorized by barcode for PL15 (7,045 sequences), J1 (3,055 sequences), J2 (13,130 sequences) and J3 (1,890 sequences). Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria) was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities. PMID:23577162

  20. Characterisation of the bacterial populations in a saline heat storage aquifer in the North German Basin

    NASA Astrophysics Data System (ADS)

    Alawi, M.; Lerm, S.; Vetter, A.; Vieth, A.; Mangelsdorf, K.; Seibt, A.; Wolfgramm, M.; Würdemann, H.

    2009-04-01

    The colonization and the ecology of microorganisms in the deep biosphere arouse increasing interest of scientists because of utilizing the subsurface for e.g. energy storage and recovery. The research project AquiScreen investigates the operational reliability of eight geothermally used groundwater systems in Germany under microbial, geochemical, mineralogical, and petrological aspects. This study shows the results of the heat storage in Neubrandenburg (depth: 1250 m), a typical site for saline fluids in the North German Basin. The seasonal alternation in charge and discharge mode enabled sampling the warm (75˚ C) and the cold (45˚ C) side of the geothermal doublet. The analyses focus on microbially induced corrosion on plant components and scaling resulting in filter and/or formation clogging. Microbiological analyses were carried out with fluid and solid phase samples by 16S rDNA based Single Strand Conformation Polymorphism (SSCP) fingerprinting. The analyses are utilized to evaluate the impact of microbial populations on such systems. The genetic fingerprinting revealed significant differences in the bacterial community structure between the warm and cold side of the heat storage. Since the geochemical analyses revealed no remarkable differences, the temperature might be crucial for the different community structures. At the warm side of the aquifer the identified bacteria are closely related to Variovorax and Sphingomonas. At the cold side of the heat storage sulphate reducing and fermentative bacteria were detected. These results correspond with locally observed iron sulphide precipitation and corrosion processes on plant components. Particularly the bacterial population of the cold side was studied over a period of two years. Thereby seasonal changes in the abundance of the identified bacteria, depending on the operational mode of the geothermal plant, were observed. After a malfunction in the pump system of the cold side of the heat storage changes in

  1. Bacterial Population in Intestines of Litopenaeus vannamei Fed Different Probiotics or Probiotic Supernatant.

    PubMed

    Sha, Yujie; Liu, Mei; Wang, Baojie; Jiang, Keyong; Qi, Cancan; Wang, Lei

    2016-10-28

    The interactions of microbiota in the gut play an important role in promoting or maintaining the health of hosts. In this study, in order to investigate and compare the effects of dietary supplementation with Lactobacillus pentosus HC-2 (HC-2), Enterococcus faecium NRW-2, or the bacteria-free supernatant of a HC-2 culture on the bacterial composition of Litopenaeus vannamei, Illumina sequencing of the V1-V2 region of the 16S rRNA gene was used. The results showed that unique species exclusively existed in specific dietary groups, and the abundance of Actinobacteria was significantly increased in the intestinal bacterial community of shrimp fed with the bacteria-free supernatant of an HC-2 culture compared with the control. In addition, the histology of intestines of the shrimp from the four dietary groups was also described, but no obvious improvements in the intestinal histology were observed. The findings in this work will help to promote the understanding of the roles of intestinal bacteria in shrimps when fed with probiotics or probiotic supernatant.

  2. Multiplicity of Quorum Quenching Enzymes: A Potential Mechanism to Limit Quorum Sensing Bacterial Population.

    PubMed

    Koul, Shikha; Kalia, Vipin Chandra

    2017-03-01

    Bacteria express certain of their characteristics especially, pathogenicity factors at high cell densities. The process is termed as quorum sensing (QS). QS operates via signal molecules such as acylhomoserine lactones (AHLs). Other bacteria inhibit QS through the inactivation of AHL signals by producing enzymes like AHL-lactonases and -acylases. Comparative genomic analysis has revealed the multiplicity of genes for AHL lactonases (up to 12 copies per genome) among Bacillus spp. and that of AHL-acylases (up to 5 copies per genome) among Pseudomonas spp. This genetic evolution can be envisaged to enable host to withstand the attacks from bacterial population, which regulates its functioning through QS.

  3. Are nasopharyngeal cultures useful in diagnosis of acute bacterial sinusitis in children?

    PubMed

    Shaikh, Nader; Hoberman, Alejandro; Colborn, D Kathleen; Kearney, Diana H; Jeong, Jong H; Kurs-Lasky, Marcia; Barbadora, Karen A; Bowen, A'delbert; Flom, Lynda L; Wald, Ellen R

    2013-12-01

    The diagnosis of acute bacterial sinusitis can be challenging because symptoms of acute sinusitis and an upper respiratory tract infection (URI) overlap. A rapid test, if accurate in differentiating sinusitis from URI, could be helpful in the diagnostic process. We examined the utility of nasopharyngeal cultures in identifying the subgroup of children with a clinical diagnosis of acute sinusitis who are least likely to benefit from antimicrobial therapy (those with completely normal sinus radiographs). Nasopharyngeal swabs were collected from 204 children meeting a priori clinical criteria for acute sinusitis. All children had sinus X-rays at the time of diagnosis. To determine if negative nasopharyngeal culture results could reliably identify the subgroup of children with normal radiographs, we calculated negative predictive values and negative likelihood ratios. Absence of pathogens in the nasopharynx was not helpful in identifying this low-risk subgroup.

  4. Isolation and characterization of culturable seed-associated bacterial endophytes from gnotobiotically grown Marama bean seedlings.

    PubMed

    Chimwamurombe, Percy Maruwa; Grönemeyer, Jann Lasse; Reinhold-Hurek, Barbara

    2016-06-01

    Marama bean (Tylosema esculentum) is an indigenous non-nodulating legume to the arid agro-ecological parts of Southern Africa. It is a staple food for the Khoisan and Bantu people from these areas. It is intriguing how it is able to synthesize the high-protein content in the seeds since its natural habitat is nitrogen deficient. The aim of the study was to determine the presence of seed transmittable bacterial endophytes that may have growth promoting effects, which may be particularly important for the harsh conditions. Marama bean seeds were surface sterilized and gnotobiotically grown to 2 weeks old seedlings. From surface-sterilized shoots and roots, 123 distinct bacterial isolates were cultured using three media, and identified by BOX-PCR fingerprinting and sequence analyses of the 16S rRNA and nifH genes. Phylogenetic analyses of 73 putative endophytes assigned them to bacterial species from 14 genera including Proteobacteria (Rhizobium, Massilia, Kosakonia, Pseudorhodoferax, Caulobacter, Pantoea, Sphingomonas, Burkholderia, Methylobacterium), Firmicutes (Bacillus), Actinobacteria (Curtobacterium, Microbacterium) and Bacteroidetes (Mucilaginibacter, Chitinophaga). Screening for plant growth-promoting activities revealed that the isolates showed production of IAA, ACC deaminase, siderophores, endoglucanase, protease, AHLs and capacities to solubilize phosphate and fix nitrogen. This is the first report that marama bean seeds may harbor endophytes that can be cultivated from seedlings; in this community of bacteria, physiological characteristics that are potentially plant growth promoting are widespread.

  5. Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing

    PubMed Central

    Riba, J.; Gleichmann, T.; Zimmermann, S.; Zengerle, R.; Koltay, P.

    2016-01-01

    The isolation and analysis of single prokaryotic cells down to 1 μm and less in size poses a special challenge and requires micro-engineered devices to handle volumes in the picoliter to nanoliter range. Here, an advanced Single-Cell Printer (SCP) was applied for automated and label-free isolation and deposition of bacterial cells encapsulated in 35 pl droplets by inkjet-like printing. To achieve this, dispenser chips to generate micro droplets have been fabricated with nozzles 20 μm in size. Further, the magnification of the optical system used for cell detection was increased. Redesign of the optical path allows for collision-free addressing of any flat substrate since no compartment protrudes below the nozzle of the dispenser chip anymore. The improved system allows for deterministic isolation of individual bacterial cells. A single-cell printing efficiency of 93% was obtained as shown by printing fluorescent labeled E. coli. A 96-well plate filled with growth medium is inoculated with single bacteria cells on average within about 8 min. Finally, individual bacterial cells from a heterogeneous sample of E. coli and E. faecalis were isolated for clonal culturing directly on agar plates in user-defined array geometry. PMID:27596612

  6. Diversity, antimicrobial and antioxidant activities of culturable bacterial endophyte communities in Aloe vera.

    PubMed

    Akinsanya, Mushafau Adewale; Goh, Joo Kheng; Lim, Siew Ping; Ting, Adeline Su Yien

    2015-12-01

    Twenty-nine culturable bacterial endophytes were isolated from surface-sterilized tissues (root, stem and leaf) of Aloe vera and molecularly characterized to 13 genera: Pseudomonas, Bacillus, Enterobacter, Pantoea, Chryseobacterium, Sphingobacterium, Aeromonas, Providencia, Cedecea, Klebsiella, Cronobacter, Macrococcus and Shigella. The dominant genera include Bacillus (20.7%), Pseudomonas (20.7%) and Enterobacter (13.8%). The crude and ethyl acetate fractions of the metabolites of six isolates, species of Pseudomonas, Bacillus, Chryseobacterium and Shigella, have broad spectral antimicrobial activities against pathogenic Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus cereus, Salmonella Typhimurium, Proteus vulgaris, Klebsiella pneumoniae, Escherichia coli, Streptococcus pyogenes and Candida albicans, with inhibition zones ranging from 6.0 ± 0.57 to 16.6 ± 0.57 mm. In addition, 80% of the bacterial endophytes produced 1,1-diphenyl-2-picrylhydrazyl (DPPH) with scavenging properties of over 75% when their crude metabolites were compared with ascorbic acid (92%). In conclusion, this study revealed for the first time the endophytic bacteria communities from A. vera (Pseudomonas hibiscicola, Macrococcus caseolyticus, Enterobacter ludwigii, Bacillus anthracis) that produce bioactive compounds with high DPPH scavenging properties (75-88%) and (Bacillus tequilensis, Pseudomonas entomophila, Chryseobacterium indologenes, Bacillus aerophilus) that produce bioactive compounds with antimicrobial activities against bacterial pathogens. Hence, we suggest further investigation and characterization of their bioactive compounds.

  7. Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing

    NASA Astrophysics Data System (ADS)

    Riba, J.; Gleichmann, T.; Zimmermann, S.; Zengerle, R.; Koltay, P.

    2016-09-01

    The isolation and analysis of single prokaryotic cells down to 1 μm and less in size poses a special challenge and requires micro-engineered devices to handle volumes in the picoliter to nanoliter range. Here, an advanced Single-Cell Printer (SCP) was applied for automated and label-free isolation and deposition of bacterial cells encapsulated in 35 pl droplets by inkjet-like printing. To achieve this, dispenser chips to generate micro droplets have been fabricated with nozzles 20 μm in size. Further, the magnification of the optical system used for cell detection was increased. Redesign of the optical path allows for collision-free addressing of any flat substrate since no compartment protrudes below the nozzle of the dispenser chip anymore. The improved system allows for deterministic isolation of individual bacterial cells. A single-cell printing efficiency of 93% was obtained as shown by printing fluorescent labeled E. coli. A 96-well plate filled with growth medium is inoculated with single bacteria cells on average within about 8 min. Finally, individual bacterial cells from a heterogeneous sample of E. coli and E. faecalis were isolated for clonal culturing directly on agar plates in user-defined array geometry.

  8. Imaging the Population Dynamics of Bacterial Communities in the Zebrafish Gut

    NASA Astrophysics Data System (ADS)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Zac Stephens, W.; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

    2013-03-01

    The vertebrate gut is home to a diverse microbial ecosystem whose composition has a strong influence on the development and health of the host organism. While researchers are increasingly able to identify the constituent members of the microbiome, very little is known about the spatial and temporal dynamics of commensal microbial communities, including the mechanisms by which communities nucleate, grow, and interact. We address these issues using a model organism: the larval zebrafish (Danio rerio) prepared microbe-free and inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging with light sheet fluorescence microscopy enables visualization of individual bacterial cells as well as growing colonies over the entire volume of the gut over periods up to 24 hours. We analyze the structure and dynamics of imaged bacterial communities, uncovering correlations between population size, growth rates, and the timing of inoculations that suggest the existence of active changes in the host environment induced by early bacterial exposure. Our data provide the first visualizations of gut microbiota development over an extended period of time in a vertebrate.

  9. Bacterial Diversity Associated with Wild Caught Anopheles Mosquitoes from Dak Nong Province, Vietnam Using Culture and DNA Fingerprint

    PubMed Central

    Ngo, Chung Thuy; Aujoulat, Fabien; Veas, Francisco; Jumas-Bilak, Estelle; Manguin, Sylvie

    2015-01-01

    Background Microbiota of Anopheles midgut can modulate vector immunity and block Plasmodium development. Investigation on the bacterial biodiversity in Anopheles, and specifically on the identification of bacteria that might be used in malaria transmission blocking approaches, has been mainly conducted on malaria vectors of Africa. Vietnam is an endemic country for both malaria and Bancroftian filariasis whose parasitic agents can be transmitted by the same Anopheles species. No information on the microbiota of Anopheles mosquitoes in Vietnam was available previous to this study. Method The culture dependent approach, using different mediums, and culture independent (16S rRNA PCR – TTGE) method were used to investigate the bacterial biodiversity in the abdomen of 5 Anopheles species collected from Dak Nong Province, central-south Vietnam. Molecular methods, sequencing and phylogenetic analysis were used to characterize the microbiota. Results and Discussion The microbiota in wild-caught Anopheles was diverse with the presence of 47 bacterial OTUs belonging to 30 genera, including bacterial genera impacting Plasmodium development. The bacteria were affiliated with 4 phyla, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, the latter being the dominant phylum. Four bacterial genera are newly described in Anopheles mosquitoes including Coxiella, Yersinia, Xanthomonas, and Knoellia. The bacterial diversity per specimen was low ranging from 1 to 4. The results show the importance of pairing culture and fingerprint methods to better screen the bacterial community in Anopheles mosquitoes. Conclusion Sampled Anopheles species from central-south Vietnam contained a diverse bacterial microbiota that needs to be investigated further in order to develop new malaria control approaches. The combination of both culture and DNA fingerprint methods allowed a thorough and complementary screening of the bacterial community in Anopheles mosquitoes. PMID:25747513

  10. Specific PCR, bacterial culture, serology and pharyngeal sampling to enhance the aetiological diagnosis of cellulitis.

    PubMed

    Toleman, Michelle S; Vipond, I Barry; Brindle, Richard

    2016-01-01

    It is often difficult to obtain a bacteriological diagnosis in patients with cellulitis. We examined the utility of molecular techniques and skin and throat cultures, as well as serology, in providing evidence of either Staphylococcus aureus or group A Streptococcus (GAS) presence inpatients with cellulitis. Samples were collected from patients with a clinical diagnosis of cellulitis who were recruited into a prospective placebo-controlled clinical trial (C4C study, EudraCT 2013-001218-14). Specific PCR, paired serology and culture for both organisms were carried out on a variety of samples where appropriate. Despite utilizing a range of diagnostic methods,a bacteriological diagnosis was only achieved in 43 % of patients with a clinical diagnosis of cellulitis. Seventeen per cent of patients tested positive for GAS by any method but only 4 % were positive by PCR, whilst S. aureus was detected in 34% of samples. Bacterial diagnosis in cases of cellulitis remains challenging. This is probably due to a very low bacterial burden with toxin production resulting in inflammation mediating skin damage. Further consideration for the need for long courses of antimicrobial therapy for cellulitis therefore appears merited.

  11. Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils.

    PubMed

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2015-07-01

    Cypermethrin is widely used for insect control; however, its toxicity toward aquatic life requires its complete removal from contaminated areas where the natural degradation ability of microbes can be utilized. Agricultural soil with extensive history of CM application was used to prepare enrichment cultures using cypermethrin as sole carbon source for isolation of cypermethrin degrading bacteria and bacterial community analysis using PCR-DGGE of 16 S rRNA gene. DGGE analysis revealed that dominant members of CM enrichment culture were associated with α-proteobacteria followed by γ-proteobacteria, Firmicutes, and Actinobacteria. Three potential CM-degrading isolates identified as Ochrobactrum anthropi JCm1, Bacillus megaterium JCm2, and Rhodococcus sp. JCm5 degraded 86-100% of CM (100 mg L(-1) ) within 10 days. These isolates were also able to degrade other pyrethroids, carbofuran, and cypermethrin degradation products. Enzyme activity assays revealed that enzymes involved in CM-degradation were inducible and showed activity when strains were grown on cypermethrin. Degradation kinetics of cypermethrin (200 mg kg(-1)) in soils inoculated with isolates JCm1, JCm2, and JCm5 suggested time-dependent disappearance of cypermethrin with rate constants of 0.0516, 0.0425, and 0.0807 d(-1), respectively, following first order rate kinetics. The isolated bacterial strains were among dominant genera selected under CM enriched conditions and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  12. Inhibition of bacterial growth in sweet cheese whey by carbon dioxide as determined by culture-independent community profiling.

    PubMed

    Lo, Raquel; Xue, Tian; Weeks, Mike; Turner, Mark S; Bansal, Nidhi

    2016-01-18

    Whey is a valuable co-product from cheese making that serves as a raw material for a wide range of products. Its rich nutritional content lends itself to rapid spoilage, thus it typically needs to be pasteurised and refrigerated promptly. Despite the extensive literature on milk spoilage bacteria, little is known about the spoilage bacteria of whey. The utility of carbon dioxide (CO2) to extend the shelf-life of raw milk and cottage cheese has been well established, but its application in whey preservation has not yet been explored. This study aims to characterise the microbial populations of fresh and spoiled sweet whey by culture-independent community profiling using 454 pyrosequencing of 16S rRNA gene amplicons and to determine whether carbonation is effective in inhibiting bacterial growth in sweet whey. The microbiota of raw Cheddar and Mozzarella whey was dominated by cheese starter bacteria. After pasteurisation, two out of the three samples studied became dominated by diverse environmental bacteria from various phyla, with Proteobacteria being the most dominant. Diverse microbial profiles were maintained until spoilage occurred, when the entire population was dominated by just one or two genera. Whey spoilage bacteria were found to be similar to those of milk. Pasteurised Cheddar and Mozzarella whey was spoiled by Bacillus sp. or Pseudomonas sp., and raw Mozzarella whey was spoiled by Pseudomonas sp., Serratia sp., and other members of the Enterobacteriaceae family. CO2 was effective in inhibiting bacterial growth of pasteurised Cheddar and Mozzarella whey stored at 15°C and raw Mozzarella whey stored at 4°C. The spoilage bacteria of the carbonated samples were similar to those of the non-carbonated controls.

  13. What is Growth? Concurrent determination of a bacterial population's many shades of growth

    NASA Astrophysics Data System (ADS)

    Lambert, Guillaume; Kussell, Edo

    2013-03-01

    One of the most exciting developments in the study of the physics of microbial life is the ability to precisely monitor stochastic variations of gene expression in individual cells. A fundamental question is whether these variations improve the long-term ability of a population to adapt to new environments. While variations in gene expression in bacteria are easily measured through the use of reporter systems such as green fluorescent proteins and its variants, precise determination of a cell's growth rate, and how it is influenced by its immediate environment, remains challenging. Here, we show that many conflicting and ambiguous definitions of bacterial growth can actually be used interchangeably in E. coli. Indeed, by monitoring small populations of E. coli bacteria inside a microfluidic device, we show that seemingly independent measurements of growth (elongation rate and the average division time, for instance) agree very precisely with one another. We combine these definitions with the population's length and age distribution to very precisely quantify the influence of temperature variations on a population's growth rate. We conclude by using coalescence theory to describe the evolution of a population's genetic structure over time.

  14. Evaluation of Sulfadiazine Degradation in Three Newly Isolated Pure Bacterial Cultures

    PubMed Central

    Mulla, Sikandar I.; Sun, Qian; Hu, Anyi; Wang, Yuwen; Ashfaq, Muhammad; Eqani, Syed Ali Musstjab Akber Shah; Yu, Chang-Ping

    2016-01-01

    This study is aimed to assess the biodegradation of sulfadiazine (SDZ) and characterization of heavy metal resistance in three pure bacterial cultures and also their chemotactic response towards 2-aminopyrimidine. The bacterial cultures were isolated from pig manure, activated sludge and sediment samples, by enrichment technique on SDZ (6 mg L-1). Based on the 16S rRNA gene sequence analysis, the microorganisms were identified within the genera of Paracoccus, Methylobacterium and Kribbella, which were further designated as SDZ-PM2-BSH30, SDZ-W2-SJ40 and SDZ-3S-SCL47. The three identified pure bacterial strains degraded up to 50.0, 55.2 and 60.0% of SDZ (5 mg L-1), respectively within 290 h. On the basis of quadrupole time-of-flight mass spectrometry and high performance liquid chromatography, 2-aminopyrimidine and 4-hydroxy-2-aminopyrimidine were identified as the main intermediates of SDZ biodegradation. These bacteria were also able to degrade the metabolite, 2-aminopyrimidine, of the SDZ. Furthermore, SDZ-PM2-BSH30, SDZ-W2-SJ40 and SDZ-3S-SCL47 also showed resistance to various heavy metals like copper, cadmium, chromium, cobalt, lead, nickel and zinc. Additionally, all three bacteria exhibited positive chemotaxis towards 2-aminopyrimidine based on the drop plate method and capillary assay. The results of this study advanced our understanding about the microbial degradation of SDZ, which would be useful towards the future SDZ removal in the environment. PMID:27755578

  15. Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

    NASA Astrophysics Data System (ADS)

    Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

    2011-12-01

    The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum

  16. Polyphasic approach to bacterial dynamics during the ripening of Spanish farmhouse cheese, using culture-dependent and -independent methods.

    PubMed

    Martín-Platero, Antonio M; Valdivia, Eva; Maqueda, Mercedes; Martín-Sánchez, Inés; Martínez-Bueno, Manuel

    2008-09-01

    We studied the dynamics of the microbial population during ripening of Cueva de la Magahá cheese using a combination of classical and molecular techniques. Samples taken during ripening of this Spanish goat's milk cheese in which Lactococcus lactis and Streptococcus thermophilus were used as starter cultures were analyzed. All bacterial isolates were clustered by using randomly amplified polymorphic DNA (RAPD) and identified by 16S rRNA gene sequencing, species-specific PCR, and multiplex PCR. Our results indicate that the majority of the 225 strains isolated and enumerated on solid media during the ripening period were nonstarter lactic acid bacteria, and Lactobacillus paracasei was the most abundant species. Other Lactobacillus species, such as Lactobacillus plantarum and Lactobacillus parabuchneri, were also detected at the beginning and end of ripening, respectively. Non-lactic-acid bacteria, mainly Kocuria and Staphylococcus strains, were also detected at the end of the ripening period. Microbial community dynamics determined by temporal temperature gradient gel electrophoresis provided a more precise estimate of the distribution of bacteria and enabled us to detect Lactobacillus curvatus and the starter bacteria S. thermophilus and L. lactis, which were not isolated. Surprisingly, the bacterium most frequently found using culture-dependent analysis, L. paracasei, was scarcely detected by this molecular approach. Finally, we studied the composition of the lactobacilli and their evolution by using length heterogeneity PCR.

  17. Polyphasic Approach to Bacterial Dynamics during the Ripening of Spanish Farmhouse Cheese, Using Culture-Dependent and -Independent Methods▿

    PubMed Central

    Martín-Platero, Antonio M.; Valdivia, Eva; Maqueda, Mercedes; Martín-Sánchez, Inés; Martínez-Bueno, Manuel

    2008-01-01

    We studied the dynamics of the microbial population during ripening of Cueva de la Magahá cheese using a combination of classical and molecular techniques. Samples taken during ripening of this Spanish goat's milk cheese in which Lactococcus lactis and Streptococcus thermophilus were used as starter cultures were analyzed. All bacterial isolates were clustered by using randomly amplified polymorphic DNA (RAPD) and identified by 16S rRNA gene sequencing, species-specific PCR, and multiplex PCR. Our results indicate that the majority of the 225 strains isolated and enumerated on solid media during the ripening period were nonstarter lactic acid bacteria, and Lactobacillus paracasei was the most abundant species. Other Lactobacillus species, such as Lactobacillus plantarum and Lactobacillus parabuchneri, were also detected at the beginning and end of ripening, respectively. Non-lactic-acid bacteria, mainly Kocuria and Staphylococcus strains, were also detected at the end of the ripening period. Microbial community dynamics determined by temporal temperature gradient gel electrophoresis provided a more precise estimate of the distribution of bacteria and enabled us to detect Lactobacillus curvatus and the starter bacteria S. thermophilus and L. lactis, which were not isolated. Surprisingly, the bacterium most frequently found using culture-dependent analysis, L. paracasei, was scarcely detected by this molecular approach. Finally, we studied the composition of the lactobacilli and their evolution by using length heterogeneity PCR. PMID:18658288

  18. Comparative analysis of bacterial community composition in bulk tank raw milk by culture-dependent and culture-independent methods using the viability dye propidium monoazide.

    PubMed

    Weber, Mareike; Geißert, Janina; Kruse, Myriam; Lipski, André

    2014-11-01

    Microbial diversity of 3 raw milk samples after 72 h of storage at 4 °C in a bulk tank was analyzed by culture-dependent and -independent methods. The culture-dependent approach was based on the isolation of bacteria on complex and selective media, chemotaxonomic differentiation of isolates, and subsequent identification by 16S rRNA gene sequencing. The culture-independent approach included the treatment of raw milk with the dye propidium monoazide before direct DNA extraction by mechanic and enzymatic cell lysis approaches, and cloning and sequencing of the 16S rRNA genes. The selective detection of viable bacteria improved the comparability between bacterial compositions of raw milk based on culture-dependent and -independent methods, which was the major objective of this study. Several bacterial species of the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria were detected by the culture-dependent method, whereas mainly bacteria of the phylum Proteobacteria as well as low proportions of the phyla Bacteroidetes and Actinobacteria were detected by the culture-independent method. This led to the conclusion that the phylum Firmicutes was strongly discriminated by the culture-independent approach. Generally, species richness detected by the culture-dependent method was higher than that detected by the culture-independent method for all samples. However, few taxa could be detected solely by the direct DNA-based method. In conclusion, the combination of culture-dependent and -independent methods led to the detection of the highest bacterial diversity for the raw milk samples analyzed. It was shown that DNA extraction from raw milk as the essential step in culture-independent methods causes the discrimination of taxa by incomplete cell lysis. Treatment of raw milk with the viability dye propidium monoazide was optimized for the application in raw milk without former removal of milk ingredients and proved to be a suitable tool to ensure comparability

  19. Biodegradation of methyl tert-butyl ether by cold-adapted mixed and pure bacterial cultures.

    PubMed

    Zaitsev, G M; Uotila, J S; Häggblom, M M

    2007-04-01

    An aerobic mixed bacterial culture (CL-EMC-1) capable of utilizing methyl tert-butyl ether (MTBE) as the sole source of carbon and energy with a growth temperature range of 3 to 30 degrees C and optimum of 18 to 22 degrees C was enriched from activated sludge. Transient accumulation of tert-butanol (TBA) occurred during utilization of MTBE at temperatures from 3 degrees C to 14 degrees C, but TBA did not accumulate above 18 degrees C. The culture utilized MTBE at a concentration of up to 1.5 g l(-1) and TBA of up to 7 g l(-1). The culture grew on MTBE at a pH range of 5 to 9, with an optimum pH of 6.5 to 7.1. The specific growth rate of the CL-EMC-1 culture on 0.1 g l(-1) of MTBE at 22 degrees C and pH 7.1 was 0.012 h(-1), and the growth yield was 0.64 g (dry weight) g(-1). A new MTBE-utilizing bacterium, Variovorax paradoxus strain CL-8, isolated from the mixed culture utilized MTBE, TBA, 2-hydroxy isobutyrate, lactate, methacrylate, and acetate as sole sources of carbon and energy but not 2-propanol, acetone, methanol, formaldehyde, or formate. Two other isolates, Hyphomicrobium facilis strain CL-2 and Methylobacterium extorquens strain CL-4, isolated from the mixed culture were able to grow on C(1) compounds. The combined consortium could thus utilize all of the carbon of MTBE.

  20. Bacterial communities associated with invasive populations of Bactrocera dorsalis (Diptera: Tephritidae) in China.

    PubMed

    Liu, L J; Martinez-Sañudo, I; Mazzon, L; Prabhakar, C S; Girolami, V; Deng, Y L; Dai, Y; Li, Z H

    2016-12-01

    The oriental fruit fly Bactrocera dorsalis (Hendel) is a destructive insect pest of a wide range of fruits and vegetables. This pest is an invasive species and is currently distributed in some provinces of China. To recover the symbiotic bacteria of B. dorsalis from different invasion regions in China, we researched the bacterial diversity of this fruit fly among one laboratory colony (Guangdong, China) and 15 wild populations (14 sites in China and one site in Thailand) using DNA-based approaches. The construction of 16S rRNA gene libraries allowed the identification of 24 operational taxonomic units of associated bacteria at the 3% distance level, and these were affiliated with 3 phyla, 5 families, and 13 genera. The higher bacterial diversity was recovered in wild populations compared with the laboratory colony and in samples from early term invasion regions compared with samples from late term invasion regions. Moreover, Klebsiella pneumoniae and Providencia sp. were two of the most frequently recovered bacteria, present in flies collected from three different regions in China where B. dorsalis is invasive. This study for the first time provides a systemic investigation of the symbiotic bacteria of B. dorsalis from different invasion regions in China.

  1. Optimal Control Strategies for Disinfection of Bacterial Populations with Persister and Susceptible Dynamics

    PubMed Central

    Brown, Jason; Darres, Kyle; Petty, Katherine

    2012-01-01

    It is increasingly clear that bacteria manage to evade killing by antibiotics and antimicrobials in a variety of ways, including mutation, phenotypic variations, and formation of biofilms. With recent advances in understanding the dynamics of the tolerance mechanisms, there have been subsequent advances in understanding how to manipulate the bacterial environments to eradicate the bacteria. This study focuses on using mathematical techniques to find the optimal disinfection strategy to eliminate the bacteria while managing the load of antibiotic that is applied. In this model, the bacterial population is separated into those that are tolerant to the antibiotic and those that are susceptible to disinfection. There are transitions between the two populations whose rates depend on the chemical environment. Our results extend previous mathematical studies to include more realistic methods of applying the disinfectant. The goal is to provide experimentally testable predictions that have been lacking in previous mathematical studies. In particular, we provide the optimal disinfection protocol under a variety of assumptions within the model that can be used to validate or invalidate our simplifying assumptions and the experimental hypotheses that we used to develop the model. We find that constant dosing is not the optimal method for disinfection. Rather, cycling between application and withdrawal of the antibiotic yields the fastest killing of the bacteria. PMID:22751538

  2. EFFECT OF SITE ON BACTERIAL POPULATIONS IN THE SAPWOOD OF COARSE WOODY DEBRIS.

    SciTech Connect

    Porter, Emma, G.,; Waldrop, Thomas, A.; McElreath, Susan, D.; Tainter, Frank, H.

    1998-01-01

    Porter, Emma G., T.A. Waldrop, Susan D. McElreath, and Frank H. Tainter. 1998. Effect of site on bacterial populations in the sapwood of coarse woody debris. Pp. 480-484. In: Proc. 9th Bienn. South. Silv. Res. Conf. T.A. Waldrop (ed). USDA Forest Service, Southern Research Station. Gen. Tech. Rep. SRS-20. Abstract: Coarse woody debris (CWD) is an important structural component of southeastern forest ecosystems, yet little is known about its dynamics in these systems. This project identified bacterial populations associated with CWD and their dynamics across landscape ecosystem classification (LEC) units. Bolts of red oak and loblolly pine were placed on plots at each of three hydric, mesic, and xeric sites at the Savannah River Station. After the controls were processed, samples were taken at four intervals over a 16-week period. Samples were ground within an anaerobe chamber using nonselective media. Aerobic and facultative anaerobic bacteria were identified using the Biolog system and the anaerobes were identified using the API 20A system. Major genera isolated were: Bacillus, Buttiauxella, Cedecea, Enterobacter, Erwinia, Escherichia, Klebsiella, Pantoea, Pseudomonas, Serratia, and Xanthomonas. The mean total isolates were determined by LEC units and sample intervals. Differences occurred between the sample intervals with total isolates of 6.67, 13.33, 10.17, and 9.50 at 3, 6, 10, and 16 weeks, respectively. No significant differences in the numbers of bacteria isolated were found between LEC units.

  3. Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis

    PubMed Central

    Lopez, Isabel; Ruiz-Larrea, Fernanda; Cocolin, Luca; Orr, Erica; Phister, Trevor; Marshall, Megan; VanderGheynst, Jean; Mills, David A.

    2003-01-01

    Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria. PMID:14602643

  4. Phage mutations in response to CRISPR diversification in a bacterial population.

    PubMed

    Sun, Christine L; Barrangou, Rodolphe; Thomas, Brian C; Horvath, Philippe; Fremaux, Christophe; Banfield, Jillian F

    2013-02-01

    Interactions between bacteria and their coexisting phage populations impact evolution and can strongly influence biogeochemical processes in natural ecosystems. Periodically, mutation or migration results in exposure of a host to a phage to which it has no immunity; alternatively, a phage may be exposed to a host it cannot infect. To explore the processes by which coexisting, co-evolving hosts and phage populations establish, we cultured Streptococcus thermophilus DGCC7710 with phage 2972 and tracked CRISPR (clustered regularly interspaced short palindromic repeats) diversification and host-phage co-evolution in a population derived from a colony that acquired initial CRISPR-encoded immunity. After 1 week of co-culturing, the coexisting host-phage populations were metagenomically characterized using 454 FLX Titanium sequencing. The evolved genomes were compared with reference genomes to identify newly incorporated spacers in S. thermophilus DGCC7710 and recently acquired single-nucleotide polymorphisms (SNPs) in phage 2972. Following phage exposure, acquisition of immune elements (spacers) led to a genetically diverse population with multiple subdominant strain lineages. Phage mutations that circumvented three early immunization events were localized in the proto-spacer adjacent motif (PAM) or near the PAM end of the proto-spacer, suggesting a strong selective advantage for the phage that mutated in this region. The sequential fixation or near fixation of these single mutations indicates selection events so severe that single phage genotypes ultimately gave rise to all surviving lineages and potentially carried traits unrelated to immunity to fixation.

  5. Detection of carboxylesterase and esterase activity in culturable gut bacterial flora isolated from diamondback moth, Plutella xylostella (Linnaeus), from India and its possible role in indoxacarb degradation.

    PubMed

    Ramya, Shanivarsanthe Leelesh; Venkatesan, Thiruvengadam; Srinivasa Murthy, Kottilingam; Jalali, Sushil Kumar; Verghese, Abraham

    2016-01-01

    Diamondback moth (DBM), Plutella xylostella (Linnaeus), is a notorious pest of brassica crops worldwide and is resistant to all groups of insecticides. The insect system harbors diverse groups of microbiota, which in turn helps in enzymatic degradation of xenobiotic-like insecticides. The present study aimed to determine the diversity of gut microflora in DBM, quantify esterase activity and elucidate their possible role in degradation of indoxacarb. We screened 11 geographic populations of DBM in India and analyzed them for bacterial diversity. The culturable gut bacterial flora underwent molecular characterization with 16S rRNA. We obtained 25 bacterial isolates from larvae (n=13) and adults (n=12) of DBM. In larval gut isolates, gammaproteobacteria was the most abundant (76%), followed by bacilli (15.4%). Molecular characterization placed adult gut bacterial strains into three major classes based on abundance: gammaproteobacteria (66%), bacilli (16.7%) and flavobacteria (16.7%). Esterase activity from 19 gut bacterial isolates ranged from 0.072 to 2.32μmol/min/mg protein. Esterase bands were observed in 15 bacterial strains and the banding pattern differed in Bacillus cereus - KC985225 and Pantoea agglomerans - KC985229. The bands were characterized as carboxylesterase with profenofos used as an inhibitor. Minimal media study showed that B. cereus degraded indoxacarb up to 20%, so it could use indoxacarb for metabolism and growth. Furthermore, esterase activity was greater with minimal media than control media: 1.87 versus 0.26μmol/min/mg protein. Apart from the insect esterases, bacterial carboxylesterase may aid in the degradation of insecticides in DBM.

  6. Quantitative high-throughput population dynamics in continuous-culture by automated microscopy

    PubMed Central

    Merritt, Jason; Kuehn, Seppe

    2016-01-01

    We present a high-throughput method to measure abundance dynamics in microbial communities sustained in continuous-culture. Our method uses custom epi-fluorescence microscopes to automatically image single cells drawn from a continuously-cultured population while precisely controlling culture conditions. For clonal populations of Escherichia coli our instrument reveals history-dependent resilience and growth rate dependent aggregation. PMID:27616752

  7. Characterization of methanotrophic bacterial populations in natural and agricultural aerobic soils of the European Russia

    NASA Astrophysics Data System (ADS)

    Kravchenko, Irina; Sukhacheva, Marina; Kizilova, Anna

    2014-05-01

    out to be much low diverse and dominated by uncultivated methanotrophs.. In Podzoluvisol, Luvisol and Meadow Kastanozem we have identified deeply-branching pmoA sequences of Alphaproteobacteria, only distantly related to Crenothrix polyspora, and formed a monophyletic cluster with uncultured methanotrophs from Hawaiian forest soil, soils in Greenland and Cluster I from arctic tundra soils, referred as UNSC (uncultivated natural soil cluster). A new pmoA gene-based PCR primer set was designed for detection of UNSC methanotrophs, and the copy numbers in Podzoluvisol was found to be 8.6 × 105copies g-1 of soil sampled in September 2013. We observed a pronounced shift to cultured methanotrophs with high similarity to Methylosinus, Methylocystis, Methylomicrobium, Methylobacter, and Methylocaldum in the same soils after agricultural loading. Soils from agricultural sites had larger diversity of methanotrophs, but they failed to make a significant contribution to elimination of methane as observed in both in situ and laboratory experiments. In summary, our study demonstrated that uncultured methanotrophs with pmoA monooxygenase distantly related to and Crenothrix polyspora and cluster I methanotrophs dominated in methane-oxidizing bacterial communities in unmanaged soils. Thereby, our results highlight the necessity for further studies to be addressed at studying of this group. The study was partially supported by RFBR research project # 13-04-00603_a. .

  8. Bacterial and archaeal populations at two shallow hydrothermal vents off Panarea Island (Eolian Islands, Italy).

    PubMed

    Maugeri, Teresa Luciana; Lentini, Valeria; Gugliandolo, Concetta; Italiano, Francesco; Cousin, Sylvie; Stackebrandt, Erko

    2009-01-01

    The aim of this study was to investigate the microbial community thriving at two shallow hydrothermal vents off Panarea Island (Italy). Physico-chemical characteristics of thermal waters were examined in order to establish the effect of the vents on biodiversity of both Bacteria and Archaea. Water and adjacent sediment samples were collected at different times from two vents, characterised by different depth and temperature, and analysed to evaluate total microbial abundances, sulphur-oxidising and thermophilic aerobic bacteria. Total microbial abundances were on average of the order of 10(5) cells ml(-1), expressed as picoplanktonic size fraction. Picophytoplanktonic cells accounted for 0.77-3.83% of the total picoplanktonic cells. The contribution of bacterial and archaeal taxa to prokaryotic community diversity was investigated by PCR-DGGE fingerprinting method. The number of bands derived from bacterial DNA was highest in the DGGE profiles of water sample from the warmest and deepest site (site 2). In contrast, archaeal richness was highest in the water of the coldest and shallowest site (site 1). Sulphur-oxidising bacteria were detected by both culture-dependent and -independent methods. The primary production at the shallow hydrothermal system of Panarea is supported by a complex microbial community composed by phototrophs and chemolithotrophs.

  9. Population dynamics of an algal bacterial cenosis in closed ecological system

    NASA Astrophysics Data System (ADS)

    Pisman, T. I.; Galayda, Ya. V.; Loginova, N. S.

    The paper deals with microalgae-bacteria interrelationships in the "autotroph-heterotroph" aquatic biotic cycle. Explanations of why and how algal-bacterial ecosystems are formed still remain controversial. The paper presents results of experimental and theoretical investigations of the functioning of the algal-bacterial cenosis (the microalga Chlorella vulgaris and concomitant microflora). The Chlorella microbial community is dominated by representatives of the genus Pseudomonas. Experiments with non-sterile batch cultures of Chlorella on Tamiya medium showed that the biomass of microorganisms increases simultaneously with the increase in microalgal biomass. The microflora of Chlorella can grow on organic substances released by photosynthesizing Chlorella. Microorganisms can also use dying Chlorella cells, i.e. form a "producer-reducer" biocycle. To get a better insight into the cenosis-forming role of microalgae, a mathematical model of the "autotroph-heterotroph" aquatic biotic cycle has been constructed, taking into account the utilization of Chlorella photosynthates and dead cells by microorganisms and the contribution of the components to the nitrogen cycle. A theoretical study showed that the biomass of concomitant bacteria grown on glucose and detritus is larger than the biomass of bacteria utilizing only microalgal photosynthates, which agrees well with the experimental data.

  10. Magnesium aminoclay enhances lipid production of mixotrophic Chlorella sp. KR-1 while reducing bacterial populations.

    PubMed

    Kim, Bohwa; Praveenkumar, Ramasamy; Lee, Jiye; Nam, Bora; Kim, Dong-Myung; Lee, Kyubock; Lee, Young-Chul; Oh, You-Kwan

    2016-11-01

    Improving lipid productivity and preventing overgrowth of contaminating bacteria are critical issues relevant to the commercialization of the mixotrophic microalgae cultivation process. In this paper, we report the use of magnesium aminoclay (MgAC) nanoparticles for enhanced lipid production from oleaginous Chlorella sp. KR-1 with simultaneous control of KR-1-associated bacterial growth in mixotrophic cultures with glucose as the model substrate. Addition of 0.01-0.1g/L MgAC promoted microalgal biomass production better than the MgAC-less control, via differential biocidal effects on microalgal and bacterial cells (the latter being more sensitive to MgAC's bio-toxicity than the former). The inhibition effect of MgAC on co-existing bacteria was, as based on density-gradient-gel-electrophoresis (DGGE) analysis, largely dosage-dependent and species-specific. MgAC also, by inducing an oxidative stress environment, increased both the cell size and lipid content of KR-1, resulting in a considerable, ∼25% improvement of mixotrophic algal lipid productivity (to ∼410mgFAME/L/d) compared with the untreated control.

  11. Lipid biomarkers for bacterial ecosystems: studies of cultured organisms, hydrothermal environments and ancient sediments

    NASA Technical Reports Server (NTRS)

    Summons, R. E.; Jahnke, L. L.; Simoneit, B. R.

    1996-01-01

    This paper forms part of our long-term goal of using molecular structure and carbon isotopic signals preserved as hydrocarbons in ancient sediments to improve understanding of the early evolution of Earth's surface environment. We are particularly concerned with biomarkers which are informative about aerobiosis. Here, we combine bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems to construct models for the nature, behaviour and preservation potential of primitive microbial communities. We use a combined molecular and isotopic approach to characterize lipids produced by cultured bacteria and test a variety of culture conditions which affect their biosynthesis. This information is then compared with lipid mixtures isolated from contemporary hot springs and evaluated for the kinds of chemical change that would accompany burial and incorporation into the sedimentary record. In this study we have shown that growth temperature does not appear to alter isotopic fractionation within the lipid classes produced by a methanotropic bacterium. We also found that cultured cyanobacteria biosynthesize diagnostic methylalkanes and dimethylalkanes with the latter only made when growing under low pCO2. In an examination of a microbial mat sample from Octopus Spring, Yellowstone National Park (USA), we could readily identify chemical structures with 13C contents which were diagnostic for the phototrophic organisms such as cyanobacteria and Chloroflexus. We could not, however, find molecular evidence for operation of a methane cycle in the particular mat samples we studied.

  12. Effects of culturing on the population structure of a hyperthermophilic virus from Yellowstone National Park

    SciTech Connect

    J. C. Snyder; J. Spuhler; B. Wiedenheft; F. F. Roberto; M. J. Young

    2004-12-01

    The existence of a culturing bias has long been known when sampling organisms from the environment. This bias underestimates microbial diversity and does not accurately reflect the most ecologically relevant species. Until now no study has examined the effects of culture bias on viral populations. We have employed culture independent methods to assess the diversity of Sulfolobus spindle–shaped viruses (SSVs) from extremely hyperthermal environments. This diversity is then compared to the viral diversity of cultured samples. We detected a clear culturing bias between environmental samples and cultured isolates. This is first study identifying a culture bias in a viral population.

  13. High level multiple antibiotic resistance among fish surface associated bacterial populations in non-aquaculture freshwater environment.

    PubMed

    Ozaktas, Tugba; Taskin, Bilgin; Gozen, Ayse G

    2012-12-01

    Freshwater fish, Alburnus alburnus (bleak), were captured from Lake Mogan, situated in Ankara, during spring. The surface mucus of the fish was collected and associated bacteria were cultured and isolated. By sequencing PCR-amplified 16S RNA encoding genes, the isolates were identified as members of 12 different genera: Acinetobacter, Aeromonas, Bacillus, Brevundimonas, Gordonia, Kocuria, Microbacterium, Mycobacterium, Pseudomonas, Rhodococcus, and Staphylococcus, in addition to one strain that was unidentified. The mucus-dwelling bacterial isolates were tested for resistance against ampicillin, kanamycin, streptomycin and chloramphenicol. About 95% of the isolates were found to be resistant to ampicillin, 93% to chloramphenicol, and 88% to kanamycin and streptomycin. A Microbacterium oxydans and the unidentified environmental isolate were resistant to all four antibiotics tested at very high levels (>1600 μg/ml ampicillin and streptomycin; >1120 μg/ml kanamycin; >960 μg/ml chloramphenicol). Only a Kocuria sp. was sensitive to all four antibiotics at the lowest concentrations tested (3.10 μg/ml ampicillin and streptomycin; 2.15 μg/ml kanamycin; 1.85 μg/ml chloramphenicol). The rest of the isolates showed different resistance levels. Plasmid isolations were carried out to determine if the multiple antibiotic resistance could be attributed to the presence of plasmids. However, no plasmid was detected in any of the isolates. The resistance appeared to be mediated by chromosome-associated functions. This study indicated that multiple antibiotic resistance at moderate to high levels is common among the current phenotypes of the fish mucus-dwelling bacterial populations in this temperate, shallow lake which has not been subjected to any aquaculturing so far but under anthropogenic effect being in a recreational area.

  14. Adherence, accumulation, and cell division of a natural adherent bacterial population.

    PubMed Central

    Bloomquist, C G; Reilly, B E; Liljemark, W F

    1996-01-01

    Developing dental bacterial plaques formed in vivo on enamel surfaces were examined in specimens from 18 adult volunteers during the first day of plaque formation. An intraoral model placing enamel pieces onto teeth was used to study bacterial plaque populations developing naturally to various cell densities per square millimeter of surface area of the enamel (W. F. Liljemark, C. G. Bloomquist, C. L. Bandt, B. L. Philstrom, J. E. Hinrichs, and L. F. Wolff, Oral Microbiol. Immunol. 8:5-15, 1993). Radiolabeled nucleoside incorporation was used to measure DNA synthesis concurrent with the taking of standard viable cell counts of the plaque samples. Results showed that in vivo plaque formation began with the rapid adherence of bacteria until ca. 12 to 32% of the enamel's salivary pellicle was saturated (ca. 2.5 x 10(5) to 6.3 x 10(5) cells per mm2). The pioneer adherent species were predominantly those of the "sanguis streptococci." At the above-noted density, the bacteria present on the salivary pellicle incorporated low levels of radiolabeled nucleoside per viable cell. As bacterial numbers reached densities between 8.0 x 10(5) and 2.0 x 10(6) cells per mm2, there was a small increase in the incorporation of radiolabeled nucleosides per cell. At 2.5 x 10(6) to 4.0 x 10(6) cells per mm2 of enamel surface, there was a marked increase in the incorporation of radiolabeled nucleosides per cell which appeared to be cell-density dependent. The predominant species group in developing dental plaque films during density-dependent growth was the sanguis streptococci; however, most other species present showed similar patterns of increased DNA synthesis as the density noted above approached 2.5 x 10(6) to 4.0 x 10(6) cells per mm2. PMID:8576054

  15. Identification of bacterial and fungal pathogens from positive blood culture bottles: a microarray-based approach.

    PubMed

    Raich, Teresa; Powell, Scott

    2015-01-01

    Rapid identification and characterization of bacterial and fungal pathogens present in the bloodstream are essential for optimal patient management and are associated with improved patient outcomes, improved antimicrobial stewardship, improved infection control, and reduced healthcare costs. Microarrays serve as reliable platforms for the identification of these bloodstream pathogens and their associated antimicrobial resistance genes, if present. Nanosphere's (Nanosphere, Inc., Northbrook, IL, USA) Verigene Gram-Positive Blood Culture Nucleic-Acid Test (BC-GP) is one such microarray-based approach for the detection of bacteria that cause bloodstream infection. Here, we describe the design of the microarray-based Verigene BC-GP Test, the steps necessary for performing the test, and the different components of the test including nucleic acid extraction and hybridization of target nucleic acid to a microarray.

  16. Culturable bacterial communities associated to Brazilian Oscarella species (Porifera: Homoscleromorpha) and their antagonistic interactions.

    PubMed

    Laport, Marinella Silva; Bauwens, Mathieu; de Oliveira Nunes, Suzanne; Willenz, Philippe; George, Isabelle; Muricy, Guilherme

    2017-04-01

    Sponges offer an excellent model to investigate invertebrate-microorganism interactions. Furthermore, bacteria associated with marine sponges represent a rich source of bioactive metabolites. The aim of this study was to characterize the bacteria inhabiting a genus of sponges, Oscarella, and their potentiality for antimicrobial production. Bacterial isolates were recovered from different Oscarella specimens, among which 337 were phylogenetically identified. The culturable community was dominated by Proteobacteria and Firmicutes, and Vibrio was the most frequently isolated genus, followed by Shewanella. When tested for antimicrobial production, bacteria of the 12 genera isolated were capable of producing antimicrobial substances. The majority of strains were involved in antagonistic interactions and inhibitory activities were also observed against bacteria of medical importance. It was more pronounced in some isolated genera (Acinetobacter, Bacillus, Photobacterium, Shewanella and Vibrio). These findings suggest that chemical antagonism could play a significant role in shaping bacterial communities within Oscarella, a genus classified as low-microbial abundance sponge. Moreover, the identified strains may contribute to the search for new sources of antimicrobial substances, an important strategy for developing therapies to treat infections caused by multidrug-resistant bacteria. This study was the first to investigate the diversity and antagonistic activity of bacteria isolated from Oscarella spp. It highlights the biotechnological potential of sponge-associated bacteria.

  17. Molecular versus conventional culture for detection of respiratory bacterial pathogens in poultry.

    PubMed

    Ammar, A M; Abd El-Aziz, N K; Abd El Wanis, S; Bakry, N R

    2016-02-29

    Acute respiratory tract infections are leading causes of morbidity in poultry farms allover the world. Six pathogens; Escherichia coli, Mycoplasma gallisepticum, Staphylococcus aureus, Pasteurella multocida, Mannheimia haemolytica and Pseudomonas aeruginosa were involved in respiratory infections in poultry. Herein, conventional identification procedures and polymerase chain reaction (PCR) were applied for detection of the most common respiratory bacterial pathogens in clinical specimens of poultry obtained from 53 Egyptian farms with various respiratory problems and the results were compared statistically. The analyzed data demonstrated a significantly higher rate of detection of the most recovered microorganisms (P<0.05) by PCR comparing to classical culture procedures. Further, multiplex PCR could detect E. coli, M. gallisepticum, S. aureus and Ps. aeruginosa in a single reaction, however, M. haemolytica was reported in a uinplex system. According to PCR results, the most commonly recorded bacterial pathogens in examined poultry farms were E. coli and Ps. aeruginosa (54.71% each), followed by M. haemolylica (35.85%) and M. gallisepticum (20.75%). In conclusion, PCR assay offered an effective alternative to traditional typing methods for the identification and simultaneous detection of the most clinically relevant respiratory pathogens in poultry.

  18. A Culture-Independent Survey of the Bacterial Community in a Radon Hot Spring

    NASA Astrophysics Data System (ADS)

    Anitori, Roberto P.; Trott, Cherida; Saul, David J.; Bergquist, Peter L.; Walter, Malcolm R.

    2002-08-01

    Paralana is an active, radon-containing hot spring situated in a region of South Australia's Flinders Ranges with a long history of hydrothermal activity. Our aim was to determine the bacterial composition of Paralana using a culture-independent, 16S rRNA-based technique. The presence of a diverse bacterial community was strongly suggested by the large number (~180) of different ribotypes obtained upon analysis of nine hot spring samples. DNA sequencing of Paralana 16S rRNA genes corroborated this observation, identifying representatives of seven confirmed and two candidate divisions of the domain Bacteria. These included Cyanobacteria, Proteobacteria (both β and δ subdivisions), the Cytophaga-Flexibacter-Bacteroides group, Low G+C Gram-positives, Nitrospira, green non-sulfur bacteria, green sulfur bacteria, OP8, and OP12. No known ionizing radiation-resistant Bacteria were identified. Only one Paralana 16S rRNA sequence type (recombinant B5D) was homologous to a sequence previously identified from a radioactive environment.

  19. Application of real-time PCR for total airborne bacterial assessment: Comparison with epifluorescence microscopy and culture-dependent methods

    NASA Astrophysics Data System (ADS)

    Rinsoz, Thomas; Duquenne, Philippe; Greff-Mirguet, Guylaine; Oppliger, Anne

    Traditional culture-dependent methods to quantify and identify airborne microorganisms are limited by factors such as short-duration sampling times and inability to count non-culturable or non-viable bacteria. Consequently, the quantitative assessment of bioaerosols is often underestimated. Use of the real-time quantitative polymerase chain reaction (Q-PCR) to quantify bacteria in environmental samples presents an alternative method, which should overcome this problem. The aim of this study was to evaluate the performance of a real-time Q-PCR assay as a simple and reliable way to quantify the airborne bacterial load within poultry houses and sewage treatment plants, in comparison with epifluorescence microscopy and culture-dependent methods. The estimates of bacterial load that we obtained from real-time PCR and epifluorescence methods, are comparable, however, our analysis of sewage treatment plants indicate these methods give values 270-290 fold greater than those obtained by the "impaction on nutrient agar" method. The culture-dependent method of air impaction on nutrient agar was also inadequate in poultry houses, as was the impinger-culture method, which gave a bacterial load estimate 32-fold lower than obtained by Q-PCR. Real-time quantitative PCR thus proves to be a reliable, discerning, and simple method that could be used to estimate airborne bacterial load in a broad variety of other environments expected to carry high numbers of airborne bacteria.

  20. Biological treatment of sewage treatment plant sludge by pure bacterial culture with optimum process conditions in a stirred tank bioreactor.

    PubMed

    Alam, M Z; Muyibi, Suleyman A; Jamal, P

    2007-09-01

    Biological treatment of sewage treatment plant (STP) sludge by potential pure bacterial culture (Bacillus sp.) with optimum process conditions for effective biodegradation and bioseparation was carried out in the laboratory. The effective and efficient bioconversion was evaluated with the treatment of pure bacterial culture and existing microbes (uninnoculated) in sludge. The optimum process conditions i.e., temperature, 40 degrees C; pH, 6; inoculum, 5% (v/v); aeration, 1 vvm; agitation speed, 50 rpm obtained from the previous studies with chemical oxygen demand COD at 30 mgL(-1) were applied for the biological treatment of sludge. The results indicated that pure bacterial culture (Bacillus sp.) showed higher degradation and separation of treated sludge compared to treatment with the existing mixed microbes in a stirred tank bioreactor. The treated STP sludge by potential pure bacterial culture and existing microbes gave 30% and 11%; 91.2% and 59.1; 88.5% and 52.3%; 98.4% and 51.3%; 96.1% and 75.2%; 99.4% and 72.8% reduction of total suspended solids (TSS, biosolids), COD, soluble protein, turbidity, total dissolved solids (TDS) and specific resistance to filtration (SRF), respectively within 7 days of treatment. The pH was observed at 6.5 and 4 during the treatment of sludge by pure culture and existing microbes, respectively.

  1. Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms

    PubMed Central

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang; Adav, Sunil S.; Salido, May Margarette; Liu, Yang; Givskov, Michael; Sze, Siu Kwan; Tolker-Nielsen, Tim; Yang, Liang

    2016-01-01

    Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a ‘last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance development. The macrolide erythromycin, which has been previously shown to inhibit the motility and QS of P. aeruginosa, boosts biofilm eradication by colistin. Our work provides insights on the mechanisms underlying the formation of antibiotic-tolerant populations in bacterial biofilms and indicates research avenues for designing more efficient treatments against biofilm-associated infections. PMID:26892159

  2. p-Cresol mineralization and bacterial population dynamics in a nitrifying sequential batch reactor.

    PubMed

    Silva, Carlos David; Beristain-Montiel, Lizeth; de Maria Cuervo-López, Flor; Texier, Anne-Claire

    2014-09-01

    The ability of a nitrifying sludge to oxidize p-cresol was evaluated in a sequential batch reactor (SBR). p-Cresol was first transformed to p-hydroxybenzaldehyde and p-hydroxybenzoate, which were later mineralized. The specific rates of p-cresol consumption increased throughout the cycles. The bacterial population dynamics were monitored by using denaturing gradient gel electrophoresis (DGGE) and sequencing of DGGE fragments. The ability of the sludge to consume p-cresol and intermediates might be related to the presence of species such as Variovorax paradoxus and Thauera mechernichensis. p-Cresol (25 to 200mgC/L) did not affect the nitrifying SBR performance (ammonium consumption efficiency and nitrate production yield were close to 100% and 1, respectively). This may be related to the high stability observed in the nitrifying communities. It was shown that a nitrifying SBR may be a good alternative to eliminate simultaneously ammonium and p-cresol, maintaining stable the respiratory process as the bacterial community.

  3. Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms

    PubMed Central

    Santegoeds, Cecilia M.; Ferdelman, Timothy G.; Muyzer, Gerard; de Beer, Dirk

    1998-01-01

    We describe the combined application of microsensors and molecular techniques to investigate the development of sulfate reduction and of sulfate-reducing bacterial populations in an aerobic bacterial biofilm. Microsensor measurements for oxygen showed that anaerobic zones developed in the biofilm within 1 week and that oxygen was depleted in the top 200 to 400 μm during all stages of biofilm development. Sulfate reduction was first detected after 6 weeks of growth, although favorable conditions for growth of sulfate-reducing bacteria (SRB) were present from the first week. In situ hybridization with a 16S rRNA probe for SRB revealed that sulfate reducers were present in high numbers (approximately 108 SRB/ml) in all stages of development, both in the oxic and anoxic zones of the biofilm. Denaturing gradient gel electrophoresis (DGGE) showed that the genetic diversity of the microbial community increased during the development of the biofilm. Hybridization analysis of the DGGE profiles with taxon-specific oligonucleotide probes showed that Desulfobulbus and Desulfovibrio were the main sulfate-reducing bacteria in all biofilm samples as well as in the bulk activated sludge. However, different Desulfobulbus and Desulfovibrio species were found in the 6th and 8th weeks of incubation, respectively, coinciding with the development of sulfate reduction. Our data indicate that not all SRB detected by molecular analysis were sulfidogenically active in the biofilm. PMID:9758792

  4. Oral bacterial adhesion on amorphous carbon and titanium films: effect of surface roughness and culture media.

    PubMed

    Almaguer-Flores, A; Ximénez-Fyvie, L A; Rodil, S E

    2010-01-01

    Implant infections can cause severe problems from malfunctioning to dangerous sepsis affecting the health of the patient. For many years, titanium has been the most common material used on dental implants due to their mechanical and biocompatibility properties. Recent studies suggest that amorphous carbon (a-C) films can be possible candidates for coating dental implants, improving some important features like biocompatibility and bone formation. In the oral cavity, the risk of an implant infection is high due to multiple species are capable to colonize this site and these biofilm infections can limit the use of these medical devices. The purpose of this study was to evaluate the influence of the surface chemistry, roughness, and culture media in the bacterial colonization process. To achieve this, a-C and Ti films were deposited on rough and smooth surfaces and cultured with different microorganisms belonging to the oral microbiota with mycoplasma medium (MM) or human saliva (HS). Samples were incubated for 24 h, after this, samples were sonicated and the number of attached bacteria was determined by counting the colony-forming units (CFU's) from each sample. The proportion of the species in the biofilms was determined using checkerboard DNA-DNA hybridization. Data were analyzed by Student's t test using Bonferroni's modification of Student's t test and differences on the proportion of the bacterial species attached to each surface were determined using the Mann-Whitney test. Results show an increased number of CFU's on rough surfaces, especially on the a-C surfaces. The incubation media were an important factor on the adhesion of certain taxa, whereas other species were more sensitive to surface chemistry and others to surface roughness.

  5. A quasi-universal medium to break the aerobic/anaerobic bacterial culture dichotomy in clinical microbiology.

    PubMed

    Dione, N; Khelaifia, S; La Scola, B; Lagier, J C; Raoult, D

    2016-01-01

    In the mid-19th century, the dichotomy between aerobic and anaerobic bacteria was introduced. Nevertheless, the aerobic growth of strictly anaerobic bacterial species such as Ruminococcus gnavus and Fusobacterium necrophorum, in a culture medium containing antioxidants, was recently demonstrated. We tested aerobically the culture of 623 bacterial strains from 276 bacterial species including 82 strictly anaerobic, 154 facultative anaerobic, 31 aerobic and nine microaerophilic bacterial species as well as ten fungi. The basic culture medium was based on Schaedler agar supplemented with 1 g/L ascorbic acid and 0.1 g/L glutathione (R-medium). We successively optimized this media, adding 0.4 g/L uric acid, using separate autoclaving of the component, or adding haemin 0.1 g/L or α-ketoglutarate 2 g/L. In the basic medium, 237 bacterial species and ten fungal species grew but with no growth of 36 bacterial species, including 22 strict anaerobes. Adding uric acid allowed the growth of 14 further species including eight strict anaerobes, while separate autoclaving allowed the growth of all tested bacterial strains. To extend its potential use for fastidious bacteria, we added haemin for Haemophilus influenzae, Haemophilus parainfluenzae and Eikenella corrodens and α-ketoglutarate for Legionella pneumophila. This medium allowed the growth of all tested strains with the exception of Mycobacterium tuberculosis and Mycobacterium bovis. Testing primoculture and more fastidious species will constitute the main work to be done, but R-medium coupled with a rapid identification method (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) will facilitate the anaerobic culture in clinical microbiology laboratories.

  6. Nonlinearity in bacterial population dynamics: proposal for experiments for the observation of abrupt transitions in patches.

    PubMed

    Kenkre, V M; Kumar, Niraj

    2008-12-02

    An explicit proposal for experiments leading to abrupt transitions in spatially extended bacterial populations in a Petri dish is presented on the basis of an exact formula obtained through an analytic theory. The theory provides accurately the transition expressions despite the fact that the actual solutions, which involve strong nonlinearity, are inaccessible to it. The analytic expressions are verified through numerical solutions of the relevant nonlinear equation. The experimental setup suggested uses opaque masks in a Petri dish bathed in ultraviolet radiation [Lin A-L, et al. (2004) Biophys J 87:75-80 and Perry N (2005) J R Soc Interface 2:379-387], but is based on the interplay of two distances the bacteria must traverse, one of them favorable and the other adverse. As a result of this interplay feature, the experiments proposed introduce highly enhanced reliability in interpretation of observations and in the potential for extraction of system parameters.

  7. Effect of antibiotics on bacterial populations: a multi-hierachical selection process

    PubMed Central

    Martínez, José Luis

    2017-01-01

    Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats. PMID:28163908

  8. Effect of antibiotics on bacterial populations: a multi-hierachical selection process.

    PubMed

    Martínez, José Luis

    2017-01-01

    Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.

  9. Bacterial species associated with traditional starter cultures used for fermented bamboo shoot production in Manipur state of India.

    PubMed

    Jeyaram, K; Romi, W; Singh, Th Anand; Devi, A Ranjita; Devi, S Soni

    2010-09-30

    Soidon is a non-salted acidic fermented food prepared from the succulent bamboo shoot tip of Schizostachyum capitatum Munro by using a traditional liquid starter called "soidon mahi" in Manipur state of India. In this study, 163 bacterial isolates associated with this starter samples were identified and their population distribution was investigated by amplified ribosomal DNA restriction analysis (ARDRA), 16S rDNA sequencing and randomly amplified polymorphic DNA (RAPD) analysis. This acidic starter (pH 4.5+/-0.15) was dominated by a characteristic association of Bacillus and lactic acid bacteria (LAB) together. The population distribution of dominant species were Bacillus subtilis 29.3%, Bacillus cereus 35.7%, Bacillus pumilus 2.6%, Lactobacillus brevis 9.6%, Lactobacillus plantarum 5.1%, Carnobacterium sp. 11.9%, Enterococcus faecium 1.2% and Pseudomonas fluorescens 4.6%. Alarming population load (10(6)-10(7)cfu/ml) of B. cereus in 87% of starter samples studied should raise concern regarding biosafety of soidon consumption. PCR amplification of 16S-23S rDNA intergenic transcribed spacer (ITS) region and ITS-RFLP profiles revealed a high diversity with eight subgroups in B. subtilis, five subgroups in B. cereus and three subgroups in L. brevis isolates. The most abundant B. subtilis subgroup IB.1 distributed in most of the samples showed very less clonal variability during RAPD analysis. The molecular methods used in this study identified the dominant strains of Bacillus and LAB distributed in most of the starter samples. These dominant strains of B. subtilis, L. brevis and L. plantarum would allow for developing a defined starter culture for the production of quality soidon.

  10. Bacterial populations and metabolites in the feces of free roaming and captive grizzly bears.

    PubMed

    Schwab, Clarissa; Cristescu, Bogdan; Boyce, Mark S; Stenhouse, Gordon B; Gänzle, Michael

    2009-12-01

    Gut physiology, host phylogeny, and diet determine the composition of the intestinal microbiota. Grizzly bears (Ursus arctos horribilis) belong to the Order Carnivora, yet feed on an omnivorous diet. The role of intestinal microflora in grizzly bear digestion has not been investigated. Microbiota and microbial activity were analysed from the feces of wild and captive grizzly bears. Bacterial composition was determined using culture-dependent and culture-independent methods. The feces of wild and captive grizzly bears contained log 9.1 +/- 0.5 and log 9.2 +/- 0.3 gene copies x g(-1), respectively. Facultative anaerobes Enterobacteriaceae and enterococci were dominant in wild bear feces. Among the strict anaerobes, the Bacteroides-Prevotella-Porphyromonas group was most prominent. Enterobacteriaceae were predominant in the feces of captive grizzly bears, at log 8.9 +/- 0.5 gene copies x g(-1). Strict anaerobes of the Bacteroides-Prevotella-Porphyromonas group and the Clostridium coccoides cluster were present at log 6.7 +/- 0.9 and log 6.8 +/- 0.8 gene copies x g(-1), respectively. The presence of lactate and short-chain fatty acids (SCFAs) verified microbial activity. Total SCFA content and composition was affected by diet. SCFA composition in the feces of captive grizzly bears resembled the SCFA composition of prey-consuming wild animals. A consistent data set was obtained that associated fecal microbiota and metabolites with the distinctive gut physiology and diet of grizzly bears.

  11. Critical dynamics of self-gravitating Langevin particles and bacterial populations.

    PubMed

    Sire, Clément; Chavanis, Pierre-Henri

    2008-12-01

    We study the critical dynamics of the generalized Smoluchowski-Poisson system (for self-gravitating Langevin particles) or generalized Keller-Segel model (for the chemotaxis of bacterial populations). These models [P. H. Chavanis and C. Sire, Phys. Rev. E 69, 016116 (2004)] are based on generalized stochastic processes leading to the Tsallis statistics. The equilibrium states correspond to polytropic configurations with index n similar to polytropic stars in astrophysics. At the critical index n_{3}=d(d-2) (where d>or=2 is the dimension of space), there exists a critical temperature Theta_{c} (for a given mass) or a critical mass M_{c} (for a given temperature). For Theta>Theta_{c} or MM_{c} the system collapses and forms, in a finite time, a Dirac peak containing a finite fraction M_{c} of the total mass surrounded by a halo. We study these regimes numerically and, when possible, analytically by looking for self-similar or pseudo-self-similar solutions. This study extends the critical dynamics of the ordinary Smoluchowski-Poisson system and Keller-Segel model in d=2 corresponding to isothermal configurations with n_{3}-->+infinity . We also stress the analogy between the limiting mass of white dwarf stars (Chandrasekhar's limit) and the critical mass of bacterial populations in the generalized Keller-Segel model of chemotaxis.

  12. Strain-specific differentiation of lactococci in mixed starter culture populations using randomly amplified polymorphic DNA-derived probes.

    PubMed Central

    Erlandson, K; Batt, C A

    1997-01-01

    A hydrophobic grid membrane filtration (HGMF) colony hybridization assay was developed that allows strain-specific differentiation of defined bacterial populations. The randomly amplified polymorphic DNA (RAPD) fingerprinting technique was used to identify potential signature nucleic acid sequences unique to each member of a commercial cheese starter culture blend. The blend consisted of two closely related Lactococcus lactis subsp. cremoris strains, 160 and 331, and one L. lactis subsp. lactis strain, 210. Three RAPD primers (OPX 1, OPX 12, and OPX 15) generated a total of 32 products from these isolates, 20 of which were potential strain-specific markers. Southern hybridization analyses revealed, that the RAPD-generated signature sequences OPX15-0.95 and a 0.36-kb HaeIII fragment of OPX1-1.0b were specific for strains 331 and 210, respectively, within the context of the test starter culture blend. These strain-specific probes were used in a HGMF colony hybridization assay. Colony lysis, hybridization, and nonradioactive detection parameters were optimized to allow specific differentiation and quantitation of the target strains in the mixed starter culture population. When the 210 and 331 probes were tested at their optimal hybridization temperatures against single cultures, they detected 100% of the target strain CFUs, without cross-reactivity to the other strains. The probes for strains 210 and 331 also successfully detected their targets in blended cultures even with a high background of the other two strains. PMID:9212417

  13. Strain-specific differentiation of lactococci in mixed starter culture populations using randomly amplified polymorphic DNA-derived probes.

    PubMed

    Erlandson, K; Batt, C A

    1997-07-01

    A hydrophobic grid membrane filtration (HGMF) colony hybridization assay was developed that allows strain-specific differentiation of defined bacterial populations. The randomly amplified polymorphic DNA (RAPD) fingerprinting technique was used to identify potential signature nucleic acid sequences unique to each member of a commercial cheese starter culture blend. The blend consisted of two closely related Lactococcus lactis subsp. cremoris strains, 160 and 331, and one L. lactis subsp. lactis strain, 210. Three RAPD primers (OPX 1, OPX 12, and OPX 15) generated a total of 32 products from these isolates, 20 of which were potential strain-specific markers. Southern hybridization analyses revealed, that the RAPD-generated signature sequences OPX15-0.95 and a 0.36-kb HaeIII fragment of OPX1-1.0b were specific for strains 331 and 210, respectively, within the context of the test starter culture blend. These strain-specific probes were used in a HGMF colony hybridization assay. Colony lysis, hybridization, and nonradioactive detection parameters were optimized to allow specific differentiation and quantitation of the target strains in the mixed starter culture population. When the 210 and 331 probes were tested at their optimal hybridization temperatures against single cultures, they detected 100% of the target strain CFUs, without cross-reactivity to the other strains. The probes for strains 210 and 331 also successfully detected their targets in blended cultures even with a high background of the other two strains.

  14. Frequency of caseous lymphadenitis (CLA) in sheep slaughtered in an abattoir in Tabriz: comparison of bacterial culture and pathological study.

    PubMed

    Zavoshti, Fereydon Rezazadeh; Khoojine, Amir Babak Sioofy; Helan, Javad Ashrafi; Hassanzadeh, Belal; Heydari, Ali Akbar

    2012-10-01

    From January to February 2008, 468 sheep carcasses (335 male and 133 female) in a Khosroshahr (suburb of Tabriz, East Azerbaijan province, Iran) abattoir were randomly selected for inspection. The aim of the study was to estimate the frequency of caseous lymphadenitis (CLA) in sheep and to compare the results of bacterial cultures and histopathology of suspected cases. The mean age of the population was 2.5 years. One hundred ninety-seven cases containing 153 (77.7%) males and 44 (22.3%) females had prominent enlargement of one of the lymph nodes (i.e., prescapular, prefemoral, inguinal, supramammary, or midiastinal); these were removed with the surrounding tissue for further evaluation. For confirmed diagnosis of CLA, samples were sent for microbiology and pathology analysis. Standard bacteriological culture methods for isolation of Corynebacterium pseudotuberculosis and tissue preparations for histopathological sections were performed. To evaluate the effect of age on the frequency of CLA, animals were categorized in four groups: under 1, 1-2, 2-3, and over 3 years of age. Based on the results, in 59 (12.60%) carcasses C. pseudotuberculosis was isolated, and in 94 (20.08%) of the cases histopathological studies revealed pathognomonic signs (lamellated exudates or onion ring) of CLA. The frequency of CLA based on bacteriological culture was 12.60% and on histopathological study 20.08%. In 37 (18.8%) of the carcasses, both bacteriological and histopathological studies confirmed CLA. The frequency of CLA following microscopic examination (20.08%) presented a more precise diagnosis compared to bacteriological culture (12.60%) and macroscopic evaluation of the lymph nodes (P < 0.05). Furthermore, there was a positive correlation rate between the bacteriological culture and histopathological study (r = 0.196, P = 0.006). The prescapular lymph node had the highest infection rate with 54 (1.70 ± 0.97) and supramammary lymph node had the lowest with two

  15. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives

    PubMed Central

    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

  16. Differences in bacterial diversity of host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory.

    PubMed

    Medina, R F; Nachappa, P; Tamborindeguy, C

    2011-04-01

    Host-associated differentiation (HAD) is the presence of genetically divergent, host-associated populations. It has been suggested that microbial symbionts of insect herbivores may play a role in HAD by allowing their insect hosts to use different plant species. The objective of this study was to document if host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory corresponded with differences in the composition of their associated bacteria. To test this hypothesis, we characterized the symbionts present in P. notabilis associated with these two tree species through metagenomic analyses using 454 sequencing. Differences in bacterial diversity were found between P. notabilis populations associated with pecan and water hickory. The bacteria, Pantoea agglomerans and Serratia marcescens, were absent in the P. notabilis water hickory population, whereas both species accounted for more than 69.72% of bacterial abundance in the pecan population.

  17. An investigation of total bacterial communities, culturable antibiotic-resistant bacterial communities and integrons in the river water environments of Taipei city.

    PubMed

    Yang, Chu-Wen; Chang, Yi-Tang; Chao, Wei-Liang; Shiung, Iau-Iun; Lin, Han-Sheng; Chen, Hsuan; Ho, Szu-Han; Lu, Min-Jheng; Lee, Pin-Hsuan; Fan, Shao-Ning

    2014-07-30

    The intensive use of antibiotics may accelerate the development of antibiotic-resistant bacteria (ARB). The global geographical distribution of environmental ARB has been indicated by many studies. However, the ARB in the water environments of Taiwan has not been extensively investigated. The objective of this study was to investigate the communities of ARB in Huanghsi Stream, which presents a natural acidic (pH 4) water environment. Waishuanghsi Stream provides a neutral (pH 7) water environment and was thus also monitored to allow comparison. The plate counts of culturable bacteria in eight antibiotics indicate that the numbers of culturable carbenicillin- and vancomycin-resistant bacteria in both Huanghsi and Waishuanghsi Streams are greater than the numbers of culturable bacteria resistant to the other antibiotics tested. Using a 16S rDNA sequencing approach, both the antibiotic-resistant bacterial communities (culture-based) and the total bacterial communities (metagenome-based) in Waishuanghsi Stream exhibit a higher diversity than those in Huanghsi Stream were observed. Of the three classes of integron, only class I integrons were identified in Waishuanghsi Stream. Our results suggest that an acidic (pH 4) water environment may not only affect the community composition of antibiotic-resistant bacteria but also the horizontal gene transfer mediated by integrons.

  18. Changes in bacterial communities from swine feces during continuous culture with starch.

    PubMed

    Ricca, D M; Ziemer, C J; Kerr, B J

    2010-10-01

    Bacteria from swine feces were grown in continuous culture with starch as the sole carbohydrate in order to monitor changes during fermentation and to determine how similar fermenter communities were to each other. DNA extracted from fermenter samples was analyzed by denaturing gradient gel electrophoresis (DGGE). A significant decrease in diversity was observed, the Shannon-Weaver index dropped from 1.92 to 1.13 after 14 days of fermentation. Likewise, similarity of fermenter communities to those in the fecal inoculum also decreased over time. Both diversity and similarity to the inoculum decreased most rapidly in the first few days of fermentation, reflecting a period of adaptation. Sequencing of DGGE bands indicated that the same species were present in replicate fermenters. Most of these bacteria were placed in the Clostridium coccoides/Eubacterium rectale group (likely saccharolytic butyrate producers), a dominant bacterial group in the intestinal tract of pigs. DGGE proved useful to monitor swine fecal communities in vitro and indicated the selection and maintenance of native swine intestinal bacteria during continuous culture.

  19. Diversity of Vaginal Lactic Acid Bacterial Microbiota in 15 Algerian Pregnant Women with and without Bacterial Vaginosis by using Culture Independent Method

    PubMed Central

    Abdi, Akila; Fhoula, Imène; Bringel, Françoise; Boudabous, Abdelatif; Ouzari, Imene Hadda

    2016-01-01

    Introduction Bacterial Vaginosis (BV) is the most common lower genital tract disorder among women of reproductive age (pregnant and non-pregnant) and a better knowledge of Lactobacillus species richness in healthy and infected vaginal microbiota is needed to efficiently design better probiotic products to promote the maintenance of normal flora which will help prevent bacterial vaginosis. Aim To evaluate and compare the diversity of lactic acid bacterial species in pregnant women with and without BV. Materials and Methods A pilot study was carried out during November-2014 to March-2015 in University Badji Mokhtar, Annaba, Algeria. Vaginal swabs were collected from 15 pregnant women aged between 19 and 35 years (mean 27.6 years; n=15) living in the East of Algeria visiting Gynecology service, hospital Abdallah Nouaouria- El bouni, Annaba. Vaginal samples were gram-stained, and scored by the Nugent method. The cohort included cases of women with healthy “normal” vaginal flora, infected flora with bacterial vaginosis and women with “intermediate” flora. The vaginal LAB community from pregnant women was identified by culture independent method based on Denaturing Gradient Gel Electrophoresis (DGGE), with the 16S rRNA gene sequencing. Results A majority of LAB affiliated to the genus Lactobacillus was found in “normal” and “intermediate” flora (87.5% and 43.75% respectively), while a majority of LAB affiliated to the genus Enterococcus was identified in women with bacterial vaginosis and intermediate flora (60% and 46.75% respectively). Our results showed that the presence of Lactobacillus iners and Lactobacillus delbruekii promotes stability of the vaginal microbiota. Conclusion This result confirms the findings of previous studies suggesting that the occurrence of predominant Lactobacillus negatively correlates with bacterial vaginosis incidence and their current use as probiotics. Lactobacillus iners and Lactobacillus delbruekii can be defined as

  20. [Analysis of bacterial composition of the pink mat from spectacles hot spring in Tengchong by culture-independent approach].

    PubMed

    Zhang, Dong-Hua; Li, Qin-Yuan; Liu, Yang; Peng, Qian

    2004-12-01

    The bacterial composition of the pink mat was studied by culture-independent approach. 23 complete 16S rDNA sequences were obtained. According to the sequences alignment and analysis of comparability, the bacteria of the pink mat was consisted of Proteobacteria, Firmicutes, Bacteroidetes, Actinobacter, Deinococcus-thermus, Aquificals. And compared with bacterial composition of the mats from Octopus spring in Yellowstone Park and Haegindi and Fluidir spring, Olkelduhals, Grensdalur spring in Iceland, the pink mat in spectacles spring had highest bacterial diversity among them because it perhaps included lots of bacteria at lower temperature. And the result indicated the same community lived in the same niche and Aquficales was dominant group among bacterial composition of the mat in higher temperature and near-neutral hot spring.

  1. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

    PubMed Central

    Olm, Matthew R.; Brown, Christopher T.; Brooks, Brandon; Firek, Brian; Baker, Robyn; Burstein, David; Soenjoyo, Karina; Thomas, Brian C.; Morowitz, Michael; Banfield, Jillian F.

    2017-01-01

    The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity. PMID:28073918

  2. Antimicrobial susceptibility testing of Gram-positive and -negative bacterial isolates directly from spiked blood culture media with Raman spectroscopy.

    PubMed

    Dekter, H E; Orelio, C C; Morsink, M C; Tektas, S; Vis, B; Te Witt, R; van Leeuwen, W B

    2017-01-01

    Patients suffering from bacterial bloodstream infections have an increased risk of developing systematic inflammatory response syndrome (SIRS), which can result in rapid deterioration of the patients' health. Diagnostic methods for bacterial identification and antimicrobial susceptibility tests are time-consuming. The aim of this study was to investigate whether Raman spectroscopy would be able to rapidly provide an antimicrobial susceptibility profile from bacteria isolated directly from positive blood cultures. First, bacterial strains (n = 133) were inoculated in tryptic soy broth and incubated in the presence or absence of antibiotics for 5 h. Antimicrobial susceptibility profiles were analyzed by Raman spectroscopy. Subsequently, a selection of strains was isolated from blood cultures and analyzed similarly. VITEK®2 technology and broth dilution were used as the reference methods. Raman spectra from 67 antibiotic-susceptible strains showed discriminatory spectra in the absence or at low concentrations of antibiotics as compared to high antibiotic concentrations. For 66 antibiotic-resistant strains, no antimicrobial effect was observed on the bacterial Raman spectra. Full concordance with VITEK®2 data and broth dilution was obtained for the antibiotic-susceptible strains, 68 % and 98 %, respectively, for the resistant strains. Discriminative antimicrobial susceptibility testing (AST) profiles were obtained for all bacterial strains isolated from blood cultures, resulting in full concordance with the VITEK®2 data. It can be concluded that Raman spectroscopy is able to detect the antimicrobial susceptibility of bacterial species isolated from a positive blood culture bottle within 5 h. Although Raman spectroscopy is cheap and rapid, further optimization is required, to fulfill a great promise for future AST profiling technology development.

  3. Hierarchical population model with a carrying capacity distribution for bacterial biofilms.

    PubMed

    Indekeu, J O; Sznajd-Weron, K

    2003-12-01

    In order to describe biological colonies with a conspicuous hierarchical structure, a time- and space-discrete model for the growth of a rapidly saturating local biological population N(x,t) is derived from a hierarchical random deposition process previously studied in statistical physics. Two biologically relevant parameters, the probabilities of birth, B, and of death, D, determine the carrying capacity K. Due to the randomness the population depends strongly on position x and there is a distribution of carrying capacities, Pi(K). This distribution has self-similar character owing to the exponential slowing down of the growth, assumed in this hierarchical model. The most probable carrying capacity and its probability are studied as a function of B and D. The effective growth rate decreases with time, roughly as in a Verhulst process. The model is possibly applicable, for example, to bacteria forming a "towering pillar" biofilm, a structure poorly described by standard Eden or diffusion-limited-aggregation models. The bacteria divide on randomly distributed nutrient-rich regions and are exposed to a random local bactericidal agent (antibiotic spray). A gradual overall temperature or chemical change away from optimal growth conditions reduces bacterial reproduction, while biofilm development degrades antimicrobial susceptibility, causing stagnation into a stationary state.

  4. Genomic evolution of bacterial populations under coselection by antibiotics and phage.

    PubMed

    Cairns, Johannes; Frickel, Jens; Jalasvuori, Matti; Hiltunen, Teppo; Becks, Lutz

    2016-12-15

    Bacteria live in dynamic systems where selection pressures can alter rapidly, forcing adaptation to the prevailing conditions. In particular, bacteriophages and antibiotics of anthropogenic origin are major bacterial stressors in many environments. We previously observed that populations of the bacterium Pseudomonas fluorescens SBW25 exposed to the lytic bacteriophage SBW25Φ2 and a noninhibitive concentration of the antibiotic streptomycin (coselection) achieved higher levels of phage resistance compared to populations exposed to the phage alone. In addition, the phage became extinct under coselection while remaining present in the phage alone environment. Further, phenotypic tests indicated that these observations might be associated with increased mutation rate under coselection. In this study, we examined the genetic causes behind these phenotypes by whole-genome sequencing clones isolated from the end of the experiments. We were able to identify genetic factors likely responsible for streptomycin resistance, phage resistance and hypermutable (mutator) phenotypes. This constitutes genomic evidence in support of the observation that while the presence of phage did not affect antibiotic resistance, the presence of antibiotic affected phage resistance. We had previously hypothesized an association between mutators and elevated levels of phage resistance under coselection. However, our evidence regarding the mechanism was inconclusive, as although with phage mutators were only found under coselection, additional genomic evidence was lacking and phage resistance was also observed in nonmutators under coselection. More generally, our study provides novel insights into evolution between univariate and multivariate selection (here two stressors), as well as the potential role of hypermutability in natural communities.

  5. Monolayer culture systems with respiratory epithelial cells for evaluation of bacterial invasiveness.

    PubMed

    Hirakata, Yoichi; Yano, Hisakazu; Arai, Kazuaki; Endo, Shiro; Kanamori, Hajime; Aoyagi, Tetsuji; Hirotani, Ayako; Kitagawa, Miho; Hatta, Masumitsu; Yamamoto, Natsuo; Kunishima, Hiroyuki; Kawakami, Kazuyoshi; Kaku, Mitsuo

    2010-01-01

    Pseudomonas (P.) aeruginosa is a major opportunistic pathogen especially in immunocompromised patients. To evaluate the invasiveness of respiratory pathogens, we developed monolayer culture systems and examined the degree of invasion by P. aeruginosa and invasive Salmonella (S.) typhimurium strains using human respiratory cell lines: A549 (derived from lung cancer), BEAS-2B (normal bronchial epithelium), and Calu-3 (pleural effusion of a patient with adenocarcinoma of the lung). Cells were seeded into filter units containing 0.33 cm(2) filter membranes with 3.0 microm pores, and were incubated at 37 degrees C under 5% CO(2) for 4-10 days. By monitoring the trans-monolayer electrical resistance (TER), we judged that BEAS-2B cells (TER values: 436.2 +/- 16.8 to 628.8 +/- 66.3 Omega cm(2)) and Calu-3 cells (TER values: 490.5 +/- 25.2 to 547.8 +/- 21.6 Omega cm(2)) formed monolayers with tight junctions, but not A549 cells. On day 8 of culture, monolayer cultures were infected with bacteria, and the number of microorganisms penetrating into the basolateral medium was counted. Wild-type P. aeruginosa PAO1 (PAO1 WT) and S. typhimurium SL1344 were detected in the basolateral medium of BEAS-2B monolayer system by 3 h after inoculation, while only P. aeruginosa PAO1 WT was detected in the basolateral medium of Calu-3 monolayer, indicating poor invasiveness of S. typhimurium SL1344 in the Calu-3 system. These findings suggest that BEAS-2B or Calu-3 monolayer system could be useful for evaluating the invasiveness of respiratory pathogens. Because of the difference in bacterial invasiveness, we may need to choose a suitable cell system for each target pathogen.

  6. Investigating bacterial population structure and dynamics in traditional koumiss from Inner Mongolia using single molecule real-time sequencing.

    PubMed

    Gesudu, Qimu; Zheng, Yi; Xi, Xiaoxia; Hou, Qiang Chuan; Xu, Haiyan; Huang, Weiqiang; Zhang, Heping; Menghe, Bilige; Liu, Wenjun

    2016-10-01

    Koumiss is considered as a complete dairy product high in nutrients and with medicinal properties. The bacterial communities involved in production of koumiss play a crucial role in the fermentation cycle. To reveal bacterial biodiversity in koumiss and the dynamics of succession in bacterial populations during fermentation, 22 samples were collected from 5 sampling sites and the full length of the 16S ribosomal RNA genes sequenced using single molecule real-time sequencing technology. One hundred forty-eight species were identified from 82 bacterial genera and 8 phyla. These results suggested that the structural difference in the bacterial community could be attributed to geographical location. The most significant difference in bacterial composition occurred in samples from group D compared with other groups. The sampling location of group D was distant from the city and maintained the primitive local nomadic life. The dynamics of succession in bacterial communities showed that Lactobacillus helveticus increased in abundance from 0 to 9h and reached its peak at 9h and then decreased. In contrast, Enterococcus faecalis, Enterococcus durans, and Enterococcus casseliflavus increased gradually throughout the fermentation process, and reached a maximum after 24h.

  7. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus.

    PubMed

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-02-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts.

  8. Comparative usefulness of inflammatory markers to indicate bacterial infection-analyzed according to blood culture results and related clinical factors.

    PubMed

    Nishikawa, Hirokazu; Shirano, Michinori; Kasamatsu, Yu; Morimura, Ayumi; Iida, Ko; Kishi, Tomomi; Goto, Tetsushi; Okamoto, Saki; Ehara, Eiji

    2016-01-01

    To assess relationships of inflammatory markers and 2 related clinical factors with blood culture results, we retrospectively investigated inpatients' blood culture and blood chemistry findings that were recorded from January to December 2014 using electronic medical records and analyzed the data of 852 subjects (426 culture-positive and 426 culture-negative). Results suggested that the risk of positive blood culture statistically increased as inflammatory marker levels and the number of related factors increased. Concerning the effectiveness of inflammatory markers, when the outcome definition was also changed for C-reactive protein (CRP), the odds ratio had a similar value, whereas when the outcome definition of blood culture positivity was used for procalcitonin (PCT), the greatest effectiveness of that was detected. Therefore, the current results suggest that PCT is more useful than CRP as an auxiliary indication of bacterial infection.

  9. Comparison of human optimized bacterial luciferase, firefly luciferase, and green fluorescent protein for continuous imaging of cell culture and animal models

    NASA Astrophysics Data System (ADS)

    Close, Dan M.; Hahn, Ruth E.; Patterson, Stacey S.; Baek, Seung J.; Ripp, Steven A.; Sayler, Gary S.

    2011-04-01

    Bioluminescent and fluorescent reporter systems have enabled the rapid and continued growth of the optical imaging field over the last two decades. Of particular interest has been noninvasive signal detection from mammalian tissues under both cell culture and whole animal settings. Here we report on the advantages and limitations of imaging using a recently introduced bacterial luciferase (lux) reporter system engineered for increased bioluminescent expression in the mammalian cellular environment. Comparison with the bioluminescent firefly luciferase (Luc) system and green fluorescent protein system under cell culture conditions demonstrated a reduced average radiance, but maintained a more constant level of bioluminescent output without the need for substrate addition or exogenous excitation to elicit the production of signal. Comparison with the Luc system following subcutaneous and intraperitoneal injection into nude mice hosts demonstrated the ability to obtain similar detection patterns with in vitro experiments at cell population sizes above 2.5 × 104 cells but at the cost of increasing overall image integration time.

  10. [A retrospective study of the relationship between bacterial numbers from central venous catheter tip cultures and blood cultures for evaluating central line-associated bloodstream infections].

    PubMed

    Ohtaki, Hirofumi; Ohkusu, Kiyofumi; Nakayama, Asami; Yonetamari, Jun; Ando, Kohei; Miyazaki, Takashi; Ohta, Hirotoshi; Furuta, Nobuyuki; Watanabe, Tamayo; Ito, Hiroyasu; Murakami, Nobuo; Seishima, Mitsuru

    2014-01-01

    Catheter-related bloodstream infection (CRBSI) is an infectious disease requiring special attention. It is a common cause of nosocomial infections; catheter insertion into the central veins particularly increases the risk of infection (CLA-BSI: central line-associated bloodstream infection). We examined the relationship between the number of bacterial colonies cultured from shredded central venous catheter (CVC) tips and from blood cultures in our hospital from 2011 to 2012. Coagulase-negative staphylococci topped the list of microbe isolated from the CVC tip culture, followed by Pseudomonas aeruginosa, Staphylococcus aureus, and Candida spp. S. aureus and Candida spp., with growth of over 15 colony-forming units in the CVC tip culture, were also detected at high rates in the blood culture. However, gramnegative bacilli (Enterobacteriaceae and P. aeruginosa) did not show a similar increase in colony number in the CVC tip culture. Because microbes adhering to shredded catheter tips are readily detected by culture, this method is useful as a routine diagnostic test. In addition, prompt clinical reporting of the bacterial number of serious CLA-BSI-causing S. aureus and Candida spp. isolated from CVC tips could contribute to earlier CLA-BSI diagnosis.

  11. Development of polyvinyl chloride biofilms for succession of selected marine bacterial populations.

    PubMed

    Balasubramanian, V; Palanichamy, S; Subramanian, G; Rajaram, R

    2012-01-01

    Present investigation was made to bring out the pattern of biofilm formation by heterotrophic bacteria on nontoxic material, polyvinyl chloride (PVC) sheet fitted wooden rack that was immersed in seawater and the study was conducted in Tuticorin coast. Samplings were made over a period of 7 days with the following time period intervals: 30 min, 1, 2, 4, 24, 48, 72, 96, 120 and 144 hr. Bacterial enumeration was made by spread plate method on nutrient agar medium and characterization of bacterial isolates up to generic level was done. Gram-negative bacteria like Pseudomonas sp., Enterobacter sp., Aeromonas sp., Cytophaga sp. and Flavobacterium sp. were found to be the pioneer in colonizing the surface within 30 min and seven genera were represented in the biofilm. Among them two genera were found belonging to Gram-positive groups which included Micrococcus and Bacillus sp. The early stage biofilm i.e. up to 24th hr was wholly constituted by Gram-negative groups. However, the population density of Pseudomonas sp. was found to be higher (315 CFU) when compared to other Gram-negative forms. Occurrence of Gram-positive group was noted only at 48th hr old biofilm (28 to 150 CFU). The period between 48 and 96th hr was the transition where both the Gram-negative and Gram-positive groups co- existed. After 96th hr, the biofilm was found constituted only by Gram-positive groups. The isolates of early stage biofilm were found to produce allelopathic substance like bacteriocin.

  12. Investigation of Endophytic Bacterial Community in Supposedly Axenic Cultures of Pineapple and Orchids with Evidence on Abundant Intracellular Bacteria.

    PubMed

    Esposito-Polesi, Natalia Pimentel; de Abreu-Tarazi, Monita Fiori; de Almeida, Cristina Vieira; Tsai, Siu Mui; de Almeida, Marcílio

    2017-01-01

    Asepsis, defined as the absence of microbial contamination, is one of the most important requirements of plant micropropagation. In long-term micropropagated cultures, there may occasionally occur scattered microorganism growth in the culture medium. These microorganisms are common plant components and are known as latent endophytes. Thus, the aim of this research was to investigate the presence of endophytic bacteria in asymptomatic pineapple and orchid microplants, which were cultivated in three laboratories for 1 year. Isolation and characterization of bacterial isolates, PCR-DGGE from total genomic DNA of microplants and ultrastructural analysis of leaves were performed. In the culture-dependent technique, it was only possible to obtain bacterial isolates from pineapple microplants. In this case, the bacteria genera identified in the isolation technique were Bacillus, Acinetobacter, and Methylobacterium. The scanning electron microscopy and transmission electron microscopy (SEM and TEM) analyses revealed the presence of endophytic bacteria in intracellular spaces in the leaves of pineapple and orchid microplants, independent of the laboratory or cultivation protocol. Our results strongly indicate that there are endophytic bacterial communities inhabiting the microplants before initiation of the in vitro culture and that some of these endophytes persist in their latent form and can also grow in the culture medium even after long-term micropropagation, thus discarding the concept of "truly axenic plants."

  13. A surface swab method for culturing Foley catheters assays the pericatheter (urethral) but not the urine (luminal) microbial population.

    PubMed

    Johnson, J R; Dykstra, D; Brown, J J; Kringstad, B; Pryor, J L

    1997-07-01

    Assessment of the urethral flora in patients with indwelling bladder catheters is problematic in the presence of urinary tract infection (UTI). A new surface swab method that samples the external catheter surface without interference from contaminated luminal contents is described. In vitro, recovery of adherent bacteria from the external catheter surface by the surface swab method was proportional to the bacterial density as measured by a comparison scrape method. In a prospective longitudinal assessment of three chronically catheterized subjects with polymicrobial catheter-associated UTI, a conventional roll plate catheter culture method suggested substantial overlap between the urethral and urine microbial populations, possibly a result of contamination of catheter cultures by infected urine. In contrast, the surface swab method revealed little overlap between these floras, evidence suggesting a predominantly luminal (rather than meatal) route of UTI acquisition. The new surface swab method should prove useful in future studies of the pathogenesis and prevention of catheter-associated UTI.

  14. Weighted ssGBLUP improves genomic selection accuracy for bacterial cold water disease resistance in a rainbow trout population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to compare methods for genomic evaluation in a Rainbow Trout (Oncorhynchus mykiss) population for survival when challenged by Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). The used methods were: 1)regular ssGBLUP that assume...

  15. Emergence of Competitive Dominant Ammonia-Oxidizing Bacterial Populations in a Full-Scale Industrial Wastewater Treatment Plant

    PubMed Central

    Layton, Alice C.; Dionisi, Hebe; Kuo, H.-W.; Robinson, Kevin G.; Garrett, Victoria M.; Meyers, Arthur; Sayler, Gary S.

    2005-01-01

    Ammonia-oxidizing bacterial populations in an industrial wastewater treatment plant were investigated with amoA and 16S rRNA gene real-time PCR assays. Nitrosomonas nitrosa initially dominated, but over time RI-27-type ammonia oxidizers, also within the Nitrosomonas communis lineage, increased from below detection to codominance. This shift occurred even though nitrification remained constant. PMID:15691975

  16. Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations

    PubMed Central

    2011-01-01

    Background Common bacterial blight (CBB), incited by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Host resistance is practically the most effective and environmentally-sound approach to control CBB. Unlike conventional QTL discovery strategies, in which bi-parental populations (F2, RIL, or DH) need to be developed, association mapping-based strategies can use plant breeding populations to synchronize QTL discovery and cultivar development. Results A population of 469 dry bean lines of different market classes representing plant materials routinely developed in a bean breeding program were used. Of them, 395 lines were evaluated for CBB resistance at 14 and 21 DAI (Days After Inoculation) in the summer of 2009 in an artificially inoculated CBB nursery in south-western Ontario. All lines were genotyped using 132 SNPs (Single Nucleotide Polymorphisms) evenly distributed across the genome. Of the 132 SNPs, 26 SNPs had more than 20% missing data, 12 SNPs were monomorphic, and 17 SNPs had a MAF (Minor Allelic Frequency) of less than 0.20, therefore only 75 SNPs were used for association study, based on one SNP per locus. The best possible population structure was to assign 36% and 64% of the lines into Andean and Mesoamerican subgroups, respectively. Kinship analysis also revealed complex familial relationships among all lines, which corresponds with the known pedigree history. MLM (Mixed Linear Model) analysis, including population structure and kinship, was used to discover marker-trait associations. Eighteen and 22 markers were significantly associated with CBB rating at 14 and 21 DAI, respectively. Fourteen markers were significant for both dates and the markers UBC420, SU91, g321, g471, and g796 were highly significant (p ≤ 0.001). Furthermore, 12 significant SNP markers were co-localized with or close to the CBB-QTLs identified previously in bi-parental QTL mapping

  17. Cultural Factors and Population in Developing Countries. Occasional Monograph Series, No. Six. ICP Work Agreement Reports.

    ERIC Educational Resources Information Center

    Smithsonian Institution, Washington, DC.

    Five studies focus on the cultural components of population issues in Thailand, Jamaica, Korea, Kenya, and Indonesia. The reports explore the influence of cultural factors on contraceptive practice, family planning, abortion, and education. Recommendations are made for policymakers in areas that impinge on population growth. "Birth Control…

  18. Impact of Bioreactor Environment and Recovery Method on the Profile of Bacterial Populations from Water Distribution Systems

    PubMed Central

    Luo, Xia; Jellison, Kristen L.; Huynh, Kevin; Widmer, Giovanni

    2015-01-01

    Multiple rotating annular reactors were seeded with biofilms flushed from water distribution systems to assess (1) whether biofilms grown in bioreactors are representative of biofilms flushed from the water distribution system in terms of bacterial composition and diversity, and (2) whether the biofilm sampling method affects the population profile of the attached bacterial community. Biofilms were grown in bioreactors until thickness stabilized (9 to 11 weeks) and harvested from reactor coupons by sonication, stomaching, bead-beating, and manual scraping. High-throughput sequencing of 16S rRNA amplicons was used to profile bacterial populations from flushed biofilms seeded into bioreactors as well as biofilms recovered from bioreactor coupons by different methods. β diversity between flushed and reactor biofilms was compared to β diversity between (i) biofilms harvested from different reactors and (ii) biofilms harvested by different methods from the same reactor. These analyses showed that average diversity between flushed and bioreactor biofilms was double the diversity between biofilms from different reactors operated in parallel. The diversity between bioreactors was larger than the diversity associated with different biofilm recovery methods. Compared to other experimental variables, the method used to recover biofilms had a negligible impact on the outcome of water biofilm analyses based on 16S amplicon sequencing. Results from this study show that biofilms grown in reactors over 9 to 11 weeks are not representative models of the microbial populations flushed from a distribution system. Furthermore, the bacterial population profile of biofilms grown in replicate reactors from the same flushed water are likely to diverge. However, four common sampling protocols, which differ with respect to disruption of bacterial cells, provide similar information with respect to the 16S rRNA population profile of the biofilm community. PMID:26196282

  19. Impact of Bioreactor Environment and Recovery Method on the Profile of Bacterial Populations from Water Distribution Systems.

    PubMed

    Luo, Xia; Jellison, Kristen L; Huynh, Kevin; Widmer, Giovanni

    2015-01-01

    Multiple rotating annular reactors were seeded with biofilms flushed from water distribution systems to assess (1) whether biofilms grown in bioreactors are representative of biofilms flushed from the water distribution system in terms of bacterial composition and diversity, and (2) whether the biofilm sampling method affects the population profile of the attached bacterial community. Biofilms were grown in bioreactors until thickness stabilized (9 to 11 weeks) and harvested from reactor coupons by sonication, stomaching, bead-beating, and manual scraping. High-throughput sequencing of 16S rRNA amplicons was used to profile bacterial populations from flushed biofilms seeded into bioreactors as well as biofilms recovered from bioreactor coupons by different methods. β diversity between flushed and reactor biofilms was compared to β diversity between (i) biofilms harvested from different reactors and (ii) biofilms harvested by different methods from the same reactor. These analyses showed that average diversity between flushed and bioreactor biofilms was double the diversity between biofilms from different reactors operated in parallel. The diversity between bioreactors was larger than the diversity associated with different biofilm recovery methods. Compared to other experimental variables, the method used to recover biofilms had a negligible impact on the outcome of water biofilm analyses based on 16S amplicon sequencing. Results from this study show that biofilms grown in reactors over 9 to 11 weeks are not representative models of the microbial populations flushed from a distribution system. Furthermore, the bacterial population profile of biofilms grown in replicate reactors from the same flushed water are likely to diverge. However, four common sampling protocols, which differ with respect to disruption of bacterial cells, provide similar information with respect to the 16S rRNA population profile of the biofilm community.

  20. Combination of culture-independent and culture-dependent molecular methods for the determination of bacterial community of iru, a fermented Parkia biglobosa seeds

    PubMed Central

    Adewumi, Gbenga A.; Oguntoyinbo, Folarin A.; Keisam, Santosh; Romi, Wahengbam; Jeyaram, Kumaraswamy

    2013-01-01

    In this study, bacterial composition of iru produced by natural, uncontrolled fermentation of Parkia biglobosa seeds was assessed using culture-independent method in combination with culture-based genotypic typing techniques. PCR-denaturing gradient gel electrophoresis (DGGE) revealed similarity in DNA fragments with the two DNA extraction methods used and confirmed bacterial diversity in the 16 iru samples from different production regions. DNA sequencing of the highly variable V3 region of the 16S rRNA genes obtained from PCR-DGGE identified species related to Bacillus subtilis as consistent bacterial species in the fermented samples, while other major bands were identified as close relatives of Staphylococcus vitulinus, Morganella morganii, B. thuringiensis, S. saprophyticus, Tetragenococcus halophilus, Ureibacillus thermosphaericus, Brevibacillus parabrevis, Salinicoccus jeotgali, Brevibacterium sp. and uncultured bacteria clones. Bacillus species were cultured as potential starter cultures and clonal relationship of different isolates determined using amplified ribosomal DNA restriction analysis (ARDRA) combined with 16S–23S rRNA gene internal transcribed spacer (ITS) PCR amplification, restriction analysis (ITS-PCR-RFLP), and randomly amplified polymorphic DNA (RAPD-PCR). This further discriminated B. subtilis and its variants from food-borne pathogens such as B. cereus and suggested the need for development of controlled fermentation processes and good manufacturing practices (GMP) for iru production to achieve product consistency, safety quality, and improved shelf life. PMID:23316189

  1. Methylmercury decomposition in sediments and bacterial cultures: Involvement of methanogens and sulfate reducers in oxidative demethylation

    USGS Publications Warehouse

    Oremland, R.S.; Culbertson, C.W.; Winfrey, M.R.

    1991-01-01

    Demethylation of monomethylmercury in freshwater and estuarine sediments and in bacterial cultures was investigated with 14CH3HgI. Under anaerobiosis, results with inhibitors indicated partial involvement of both sulfate reducers and methanogens, the former dominating estuarine sediments, while both were active in freshwaters. Aerobes were the most significant demethylators in estuarine sediments, but were unimportant in freshwater sediments. Products of anaerobic demethylation were mainly 14CO2 as well as lesser amounts of 14CH4. Acetogenic activity resulted in fixation of some 14CO2 produced from 14CH3HgI into acetate. Aerobic demethylation in estuarine sediments produced only 14CH4, while aerobic demethylation in freshwater sediments produced small amounts of both 14CH4 and 14CO2. Two species of Desulfovibrio produced only traces of 14CH4 from 14CH3HgI, while a culture of a methylotrophic methanogen formed traces of 14CO2 and 14CH4 when grown on trimethylamine in the presence of the 14CH3HgI. These results indicate that both aerobes and anaerobes demethylate mercury in sediments, but that either group may dominate in a particular sediment type. Aerobic demethylation in the estuarine sediments appeared to proceed by the previously characterized organomercurial-lyase pathway, because methane was the sole product. However, aerobic demethylation in freshwater sediments as well as anaerobic demethylation in all sediments studied produced primarily carbon dioxide. This indicates the presence of an oxidative pathway, possibly one in which methylmercury serves as an analog of one-carbon substrates.

  2. Methylmercury decomposition in sediments and bacterial cultures: Involvement of methanogens and sulfate reducers in oxidative demethylation

    SciTech Connect

    Oremland, R.S.; Culbertson, C.W. ); Winfrey, M.R. )

    1991-01-01

    The biogeochemical cycling of mercury has received considerable attention because of the toxicity of methylmercury, its bioaccumulation in biota, and its biomagnification in aquatic food chains. The formation of methylmercury is mediated primarily by microorganisms. Demethylation of monomethylmercury in freshwater and estuarine sediments and in bacterial cultures was investigated with {sup 14}CH{sub 3}HgI. Under anaerobiosis, results with inhibitors indicated partial involvement of both sulfate reducers and methanogens, the former dominated estuarine sediments, while both were active in freshwaters. Aerobes were the most significant demethylators in estuarine sediments, but were unimportant in freshwater sediments. Products of anaerobic demthylation were mainly {sup 14}CO{sub 2} as well as lesser amounts of {sup 14}CH{sub 4}. Acetogenic activity resulted in fixation of some {sup 14}CO{sub 2} produced from {sup 14}CH{sub 3}HgI into acetate. Aerobic demethylation in estuarine sediments produced only {sup 14}CH{sub 4}, while aerobic demethylation in freshwater sediments produced small amounts of both {sup 14}CH{sub 4} and {sup 14}CO{sub 2}. Two species of Desulfovibrio produced only traces of {sup 14}CH{sub 4} from {sup 14}CH{sub 3}HgI, while a culture of a methylotrophic methanogen formed traces of {sup 14}CO{sub 2} and {sup 14}CH{sub 4} when grown on trimethylamine in the presence of the {sup 14}CH{sub 3}HgI. These results indicate that both aerobes and anaerobes demethylate mercury in sediments, but that either group may dominate in a particular sediment type. Aerobic demethylation in the estuarine sediments appeared to proceed by the previously characterized organomercurial-lyase pathway, because methane was the sole product. This indicates the presence of an oxidative pathway, possibly one in which methylmercury serves as an analog of one-carbon substrates.

  3. Culturally Grounded Prevention for Minority Youth Populations: A Systematic Review of the Literature

    PubMed Central

    Lauricella, Michela; Valdez, Jessica K.; Okamoto, Scott K.; Helm, Susana; Zaremba, Colleen

    2016-01-01

    Contemporary prevention science has focused on the application of cultural adaptations of evidence-based prevention programs for minority youth populations. Far less is known about culturally grounded methods that are intended to organically develop prevention programs within specific populations and communities. This article systematically reviews recent literature on culturally grounded interventions used to prevent health disparities in ethnic minority youth populations. In this review, we assessed 31 peer-reviewed articles published in 2003 or later that fit inclusionary criteria pertaining to the development and evaluation of culturally grounded prevention programs. The evaluated studies indicated different approaches toward cultural grounding, as well as specific populations, geographic regions, and health issues that have been targeted. Specifically, the findings indicated that most of the studies focused on the development and evaluation of culturally grounded HIV/STI and substance abuse prevention programs for Mexican American, African American, and American Indian/Alaska Native youth residing in the South or Southwestern U.S. These studies largely relied on community-based participatory or qualitative research methods to develop programs from the “ground up.” This review has implications for the development of future culturally grounded and culturally adapted prevention programs targeting underserved minority youth populations and geographic regions. Specifically, it identifies populations and regions where culturally grounded prevention efforts are underdeveloped or non-existent, providing some scientific direction for the future development of these types of programs. PMID:26733384

  4. Characterization of polyhydroxyalkanoates synthesized from microbial mixed cultures and of their nanobiocomposites with bacterial cellulose nanowhiskers.

    PubMed

    Martínez-Sanz, Marta; Villano, Marianna; Oliveira, Catarina; Albuquerque, Maria G E; Majone, Mauro; Reis, Maria; Lopez-Rubio, Amparo; Lagaron, Jose M

    2014-06-25

    The present work reports on the production and characterization of polyhydroxyalkanoates (PHAs) with different valerate contents, which were synthesized from microbial mixed cultures, and the subsequent development of nanocomposites incorporating bacterial cellulose nanowhiskers (BCNW) via solution casting processing. The characterization of the pure biopolyesters showed that the properties of PHAs may be strongly modified by varying the valerate ratio in the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) copolymer, as expected. Increasing the valerate content was seen to greatly decrease the melting temperature and enthalpy of the material, as well as its rigidity and stiffness, resulting in a more ductile behaviour. Additionally, the higher valerate PHA displayed higher permeability to water and oxygen and higher moisture sensitivity. Subsequently, BCNW were incorporated into both PHA grades, achieving a high level of dispersion for a 1 wt.-% loading, whereas some agglomeration took place for 3 wt.-% BCNW. As evidenced by DSC analyses, BCNW presented a nucleating effect on the PHA matrices. BCNW also increased the thermal stability of the polymeric matrices when properly dispersed due to strong matrix-filler interactions. Barrier properties were seen to depend on relative humidity and improved at low nanofiller loadings and low relative humidity.

  5. Influence of chemical surfactants on the biodegradation of crude oil by a mixed bacterial culture.

    PubMed

    Van Hamme, J D; Ward, O P

    1999-02-01

    The effects of surfactant physicochemical properties, such as the hydrophile-lipophile balance (HLB) and molecular structure, on the biodegradation of 2% w/v Bow River crude oil by a mixed-bacterial culture were examined. Viable counts increased 4.6-fold and total petroleum hydrocarbon (TPH) biodegradation increased 57% in the presence of Igepal CO-630, a nonylphenol ethoxylate (HLB 13, 0.625 g/L). Only the nonylphenol ethoxylate with an HLB value of 13 substantially enhanced biodegradation. The surfactants from other chemical classes with HLB values of 13 (0.625 g/L) had no effect or were inhibitory. TPH biodegradation enhancement by Igepal CO-630 occurred at concentrations above the critical micelle concentration. When the effect of surfactant on individual oil fractions was examined, the biodegradation enhancement for the saturate and aromatic fractions was the same. In all cases, biodegradation resulted in increased resin and asphaltene concentrations. Optimal surfactant concentrations for TPH biodegradation reduced resin and asphaltene formation. Chemical surfactants have the potential to improve crude oil biodegradation in complex microbial systems, and surfactant selection should consider factors such as molecular structure, HLB, and surfactant concentration.

  6. Breast Cancer Screening: Cultural Beliefs and Diverse Populations

    ERIC Educational Resources Information Center

    Simon, Cassandra E.

    2006-01-01

    This article addresses the role of culture in breast cancer screening behavior among African American, American Indian/Alaskan Native, Asian American/Pacific Islander, and Hispanic/Latina women. It reviews cultural beliefs, attitudes, and knowledge and their relative influence on women's decisions regarding health tests. The article explores how…

  7. Does dormancy increase fitness of bacterial populations in time-varying environments?

    PubMed

    Malik, Tufail; Smith, Hal L

    2008-05-01

    A simple family of models of a bacterial population in a time varying environment in which cells can transit between dormant and active states is constructed. It consists of a linear system of ordinary differential equations for active and dormant cells with time-dependent coefficients reflecting an environment which may be periodic or random, with alternate periods of low and high resource levels. The focus is on computing/estimating the dominant Lyapunov exponent, the fitness, and determining its dependence on various parameters and the two strategies-responsive and stochastic-by which organisms switch between dormant and active states. A responsive switcher responds to good and bad times by making timely and appropriate transitions while a stochastic switcher switches continuously without regard to the environmental state. The fitness of a responsive switcher is examined and compared with fitness of a stochastic switcher, and with the fitness of a dormancy-incapable organism. Analytical methods show that both switching strategists have higher fitness than a dormancy-incapable organism when good times are rare and that responsive switcher has higher fitness than stochastic switcher when good times are either rare or common. Numerical calculations show that stochastic switcher can be most fit when good times are neither too rare or too common.

  8. Population densities of five migratory endoparasitic nematodes in carrot disk cultures.

    PubMed

    Verdejo-Lucas, S; Pinochet, J

    1992-03-01

    Numbers of nematodes recovered per culture varied greatly among five species cultured on carrot disks. Radopholus similis and Pratylenchus vulnus showed the highest population densities, with 23,400-fold and 16,600-fold increases, respectively, in 90 days. Final populations of P. thornei and Zygotytenchus guevarai were similar but lower than those of R. similis and P. vulnus. The population of P. neglectus increased 74 times. Species with the greatest reproduction in this study reproduce sexually.

  9. Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage.

    PubMed

    Reboleiro-Rivas, P; Martín-Pascual, J; Morillo, J A; Juárez-Jiménez, B; Poyatos, J M; Rodelas, B; González-López, J

    2016-01-01

    Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs.

  10. Bacterial Communities and Midgut Microbiota Associated with Mosquito Populations from Waste Tires in East-Central Illinois.

    PubMed

    Kim, Chang-Hyun; Lampman, Richard L; Muturi, Ephantus J

    2015-01-01

    Mosquito-microbe interactions tend to influence larval nutrition, immunity, and development, as well as fitness and vectorial capacity of adults. Understanding the role of different bacterial species not only improves our knowledge of the physiological and ecological consequences of these interactions, but also provides the basis for developing novel strategies for controlling mosquito-borne diseases. We used culture-dependent and culture-independent techniques to characterize the bacterial composition and abundance in water and midgut samples of larval and adult females of Aedes japonicus (Theobald), Aedes triseriatus (Say), and Culex restuans (Theobald) collected from waste tires at two wooded study sites in Urbana, IL. The phylum-specific real-time quantitative polymerase chain reaction assay revealed a higher proportion of Actinobacteria and a lower proportion of gamma-Proteobacteria and Bacteroidetes in water samples and larval midguts compared to adult female midguts. Only 15 of the 57 bacterial species isolated in this study occurred in both study sites. The number of bacterial species was highest in water samples (28 species from Trelease Woods; 25 species from South Farms), intermediate in larval midguts (13 species from Ae. japonicus; 12 species from Ae. triseriatus; 8 species from Cx. restuans), and lowest in adult female midguts (2 species from Ae. japonicus; 3 species from Ae. triseriatus). These findings suggest that the composition and richness of bacterial communities varies both between habitats and among mosquito species and that the reduction in bacteria diversity during metamorphosis is more evident among bacteria detected using the culture-dependent method.

  11. Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder

    PubMed Central

    Hilt, Evann E.; McKinley, Kathleen; Pearce, Meghan M.; Rosenfeld, Amy B.; Zilliox, Michael J.; Mueller, Elizabeth R.; Brubaker, Linda; Gai, Xiaowu; Wolfe, Alan J.

    2014-01-01

    Our previous study showed that bacterial genomes can be identified using 16S rRNA sequencing in urine specimens of both symptomatic and asymptomatic patients who are culture negative according to standard urine culture protocols. In the present study, we used a modified culture protocol that included plating larger volumes of urine, incubation under varied atmospheric conditions, and prolonged incubation times to demonstrate that many of the organisms identified in urine by 16S rRNA gene sequencing are, in fact, cultivable using an expanded quantitative urine culture (EQUC) protocol. Sixty-five urine specimens (from 41 patients with overactive bladder and 24 controls) were examined using both the standard and EQUC culture techniques. Fifty-two of the 65 urine samples (80%) grew bacterial species using EQUC, while the majority of these (48/52 [92%]) were reported as no growth at 103 CFU/ml by the clinical microbiology laboratory using the standard urine culture protocol. Thirty-five different genera and 85 different species were identified by EQUC. The most prevalent genera isolated were Lactobacillus (15%), followed by Corynebacterium (14.2%), Streptococcus (11.9%), Actinomyces (6.9%), and Staphylococcus (6.9%). Other genera commonly isolated include Aerococcus, Gardnerella, Bifidobacterium, and Actinobaculum. Our current study demonstrates that urine contains communities of living bacteria that comprise a resident female urine microbiota. PMID:24371246

  12. [The process of bacterial population splitting into dissociants and long-term batch cultivation of bacteria].

    PubMed

    Mil'ko, E S; Mil'ko, D M

    2014-01-01

    The growth and composition of a population were studied during long-term (up to 50 days) batch cultivation of mono and mixed cultures of Pseudomonas aeruginosa S- and M-dissociants and Rhodobacter sphaeroides R- and M-dissociants without the addition of nutrients. During the cultivation of P. aeruginosa on a glucose-containing mineral medium, periodic lysis followed by polyculture growth resumption in the late stationary phase occurred on account of the M-dissociant: the change in its cell number corresponded to the change in the total cell number of the association. It was shown that the periodic occurrence of reducing sugars in the medium preceded the resumption ofpolyculture growth.

  13. Human mixed lymphocyte culture using separated lymphocyte populations.

    PubMed Central

    Potter, M R; Moore, M

    1977-01-01

    The ability of human blood lymphocyte populations enriched with T or B cells to act as responder and stimulator populations in the one-way mixed lymphocyte reaction (MLR) was investigated. T- and B-cell-enriched populations were obtained by separation of rosette-forming and non rosette-forming cells and T-cell-enriched populations were also obtained by nylon-fibre column filtration. Using cells prepared by rosette sedimentation, control unseparated and T-cell-enriched populations responded well when stimulated by mitomycin C-treated unseparated cells from a second individual; and stimulation by T- and B-enriched populations generally produced some response, although the magnitude was variable. B-cell-enriched populations gave virtually no response regardless of the composition of the stimulating populations. Nylon-column-enriched T-cell populations responded to stimulation by control unseparated cells but not to T cells purified by the same procedure. T-cell enriched populations prepared by the two methods thus had different activities in the MLR despite containing similar numbers of T cells suggesting that other factors, such as the presence of small numbers of accessory cells, are important in determining the magnitude of the MLR. PMID:139361

  14. Biodegradation of phenanthrene, spatial distribution of bacterial populations and dioxygenase expression in the mycorrhizosphere of Lolium perenne inoculated with Glomus mosseae.

    PubMed

    Corgié, S C; Fons, F; Beguiristain, T; Leyval, C

    2006-05-01

    Interactions between the plant and its microbial communities in the rhizosphere control microbial polycyclic aromatic hydrocarbons (PAH) biodegradation processes. Arbuscular mycorrhizal (AM) fungi can influence plant survival and PAH degradation in polluted soil. This work was aimed at studying the contribution of the mycorrhizosphere to PAH biodegradation in the presence of ryegrass (Lolium perenne L., cv. Barclay) inoculated with Glomus mosseae (BEG 69) by taking into account the structure and activity of bacterial communities, PAH degrading culturable bacteria as a function of the distance from roots. Ryegrass was grown in compartmentalized systems designed to harvest successive sections of rhizosphere in lateral compartments polluted or not with phenanthrene (PHE). Colonization of roots by G. mosseae (BEG 69) modified the structure and density of bacterial populations in the mycorrhizosphere, compared to the rhizosphere of non-mycorrhizal plants. G. mosseae increased the density of culturable heterotrophic and PAH degrading bacteria beyond the immediate rhizosphere in the presence of PHE, and increased the density of PAH degraders in the absence of the pollutant. Biodegradation was not significantly increased in the mycorrhizosphere, compared to control non-mycorrhizal plants, where PHE biodegradation already reached 92% after 6 weeks. However, dioxygenase transcriptional activity was found to be higher in the immediate mycorrhizosphere in the presence of G. mosseae (BEG 69).

  15. Why we don't get sick: the within-host population dynamics of bacterial infections.

    PubMed

    Levin, B R; Antia, R

    2001-05-11

    To pathogenic microparasites (viruses, bacteria, protozoa, or fungi), we and other mammals (living organisms at large) are little more than soft, thin-walled flasks of culture media. Almost every time we eat, brush our teeth, scrape our skin, have sex, get bitten by insects, and inhale, we are confronted with populations of microbes that are capable of colonizing the mucosa lining our orifices and alimentary tract and proliferating in fluids and cells within us. Nevertheless, we rarely get sick, much less succumb to these infections. The massive numbers of bacteria and other micro- and not-so-micro organisms that abound and replicate in our alimentary tract and cover our skin and the mucosa lining our orifices normally maintain their communities in seemingly peaceful coexistence with the somatic cells that define us. Why don't these microbes invade and proliferate in the culture media within the soft, thin-walled flask that envelops us? Why don't they cause disease and lead to our rapid demise?

  16. Effect of Lactobacillus johnsonii CRL1647 on different parameters of honeybee colonies and bacterial populations of the bee gut.

    PubMed

    Audisio, M C; Sabaté, D C; Benítez-Ahrendts, M R

    2015-01-01

    Lactobacillus johnsonii CRL1647, isolated from the intestinal tract of a worker-bee in Salta, Argentina, was delivered to Apis mellifera L. honey bee colonies according to two different administration schedules: 1×10(5) cfu/ml every 15 days (2011) or monthly (2012). The effect of each treatment on the bee-colony performance was monitored by measuring honey production, and the prevalence of varroasis and nosemosis. Worker bees from each assay were randomly captured 3 days after administration and assayed for the following intestinal culturable and defined bacterial populations: total aerobic microorganisms, Bacillus spp. spores, Lactobacillus spp., Enterococcus spp. and enterobacteria. Interestingly, both treatments generated a similar increase in honey production in treated colonies compared to controls: 36.8% (every 15 days) and 36.3% (monthly). Nosema index always exhibited a reduction when lactobacilli were administered; in turn, Varroa incidence was lower when the lactobacilli were administered once a month. Moreover, the administration of L. johnsonii CRL1647 every 15 days produced an increase in the total number of aerobic microorganisms and in bacteria belonging to the genera Lactobacillus and Enterococcus; at the same time, a decrease was observed in the number of total spores at the end of the treatment. The number of enterobacteria was constant and remained below that of control hives at the end of the assay. On the other hand, the delivery of lactobacilli once a month only showed an increase in the number of bacteria belonging to the genus Lactobacillus; meanwhile, viable counts of the remaining microorganisms assayed were reduced. Even though it seems that both treatments were similar, those bee colonies that received L. johnsonii CRL1647 every 15 days became so strong that they swarmed.

  17. Environmental factors shaping cultured free-living amoebae and their associated bacterial community within drinking water network.

    PubMed

    Delafont, Vincent; Bouchon, Didier; Héchard, Yann; Moulin, Laurent

    2016-09-01

    Free-living amoebae (FLA) constitute an important part of eukaryotic populations colonising drinking water networks. However, little is known about the factors influencing their ecology in such environments. Because of their status as reservoir of potentially pathogenic bacteria, understanding environmental factors impacting FLA populations and their associated bacterial community is crucial. Through sampling of a large drinking water network, the diversity of cultivable FLA and their bacterial community were investigated by an amplicon sequencing approach, and their correlation with physicochemical parameters was studied. While FLA ubiquitously colonised the water network all year long, significant changes in population composition were observed. These changes were partially explained by several environmental parameters, namely water origin, temperature, pH and chlorine concentration. The characterisation of FLA associated bacterial community reflected a diverse but rather stable consortium composed of nearly 1400 OTUs. The definition of a core community highlighted the predominance of only few genera, majorly dominated by Pseudomonas and Stenotrophomonas. Co-occurrence analysis also showed significant patterns of FLA-bacteria association, and allowed uncovering potentially new FLA - bacteria interactions. From our knowledge, this study is the first that combines a large sampling scheme with high-throughput identification of FLA together with associated bacteria, along with their influencing environmental parameters. Our results demonstrate the importance of physicochemical parameters in the ecology of FLA and their bacterial community in water networks.

  18. Culture free DGGE and cloning based monitoring of changes in bacterial communities of salad due to processing.

    PubMed

    Handschur, M; Pinar, G; Gallist, B; Lubitz, W; Haslberger, A G

    2005-11-01

    To assess the possibilities of a culture-independent monitoring of bacterial communities in the food chain, samples of salad from farming sites as well as corresponding, processed products in stores were analysed. The bacterial DNA was extracted using a modified soil extraction protocol. Amplification of 16S rDNA was carried out using primers specific for eubacteria and enterobacteriaceae. Fingerprints of 200/370 bp respectively were obtained by denaturing gradient gel electrophoresis (DGGE) analysis following PCR and nested PCR amplification. In parallel to DGGE analysis, clone libraries containing PCR fragments of the ribosomal gene were constructed and clones were screened by DGGE. DGGE analysis indicated a high diversity of bacterial communities in salad samples. Fingerprints indicated clearly reduced diversity of bacterial communities in processed samples from markets compared to field-grown salads. Surprisingly, primers pointed out in literature as specific for enterobacteriaceae did amplify pseudomonadeceae as well. Therefore, the more specific primers fD2 and rP1 were used subsequently in this study to amplify specific members of the family enterobacteriaceae. A total of 11 different 16S rDNA sequences were obtained and subjected to sequencing and phylogenetic affiliation. Sequences derived from the eubacterial clone library from organically farmed salad were affiliated to the family microbacteriaceae and pseudomonadaceae. In addition, a potential new genus within the family of enterobacteriaceae was detected. Furthermore, a sequence showing 98.9% similarity to Pseudomonas libaniensis (fluorescence subgroup) was found in a processed salad sample but not in the corresponding field samples. This species is generally known as an opportunistic pathogen. Whereas molecular based monitoring of bacterial communities in food still may need more experience and standardisation to detect specific bacteria present, the monitoring strategy presented in this paper

  19. Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus

    PubMed Central

    Su, Xiao-Mei; Liu, Yin-Dong; Hashmi, Muhammad Zaffar; Ding, Lin-Xian; Shen, Chao-Feng

    2015-01-01

    Biphenyl (BP)-degrading bacteria were identified to degrade various polychlorinated BP (PCB) congers in long-term PCB-contaminated sites. Exploring BP-degrading capability of potentially useful bacteria was performed for enhancing PCB bioremediation. In the present study, the bacterial composition of the PCB-contaminated sediment sample was first investigated. Then extracellular organic matter (EOM) from Micrococcus luteus was used to enhance BP biodegradation. The effect of the EOM on the composition of bacterial community was investigated by combining with culture-dependent and culture-independent methods. The obtained results indicate that Proteobacteria and Actinobacteria were predominant community in the PCB-contaminated sediment. EOM from M. luteus could stimulate the activity of some potentially difficult-to-culture BP degraders, which contribute to significant enhancement of BP biodegradation. The potentially difficult-to-culture bacteria in response to EOM addition were mainly Rhodococcus and Pseudomonas belonging to Gammaproteobacteria and Actinobacteria respectively. This study provides new insights into exploration of functional difficult-to-culture bacteria with EOM addition and points out broader BP/PCB degrading, which could be employed for enhancing PCB-bioremediation processes. PMID:25675850

  20. Pentachlorophenol degradation: a pure bacterial culture and an epilithic microbial consortium.

    PubMed Central

    Brown, E J; Pignatello, J J; Martinson, M M; Crawford, R L

    1986-01-01

    The steady-state growth of a Flavobacterium strain known to utilize pentachlorophenol (PCP) was examined when cellobiose and PCP simultaneously limited its growth rate in continuous culture. A concentration of 600 mg of PCP per liter in influent medium could be continuously degraded without affecting steady-state growth. We measured specific rates of PCP carbon degradation as high as 0.15 +/- 0.01 g (dry weight) of C per h at a growth rate of 0.045 h-1. Comparable specific rates of PCP degradation were obtained and maintained by PCP-adapted, natural consortia of epilithic microorganisms. The consortium results suggest that a fixed-film bioreactor containing a PCP-adapted natural microbial population could be used to treat PCP-contaminated water. PMID:3729408

  1. Pentachlorophenol degradation: a pure bacterial culture and an epilithic microbial consortium

    SciTech Connect

    Brown, E.J.; Pignatello, J.J.; Martinson, M.M.; Crawford, R.L.

    1986-07-01

    The steady-state growth of a Flavobacterium strain known to utilize pentachlorophenol (PCP) was examined when cellobiose and PCP simultaneously limited its growth rate in continuous culture. A concentration of 600 mg of PCP per liter in influent medium could be continuously degraded without affecting steady-state growth. We measured specific rates of PCP carbon degradation as high as 0.15 +/- 0.01 g (dry weight) of C per h at a growth rate of 0.045 h-1. Comparable specific rates of PCP degradation were obtained and maintained by PCP-adapted, natural consortia of epilithic microorganisms. The consortium results suggest that a fixed-film bioreactor containing a PCP-adapted natural microbial population could be used to treat PCP-contaminated water.

  2. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature.

    PubMed

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N; Golyshina, Olga V; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I; Golyshin, Peter N; Yakimov, Michail M; Daffonchio, Daniele; Ferrer, Manuel

    2015-06-29

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.

  3. Linkage disequilibrium in wild and cultured populations of Pacific oyster ( Crassostrea gigas)

    NASA Astrophysics Data System (ADS)

    Guo, Xiang; Li, Qi; Kong, Lingfeng; Yu, Hong

    2016-04-01

    Linkage disequilibrium (LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping. The feasibility and efficacy of association studies are strongly dependent on the extent of LD which determines the number and density of markers in the studied population, as well as the experimental design for an association analysis. In this study, we first characterized the extent of LD in a wild population and a cultured mass-selected line of Pacific oyster ( Crassostrea gigas). A total of 88 wild and 96 cultured individuals were selected to assess the level of genome-wide LD with 53 microsatellites, respectively. For syntenic marker pairs, no significant association was observed in the wild population; however, three significant associations occurred in the cultured population, and the significant LD extended up to 12.7 cM, indicating that strong artificial selection is a key force for substantial increase of genome-wide LD in cultured population. The difference of LD between wild and cultured populations showed that association studies in Pacific oyster can be achieved with reasonable marker densities at a relatively low cost by choosing an association mapping population. Furthermore, the frequent occurrence of LD between non-syntenic loci and rare alleles encourages the joint application of linkage analysis and LD mapping when mapping genes in oyster. The information on the linkage disequilibrium in the cultured population is useful for future association mapping in oyster.

  4. Monitoring Bacterial Communities in Raw Milk and Cheese by Culture-Dependent and -Independent 16S rRNA Gene-Based Analyses▿

    PubMed Central

    Delbès, Céline; Ali-Mandjee, Leila; Montel, Marie-Christine

    2007-01-01

    The diversity and dynamics of bacterial populations in Saint-Nectaire, a raw-milk, semihard cheese, were investigated using a dual culture-dependent and direct molecular approach combining single-strand conformation polymorphism (SSCP) fingerprinting and sequencing of 16S rRNA genes. The dominant clones, among 125 16S rRNA genes isolated from milk, belonged to members of the Firmicutes (58% of the total clones) affiliated mainly with the orders Clostridiales and the Lactobacillales, followed by the phyla Proteobacteria (21.6%), Actinobacteria (16.8%), and Bacteroidetes (4%). Sequencing the 16S rRNA genes of 126 milk isolates collected from four culture media revealed the presence of 36 different species showing a wider diversity in the Gammaproteobacteria phylum and Staphylococcus genus than that found among clones. In cheese, a total of 21 species were obtained from 170 isolates, with dominant species belonging to the Lactobacillales and subdominant species affiliated with the Actinobacteria, Bacteroidetes (Chryseobacterium sp.), or Gammaproteobacteria (Stenotrophomonas sp.). Fingerprinting DNA isolated from milk by SSCP analysis yielded complex patterns, whereas analyzing DNA isolated from cheese resulted in patterns composed of a single peak which corresponded to that of lactic acid bacteria. SSCP fingerprinting of mixtures of all colonies harvested from plate count agar supplemented with crystal violet and vancomycin showed good potential for monitoring the subdominant Proteobacteria and Bacteroidetes (Flavobacteria) organisms in milk and cheese. Likewise, analyzing culturable subcommunities from cheese-ripening bacterial medium permitted assessment of the diversity of halotolerant Actinobacteria and Staphylococcus organisms. Direct and culture-dependent approaches produced complementary information, thus generating a more accurate view of milk and cheese microbial ecology. PMID:17259356

  5. Quantitative and qualitative analyses of the bacterial microbiota of tilapia (Oreochromis niloticus) cultured in earthen ponds in the Philippines.

    PubMed

    Pakingking, Rolando; Palma, Peter; Usero, Roselyn

    2015-02-01

    The quantity and composition of the bacterial microbiota in the rearing water, sediment, gills and intestines of tilapia Oreochromis niloticus collected every 2 weeks from Day 30 to Day 120 after stocking for grow-out culture in 6 earthen brackish water ponds in the Philippines were examined. The total heterotrophic aerobic bacterial counts obtained in the water, sediment, gills and intestines of tilapia ranged from 10(3) to 10(4) c.f.u. ml(-1), 10(3)-10(5), 10(5)-10(7) and 10(4)-10(7) c.f.u. g(-1), respectively. In terms of composition, a total of 20 bacterial genera and 31 species were identified with the preponderance of gram-negative bacteria constituting 84 % of all bacterial isolates examined. Aeromonas hydrophila, Bacillus spp., Plesiomonas shigelloides, Shewanella putrefaciens, Pseudomonas fluorescens, Staphylococcus spp. and Vibrio cholerae were the dominant bacteria identified in the gills and intestine of tilapia. These bacteria also dominated in the pond sediment and rearing water, except for the nil isolation of S. putrefaciens and V. cholerae in the water samples examined, indicating that resident bacteria in the pond water and sediment congruently typify the composition of bacterial microbiota in the gills and intestine of tilapia which under stressful conditions may propel the ascendance of disease epizootics.

  6. Fitness and proteome changes accompanying the development of erythromycin resistance in a population of Escherichia coli grown in continuous culture.

    PubMed

    Petráčková, Denisa; Janeček, Jiří; Bezoušková, Silvia; Kalachová, Ladislava; Techniková, Zuzana; Buriánková, Karolína; Halada, Petr; Haladová, Kateřina; Weiser, Jaroslav

    2013-10-01

    We studied the impact of a sublethal concentration of erythromycin on the fitness and proteome of a continuously cultivated population of Escherichia coli. The development of resistance to erythromycin in the population was followed over time by the gradient plate method and minimum inhibitory concentration (MIC) measurements. We measured the growth rate, standardized efficiency of synthesis of radiolabeled proteins, and translation accuracy of the system. The proteome changes were followed over time in two parallel experiments that differed in the presence or absence of erythromycin. A comparison of the proteomes at each time point (43, 68, and 103 h) revealed a group of unique proteins differing in expression. From all 35 proteins differing throughout the cultivation, only three were common to more than one time point. In the final population, a significant proportion of upregulated proteins was localized to the outer or inner cytoplasmic membranes or to the periplasmic space. In a population growing for more than 100 generations in the presence of antibiotic, erythromycin-resistant bacterial clones with improved fitness in comparison to early resistant culture predominated. This phenomenon was accompanied by distinct changes in protein expression during a stepwise, population-based development of erythromycin resistance.

  7. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus

    PubMed Central

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-01-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts. PMID:25750710

  8. Influence of zinc on bacterial populations and their proteolytic enzyme activities in freshwater environments: a cross-site comparison.

    PubMed

    Rasmussen, Lauren; Olapade, Ola A

    2016-04-01

    Temporal responses of indigenous bacterial populations and proteolytic enzyme (i.e., aminopeptidase) activities in the bacterioplankton assemblages from 3 separate freshwater environments were examined after exposure to various zinc (Zn) concentrations under controlled microcosm conditions. Zn concentrations (ranging from 0 to 10 μmol/L) were added to water samples collected from the Kalamazoo River, Rice Creek, and Huron River and examined for bacterial abundance and aminopeptidase activities at various time intervals over a 48 h incubation period in the dark. The results showed that the Zn concentrations did not significantly influence total bacterial counts directly; however, aminopeptidase activities varied significantly to increasing zinc treatments over time. Also, analysis of variance and linear regression analyses revealed significant positive relationships between bacterial numbers and their hydrolytic enzyme activities, suggesting that both probably co-vary with increasing Zn concentrations in aquatic systems. The results from this study serve as additional evidence of the ecological role of Zn as an extracellular peptidase cofactor on the dynamics of bacterial assemblages in aquatic environments.

  9. A screening algorithm for diagnosing bacterial gastroenteritis by real-time PCR in combination with guided culture.

    PubMed

    Van Lint, P; De Witte, E; Ursi, J P; Van Herendael, B; Van Schaeren, J

    2016-06-01

    We have introduced a real-time PCR for the simultaneous detection of Campylobacter jejuni, Salmonella spp., Shigella spp./enteroinvasive Escherichia coli and Yersinia enterocolitica in fecal samples in our routine laboratory. This new approach showed consistent results, with minimal inter-sample variation. When compared to conventional culture, the hands-on time decreased by 13 h/wk, and the median turnaround time drastically shortened from 73 to 29 h (P < .0001). Moreover, the detection rate of the targeted pathogens seemed to increase: the positivity rate registered over a twelve month period increased from 4.98% when using bacterial culture, compared to 8.56% when using real-time PCR (P < .0001). For antimicrobial susceptibility testing, samples that are found to be PCR positive are additionally cultured after the PCR result is known. Using this algorithm, we got a positive culture for 71.0% of the PCR positive samples. The samples missed by guided culture had significantly higher quantification cycle (Cq) values compared to the samples picked up by guided culture (P = .0003). Finally; we also tested the effect of extended sample storage on the performance of guided culture. Storage time prior to inoculation did have an effect on the positivity rate of culture; interestingly, these effects were clearly species-dependent.

  10. Structure and Origin of Xanthomonas arboricola pv. pruni Populations Causing Bacterial Spot of Stone Fruit Trees in Western Europe.

    PubMed

    Boudon, Sylvain; Manceau, Charles; Nottéghem, Jean-Loup

    2005-09-01

    ABSTRACT Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on stone fruit, was found in 1995 in several orchards in southeastern France. We studied population genetics of this emerging pathogen in comparison with populations from the United States, where the disease was first described, and from Italy, where the disease has occurred since 1920. Four housekeeping genes (atpD, dnaK, efp, and glnA) and the intergenic transcribed spacer region were sequenced from a total of 3.9 kb of sequences, and fluorescent amplified fragment length polymorphism (FAFLP) analysis was performed. A collection of 64 X. arboricola pv. pruni strains, including 23 strains from France, was analyzed. The X. arboricola pv. pruni population had a low diversity because no sequence polymorphisms were observed. Population diversity revealed by FAFLP was lower for the West European population than for the American population. The same bacterial genotype was detected from five countries on three continents, a geographic distribution that can be explained by human-aided migration of bacteria. Our data support the hypothesis that the pathogen originated in the United States and subsequently has been disseminated to other stone-fruit-growing regions of the world. In France, emergence of this disease was due to a recent introduction of the most prevalent genotype of the bacterium found worldwide.

  11. The role of indigenous bacterial and fungal soil populations in the biodegradation of crude oil in a desert soil.

    PubMed

    Embar, Keren; Forgacs, Chaim; Sivan, Alex

    2006-08-01

    The biodegradation capacity of indigenous microbial populations was examined in a desert soil contaminated with crude oil. To evaluate biodegradation, soil samples supplemented with 5, 10 or 20% (w/w) of crude oil were incubated for 90 days at 30 degrees C. The effect of augmentation of the soil with vermiculite (50% v/v) as a bulking agent providing increased surface/volume ratio and improved soil aeration was also tested. Maximal biodegradation (91%) was obtained in soil containing the highest concentration of crude oil (20%) and supplemented with vermiculite; only 74% of the oil was degraded in samples containing the same level of crude oil but lacking vermiculite. Gas chromatograms of distilled fractions of crude oil extracted from the soil before and after incubation demonstrated that most of the light and part of the intermediate weight fractions initially present in the oil extracts could not be detected after incubation. Monitoring of microbial population densities revealed an initial decline in bacterial viable counts after exposure to oil, presumably as a result of the crude oil's toxicity. This decline was followed by a steep recovery in microbial population density, then by a moderate increase that persisted until the end of incubation. By contrast, the inhibitory effect of crude oil on the fungal population was minimal. Furthermore, the overall increased growth response of the fungal population, at all three levels of contamination, was about one order of magnitude higher than that of the bacterial population.

  12. On the number of independent cultural traits carried by individuals and populations.

    PubMed

    Lehmann, Laurent; Aoki, Kenichi; Feldman, Marcus W

    2011-02-12

    In species subject to individual and social learning, each individual is likely to express a certain number of different cultural traits acquired during its lifetime. If the process of trait innovation and transmission reaches a steady state in the population, the number of different cultural traits carried by an individual converges to some stationary distribution. We call this the trait-number distribution. In this paper, we derive the trait-number distributions for both individuals and populations when cultural traits are independent of each other. Our results suggest that as the number of cultural traits becomes large, the trait-number distributions approach Poisson distributions so that their means characterize cultural diversity in the population. We then analyse how the mean trait number varies at both the individual and population levels as a function of various demographic features, such as population size and subdivision, and social learning rules, such as conformism and anti-conformism. Diversity at the individual and population levels, as well as at the level of cultural homogeneity within groups, depends critically on the details of population demography and the individual and social learning rules.

  13. Culture-independent bacterial community profiling of carbon dioxide treated raw milk.

    PubMed

    Lo, Raquel; Turner, Mark S; Weeks, Mike; Bansal, Nidhi

    2016-09-16

    Due to technical simplicity and strong inhibition against the growth of psychrotrophic bacteria in milk, CO2 treatment has emerged as an attractive processing aid to increase the storage time of raw milk before downstream processing. However, it is yet to be adopted by the industry. In order to further explore the suitability of CO2 treatment for raw milk processing, the bacterial populations of carbonated raw milk collected locally from five different sources in Australia were analysed with next-generation sequencing. Growth inhibition by CO2 was confirmed, with spoilage delayed by at least 7days compared with non-carbonated controls. All non-carbonated controls were spoiled by Gammaproteobacteria, namely Pseudomonas fluorescens group bacteria, Serratia and Erwinia. Two out of the five carbonated samples shared the same spoilage bacteria as their corresponding controls. The rest of the three carbonated samples were spoiled by the lactic acid bacterium (LAB) Leuconostoc. This is consistent with higher tolerance of LAB towards CO2 and selection of LAB in meat products stored in CO2-enriched modified atmosphere packaging. No harmful bacteria were found to be selected by CO2. LAB are generally regarded as safe (GRAS), thus the selection for Leuconostoc by CO2 in some of the samples poses no safety concern. In addition, we have confirmed previous findings that 454 pyrosequencing and Illumina sequencing of 16S rRNA gene amplicons from the same sample yield highly similar results. This supports comparison of results obtained with the two different sequencing platforms, which may be necessary considering the imminent discontinuation of 454 pyrosequencing.

  14. [The influence of solcoseryl on population and cellular parameters of HeLa and RD cultures].

    PubMed

    Magakian, Iu A; Karalian, Z A; Karalova, E M; Abroian, L O; Akopian, L A; Gasparian, M G; Dzhagatspanian, N G; Semerdzhian, Z B; Ter-Pogosian, Z R

    2010-01-01

    Changes of population and cellular parameters of HeLa and RD cultures after introducing of solcoseryl in culture medium were studied by methods of scanning cytophotometry and cytomorphometry. Monolayer density, proliferation activity, the number of dead cells in a monolayer, the number of nucleoli in nuclei and distribution of cells in the populations by this parameter, RNA and DNA masses in nuclei and nucleoli, total volumes and surface areas of the nuclei and nucleoli were determined. It has been shown that solcoseryl differently affects the cultures both on population and on cellular levels of their organization. The results of multi-parametric analysis of the influence of solseryl on the cultures allow considering it as a biologically active compound with the features typical for cell and cell population growth regulating factors.

  15. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident.

    PubMed

    Kasai, Y; Kishira, H; Syutsubo, K; Harayama, S

    2001-04-01

    In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, alpha-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10(5) to 1.6 x 10(6) bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation.

  16. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations.

    PubMed

    Shea, Patrick R; Beres, Stephen B; Flores, Anthony R; Ewbank, Amy L; Gonzalez-Lugo, Javier H; Martagon-Rosado, Alexandro J; Martinez-Gutierrez, Juan C; Rehman, Hina A; Serrano-Gonzalez, Monica; Fittipaldi, Nahuel; Ayers, Stephen D; Webb, Paul; Willey, Barbara M; Low, Donald E; Musser, James M

    2011-03-22

    Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is a human-adapted bacterium that causes a range of infections. Much effort has been expended to dissect the molecular basis of invasive (sterile-site) infections, but little is known about the genomes of strains causing pharyngitis (streptococcal "sore throat"). Additionally, there is essentially nothing known about the genetic relationships between populations of invasive and pharyngitis strains. In particular, it is unclear if invasive strains represent a distinct genetic subpopulation of strains that cause pharyngitis. We compared the genomes of 86 serotype M3 GAS pharyngitis strains with those of 215 invasive M3 strains from the same geographical location. The pharyngitis and invasive groups were highly related to each other and had virtually identical phylogenetic structures, indicating they belong to the same genetic pool. Despite the overall high degree of genetic similarity, we discovered that strains from different host environments (i.e., throat, normally sterile sites) have distinct patterns of diversifying selection at the nucleotide level. In particular, the pattern of polymorphisms in the hyaluronic acid capsule synthesis operon was especially different between the two strain populations. This finding was mirrored by data obtained from full-genome analysis of strains sequentially cultured from nonhuman primates. Our results answer the long-standing question of the genetic relationship between GAS pharyngitis and invasive strains. The data provide previously undescribed information about the evolutionary history of pathogenic microbes that cause disease in different anatomical sites.

  17. Escape from the competence state in Streptococcus mutans is governed by the bacterial population density.

    PubMed

    Dufour, D; Villemin, C; Perry, J A; Lévesque, C M

    2016-12-01

    Horizontal gene transfer through natural DNA transformation is an important evolutionary mechanism among bacteria. Transformation requires that the bacteria are physiologically competent to take and incorporate free DNA directly from the environment. Although natural genetic transformation is a remarkable feature of many naturally competent bacteria, the process is energetically expensive for the cells. Consequently, a tight control of the competence state is necessary. The objective of the present work was to help decipher the molecular mechanisms regulating the escape from the competence state in Streptococcus mutans, the principal etiological agent responsible for tooth decay in humans. Our results showed that the cessation of competence in S. mutans was abrupt, and did not involve the accumulation of a competence inhibitor nor the depletion of a competence activator in the extracellular environment. The competence state was repressed at high cell population density via concomitant repression of sigX gene encoding the master regulator of the competence regulon. Co-culture experiments performed with oral and non-oral bacteria showed that S. mutans assesses its own population density and also the microbial density of its surroundings to regulate its competence escape. Interestingly, neither the intra-species and extra-species quorum-sensing systems nor the other 13 two-component regulatory systems identified in S. mutans were involved in the cell-density-dependent escape of the competence state. Altogether, our results suggest a complex mechanism regulating the competence shut-off involving cell-density-dependent repression of sigX through an as yet undefined system, and possibly SigX protein stability.

  18. Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities.

    PubMed

    Martínez, M E; Ranilla, M J; Tejido, M L; Saro, C; Carro, M D

    2010-08-01

    Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of dietary characteristics on microbial populations and bacterial diversity. The purpose of the study was to assess how closely fermenters can mimic the differences between diets found in vivo. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 (high forage; HF) or 30:70 (high concentrate; HC) with either alfalfa hay (A) or grass hay (G) as the forage. Total bacterial numbers were greater in the rumen of sheep fed HF diets compared with those fed HC diets, whereas the opposite was found in fermenters. The numbers of cellulolytic bacteria were not affected by F:C ratio in any fermentation system, but cellulolytic numbers were 2.7 and 1.8 times greater in sheep than in fermenters for HF and HC diets, respectively. Neither total bacterial nor cellulolytic numbers were affected by the type of forage in sheep or fermenters. Decreasing F:C ratio increased total protozoa and Entodiniae numbers in sheep by about 29 and 25%, respectively, but it had no effect in fermenters. Isotrichidae and Ophryoscolecinae numbers in sheep were not affected by changing F:C ratio, but both disappeared completely from fermenters fed HC diets. Total protozoa and Entodiniae numbers were greater in sheep fed A diets than in those fed G diets, whereas the opposite was found in fermenters. Results indicate that under the conditions of the present study, protozoa population in Rusitec fermenters was not representative of that in the rumen of sheep fed the same diets. In addition, protozoa numbers in fermenters were 121 and 226 times lower than those in the sheep rumen for HF and HC diets, respectively. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the diversity of liquid- and solid-associated bacteria in both systems. A total of 170 peaks were detected in the automated ribosomal intergenic spacer analysis

  19. Universal Probe Library based real-time PCR for rapid detection of bacterial pathogens from positive blood culture bottles.

    PubMed

    Zhu, Lingxiang; Shen, Ding-Xia; Zhou, Qiming; Liu, Chao-Jun; Li, Zexia; Fang, Xiangdong; Li, Quan-Zhen

    2014-03-01

    A set of real-time PCR based assays using the locked nucleic acid probes from Roche Universal ProbeLibrary were developed for rapid detection of eight bacterial species from positive blood culture bottles. Four duplex real-time PCR reactions targeting to one Gram-positive bacterium and one Gram-negative bacterium were optimized for species identification according to Gram stain results. We also included mecA-specific primers and probes in the assays to indicate the presence of methicillin resistance in the bacterial species. The analytical sensitivity was in the range of 1-10 CFU per PCR reaction mixture. The specificity and cross reactivity of the assay was validated by 28 ATCC reference strains and 77 negative blood culture specimens. No cross-reactivity was observed in these samples thus demonstrating 100 % specificity. 72 previously characterized clinical isolates were tested by the real-time PCR assay and validated the accuracy and feasibility of the real-time PCR assay. Furthermore, 55 positive blood culture samples were tested using real-time PCR and 50 (90.9 %) of them were identified as the same species as judged by biochemical analysis. In total, real-time PCR showed 98.2 % consistent to that of traditional methods. Real-time PCR can be used as a supplement for early detection of the frequently-occurred pathogens from the positive blood cultures.

  20. Investigation of the biotransformation of pentachlorophenol and pulp paper mill effluent decolorisation by the bacterial strains in a mixed culture.

    PubMed

    Singh, Shail; Chandra, R; Patel, D K; Reddy, M M K; Rai, Vibhuti

    2008-09-01

    Mixed culture of two bacterial strains Bacillus sp. and Serratia marcescens showed potential pentachlorophenol (PCP) degradation and decolorisation of pulp paper mill effluent. The physico-chemical quality of pulp paper mill effluent has been analyzed after 168 h incubation period degraded by mixed culture. The study revealed that it has decreased high load of BOD, COD, TS, TDS, TSS, sulphate, phosphate, total nitrogen, total phenols, metals and different salts (i.e. chloride, sodium, nitrate, potassium) at 168 h incubation period. PCP degradation in pulp paper mill effluent was confirmed by HPLC analysis. Mixed culture was found to degrade PCP up to (94%) present in pulp paper mill effluent with 1% glucose and 0.5% peptone (w/v) at 30+/-1 degrees C, pH 8.0+/-0.2 at 120 rpm in 168 h incubation period. The simultaneous release of chloride ion up to 1,200 mg/l at 168 h emphasized the bacterial dechlorination in the medium. The pulp paper mill effluent degradation was also supported by decline in pH, AOX (absorbable organic halides), color, D.O., BOD, COD and PCP. The analysis of pulp paper mill effluent degradation products by GC-MS analysis revealed the formation of low molecular weight compound like 2-chlorophenol (RT=3.8 min) and tetrachlorohydroquinone (RT=11.86 min) from PCP extracted degraded sample. Further, mixed culture may be used for bioremediation of PCP containing pulp paper mill waste in the environment.

  1. Bovine whole-blood culture as a tool for the measurement of endotoxin activities in Gram-negative bacterial vaccines.

    PubMed

    Imamura, Saiki; Nakamizo, Mari; Kawanishi, Michiko; Nakajima, Nao; Yamamoto, Kinya; Uchiyama, Mariko; Hirano, Fumiya; Nagai, Hidetaka; Kijima, Mayumi; Ikebuchi, Ryoyo; Mekata, Hirohisa; Murata, Shiro; Konnai, Satoru; Ohashi, Kazuhiko

    2013-05-15

    In order to analyze bovine immune reactions against the Gram-negative bacterial vaccine, bovine whole-blood culture was used to investigate the pro-inflammatory cytokine responses stimulated with lipopolysaccharides (LPS) extracted from Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, and Klebsiella pneumoniae. We also examined the interaction between LPS and aluminum hydroxide gel for endotoxin activity and pro-inflammatory cytokine responses of whole bovine blood. Alteration in the mRNA concentrations of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-10 in whole-blood culture at 4h after stimulation with different doses of LPS was observed and determined by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The mRNA concentrations of TNF-α and IL-1β changed in a dose-dependent manner and differed depending on the type of LPS. Limulus test revealed that endotoxin activity was remarkably reduced when aluminum hydroxide gel was added to LPS. In contrast, the mRNA concentration of TNF-α in whole bovine blood was enhanced by LPS mixed with aluminum hydroxide gel. These results suggest that bovine whole-blood culture can be utilized to detect endotoxin activity of Gram-negative bacterial vaccines. In addition, whole-blood culture offers several advantages, such as ease of performance, few preparation artifacts, and a physiological cell environment, for investigating bovine immune response compared with the Limulus test.

  2. Comparison of Two Bacterial Transport Media for Culture of Tonsilar Swabs from Bighorn Sheep ( Ovis canadensis ) and Mountain Goats ( Oreamnos americanus ).

    PubMed

    Roug, Annette; Diaz-Campos, Dubraska; Teitzel, Charlene; Besser, Thomas E

    2017-01-01

    Duplicate tonsilar swabs were collected from 77 bighorn sheep ( Ovis canadensis ) and 19 mountain goats ( Oreamnos americanus ) in Utah. Swabs were refrigerated in bacterial transport medium or frozen in cryopreservation medium prior to bacteriologic culture. The cryopreservation medium yielded comparable or superior bacterial growth while permitting more flexibility in specimen shipment to the laboratory.

  3. Bacterial meningitis in diabetes patients: a population-based prospective study

    PubMed Central

    van Veen, Kiril E. B.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2016-01-01

    Diabetes mellitus is associated with increased infection rates. We studied clinical features and outcome of community-acquired bacterial meningitis in diabetes patients. Patients were selected from a nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 2006 to October 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were prospectively collected. A total of 183 of 1447 episodes (13%) occurred in diabetes patients. The incidence of bacterial meningitis in diabetes patients was 3.15 per 100,000 patients per year and the risk of acquiring bacterial meningitis was 2.2-fold higher for diabetes patients. S. pneumoniae was the causative organism in 139 of 183 episodes (76%) and L. monocytogenes in 11 of 183 episodes (6%). Outcome was unfavourable in 82 of 183 episodes (45%) and in 43 of 183 episodes (23%) the patient died. Diabetes was associated with death with an odds ratio of 1.63 (95% CI 1.12–2.37, P = 0.011), which remained after adjusting for known predictors of death in a multivariable analysis (OR 1.98 [95% CI 1.13–3.48], P = 0.017). In conclusion, diabetes is associated with a 2-fold higher risk of acquiring bacterial meningitis. Diabetes is a strong independent risk factor for death in community-acquired adult bacterial meningitis. PMID:27845429

  4. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques

    PubMed Central

    Ceuppens, Siele; Delbeke, Stefanie; De Coninck, Dieter; Boussemaere, Jolien; Boon, Nico; Uyttendaele, Mieke

    2015-01-01

    Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth. PMID:26308033

  5. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques.

    PubMed

    Ceuppens, Siele; Delbeke, Stefanie; De Coninck, Dieter; Boussemaere, Jolien; Boon, Nico; Uyttendaele, Mieke

    2015-08-21

    Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.

  6. Culturally tailored postsecondary nutrition and health education curricula for indigenous populations

    PubMed Central

    McConnell, Sarah

    2013-01-01

    Background In preparation for the initial offering of the University of Alaska Fairbanks (UAF), Interior–Aleutians Campus Rural Nutrition Services (RNS) program, a literature review was conducted to establish the need for the proposed program and to substantiate the methodology for delivering integrated, culturally tailored postsecondary education and extension to Alaska Natives and rural Alaskans. There was a striking absence of peer-reviewed journal articles describing culturally tailored postsecondary health curricula for indigenous populations. Objective To complete and discuss a current (November 2012) literature review for culturally tailored postsecondary health curricula designed and delivered for indigenous populations. Methods/Design The author conducted an expanded online search that employed multiple configurations of key terms using Google and Google Scholar, as well as pertinent sources. The author located archived reports in person and contacted authors by email. Results The expanded search produced a modest amount of additional literature for review. A disappointing number of publications describing or evaluating culturally tailored postsecondary health curricula in mainstream institutions are available. Related resources on culturally tailored extension and resources for the development and delivery of culturally tailored nutrition and health curricula were identified. Conclusions The present results demonstrate a significant absence of literature on the topic, which may or may not indicate the absence of sufficient culturally tailored postsecondary health curricula for indigenous populations. There are indications that culturally tailored postsecondary health curricula for indigenous populations have the potential to effectively address certain issues of health literacy and health disparities. PMID:23967420

  7. Population growth and allergen accumulation of Dermatophagoides pteronyssinus cultured at 20 and 25 °C.

    PubMed

    Yella, Lakshmi; Morgan, Marjorie S; Arlian, Larry G

    2011-02-01

    The house dust mites, Dermatophagoides pteronyssinus and D. farinae are cultured commercially and in research laboratories and material is harvested from these cultures to make extracts that are used for diagnosis, immunotherapy and research. Temperature and other climatic conditions can influence population growth rates, dynamics of allergen production, and the associated endotoxin, enzyme and protein levels of the mite material harvested from these cultures. Here we determined how temperature affected these parameters. Dermatophagoides pteronyssinus was cultured at 20 and 25 °C at 75% relative humidity, and at 2-week intervals the concentrations of mites, Der p 1 and Der p 2 allergens, endotoxin, and selected enzymes were determined. Mite density increased exponentially but growth rate and final population density were greater at 25 °C compared to 20 °C. The combined allergen (Der p 1 + Der p 2) concentrations accumulated in the cultures at about the same rate at both temperatures. However, individual Der p 1 and Der p 2 accumulation rates varied independently at the two temperatures. Der p 1 accumulated faster at 20 °C whereas Der p 2 accumulated faster at 25 °C. The amount of Der p 1 in whole cultures was greater than the amount of Der p 2. The concentration of allergen for washed mites harvested from the cultures was much less than for the whole cultures. Our study demonstrated that temperature is an important factor in population growth and the dynamics of allergen production in cultured mites.

  8. Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

    USGS Publications Warehouse

    Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J.P.; Ritter, Daniel J.; McIntosh, Jennifer C.; Clark, Arthur C.; Ruppert, Leslie F.; Cunningham, Alfred B.; Vinson, David S.; Orem, William H.; Fields, Matthew W.

    2016-01-01

    Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulic conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112 to 120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ13C values (−67‰ average), high alkalinity values (22 meq/kg average), relatively positive δ13C-DIC values (4‰ average), and no detectable higher chain hydrocarbons, NO3−, or SO42−. Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situbacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down

  9. Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions.

    PubMed

    Bortolini, Cristian; Patrone, Vania; Puglisi, Edoardo; Morelli, Lorenzo

    2016-11-07

    The quality of chocolate is influenced by several parameters, one of which is bacterial diversity during fermentation and drying; a crucial factor for the generation of the optimal cocoa flavor precursors. Our understanding of the bacterial populations involved in chocolate fermentation can be improved by the use of high-throughput sequencing technologies (HTS), combined with PCR amplification of the 16S rRNA subunit. Here, we have conducted a high-throughput assessment of bacterial diversity in four processed samples of cocoa beans from different geographic origins. As part of this study, we also assessed whether different DNA extraction methods could affect the quality of our data. The dynamics of microbial populations were analyzed postharvest (fermentation and sun drying) and shipment, before entry to the industrial process. A total of 691,867 high quality sequences were obtained by Illumina MiSeq sequencing of the two bacterial 16S rRNA hypervariable regions, V3 and V4, following paired-read assembly of the raw reads. Manual curation of the 16S database allowed us to assign the correct taxonomic classifications, at species level, for 83.8% of those reads. This approach revealed a limited biodiversity and population dynamics for both the lactic acid bacteria (LAB) and acetic acid bacteria (AAB), both of which are key players during the acetification and lactic acid fermentation phases. Among the LAB, the most abundant species were Lactobacillus fermentum, Enterococcus casseliflavus, Weissella paramesenteroides, and Lactobacillus plantarum/paraplantarum. Among the AAB, Acetobacter syzygii, was most abundant, then Acetobacter senegalensis and Acetobacter pasteriuanus. Our results indicate that HTS approach has the ability to provide a comprehensive view of the cocoa bean microbiota at the species level.

  10. No Evidence for a Culturable Bacterial Tetrodotoxin Producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae) and Stylochoplana sp. (Platyhelminthes: Polycladida)

    PubMed Central

    Salvitti, Lauren R.; Wood, Susanna A.; McNabb, Paul; Cary, Stephen Craig

    2015-01-01

    Tetrodotoxin (TTX) is a potent neurotoxin found in the tissues of many taxonomically diverse organisms. Its origin has been the topic of much debate, with suggestions including endogenous production, acquisition through diet, and symbiotic bacterial synthesis. Bacterial production of TTX has been reported in isolates from marine biota, but at lower than expected concentrations. In this study, 102 strains were isolated from Pleurobranchaea maculata (Opisthobranchia) and Stylochoplana sp. (Platyhelminthes). Tetrodotoxin production was tested utilizing a recently developed sensitive method to detect the C9 base of TTX via liquid chromatography—mass spectrometry. Bacterial strains were characterized by sequencing a region of the 16S ribosomal RNA gene. To account for the possibility that TTX is produced by a consortium of bacteria, a series of experiments using marine broth spiked with various P. maculata tissues were undertaken. Sixteen unique strains from P. maculata and one from Stylochoplana sp. were isolated, representing eight different genera; Pseudomonadales, Actinomycetales, Oceanospirillales, Thiotrichales, Rhodobacterales, Sphingomonadales, Bacillales, and Vibrionales. Molecular fingerprinting of bacterial communities from broth experiments showed little change over the first four days. No C9 base or TTX was detected in isolates or broth experiments (past day 0), suggesting a culturable microbial source of TTX in P. maculata and Stylochoplana sp. is unlikely. PMID:25635464

  11. Binding domains of Bacillus anthracis phage endolysins recognize cell culture age-related features on the bacterial surface.

    PubMed

    Paskaleva, Elena E; Mundra, Ruchir V; Mehta, Krunal K; Pangule, Ravindra C; Wu, Xia; Glatfelter, Willing S; Chen, Zijing; Dordick, Jonathan S; Kane, Ravi S

    2015-01-01

    Bacteriolytic enzymes often possess a C-terminal binding domain that recognizes specific motifs on the bacterial surface and a catalytic domain that cleaves covalent linkages within the cell wall peptidoglycan. PlyPH, one such lytic enzyme of bacteriophage origin, has been reported to be highly effective against Bacillus anthracis, and can kill up to 99.99% of the viable bacteria. The bactericidal activity of this enzyme, however, appears to be strongly dependent on the age of the bacterial culture. Although highly bactericidal against cells in the early exponential phase, the enzyme is substantially less effective against stationary phase cells, thus limiting its application in real-world settings. We hypothesized that the binding domain of PlyPH may differ in affinity to cells in different Bacillus growth stages and may be primarily responsible for the age-restricted activity. We therefore employed an in silico approach to identify phage lysins differing in their specificity for the bacterial cell wall. Specifically we focused our attention on Plyβ, an enzyme with improved cell wall-binding ability and age-independent bactericidal activity. Although PlyPH and Plyβ have dissimilar binding domains, their catalytic domains are highly homologous. We characterized the biocatalytic mechanism of Plyβ by identifying the specific bonds cleaved within the cell wall peptidoglycan. Our results provide an example of the diversity of phage endolysins and the opportunity for these biocatalysts to be used for broad-based protection from bacterial pathogens.

  12. No evidence for a culturable bacterial tetrodotoxin producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae) and Stylochoplana sp. (Platyhelminthes: Polycladida).

    PubMed

    Salvitti, Lauren R; Wood, Susanna A; McNabb, Paul; Cary, Stephen Craig

    2015-01-28

    Tetrodotoxin (TTX) is a potent neurotoxin found in the tissues of many taxonomically diverse organisms. Its origin has been the topic of much debate, with suggestions including endogenous production, acquisition through diet, and symbiotic bacterial synthesis. Bacterial production of TTX has been reported in isolates from marine biota, but at lower than expected concentrations. In this study, 102 strains were isolated from Pleurobranchaea maculata (Opisthobranchia) and Stylochoplana sp. (Platyhelminthes). Tetrodotoxin production was tested utilizing a recently developed sensitive method to detect the C9 base of TTX via liquid chromatography-mass spectrometry. Bacterial strains were characterized by sequencing a region of the 16S ribosomal RNA gene. To account for the possibility that TTX is produced by a consortium of bacteria, a series of experiments using marine broth spiked with various P. maculata tissues were undertaken. Sixteen unique strains from P. maculata and one from Stylochoplana sp. were isolated, representing eight different genera; Pseudomonadales, Actinomycetales, Oceanospirillales, Thiotrichales, Rhodobacterales, Sphingomonadales, Bacillales, and Vibrionales. Molecular fingerprinting of bacterial communities from broth experiments showed little change over the first four days. No C9 base or TTX was detected in isolates or broth experiments (past day 0), suggesting a culturable microbial source of TTX in P. maculata and Stylochoplana sp. is unlikely.

  13. Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.

    PubMed

    Valenzuela-Encinas, César; Neria-González, Isabel; Alcántara-Hernández, Rocio J; Estrada-Alvarado, Isabel; Zavala-Díaz de la Serna, Francisco Javier; Dendooven, Luc; Marsch, Rodolfo

    2009-07-01

    Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m(-1) and pH 7.80 (LOW soil), with EC 56 dS m(-1) and pH 10.11 (MEDIUM soil) and with EC 159 dS m(-1) and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the alpha- and gamma-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.

  14. Drastic changes in aquatic bacterial populations from the Cuatro Cienegas Basin (Mexico) in response to long-term environmental stress.

    PubMed

    Pajares, Silvia; Eguiarte, Luis E; Bonilla-Rosso, German; Souza, Valeria

    2013-12-01

    Understanding the changes of aquatic microbial community composition in response to changes in temperature and ultraviolet irradiation is relevant for predicting biogeochemical modifications in the functioning of natural microbial communities under global climate change scenarios. Herein we investigate shifts in the bacterioplankton composition in response to long-term changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with composite aquatic microbial communities from natural pools within the Cuatro Cienegas Basin (Mexican Chihuahuan desert) and were subject to different temperatures and UV conditions. 16S rRNA gene clone libraries were obtained from water samples at the mid-point (4 months) and the end of the experiment (8 months). An increase in bacterial diversity over time was found in the treatment of constant temperature and UV protection, which suggests that stable environments promote the establishment of complex and diverse bacterial community. Drastic changes in the phylogenetic bacterioplankton composition and structure were observed in response to fluctuating temperature and increasing UV radiation and temperature. Fluctuating temperature induced the largest decrease of bacterial richness during the experiment, indicating that frequent temperature changes drive the reduction in abundance of several species, most notably autotrophs. The long-term impact of these environmental stresses reduced diversity and selected for generalist aquatic bacterial populations, such as Porphyrobacter. These changes at the community level occur at an ecological time scale, suggesting that under global warming scenarios cascade effects on the food web are possible if the microbial diversity is modified.

  15. Identification of a New Marine Bacterial Strain SD8 and Optimization of Its Culture Conditions for Producing Alkaline Protease.

    PubMed

    Cui, Hongxia; Yang, Muyang; Wang, Liping; Xian, Cory J

    2015-01-01

    While much attention has been given to marine microorganisms for production of enzymes, which in general are relatively more stable and active compared to those from plants and animals, studies on alkaline protease production from marine microorganisms have been very limited. In the present study, the alkaline protease producing marine bacterial strain SD8 isolated from sea muds in the Geziwo Qinhuangdao sea area of China was characterized and its optimal culture conditions were investigated. Strain SD8 was initially classified to belong to genus Pseudomonas by morphological, physiological and biochemical characterizations, and then through 16S rDNA sequence it was identified to be likely Pseudomonas hibiscicola. In addition, the culture mediums, carbon sources and culture conditions of strain SD8 were optimized for maximum production of alkaline protease. Optimum enzyme production (236U/mL when cultured bacteria being at 0.75 mg dry weight/mL fermentation broth) was obtained when the isolate at a 3% inoculum size was grown in LB medium at 20 mL medium/100mL Erlenmeyer flask for 48h culture at 30°C with an initial of pH 7.5. This was the first report of strain Pseudomonas hibiscicola secreting alkaline protease, and the data for its optimal cultural conditions for alkaline protease production has laid a foundation for future exploration for the potential use of SD8 strain for alkaline protease production.

  16. Identification of a New Marine Bacterial Strain SD8 and Optimization of Its Culture Conditions for Producing Alkaline Protease

    PubMed Central

    Cui, Hongxia; Yang, Muyang; Wang, Liping; Xian, Cory J.

    2015-01-01

    While much attention has been given to marine microorganisms for production of enzymes, which in general are relatively more stable and active compared to those from plants and animals, studies on alkaline protease production from marine microorganisms have been very limited. In the present study, the alkaline protease producing marine bacterial strain SD8 isolated from sea muds in the Geziwo Qinhuangdao sea area of China was characterized and its optimal culture conditions were investigated. Strain SD8 was initially classified to belong to genus Pseudomonas by morphological, physiological and biochemical characterizations, and then through 16S rDNA sequence it was identified to be likely Pseudomonas hibiscicola. In addition, the culture mediums, carbon sources and culture conditions of strain SD8 were optimized for maximum production of alkaline protease. Optimum enzyme production (236U/mL when cultured bacteria being at 0.75 mg dry weight/mL fermentation broth) was obtained when the isolate at a 3% inoculum size was grown in LB medium at 20 mL medium/100mL Erlenmeyer flask for 48h culture at 30°C with an initial of pH 7.5. This was the first report of strain Pseudomonas hibiscicola secreting alkaline protease, and the data for its optimal cultural conditions for alkaline protease production has laid a foundation for future exploration for the potential use of SD8 strain for alkaline protease production. PMID:26716833

  17. Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

    PubMed Central

    2012-01-01

    Background Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-independent approaches performed in the AMD of Carnoulès (France) confirmed this low species richness. However, very little is known about the cultured bacteria in this ecosystem. The aims of the study were firstly to apply novel culture methods in order to access to the largest cultured bacterial diversity, and secondly to better define the robustness of the community for 3 important functions: As(III) oxidation, cellulose degradation and cobalamine biosynthesis. Results Despite the oligotrophic and acidic conditions found in AMDs, the newly designed media covered a large range of nutrient concentrations and a pH range from 3.5 to 9.8, in order to target also non-acidophilic bacteria. These approaches generated 49 isolates representing 19 genera belonging to 4 different phyla. Importantly, overall diversity gained 16 extra genera never detected in Carnoulès. Among the 19 genera, 3 were previously uncultured, one of them being novel in databases. This strategy increased the overall diversity in the Carnoulès sediment by 70% when compared with previous culture-independent approaches, as specific phylogenetic groups (e.g. the subclass Actinobacteridae or the order Rhizobiales) were only detected by culture. Cobalamin auxotrophy, cellulose degradation and As(III)-oxidation are 3 crucial functions in this ecosystem, and a previous meta- and proteo-genomic work attributed each function to only one taxon. Here, we demonstrate that other members of this community can also assume these functions, thus increasing the overall community robustness. Conclusions This work highlights that bacterial diversity in AMDs is much higher than previously envisaged, thus pointing out that the AMD system is functionally more robust than expected. The isolated bacteria

  18. The Driving Forces of Cultural Complexity : Neanderthals, Modern Humans, and the Question of Population Size.

    PubMed

    Fogarty, Laurel; Wakano, Joe Yuichiro; Feldman, Marcus W; Aoki, Kenichi

    2017-03-01

    The forces driving cultural accumulation in human populations, both modern and ancient, are hotly debated. Did genetic, demographic, or cognitive features of behaviorally modern humans (as opposed to, say, early modern humans or Neanderthals) allow culture to accumulate to its current, unprecedented levels of complexity? Theoretical explanations for patterns of accumulation often invoke demographic factors such as population size or density, whereas statistical analyses of variation in cultural complexity often point to the importance of environmental factors such as food stability, in determining cultural complexity. Here we use both an analytical model and an agent-based simulation model to show that a full understanding of the emergence of behavioral modernity, and the cultural evolution that has followed, depends on understanding and untangling the complex relationships among culture, genetically determined cognitive ability, and demographic history. For example, we show that a small but growing population could have a different number of cultural traits from a shrinking population with the same absolute number of individuals in some circumstances.

  19. Yeast and bacterial diversity along a transect in an acidic, As-Fe rich environment revealed by cultural approaches.

    PubMed

    Delavat, François; Lett, Marie-Claire; Lièvremont, Didier

    2013-10-01

    Acid mine drainages (AMDs) are often thought to harbour low biodiversity, yet little is known about the diversity distribution along the drainages. Using culture-dependent approaches, the microbial diversity from the Carnoulès AMD sediment was investigated for the first time along a transect showing progressive environmental stringency decrease. In total, 20 bacterial genera were detected, highlighting a higher bacterial diversity than previously thought. Moreover, this approach led to the discovery of 16 yeast species, demonstrating for the first time the presence of this important phylogenetic group in this AMD. All in all, the location of the microbes along the transect helps to better understand their distribution in a pollution gradient.

  20. In Vitro Study of the Effect of Cationic Biocides on Bacterial Population Dynamics and Susceptibility▿

    PubMed Central

    Moore, Louise E.; Ledder, Ruth G.; Gilbert, Peter; McBain, Andrew J.

    2008-01-01

    Cationic biocides (CBs) are widely used in domestic and public hygiene and to control biofouling and microbial contamination in industry. The increased use of biocides has led to concern regarding possible reductions in biocide effectiveness. Domestic drain microcosms were stabilized for 5 months and then exposed to polyhexamethylene biguanide (PHMB) at 0.1, 0.2, and 0.4g liter−1 over 6 months and characterized throughout by differential culture, together with eubacterial-specific PCR-denaturing gradient gel electrophoresis. Additionally, MICs and minimal bactericidal concentrations (MBCs) for bacteria previously isolated from a domestic drain (n = 18) and the human skin (n = 13) were determined before, during, and after escalating, sublethal exposure (14 passages) to two quaternary ammonium compounds (QAC1 and QAC2), the bisbiguanide chlorhexidine (CHX), and PHMB. Exposure of the drain microcosm to PHMB did not decrease the total viable count although significant (P < 0.01) decreases in recovery were observed for the gram-positive cocci with associated clonal expansion of pseudomonads (from ca. 0.1% of the population to ca. 10%). This clonal expansion was also manifested as elevations in bacteria that could grow in the presence of PHMB, CHX, and QAC1. Decreases in susceptibility (greater than twofold) occurred for 10/31 of the test bacteria for QAC1, 14/31 for QAC2, 10/31 for CHX, and 7/31 for PHMB. Exposure of microcosms to PHMB targeted gram-positive species and caused the clonal expansion of pseudomonads. In terms of prolonged-sublethal passage on CBs, exposure to all the biocides tested resulted in susceptibility decreases for a proportion of test bacteria, but refractory clones were not generated. PMID:18515475

  1. Comprehensive Analysis of Bacterial Flora in Postoperative Maxillary Cyst Fluid by 16S rRNA Gene and Culture Methods

    PubMed Central

    Sano, Naoto; Yamashita, Yoshio; Fukuda, Kazumasa; Taniguchi, Hatsumi; Goto, Masaaki; Miyamoto, Hiroshi

    2012-01-01

    Intracystic fluid was aseptically collected from 11 patients with postoperative maxillary cyst (POMC), and DNA was extracted from the POMC fluid. Bacterial species were identified by sequencing after cloning of approximately 580 bp of the 16S rRNA gene. Identification of pathogenic bacteria was also performed by culture methods. The phylogenetic identity was determined by sequencing 517–596 bp in each of the 1139 16S rRNA gene clones. A total of 1114 clones were classified while the remaining 25 clones were unclassified. A total of 103 bacterial species belonging to 42 genera were identified in POMC fluid samples by 16S rRNA gene analysis. Species of Prevotella (91%), Neisseria (73%), Fusobacterium (73%), Porphyromonas (73%), and Propionibacterium (73%) were found to be highly prevalent in all patients. Streptococcus mitis (64%), Fusobacterium nucleatum (55%), Propionibacterium acnes (55%), Staphylococcus capitis (55%), and Streptococcus salivarius (55%) were detected in more than 6 of the 11 patients. The results obtained by the culture method were different from those obtained by 16S rRNA gene analysis, but both approaches may be necessary for the identification of pathogens, especially of bacteria that are difficult to detect by culture methods, and the development of rational treatments for patients with POMC. PMID:22685668

  2. Enrichment and Molecular Characterization of a Bacterial Culture That Degrades Methoxy-Methyl Urea Herbicides and Their Aniline Derivatives

    PubMed Central

    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

  3. Spatial distribution of the culturable bacterial community associated with the invasive alga Caulerpa cylindracea in the Mediterranean Sea.

    PubMed

    Stabili, Loredana; Rizzo, Lucia; Pizzolante, Graziano; Alifano, Pietro; Fraschetti, Simonetta

    2017-04-01

    Understanding the mechanisms underlying the complex seaweed-bacteria associations in nature may provide information on the fitness of an invasive host. This may require the use of different approaches. In this study, we employed, for the first time, the Biolog system-Ecoplates™ to analyze the functional diversity of the culturable fraction of the bacterial assemblages associated with the surface of Caulerpa cylindracea, the invasive seaweed of the Mediterranean Sea. Seaweed samples were collected at five sites across the basin. A high similarity in the bacterial activity, expressed as Average Well Color Development (AWCD), among the study sites was observed. Culturable heterotrophic bacteria at 22 °C showed mean values ranging from 1.4 × 10(5) CFU g(-1) at Porto Cesareo (Ionian Sea, Italy) to 5.8 × 10(6) CFU g(-1) at Othonoi, Diapontine Island (Ionian Sea, Greece). The analysis of the DNA sequences on isolated bacteria demonstrated that the genera Shewanella, Marinobacter, Vibrio, Granulosicoccus and the family Rhodobacteraceae are consistently present on C. cylindracea, irrespective of its geographical origin. The present study provided new insights into the complex association between bacteria and this algal species, suggesting a specific composition and function of the associated culturable bacteria across the basin.

  4. United States Indigenous Populations and Dementia: Is There a Case for Culture-based Psychosocial Interventions?

    PubMed

    Browne, Colette V; Ka'opua, Lana Sue; Jervis, Lori L; Alboroto, Richard; Trockman, Meredith L

    2016-04-05

    Dementia is an issue of increasing importance in indigenous populations in the United States. We begin by discussing what is known about dementia prevalence and elder family caregiving in American Indian, Alaska Native, and Native Hawaiian populations. We briefly highlight examples of culture-based programming developed to address a number of chronic diseases and conditions that disproportionately affect these communities. These programs have produced positive health outcomes in American Indian, Alaska Native, and Native Hawaiian populations and may have implications for research and practice in the dementia context of culture-based interventions. Evidence-based and culture-based psychosocial programming in dementia care for indigenous populations in the United States designed by the communities they intend to serve may offer elders and families the best potential for care that is accessible, respectful, and utilized.

  5. Weight-Loss Interventions for Hispanic Populations: The Role of Culture

    PubMed Central

    Lindberg, Nangel M.; Stevens, Victor J.; Halperin, Ruben O.

    2013-01-01

    In the United States, ethnic minorities are overrepresented among the overweight and obese population, with Hispanic individuals being among the groups most at risk for obesity and obesity-related disease and disability. Most weight-loss interventions designed for the general population have been less successful with individuals from ethnic minorities and there is a pressing need to develop more effective interventions for these groups. This paper examines the importance of culture in the development of “culturally competent” weight-loss interventions for ethnic minority populations, and discusses specific culturally mediated factors that should be considered in the design and implementation of treatment interventions. While specifically focusing on Hispanic populations, we also address issues of relevance to other multiethnic societies. PMID:23533725

  6. Weight-loss interventions for Hispanic populations: the role of culture.

    PubMed

    Lindberg, Nangel M; Stevens, Victor J; Halperin, Ruben O

    2013-01-01

    In the United States, ethnic minorities are overrepresented among the overweight and obese population, with Hispanic individuals being among the groups most at risk for obesity and obesity-related disease and disability. Most weight-loss interventions designed for the general population have been less successful with individuals from ethnic minorities and there is a pressing need to develop more effective interventions for these groups. This paper examines the importance of culture in the development of "culturally competent" weight-loss interventions for ethnic minority populations, and discusses specific culturally mediated factors that should be considered in the design and implementation of treatment interventions. While specifically focusing on Hispanic populations, we also address issues of relevance to other multiethnic societies.

  7. Diversity of bacterial communities that colonize the filter units used for controlling plant pathogens in soilless cultures.

    PubMed

    Renault, David; Vallance, Jessica; Déniel, Franck; Wery, Nathalie; Godon, Jean Jacques; Barbier, Georges; Rey, Patrice

    2012-01-01

    In recent years, increasing the level of suppressiveness by the addition of antagonistic bacteria in slow filters has become a promising strategy to control plant pathogens in the recycled solutions used in soilless cultures. However, knowledge about the microflora that colonize the filtering columns is still limited. In order to get information on this issue, the present study was carried out over a 4-year period and includes filters inoculated or not with suppressive bacteria at the start of the filtering process (two or three filters were used each year). After 9 months of filtration, polymerase chain reaction (PCR)-single strand conformation polymorphism analyses point out that, for the same year of experiment, the bacterial communities from control filters were relatively similar but that they were significantly different between the bacteria-amended and control filters. To characterize the changes in bacterial communities within the filters, this microflora was studied by quantitative PCR, community-level physiological profiles, and sequencing 16SrRNA clone libraries (filters used in year 1). Quantitative PCR evidenced a denser bacterial colonization of the P-filter (amended with Pseudomonas putida strains) than control and B-filter (amended with Bacillus cereus strains). Functional analysis focused on the cultivable bacterial communities pointed out that bacteria from the control filter metabolized more carbohydrates than those from the amended filters whose trophic behaviors were more targeted towards carboxylic acids and amino acids. The bacterial communities in P- and B-filters both exhibited significantly more phylotype diversity and markedly distinct phylogenetic compositions than those in the C-filter. Although there were far fewer Proteobacteria in B- and P-filters than in the C-filter (22% and 22% rather than 69% of sequences, respectively), the percentages of Firmicutes was much higher (44% and 55% against 9%, respectively). Many Pseudomonas

  8. Effects of Fibronectin Coating on Bacterial and Osteoblast Progenitor Cells Adherence in a Co-culture Assay.

    PubMed

    Hindié, Mathilde; Wu, Dongni; Anselme, Karine; Gallet, Olivier; Di Martino, Patrick

    2016-07-06

    Bacterial adherence to the surface of implants functionalized with cell-adhesive biomolecules is a critical first step of infection development. This study was designed to determine how the immobilization of human plasmatic fibronectin (pFN) could impact bacterial and osteoblast cells interaction with the surface during concomitant exposition to the two cell-types. Calibrated suspensions of P. aeruginosa PAOI or S. aureus CIP4.83 bacteria and STRO-1(+)A osteoblast progenitor cells were mixed, co-seeded on glass coverslips coated or not with pFN and incubated at 37 °C. After 3 h of co-culture, the presence of bacteria did not modify the STRO-1(+)A cells adherence to glass. pFN coating significantly enhanced STRO-1(+)A cells, CIP4.83 and PAOI adherence to glass and bacterial interaction with STRO-1(+)A cells. Confocal laser scanning microscopy observations revealed that cells on the pFN-coated substrate exhibited a greater spreading, better organized network of cytoskeletal filaments, and an increased cellular FN expression than cells on the uncoated substrate. The use of fluorescently labeled pFN showed that adherent STRO-1(+)A cells were able to remodel and to concentrate coated pFN at the cells surface. Thus, the use of FN coating could increase the risk of bacterial adherence to the material surface, acting either directly onto the coating layer or indirectly on adherent osteoblastic cells. This may increase the infection risk in the presence of bacterial contamination.

  9. Identification of Bacterial Populations in Drinking Water Using 16S rRNA-Based Sequence Analyses

    EPA Science Inventory

    Intracellular RNA is rapidly degraded in stressed cells and is more unstable outside of the cell than DNA. As a result, RNA-based methods have been suggested to study the active microbial fraction in environmental matrices. The aim of this study was to identify bacterial populati...

  10. Polystyrene influences bacterial assemblages in Arenicola marina-populated aquatic environments in vitro.

    PubMed

    Kesy, Katharina; Oberbeckmann, Sonja; Müller, Felix; Labrenz, Matthias

    2016-12-01

    Plastic is ubiquitous in global oceans and constitutes a newly available habitat for surface-associated bacterial assemblages. Microplastics (plastic particles <5 mm) are especially susceptible to ingestion by marine organisms, as the size of these particles makes them available also to lower trophic levels. Because many marine invertebrates harbour potential pathogens in their guts, we investigated whether bacterial assemblages on polystyrene are selectively modified during their passage through the gut of the lugworm Arenicola marina and are subsequently able to develop pathogenic biofilms. We also examined whether polystyrene acts as a vector for gut biofilm assemblages after subsequent incubation of the egested particles in seawater. Our results showed that after passage through the digestive tract of A. marina, the bacterial assemblages on polystyrene particles and reference glass beads became more similar, harbouring common sediment bacteria. By contrast, only in the presence of polystyrene the potential symbiont Amphritea atlantica was enriched in the investigated biofilms, faeces, and water. Thus, especially in areas of high polystyrene contamination, this polymer may impact the bacterial composition of different habitats, with as yet unknown consequences for the respective ecosystems.

  11. Spread and transmission of bacterial pathogens in experimental populations of the nematode Caenorhabditis elegans.

    PubMed

    Diaz, S Anaid; Restif, Olivier

    2014-09-01

    Caenorhabditis elegans is frequently used as a model species for the study of bacterial virulence and innate immunity. In recent years, diverse mechanisms contributing to the nematode's immune response to bacterial infection have been discovered. Yet despite growing interest in the biochemical and molecular basis of nematode-bacterium associations, many questions remain about their ecology. Although recent studies have demonstrated that free-living nematodes could act as vectors of opportunistic pathogens in soil, the extent to which worms may contribute to the persistence and spread of these bacteria has not been quantified. We conducted a series of experiments to test whether colonization of and transmission between C. elegans nematodes could enable two opportunistic pathogens (Salmonella enterica and Pseudomonas aeruginosa) to spread on agar plates occupied by Escherichia coli. We monitored the transmission of S. enterica and P. aeruginosa from single infected nematodes to their progeny and measured bacterial loads both within worms and on the plates. In particular, we analyzed three factors affecting the dynamics of bacteria: (i) initial source of the bacteria, (ii) bacterial species, and (iii) feeding behavior of the host. Results demonstrate that worms increased the spread of bacteria through shedding and transmission. Furthermore, we found that despite P. aeruginosa's relatively high transmission rate among worms, its pathogenic effects reduced the overall number of worms colonized. This study opens new avenues to understand the role of nematodes in the epidemiology and evolution of pathogenic bacteria in the environment.

  12. Population number, viability, and taxonomic composition of the bacterial nanoforms in iron-manganic concretions

    NASA Astrophysics Data System (ADS)

    Lysak, L. V.; Kadulin, M. S.; Konova, I. A.; Lapygina, E. V.; Ivanov, A. V.; Zvyagintsev, D. G.

    2013-06-01

    It is shown for the first time that a significant part of the bacteria (up to 40%) in the iron-manganic concretions of soddy-podzolic and soddy meadow soils are represented by nanoforms; their number reaches 600-700 million cells/g. Judging from the specific luminescent coloration, the fraction of viable cells among the bacterial nanoforms is very high in the concretions and amounts up to 88-99%. For the first time, the following phyla were identified among the bacterial nanoforms in the concretions with the use of the FISH method: Alphaproteobacteria, Betaproteobacteria, Gammaproteobateria, Deltaproteobacteria, Acidobacteria, and Planctomycetes. The Gammaproteobacteria phylum predominated in the concretions from the soddy-podzolic soil, and the Deltaproteobacteria phylum predominated in the concretions from the soddy meadow soil. In the alluvial meadow soil, the Alphaproteobacteria, Betaproteobacteria, and Acidobacteria phyla were found. The significant number and portion of bacterial nanoforms in the concretions, their high vitality, and their taxonomic diversity allow us to conclude that the bacterial nanoforms play an important role in the processes taking place in the concretions.

  13. Population heterogeneity and dynamics in starter culture and lag phase adaptation of the spoilage yeast Zygosaccharomyces bailii to weak acid preservatives.

    PubMed

    Stratford, Malcolm; Steels, Hazel; Nebe-von-Caron, Gerhard; Avery, Simon V; Novodvorska, Michaela; Archer, David B

    2014-07-02

    The food spoilage yeast Zygosaccharomyces bailii shows great resistance to weak-acid preservatives, including sorbic acid (2, 4-hexadienoic acid). That extreme resistance was shown to be due to population heterogeneity, with a small sub-population of cells resistant to a variety of weak acids, probably caused by a lower internal pH reducing the uptake of all weak acids. In the present paper, it was found that resistant cells were extremely rare in exponential cultures, but increased by up to 8000-fold in stationary phase. Inoculation of media containing sorbic acid with a population of Z. bailii cells gave rise to what appeared to be a prolonged lag phase, suggesting adaptation to the conditions before the cells entered the period of exponential growth. However, the apparent lag phase caused by sorbic acid was largely due to the time required for the resistant sub-population to grow to detectable levels. The slow growth rate of the sub-population was identical to that of the final total population. The non-resistant bulk population remained viable for 3 days but had lost viability by 6 days and, during that time, there was no indication of any development of resistance in the bulk population. The sub-population growing in sorbic acid showed very high population diversity in colony size and internal pH. After removal of sorbic acid, the population rapidly reverted back to the normal, largely non-resistant, population distribution. The data presented suggest that a reevaluation of the lag phase in microbial batch culture is required, at least for the resistance of Z. bailii to sorbic acid. Furthermore, the significance of phenotypic diversity and heterogeneity in microbial populations is discussed more broadly with potential relevance to bacterial "persisters", natural selection and evolution.

  14. Culturable Aerobic and Facultative Anaerobic Intestinal Bacterial Flora of Black Cobra (Naja naja karachiensis) in Southern Pakistan

    PubMed Central

    Iqbal, Junaid; Sagheer, Mehwish; Tabassum, Nazneen; Siddiqui, Ruqaiyyah; Khan, Naveed Ahmed

    2014-01-01

    Using morphological analysis and biochemical testing, here for the first time, we determined the culturable gut bacterial flora (aerobes and facultative anaerobes) in the venomous Black Cobra (Naja naja karachiensis) from South Asia. The findings revealed that these snakes inhabit potentially pathogenic bacteria including Serratia marcescens, Pseudomonas aeruginosa, Shewanella putrefaciens, Aeromonas hydrophila, Salmonella sp., Moraxella sp., Bacillus sp., Ochrobactrum anthropi, and Providencia rettgeri. These findings are of concern, as injury from snake bite can result in wound infections and tissue necrosis leading to sepsis/necrotizing fasciitis and/or expose consumers of snake meat/medicine in the community to infections. PMID:25002979

  15. Prevalence of gastrointestinal bacterial pathogens in a population of zoo animals.

    PubMed

    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.

  16. EPS production and bioremoval of heavy metals by mixed and pure bacterial cultures isolated from Ankara Stream.

    PubMed

    Kiliç, Nur Koçberber; Kürkçü, Güliz; Kumruoğlu, Durna; Dönmez, Gönül

    2015-01-01

    This study is focused on isolation of Ni(II), Cu(II) and Cr(VI) resistant bacteria to assess their exopolysaccharide (EPS) production and related bioremoval capacities. Mixed cultures had higher heavy metal removal capacity in media with molasses (MAS) than the control cultures lacking this carbon (AS) containing 50 mg/l of heavy metal. The yields were 32%, 75.7%, and 51.1% in MAS, while the corresponding values were 29%, 55.1%, and 34.5% in AS, respectively. Purification of the strains 1, 5 and 6 present in the mixed cultures decreased the bioremoval capacities of the mixed culture samples, although these strains produced higher EPS amounts in MAS agar. Strain 5 had the highest Cu(II) (69.1%) and Cr(VI) (43.1%) removal rates at 25 mg/l initial concentration of each pollutant with EPS amounts of 0.74 g/l and 1.05 g/l, respectively. This strain was identified as Stenotrophomonas maltophilia. The presented data show that especially mixed and also pure cultures of bacterial strains isolated from Ankara Stream could be assessed as potential bioremoval agents in the treatment of Cu(II) or Cr(VI) containing wastewaters.

  17. Decolourisation of Acid Orange 7 recalcitrant auto-oxidation coloured by-products using an acclimatised mixed bacterial culture.

    PubMed

    Bay, Hui Han; Lim, Chi Kim; Kee, Thuan Chien; Ware, Ismail; Chan, Giek Far; Shahir, Shafinaz; Ibrahim, Zaharah

    2014-03-01

    This study focuses on the biodegradation of recalcitrant, coloured compounds resulting from auto-oxidation of Acid Orange 7 (AO7) in a sequential facultative anaerobic-aerobic treatment system. A novel mixed bacterial culture, BAC-ZS, consisting of Brevibacillus panacihumi strain ZB1, Lysinibacillus fusiformis strain ZB2, and Enterococcus faecalis strain ZL bacteria were isolated from environmental samples. The acclimatisation of the mixed culture was carried out in an AO7 decolourised solution. The acclimatised mixed culture showed 98 % decolourisation within 2 h of facultative anaerobic treatment using yeast extract and glucose as co-substrate. Subsequent aerobic post treatment caused auto-oxidation reaction forming dark coloured compounds that reduced the percentage decolourisation to 73 %. Interestingly, further agitations of the mixed culture in the solution over a period of 48 h significantly decolourise the coloured compounds and increased the decolourisation percentage to 90 %. Analyses of the degradation compounds using UV-visible spectrophotometer, Fourier transform infrared spectroscopy (FTIR) and high performance liquid chromatography (HPLC) showed complete degradation of recalcitrant AO7 by the novel BAC-ZS. Phytotoxicity tests using Cucumis sativus confirmed the dye solution after post aerobic treatment were less toxic compared to the parent dye. The quantitative real-time PCR revealed that E. faecalis strain ZL was the dominant strain in the acclimatised mix culture.

  18. Culturable bacterial flora associated with the dinoflagellate green Noctiluca miliaris during active and declining bloom phases in the Northern Arabian Sea.

    PubMed

    Basu, Subhajit; Deobagkar, Deepti D; Matondkar, S G Prabhu; Furtado, Irene

    2013-05-01

    A massive algal bloom of the dinoflagellate Noctiluca miliaris (green) was located in the Northern Arabian Sea by IRS-P4-2 (OCM-II) for microbiological studies, during two consecutive cruises of February-March 2009. Culturable bacterial load during bloom were ≈ 2-3-fold higher in comparison to non-bloom waters and ranged from 3.20 × 10(5) to 6.84 × 10(5) cfu ml(-1). An analysis of the dominant heterotrophs associated with Noctiluca bloom resulted in phylogenetic and a detailed metabolic characterization of 70 bacterial isolates from an overlapping active and declining bloom phase location near north-central Arabian Sea. The active phase flora was dominated by Gram-positive forms (70.59 %), a majority of which belonged to Bacillus (35.29 %) of Firmicutes. As the bloom declined, Gram-negative forms (61.11 %) emerged dominant, and these belonged to a diverse γ-proteobacterial population consisting of Shewanella (16.67 %) and equal fractions of a Cobetia-Pseudomonas-Psychrobacter-Halomonas population (36.11 %). A Unifrac-based principal coordinate analysis of partial 16S rDNA sequences showed significant differences among the active and declining phase flora and also with reported endocytic flora of Noctiluca (red). A nonparametric multidimensional scaling (NMDS) of antibiogram helped differentiation among closely related strains. The organic matter synthesized by N. miliaris appears to be quickly utilized and remineralized as seen from the high efficiency of isolates to metabolize various complex and simple C/N substrates such as carbohydrates, proteins/amino acids, lipids, sulfide production from organic matter, and solubilize phosphates. The ability of a large fraction of these strains (50-41.67 %) to further aerobically denitrify indicates their potential for nitrogen removal from these high-organic microniches of the Noctiluca bloom in the Arabian Sea, also known for high denitrification activity. The results indicate that culturable euphotic bacterial

  19. Assessment of the bacterial diversity of human colostrum and screening of staphylococcal and enterococcal populations for potential virulence factors.

    PubMed

    Jiménez, Esther; Delgado, Susana; Fernández, Leonides; García, Natalia; Albújar, Mar; Gómez, Adolfo; Rodríguez, Juan M

    2008-01-01

    In contrast to breast milk, little is known about the bacterial composition of human colostrum. The objective of this work was to analyze the bacterial diversity of colostrum obtained from healthy women and to characterize the dominant bacterial species for the presence of possible virulence factors. Samples of colostrum obtained from 36 healthy women were inoculated into different culture media. Several isolates from each medium were selected and identified. Staphylococcal and enterococcal isolates were submitted to genetic profiling. One representative of each profile was included in a genetic and phenotypic characterization scheme, including detection of potential virulence traits/genes and sensitivity to antibiotics. Staphylococcus epidermidis and Enterococcus faecalis were the dominant species, followed by Streptococcus mitis, Propionibacterium acnes and Staphylococcus lugdunensis. Among the 48 S. epidermidis isolates selected on the basis of their genetic profiles, the biofilm-related icaD gene and the mecA gene were detected in only 11 and six isolates, respectively. In parallel, 10 enterococcal isolates were also characterized and none of them contained the cylA, vanA, vanB, vanD, vanE and vanG genes. All of them were sensitive to vancomycin. There were no indications that the colostrum samples contained harmful bacteria.

  20. A comparison of culture-dependent and culture-independent techniques used to characterize bacterial communities on healthy and white plague-diseased corals of the Montastraea annularis species complex

    NASA Astrophysics Data System (ADS)

    Cook, G. M.; Rothenberger, J. P.; Sikaroodi, M.; Gillevet, P. M.; Peters, E. C.; Jonas, R. B.

    2013-06-01

    Diseases of hermatypic corals pose a global threat to coral reefs, and investigations of bacterial communities associated with healthy corals and those exhibiting signs of disease are necessary for proper diagnosis. One disease, commonly called white plague (WP), is characterized by acute tissue loss. This investigation compared the bacterial communities associated with healthy coral tissue ( N = 15), apparently healthy tissue on WP-diseased colonies ( N = 15), and WP-diseased tissues ( N = 15) from Montastraea annularis (species complex) colonies inhabiting a Bahamian reef. Aliquots of sediment ( N = 15) and water ( N = 15) were also obtained from the proximity of each coral colony sampled. Samples for culture-dependent analyses were inoculated onto one-half strength Marine Agar (½ MA) and Thiosulfate Citrate Bile Salts Sucrose Agar to quantify the culturable communities. Length heterogeneity PCR (LH-PCR) of the 16S rRNA gene characterized the bacterial operational taxonomic units (OTU) associated with lesions on corals exhibiting signs of a white plague-like disease as well as apparently healthy tissue from diseased and non-diseased conspecifics. Analysis of Similarity was conducted on the LH-PCR fingerprints, which indicated no significant difference in the composition of bacterial communities associated with apparently healthy and diseased corals. Comparisons of the 16S rRNA gene amplicons from cultured bacterial colonies (½ MA; N = 21) with all amplicons obtained from the whole coral-associated bacterial community indicated ≥39 % of coral-associated bacterial taxa could be cultured. Amplicons from these bacterial cultures matched amplicons from the whole coral-associated bacterial community that, when combined, accounted for >70 % total bacterial abundance. An OTU with the same amplicon length as Aurantimonas coralicida (313.1 bp), the reported etiological agent of WPII, was detected in relatively low abundance (<0.1 %) on all tissue types. These findings

  1. Effect of dietary supplementation of bacteriophage on performance, egg quality and caecal bacterial populations in laying hens.

    PubMed

    Kim, J H; Kim, J W; Shin, H S; Kim, M C; Lee, J H; Kim, G-B; Kil, D Y

    2015-01-01

    1. Bacteriophages (BP) have gained increasing attention as a treatment of bacterial infection for animals. However, the data pertaining to dietary application of BP for laying hens have been limited. 2. This study aimed to investigate the effect of dietary BP on laying performance, egg quality and caecal bacterial populations in laying hens. 3. The dietary BP used in this experiment was a mixture of individual BP targeting Salmonella gallinarum, Salmonella pullorum, Salmonella typhimurium, Salmonella enteritidis, Salmonella derby and Staphylococcus aureus. 4. A total of 360 Hy-Line Brown laying hens of 32 weeks of age were allotted to one of three dietary treatments with 6 replicates in a completely randomised design. The basal diet was prepared, and 0.4 or 0.8 g/kg BP mixture was supplemented to the basal diet. Diets were fed to hens for 8 weeks. 5. Laying performance and egg quality were not affected by dietary treatments. As inclusion levels of BP mixture in diets were increased, the DNA copy numbers for Salmonella spp. in the caecal contents decreased linearly, whereas the DNA copy numbers for Escherichia coli in the caecal contents increased linearly. 6. Results indicate that dietary supplementation of BP mixture decreases the target Salmonella spp. populations but increases Escherichia coli populations in the gastrointestinal tract of laying hens with little impact on laying performance and egg quality.

  2. Coevolution of adaptive technology, maladaptive culture and population size in a producer-scrounger game.

    PubMed

    Lehmann, Laurent; Feldman, Marcus W

    2009-11-07

    Technology (i.e. tools, methods of cultivation and domestication, systems of construction and appropriation, machines) has increased the vital rates of humans, and is one of the defining features of the transition from Malthusian ecological stagnation to a potentially perpetual rising population growth. Maladaptations, on the other hand, encompass behaviours, customs and practices that decrease the vital rates of individuals. Technology and maladaptations are part of the total stock of culture carried by the individuals in a population. Here, we develop a quantitative model for the coevolution of cumulative adaptive technology and maladaptive culture in a 'producer-scrounger' game, which can also usefully be interpreted as an 'individual-social' learner interaction. Producers (individual learners) are assumed to invent new adaptations and maladaptations by trial-and-error learning, insight or deduction, and they pay the cost of innovation. Scroungers (social learners) are assumed to copy or imitate (cultural transmission) both the adaptations and maladaptations generated by producers. We show that the coevolutionary dynamics of producers and scroungers in the presence of cultural transmission can have a variety of effects on population carrying capacity. From stable polymorphism, where scroungers bring an advantage to the population (increase in carrying capacity), to periodic cycling, where scroungers decrease carrying capacity, we find that selection-driven cultural innovation and transmission may send a population on the path of indefinite growth or to extinction.

  3. The cultural gap delivering health care services to Arab American populations in the United States.

    PubMed

    Aboul-Enein, Basil H; Aboul-Enein, Faisal H

    2010-01-01

    The relationship between Middle Eastern patients and populations of Arab origin with western health care professionals are by no means free of cultural misunderstandings. The relationship is often strained by mutual cultural misunderstanding as well as communicative and linguistic hardship. Even though people from the Middle East do vary racially, they do have shared values and behavior. This can include the importance of family cohesion, and interactive attitudes toward ailments and health. Some issues and concerns in providing health care could vary from attaining adequate information to communicated suggested behavioral change by a patient. Culturally and linguistically appropriate guidelines are warranted to provide an understanding of the cultural distinctiveness of Arab Eastern patients by shortening the gap between the Arab cultures with the western medical culture thus improving their healthcare needs.

  4. Resilience of the rhizosphere Pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar.

    PubMed

    Frey, Beat; Pesaro, Manuel; Rüdt, Andreas; Widmer, Franco

    2008-06-01

    We assessed the effects of phytoextraction on the dynamics of Pseudomonas spp. and ammonia-oxidizing bacterial populations in a heavy metal (HM) polluted soil. Hybrid poplars were grown in two-compartment root containers with a medium history (> 4 years) of HM pollution for 13 weeks. Bulk and poplar rhizosphere soils were analysed by denaturing gradient gel electrophoresis (DGGE) of Pseudomonas (sensu stricto) 16S rRNA and amoA gene fragments. DGGE patterns revealed that Pseudomonas and amoA-containing populations in the contaminated soils were markedly different from those in the uncontaminated soils. Pseudomonas and amoA profiles appeared to be stable over time in the bulk soils. In contrast, contaminated rhizosphere soils revealed a clear shift of populations with removal of HM becoming similar or at least shifted to the populations of the uncontaminated soils. The effect of phytoextraction was, however, not evident in the bulk samples, which still contained large amounts of HM. Cloning and sequencing of dominant DGGE bands revealed that Pseudomonas were phylogenetically related to the Pseudomonas fluorescens cluster and the amoA sequences to Nitrosospira spp. At the last sampling, major prominent band sequences from contaminated rhizosphere soils were identical to sequences obtained from uncontaminated rhizosphere soils, indicating that the populations were dominated by the same phylotypes. This study suggests that two taxonomically different populations are able to recover after the relief of HM stress by phytoextraction practices, whereas bulk microbial activities still remained depressed.

  5. Effects of petroleum mixture types on soil bacterial population dynamics associated with the biodegradation of hydrocarbons in soil environments.

    PubMed

    Hamamura, Natsuko; Ward, David M; Inskeep, William P

    2013-07-01

    Soil bacterial population dynamics were examined to assess patterns in microbial response to contamination by different petroleum mixtures with variation in n-alkane profiles or toxic constituents such as pentachlorophenol (PCP). Three soil types from distinct areas of the United States (Montana, Oregon, and Arizona) were used in controlled perturbation experiments containing crude oil, kerosene, diesel, or diesel plus PCP spiked with (14)C-hexadecane or (14)C-tridecane. After a 50-day incubation, 30-70% of added (14)C-alkanes were mineralized to (14)CO₂ in Montana and Oregon soils. In contrast, significantly lower mineralization was observed with diesel or kerosene (< 5%) compared to crude-oil treatment (~45%) in the Arizona soil. Different hydrocarbon mixtures selected both unique and common microbial populations across all three soils. Conversely, the contamination of different soils with the same mixture selected for distinct microbial populations. The most consistent genotype observed, a Rhodococcus-like population, was present in the Montana soil with all mixture types. The addition of PCP selected for PCP-tolerant alkane-degrading specialist populations. The results indicated that petroleum mixture type influenced hydrocarbon degradation rates and microbial population selection and that soil characteristics, especially organic content, could also be an important determinant of community responses to hydrocarbon perturbation.

  6. Bacterial antibiotic resistance studies using in vitro dynamic models: Population analysis vs. susceptibility testing as endpoints of mutant enrichment.

    PubMed

    Firsov, Alexander A; Strukova, Elena N; Portnoy, Yury A; Shlykova, Darya S; Zinner, Stephen H

    2015-09-01

    Emergence of bacterial antibiotic resistance is usually characterised either by population analysis or susceptibility testing. To compare these endpoints in their ability to demonstrate clear relationships with the ratio of 24-h area under the concentration-time curve (AUC24) to the minimum inhibitory concentration (MIC), enrichment of ciprofloxacin-resistant mutants of four clinical isolates of Pseudomonas aeruginosa was studied in an in vitro dynamic model that simulates mono-exponential pharmacokinetics of ciprofloxacin over a wide range of the AUC24/MIC ratios. Each organism was exposed to twice-daily ciprofloxacin for 3 days. Amplification of resistant mutants was monitored by plating on media with 2×, 4×, 8× and 16× MIC of ciprofloxacin. Population analysis data were expressed by the area under the bacterial mutant concentration-time curve (AUBCM). Changes in P. aeruginosa susceptibility were examined by daily MIC determinations. To account for the different susceptibilities of P. aeruginosa strains, post-exposure MICs (MICfinal) were related to the MICs determined with the starting inoculum (MICinitial). For each organism, AUC24/MIC relationships both with AUBCM and MICfinal/MICinitial were bell-shaped, but the latter were more strain-specific than the former. Using combined data on all four isolates, AUBCM showed a better correlation than MICfinal/MICinitial (r(2)=0.75 vs. r(2)=0.53). The shift of MICfinal/MICinitial relative to AUBCM vs. AUC24/MIC curves resulted in a weak correlation between AUBCM and MICfinal/MICinitial (r(2)=0.41). These data suggest that population analysis is preferable to susceptibility testing in bacterial resistance studies and that these endpoints should not be considered interchangeable.

  7. Impact of arachidonic acid enrichment of live rotifer prey on bacterial communities in rotifer and larval fish cultures.

    PubMed

    Seychelles, Laurent H; Doiron, Kim; Audet, Céline; Tremblay, Réjean; Pernet, Fabrice; Lemarchand, Karine

    2013-03-01

    Rotifers (Brachionus plicatilis), commonly used at first feeding in commercial fish hatcheries, carry a large bacteria load. Because they are relatively poor in essential fatty acids, it is common practice to enrich them with fatty acids, including arachidonic acid (AA). This study aims to determine whether prey enrichment with AA may act as a prebiotic and modify the microbial community composition either in AA-enriched rotifer cultures or in larval-rearing water using winter flounder (Pseudopleuronectes americanus) as a larval fish model. AA enrichment modified the bacterial community composition in both the rotifer culture tanks and the larval-rearing tanks. We observed an increase in the number of cultivable bacteria on TCBS (thiosulfate-citrate-bile salts-sucrose) agar, used as a proxy for the abundance of Vibrio sp. The results suggest that AA may also play an indirect role in larval health.

  8. Characterization of the bacterial community associated with larvae and adults of Anoplophora chinensis collected in Italy by culture and culture-independent methods.

    PubMed

    Rizzi, Aurora; Crotti, Elena; Borruso, Luigimaria; Jucker, Costanza; Lupi, Daniela; Colombo, Mario; Daffonchio, Daniele

    2013-01-01

    The wood-boring beetle Anoplophora chinensis Forster, native to China, has recently spread to North America and Europe causing serious damage to ornamental and forest trees. The gut microbial community associated with these xylophagous beetles is of interest for potential biotechnological applications in lignocellulose degradation and development of pest-control measures. In this study the gut bacterial community of larvae and adults of A. chinensis, collected from different host trees in North Italy, was investigated by both culture and culture-independent methods. Larvae and adults harboured a moderately diverse bacterial community, dominated by Proteobacteria, Actinobacteria, and Firmicutes. The gammaproteobacterial family Enterobacteriaceae (genera Gibbsiella, Enterobacter, Raoultella, and Klebsiella) was the best represented. The abundance of such bacteria in the insect gut is likely due to the various metabolic abilities of Enterobacteriaceae, including fermentation of carbohydrates derived from lignocellulose degradation and contribution to nitrogen intake by nitrogen-fixing activity. In addition, bacteria previously shown to have some lignocellulose-degrading activity were detected at a relatively low level in the gut. These bacteria possibly act synergistically with endogenous and fungal enzymes in lignocellulose breakdown. The detection of actinobacterial symbionts could be explained by a possible role in the detoxification of secondary plant metabolites and/or protection against pathogens.

  9. Characterization of the Bacterial Community Associated with Larvae and Adults of Anoplophora chinensis Collected in Italy by Culture and Culture-Independent Methods

    PubMed Central

    Rizzi, Aurora; Crotti, Elena; Lupi, Daniela; Daffonchio, Daniele

    2013-01-01

    The wood-boring beetle Anoplophora chinensis Forster, native to China, has recently spread to North America and Europe causing serious damage to ornamental and forest trees. The gut microbial community associated with these xylophagous beetles is of interest for potential biotechnological applications in lignocellulose degradation and development of pest-control measures. In this study the gut bacterial community of larvae and adults of A. chinensis, collected from different host trees in North Italy, was investigated by both culture and culture-independent methods. Larvae and adults harboured a moderately diverse bacterial community, dominated by Proteobacteria, Actinobacteria, and Firmicutes. The gammaproteobacterial family Enterobacteriaceae (genera Gibbsiella, Enterobacter, Raoultella, and Klebsiella) was the best represented. The abundance of such bacteria in the insect gut is likely due to the various metabolic abilities of Enterobacteriaceae, including fermentation of carbohydrates derived from lignocellulose degradation and contribution to nitrogen intake by nitrogen-fixing activity. In addition, bacteria previously shown to have some lignocellulose-degrading activity were detected at a relatively low level in the gut. These bacteria possibly act synergistically with endogenous and fungal enzymes in lignocellulose breakdown. The detection of actinobacterial symbionts could be explained by a possible role in the detoxification of secondary plant metabolites and/or protection against pathogens. PMID:24069601

  10. The effect of wheat prebiotics on the gut bacterial population and iron status of iron deficient broiler chickens

    PubMed Central

    2014-01-01

    Background Currently, there is a lot of interest in improving gut health, and consequently increasing Fe absorption, by managing the colonic microbial population. This is traditionally done by the consumption of probiotics, live microbial food supplements. However, an alternative, and often very effective approach, is the consumption of food ingredients known as prebiotics. Fructans and arabinoxylans are naturally occurring non-digestible oligosaccharides in wheat that exhibit prebiotic properties and may enhance intestinal iron (Fe) absorption. The aim of this study was to assess the effect of prebiotics from wheat on Fe bioavailability in vitro (Caco-2 cells) and in vivo (broiler chickens, Gallus gallus). Methods In the current study, the effect of intra-amniotic administration of wheat samples extracts at 17 d of embryonic incubation on the Fe status and possible changes in the bacterial population in intestinal content of broiler hatchlings were investigated. A group of 144 eggs were injected with the specified solution (1 ml per egg) into the amniotic fluid. Immediately after hatch (21 d) and from each treatment group, 10 chicks were euthanized and their small intestine, liver and cecum were removed for relative mRNA abundance of intestinal Fe related transporters, relative liver ferritin amounts and bacterial analysis of cecal content, respectively. Results The in vivo results are in agreement with the in vitro observations, showing no differences in the hatchling Fe status between the treatment groups, as Fe bioavailability was not increased in vitro and no significant differences were measured in the intestinal expression of DMT1, Ferroportin and DcytB in vivo. However, there was significant variation in relative amounts of bifidobacteria and lactobacilli in the intestinal content between the treatments groups, with generally more bifidobacteria being produced with increased prebiotic content. Conclusions In this study we showed that prebiotics naturally

  11. Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes.

    PubMed

    Petrova, Olga E; Garcia-Alcalde, Fernando; Zampaloni, Claudia; Sauer, Karin

    2017-01-24

    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.

  12. The role of silicon in enhancing resistance to bacterial blight of hydroponic- and soil-cultured rice.

    PubMed

    Song, Alin; Xue, Gaofeng; Cui, Peiyuan; Fan, Fenliang; Liu, Hongfang; Yin, Chang; Sun, Wanchun; Liang, Yongchao

    2016-04-19

    Here we report for the first time that bacterial blight of rice can be alleviated by silicon (Si) added. In both inoculated and uninoculated plants, shoot dry weight was significantly higher in the +Si plants than in the -Si plants. A soil-cultured trial showed that disease severity was 24.3% lower in the Si-amended plants than in the non-Si-amended plants. Plants that were switched from -Si to +Si nutrient solution and simultaneously inoculated with Xoo also exhibited the same high resistance to bacterial blight as the plants that were treated continuously with Si, with control efficiencies of 52.8 and 62.9%, respectively. Moreover, total concentrations of soluble phenolics and lignin in rice leaves were significantly higher in the +Si plants than in the -Si plants. Polyphenoloxidase (PPO) and phenylalanine ammonia-lyase (PAL) activities in rice leaves were observed to be higher in the +Si plants than in the -Si plants. The expression levels of Os03g0109600, Prla, Rcht2 and Lox2osPil, were also higher in +Si plants than in -Si plants post-inoculation during the experimental time. Addition of Si resulted in increased Pal transcription, and inhibited CatA and Os03g0126000 expression in the earlier and later stages of bacterial inoculation, respectively.

  13. A Simple and Rapid Protocol for Producing Yeast Extract from Saccharomyces cerevisiae Suitable for Preparing Bacterial Culture Media.

    PubMed

    Zarei, Omid; Dastmalchi, Siavoush; Hamzeh-Mivehroud, Maryam

    2016-01-01

    Yeasts, especially Saccharomyces cerevisiae, are one of the oldest organisms with broad spectrum of applications, owing to their unique genetics and physiology. Yeast extract, i.e. the product of yeast cells, is extensively used as nutritional resource in bacterial culture media. The aim of this study was to develop a simple, rapid and cost benefit process to produce the yeast extract. In this procedure mechanical methods such as high temperature and pressure were utilized to produce the yeast extract. The growth of the bacteria feed with the produced yeast extract was monitored in order to assess the quality of the product. The results showed that the quality of the produced yeast extract was very promising concluded from the growth pattern of bacterial cells in media prepared from this product and was comparable with that of the three commercial yeast extracts in terms of bacterial growth properties. One of the main advantages of the current method was that no chemicals and enzymes were used, leading to the reduced production cost. The method is very simple and cost effective, and can be performed in a reasonable time making it suitable for being adopted by research laboratories. Furthermore, it can be scaled up to produce large quantities for industrial applications.

  14. A Simple and Rapid Protocol for Producing Yeast Extract from Saccharomyces cerevisiae Suitable for Preparing Bacterial Culture Media

    PubMed Central

    Zarei, Omid; Dastmalchi, Siavoush; Hamzeh-Mivehroud, Maryam

    2016-01-01

    Yeasts, especially Saccharomyces cerevisiae, are one of the oldest organisms with broad spectrum of applications, owing to their unique genetics and physiology. Yeast extract, i.e. the product of yeast cells, is extensively used as nutritional resource in bacterial culture media. The aim of this study was to develop a simple, rapid and cost benefit process to produce the yeast extract. In this procedure mechanical methods such as high temperature and pressure were utilized to produce the yeast extract. The growth of the bacteria feed with the produced yeast extract was monitored in order to assess the quality of the product. The results showed that the quality of the produced yeast extract was very promising concluded from the growth pattern of bacterial cells in media prepared from this product and was comparable with that of the three commercial yeast extracts in terms of bacterial growth properties. One of the main advantages of the current method was that no chemicals and enzymes were used, leading to the reduced production cost. The method is very simple and cost effective, and can be performed in a reasonable time making it suitable for being adopted by research laboratories. Furthermore, it can be scaled up to produce large quantities for industrial applications. PMID:28243289

  15. Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

    PubMed Central

    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

  16. The role of silicon in enhancing resistance to bacterial blight of hydroponic- and soil-cultured rice

    PubMed Central

    Song, Alin; Xue, Gaofeng; Cui, Peiyuan; Fan, Fenliang; Liu, Hongfang; Yin, Chang; Sun, Wanchun; Liang, Yongchao

    2016-01-01

    Here we report for the first time that bacterial blight of rice can be alleviated by silicon (Si) added. In both inoculated and uninoculated plants, shoot dry weight was significantly higher in the +Si plants than in the −Si plants. A soil-cultured trial showed that disease severity was 24.3% lower in the Si-amended plants than in the non-Si-amended plants. Plants that were switched from −Si to +Si nutrient solution and simultaneously inoculated with Xoo also exhibited the same high resistance to bacterial blight as the plants that were treated continuously with Si, with control efficiencies of 52.8 and 62.9%, respectively. Moreover, total concentrations of soluble phenolics and lignin in rice leaves were significantly higher in the +Si plants than in the −Si plants. Polyphenoloxidase (PPO) and phenylalanine ammonia-lyase (PAL) activities in rice leaves were observed to be higher in the +Si plants than in the −Si plants. The expression levels of Os03g0109600, Prla, Rcht2 and Lox2osPil, were also higher in +Si plants than in −Si plants post-inoculation during the experimental time. Addition of Si resulted in increased Pal transcription, and inhibited CatA and Os03g0126000 expression in the earlier and later stages of bacterial inoculation, respectively. PMID:27091552

  17. Polymerase Chain Reaction–Electrospray–Time-of-Flight Mass Spectrometry Versus Culture for Bacterial Detection in Septic Arthritis and Osteoarthritis

    PubMed Central

    Palmer, Michael P.; Melton-Kreft, Rachael; Nistico, Laura; Hiller, N. Louisa; Kim, Leon H.J.; Altman, Gregory T.; Altman, Daniel T.; Sotereanos, Nicholas G.; Hu, Fen Z.

    2016-01-01

    Background: Preliminary studies have identified known bacterial pathogens in the knees of patients with osteoarthritis (OA) before arthroplasty. Aims: The current study was designed to determine the incidence and types of bacteria present in the synovial fluid of native knee joints from adult patients with diagnoses of septic arthritis and OA. Patients and Methods: Patients were enrolled between October 2010 and January 2013. Synovial fluid samples from the affected knee were collected and evaluated with both traditional microbial culture and polymerase chain reaction–electrospray ionization–time-of-flight mass spectrometry (molecular diagnostics [MDx]) to prospectively characterize the microbial content. Patients were grouped by diagnosis into one of two cohorts, those with clinical suspicion of septic arthritis (n = 44) and those undergoing primary arthroplasty of the knee for OA (n = 21). In all cases where discrepant culture and MDx results were obtained, we performed species-specific 16S rRNA fluorescence in situ hybridization (FISH) as a confirmatory test. Results: MDx testing identified bacteria in 50% of the suspected septic arthritis cases and 29% of the arthroplasty cases, whereas culture detected bacteria in only 16% of the former and 0% of the latter group. The overall difference in detection rates for culture and MDx was very highly significant, p-value = 2.384 × 10−7. All of the culture-positive cases were typed as Staphylococcus aureus. Two of the septic arthritis cases were polymicrobial as was one of the OA cases by MDx. FISH testing of the specimens with discordant results supported the MDx findings in 91% (19/21) of the cases, including one case where culture detected S. aureus and MDx detected Streptococcus agalactiae. Conclusions: MDx were more sensitive than culture, as confirmed by FISH. FISH only identifies bacteria that are embedded or infiltrated within the tissue and is thus not susceptible to contamination. Not all

  18. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

    PubMed Central

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V.; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A.; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N.; Golyshina, Olga V.; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R.; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I.; Golyshin, Peter N.; Yakimov, Michail M.; Daffonchio, Daniele; Ferrer, Manuel

    2015-01-01

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills. PMID:26119183

  19. Population size and cultural evolution in nonindustrial food-producing societies.

    PubMed

    Collard, Mark; Ruttle, April; Buchanan, Briggs; O'Brien, Michael J

    2013-01-01

    Modeling work suggests that population size affects cultural evolution such that larger populations can be expected to have richer and more complex cultural repertoires than smaller populations. Empirical tests of this hypothesis, however, have yielded conflicting results. Here, we report a study in which we investigated whether the subsistence toolkits of small-scale food-producers are influenced by population size in the manner the hypothesis predicts. We applied simple linear and standard multiple regression analysis to data from 40 nonindustrial farming and pastoralist groups to test the hypothesis. Results were consistent with predictions of the hypothesis: both the richness and the complexity of the toolkits of the food-producers were positively and significantly influenced by population size in the simple linear regression analyses. The multiple regression analyses demonstrated that these relationships are independent of the effects of risk of resource failure, which is the other main factor that has been found to influence toolkit richness and complexity in nonindustrial groups. Thus, our study strongly suggests that population size influences cultural evolution in nonindustrial food-producing populations.

  20. Speciation of vanadium in oilsand coke and bacterial culture by high performance liquid chromatography inductively coupled plasma mass spectrometry.

    PubMed

    Li, X Sherry; Glasauer, Susan; Le, X Chris

    2007-10-17

    A simple and sensitive method for the speciation of vanadium(III), (IV), and (V) was developed by using high performance liquid chromatography and inductively coupled plasma mass spectrometry (HPLC-ICPMS). The EDTA-complexed vanadium species were separated on a strong anion exchange column with an eluent containing 2 mM EDTA, 3% acetonitrile, and 80 mM ammonium bicarbonate at pH 6. Each analysis was complete in 5 min. The detection limits were 0.6, 0.7 and 1.0 microg L(-1) for V(III), V(IV), and V(V), respectively. The method was applied to coke pore water samples from an oilsand processing/upgrading site in Fort McMurray, Alberta, Canada and to Shewanella putrefaciens CN32 bacterial cultures incubated with V(V). In the coke pore water samples, V(IV) and V(V) were found to be the major species. For the first time, V(III) was detected in the bacterial cultures incubated with V(V).

  1. Aerococcus christensenii native aortic valve subacute bacterial endocarditis (SBE) presenting as culture negative endocarditis (CNE) mimicking marantic endocarditis.

    PubMed

    Jose, Anita; Cunha, Burke A; Klein, Natalie C; Schoch, Paul E

    2014-01-01

    This is a case report of an adult who presented with apparent culture negative endocarditis (CNE) thought to be marantic endocarditis due to a B-cell lymphoproliferative disorder. This was a most perplexing case and was eventually diagnosed as subacute bacterial endocarditis (SBE) due to a rare slow growing organism. Against the diagnosis of SBE was the lack of fever, hepatomegaly, peripheral manifestations and microscopic hematuria. Also, against a diagnosis of SBE was another explanation for the patient's abnormal findings, e.g., elevated ferritin levels, elevated α1/α2 globulins on SPEP, an elevated alkaline phosphatase, flow cytometry showing B-lymphocytes expressing CD5, and a bone lesion in the right iliac. Findings compatible with both SBE and marantic endocarditis due to a B-cell lymphoproliferative disorder included an elevated ESR, and splenomegaly. Blood cultures eventually became positive during hospitalization. We report a case of native aortic valve (AV) subacute bacterial endocarditis (SBE) due to Aerococcus christensenii mimicking marantic endocarditis due to a B-cell lymphoproliferative disorder. To the best of our knowledge, this is the first reported case of native AV SBE due to A. christensenii presenting as marantic endocarditis.

  2. Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil

    PubMed Central

    Weber, Sabine; Stubner, Stephan; Conrad, Ralf

    2001-01-01

    Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), and Acidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly

  3. Comparison of human optimized bacterial luciferase, firefly luciferase, and green fluorescent protein for continuous imaging of cell culture and animal models

    PubMed Central

    Close, Dan M.; Hahn, Ruth E.; Patterson, Stacey S.; Baek, Seung J.; Ripp, Steven A.; Sayler, Gary S.

    2011-01-01

    Bioluminescent and fluorescent reporter systems have enabled the rapid and continued growth of the optical imaging field over the last two decades. Of particular interest has been noninvasive signal detection from mammalian tissues under both cell culture and whole animal settings. Here we report on the advantages and limitations of imaging using a recently introduced bacterial luciferase (lux) reporter system engineered for increased bioluminescent expression in the mammalian cellular environment. Comparison with the bioluminescent firefly luciferase (Luc) system and green fluorescent protein system under cell culture conditions demonstrated a reduced average radiance, but maintained a more constant level of bioluminescent output without the need for substrate addition or exogenous excitation to elicit the production of signal. Comparison with the Luc system following subcutaneous and intraperitoneal injection into nude mice hosts demonstrated the ability to obtain similar detection patterns with in vitro experiments at cell population sizes above 2.5 × 104 cells but at the cost of increasing overall image integration time. PMID:21529093

  4. The metabolism of neonicotinoid insecticide thiamethoxam by soil enrichment cultures, and the bacterial diversity and plant growth-promoting properties of the cultured isolates.

    PubMed

    Zhou, Guang-Can; Wang, Ying; Ma, Yuan; Zhai, Shan; Zhou, Ling-Yan; Dai, Yi-Jun; Yuan, Sheng

    2014-01-01

    A soil enrichment culture (SEC) rapidly degraded 96% of 200 mg L(-1) neonicotinoid insecticide thiamethoxam (TMX) in MSM broth within 30 d; therefore, its metabolic pathway of TMX, bacterial diversity and plant growth-promoting rhizobacteria (PGPR) activities of the cultured isolates were studied. The SEC transformed TMX via the nitro reduction pathway to form nitrso, urea metabolites and via cleavage of the oxadiazine cycle to form a new metabolite, hydroxyl CLO-tri. In addition, 16S rRNA gene-denaturing gradient gel electrophoresis analysis revealed that uncultured rhizobacteria are predominant in the SEC broth and that 77.8% of the identified bacteria belonged to uncultured bacteria. A total of 31 cultured bacterial strains including six genera (Achromobacter, Agromyces, Ensifer, Mesorhizobium, Microbacterium and Pseudoxanthomonas) were isolated from the SEC broth. The 12 strains of Ensifer adhaerens have the ability to degrade TMX. All six selected bacteria showed PGPR activities. E. adhaerens TMX-23 and Agromyces mediolanus TMX-25 produced indole-3-acetic acid, whereas E. adhaerens TMX-23 and Mesorhizobium alhagi TMX-36 are N2-fixing bacteria. The six-isolated microbes were tolerant to 200 mg L(-1) TMX, and the growth of E. adhaerens was significantly enhanced by TMX, whereas that of Achromobacter sp. TMX-5 and Microbacterium sp.TMX-6 were enhanced slightly. The present study will help to explain the fate of TMX in the environment and its microbial degradation mechanism, as well as to facilitate future investigations of the mechanism through which TMX enhances plant vigor.

  5. The impact of interspecific competition on lineage evolution and a rapid peak shift by interdemic genetic mixing in experimental bacterial populations.

    PubMed

    Nakajima, Toshiyuki

    2012-01-01

    Epistatic interactions between genes in the genome constrain the accessible evolutionary paths of lineages. Two factors involving epistasis that can affect the evolutionary path and fate of lineages were investigated. The first factor concerns the impact of competition with another species lineage that has different epistatic constraints. Five enteric bacterial populations were evolved by point mutation in medium containing a single limiting resource. Single-species and two-species cultures were used to determine whether different asexual lineages have different capacities for producing variants due to epistatic constraints, and whether their survival is determined by local inter-lineage competition with different species. Local inter-lineage competition quickly resulted in one successful lineage, with another lineage becoming extinct before finding a higher peak. The second factor concerns a peak-shifting process, and whether the sexual recombination between different demes can cause peak shifts was investigated. An Escherichia coli population consisting of a male (Hfr) and female strain (F(-)) was evolved in a single limiting resource and compared to evolving populations containing the male or female strain alone. The E. coli sexual lineage was successful due to its ability to escape lower peaks and reach a higher peak, not because of a rapid approach to the nearest local peak the male or female asexual lineage could reach. The data in this study demonstrate that lineage survivability can be determined by the ability to produce beneficial mutations and checked by local competition between lineages of different species. Interspecific competition may prevent a population from evolving through crossing fitness valleys or adaptive ridges if it requires many generations to achieve peak shifts. The data also show that genomic recombination between different conspecific lineages can rapidly carry the combined lineage to a higher peak.

  6. Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

    PubMed

    Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

    2017-01-01

    The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.

  7. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    ERIC Educational Resources Information Center

    Delpech, Roger

    2009-01-01

    This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

  8. The long-term effects of phage concentration on the inhibition of planktonic bacterial cultures.

    PubMed

    Worley-Morse, Thomas O; Zhang, Lucy; Gunsch, Claudia K

    2014-01-01

    Since the early 1920s there has been an interest in using bacteriophages (phages) for the control of bacterial pathogens. While there are many factors that have limited the success of phage bio-control, one particular problem is the variability of outcomes between phages and bacteria. Specifically, there is a significant need for a better understanding of how initial phage concentrations affect long-term bacterial inhibition. In work reported herein three phages were isolated for Escherichia coli K12, Pseudomonas aeruginosa PAO1, as well as Bacillus cereus and bio-control experiments were performed with phage concentrations ranging from 10(5) to 10(8) plaque forming units per mL over the course of 72 h. For four of the nine phages isolated there was a linear relationship between inhibition and phage concentration, suggesting the effect of phage concentration is important at longer time scales. For three of the isolated phages, phage concentrations had no effect on bacterial inhibition suggesting that even at the lowest concentration the method of action was saturated and lower concentrations might still be effective. Additionally, a cocktail was created and was compared to the previously isolated phages. There was no statistical difference between the cocktail and the best performing phage highlighting the importance of selecting the appropriate phages for treatment. These results suggest that, for certain phages, there is a strong relationship between phage concentration and long-term bacterial growth inhibition and the initial phage concentration is an important indicator of the long-term outcome.

  9. Culturable bacterial endophytes isolated from Mangrove tree (Rhizophora apiculata Blume) enhance seedling growth in Rice

    PubMed Central

    Deivanai, Subramanian; Bindusara, Amitraghata Santhanam; Prabhakaran, Guruswamy; Bhore, Subhash Janardhan

    2014-01-01

    Background: Endophytic bacteria do have several potential applications in medicine and in other various sectors of biotechnology including agriculture. Bacterial endophytes need to be explored for their potential applications in agricultural biotechnology. One of the potential applications of bacterial endophytes in agricultural is to enhance the growth of the agricultural crops. Hence, this study was undertaken to explore the plant growth promoting potential application of bacterial endophytes. Objective: The objective of this study was to examine the effect of endophytic bacteria from mangrove tree (Rhizophora apiculata Blume) for their efficacy in promoting seedling growth in rice. Materials and Methods: Eight endophytic bacterial isolates (EBIs) isolated from twig and petiole tissues of the mangrove were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequence homology. Separately, surface sterilized paddy seeds were treated with cell-free broth and cell suspension of the EBIs. Rice seedlings were analyzed by various bioassays and data was recorded. Results: The gene sequences of the isolates were closely related to two genera namely, Bacillus and Pantoea. Inoculation of EBIs from R. apiculata with rice seeds resulted in accelerated root and shoot growth with significant increase in chlorophyll content. Among the isolates, Pantoea ananatis (1MSE1) and Bacillus amyloliquefaciens (3MPE1) had shown predominance of activity. Endophytic invasion was recognized by the non-host by rapid accumulation of reactive oxygen species (ROS) and was counteracted by the production of hydrogen peroxide (H2O2) and lipid peroxide. The results demonstrated that EBIs from mangrove tree can increase the fitness of the rice seedlings under controlled conditions. Conclusion: These research findings could be useful to enhance the seedling growth and could serve as foundation in further research on enhancing the growth of the rice crop using endophytic bacteria. PMID

  10. Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities.

    PubMed

    Watanabe, K; Watanabe, K; Kodama, Y; Syutsubo, K; Harayama, S

    2000-11-01

    Petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 10(6) microorganisms ml(-1), a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacter spp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater.

  11. Seasonal effects of heat shock on bacterial populations, including artificial Vibrio parahaemolyticus exposure, in the Pacific oyster, Crassostrea gigas.

    PubMed

    Aagesen, Alisha M; Häse, Claudia C

    2014-04-01

    During the warmer summer months, oysters are conditioned to spawn, resulting in massive physiological efforts for gamete production. Moreover, the higher temperatures during the summer typically result in increased bacteria populations in oysters. We hypothesized that these animals are under multiple stresses that lead to possible immune system impairments during the summer months that can possibly lead to death. Here we show that in the summer and the fall animals exposed to a short heat stress respond similarly, resulting in a general trend of more bacteria being found in heat shocked animals than their non-heat shocked counterparts. We also show that naturally occurring bacterial populations are effected by a heat shock. In addition, oysters artificially contaminated with Vibrio parahaemolyticus were also affected by a heat shock. Heat shocked animals contained higher concentrations of V. parahaemolyticus in their tissues and hemolymph than control animals and this was consistent for animals examined during summer and fall. Finally, oyster hemocyte interactions with V. parahaemolyticus differed based on the time of the year. Overall, these findings demonstrate that seasonal changes and/or a short heat shock is sufficient to impact bacterial retention, particularly V. parahaemolyticus, in oysters and this line of research might lead to important considerations for animal harvesting procedures.

  12. Evaluating a commercial PCR assay against bacterial culture for diagnosing Streptococcus uberis and Staphylococcus aureus throughout lactation.

    PubMed

    Steele, N M; Williamson, J H; Thresher, R; Laven, R A; Hillerton, J E

    2017-02-22

    The performance of a commercial, real-time PCR assay was compared with traditional bacterial culture for the identification of Streptococcus uberis and Staphylococcus aureus in bovine milk collected at different stages of lactation. Initial validation tests using fresh and frozen quarter milk samples identified factors that affected the success of the PCR. Therefore, the standard protocol was adjusted for samples collected at the first milking postpartum (colostrum) and from clinical mastitis cases. The adjustment involved PCR testing both undiluted and diluted (1 in 10 with sterile water) DNA extracts. The performance comparison between culture and the PCR assay used milk samples collected aseptically from individual quarters of mixed-age spring-calving dairy cows, during early, mid, and late lactation. Bacterial culture results were used to select a subset of samples for PCR testing (n = 315) that represented quarters with a current or prior Strep. uberis or Staph. aureus infection. Compared with culture, PCR had a sensitivity of 86.8% and specificity of 87.7% for detecting Strep. uberis (kappa = 0.74) and 96.4% and 99.7%, respectively, for detecting Staph. aureus (kappa = 0.96). The dilution of DNA extracts for colostrum and clinical samples increased the relative sensitivity from 79.2% to 86.8% for Strep. uberis detection and from 92.9% to 96.4% for Staph. aureus, presumably through diluting unidentified PCR inhibitors. The sensitivity for detecting Strep. uberis using PCR, relative to culture, was similar throughout lactation (85-89%), whereas relative specificity was lowest immediately postcalving (64%) but improved in mid and late lactation (98%). Specificity estimates for samples collected in early lactation can be optimized by reducing the cutoff cycle threshold (Ct) value from the recommended value of 37 to 34. Although using this value improved specificity (77%), it reduced test sensitivity (77%). The PCR assay lacked agreement with culture in early

  13. Cultural Adaptation and Implementation of Family Evidence-Based Interventions with Diverse Populations.

    PubMed

    Kumpfer, Karol; Magalhães, Catia; Xie, Jing

    2016-10-18

    Family evidence-based interventions (FEBIs) are effective in creating lasting improvements and preventing children's behavioral health problems, even in genetically at-risk children. Most FEBIs, however, were designed for English-speaking families. Consequently, providers have difficulty engaging non-English-speaking populations in their own country or in other countries where the content, language, and recruitment methods of the FEBIs do not reflect their culture. The practical solution has been to culturally adapt existing FEBIs. Research suggests this can increase family engagement by about 40 %. This article covers background, theory, and research on FEBIs and the need to engage more diverse families. Steps for culturally adapting FEBIs with fidelity are presented based on our own and local implementers' experiences in 36 countries with the Strengthening Families Program. These steps, also previously recommended by a United Nations Office on Drugs and Crime panel of experts in family skills interventions, include: (1) creating a cultural advisory group, (2) assessing specific needs of cultural subgroups, (3) language translation, (4) hiring implementers from the culture, (5) developing culturally adapted training systems, (6) making cultural adaptations cautiously during repeated delivery, (7) continuous implementation quality and outcome evaluation to assure effectiveness in comparison with the original FEBI, (8) developing local and international dissemination partnerships, and (9) securing funding support for sustainability. Future efficacy trials should compare existing FEBIs to culturally adapted versions to determine comparative cost effectiveness.

  14. Lactic Acid Bacterial Starter Culture with Antioxidant and γ-Aminobutyric Acid Biosynthetic Activities Isolated from Flatfish-Sikhae Fermentation.

    PubMed

    Won, Yeong Geol; Yu, Hyun-Hee; Chang, Young-Hyo; Hwang, Han-Joon

    2015-12-01

    The aim of this study is to select a lactic acid bacterial strain as a starter culture for flatfish-Sikhae fermentation and to evaluate its suitability for application in a food system. Four strains of lactic acid bacteria isolated from commercial flatfish-Sikhae were identified and selected as starter culture candidates through investigation of growth rates, salt tolerance, food safety, and functional properties such as antioxidative and antimicrobial activities. The fermentation properties of the starter candidates were also examined in food systems prepared with these strains (candidate batch) in comparison with a spontaneous fermentation process without starter culture (control batch) at 15°C. The results showed that the candidate YG331 batch had better fermentation properties such as viable cell count, pH, and acidity than the other experimental batches, including the control batch. The results are expressed according to selection criteria based on a preliminary sensory evaluation and physiochemical investigation. Also, only a small amount of histamine was detected with the candidate YG331 batch. The radical scavenging activity of the candidate batches was better compared with the control batch, and especially candidate YG331 batch showed the best radical scavenging activity. Also, we isolated another starter candidate (identified as Lactobacillus brevis PM03) with γ-aminobutyric acid (GABA)-producing activity from commercial flatfish-Sikhae products. The sensory scores of the candidate YG331 batch were better than those of the other experimental batches in terms of flavor, color, and overall acceptance. In this study, we established selection criteria for the lactic acid bacterial starter for the flatfish-Sikhae production and finally selected candidate YG331 as the most suitable starter.

  15. [110th year Nederlands Tijdschrift voor Tandheelkunde. 2. Root canal treatment, intra-canal disinfectants and bacterial culture: past and present].

    PubMed

    Moorer, W R; Wesselink, P R

    2003-05-01

    Fifty years ago the Dutch Journal of Dentistry published methods and opinions concerning root canal treatment. Qualitative bacterial culture, inclusion of aggressive disinfectants, as well as antibiotics and widening of the apical constriction were carried out. Nowadays, because of several reasons, these are not clinical practice anymore. Controversy over the clinical consequences of bacterial presence in tubules and in the peri-apical area prevailed in the past and seem to be prevalent once again.

  16. Composition and Diversity Analysis of the Gut Bacterial Community of the Oriental Armyworm, Mythimna separata, Determined by Culture-Independent and Culture-Dependent Techniques

    PubMed Central

    He, Cai; Nan, Xiaoning; Zhang, Zhengqing; Li, Menglou

    2013-01-01

    The intestinal bacteria community structure and diversity of the Oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae), was studied by analysis of a 16S rDNA clone library, denaturing gradient gel electrophoresis,and culture-dependent techniques. The 16S rDNA clone library revealed a bacterial community diversity comprising Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes and Proteobacteria, among which Escherichia coli (Migula) (Enterobacteriales: Enterobacteriaceae) was the dominant bacteria. The intestinal bacteria isolated by PCR-denaturing gradient gel electrophoresis were classified to Firmicutes, Proteobacteria, and Gracilicutes, and E. coli was again the dominant bacteria. The culture-dependent technique showed that the intestinal bacteria belonged to Firmicutes and Actinobacteria, and Staphylococcus was the dominant bacteria. The intestinal bacteria of M. separata were widely distributed among the groups Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes, Proteobacteria, and Gracilicutes. 16S rDNA clone library, denaturing gradient gel electrophoresis, and culture-dependent techniques should be integrated to obtain precise results in terms of the microbial community and its diversity. PMID:24773514

  17. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    PubMed

    Harris, Jordan Lee; Balci, Yilmaz

    2015-01-01

    Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

  18. Identification of Common Bacterial Pathogens Causing Meningitis in Culture-Negative Cerebrospinal Fluid Samples Using Real-Time Polymerase Chain Reaction

    PubMed Central

    2016-01-01

    Background. Meningitis is a serious communicable disease with high morbidity and mortality rates. It is an endemic disease in Egypt caused mainly by Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. In some settings, bacterial meningitis is documented depending mainly on positive cerebrospinal fluid (CSF) culture results or CSF positive latex agglutination test, missing the important role of prior antimicrobial intake which can yield negative culture and latex agglutination test results. This study aimed to utilize molecular technology in order to diagnose bacterial meningitis in culture-negative CSF samples. Materials and Methods. Forty culture-negative CSF samples from suspected cases of bacterial meningitis were examined by real-time polymerase chain reaction (real-time PCR) for the presence of lytA, bexA, and ctrA genes specific for Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, respectively. Results. Positive real-time PCR results for Streptococcus pneumoniae were detected in 36 (90%) of culture-negative CSF samples while no positive results for Haemophilus influenzae or Neisseria meningitidis were detected. Four (10%) samples were negative by real-time PCR for all tested organisms. Conclusion. The use of molecular techniques as real-time PCR can provide a valuable addition to the proportion of diagnosed cases of bacterial meningitis especially in settings with high rates of culture-negative results. PMID:27563310

  19. Cultural Relevance and Working with Inner City Youth Populations to Achieve Civic Engagement

    ERIC Educational Resources Information Center

    Ward, Shakoor; Webster, Nicole

    2011-01-01

    This article helps Extension professionals consider the cultural relevant needs of inner city residents in hopes of achieving ongoing civic engagement and appropriate program activities in these communities. Having a deep understanding of how the various dimensions of marginalized community life among inner city populations affect participation in…

  20. Teaching Population Growth Using Cultures of Vinegar Eels, "Turbatrix aceti" (Nematoda)

    ERIC Educational Resources Information Center

    Wallace, Robert L.

    2005-01-01

    A simple laboratory exercise is presented that follows the population growth of the common vinegar eel, "Turbatrix aceti" (Nematoda), in a microcosm using a simple culture medium. It lends itself to an exercise in a single semester course. (Contains 4 figures.)

  1. Parental Opinion Concerning School Sexuality Education in a Culturally Diverse Population in the USA

    ERIC Educational Resources Information Center

    Heller, Janet R.; Johnson, Helen L.

    2013-01-01

    This study aimed to expand upon previous research related to parental opinion concerning school sexuality education by sampling a culturally diverse, low-income population that has been traditionally under-represented in the literature. A total of 191 parents attending an urban community college completed a written questionnaire about what topics…

  2. A novel approach to recycle bacterial culture waste for fermentation reuse via a microbial fuel cell-membrane bioreactor system.

    PubMed

    Li, Jian; Zhu, Yuan; Zhuang, Liangpeng; Otsuka, Yuichiro; Nakamura, Masaya; Goodell, Barry; Sonoki, Tomonori; He, Zhen

    2015-09-01

    Biochemical production processes require water and nutrient resources for culture media preparation, but aqueous waste is generated after the target products are extracted. In this study, culture waste (including cells) produced from a lab-scale fermenter was fed into a microbial fuel cell-membrane bioreactor (MFC-MBR) system. Electrical energy was generated via the interaction between the microbial consortia and the solid electrode in the MFC. The treated wastewater was reclaimed in this process which was reused as a solvent and a nutrient source in subsequent fermentation. Polarization testing showed that the MFC produced a maximum current density of 37.53 A m(-3) with a maximum power density of 5.49 W m(-3). The MFC was able to generate 0.04 kWh of energy per cubic meter of culture waste treated. The lab-scale fermenters containing pure cultures of an engineered Pseudomonas spp. were used to generate 2-pyrone-4,6-dicarboxylic acid (PDC), a high value platform chemical. When the MFC-MBR-treated wastewater was used for the fermenter culture medium, a specific bacterial growth rate of 1.00 ± 0.05 h(-1) was obtained with a PDC production rate of 708.11 ± 64.70 mg PDC L(-1) h(-1). Comparable values for controls using pure water were 0.95 ± 0.06 h(-1) and 621.01 ± 22.09 mg PDC L(-1) h(-1) (P > 0.05), respectively. The results provide insight on a new approach for more sustainable bio-material production while at the same time generating energy, and suggest that the treated wastewater can be used as a solvent and a nutrient source for the fermentation production of high value platform chemicals.

  3. Genetic population structure in an equatorial sparrow: roles for culture and geography.

    PubMed

    Danner, Julie E; Fleischer, Robert C; Danner, Raymond M; Moore, Ignacio T

    2017-03-10

    Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate if female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested if variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect and adjacent study sites were separated by approximately 25km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley, and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley, and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding if, and at what spatial scale, culture can affect population divergence. This article is protected by copyright. All rights reserved.

  4. Light Suppresses Bacterial Population through the Accumulation of Hydrogen Peroxide in Tobacco Leaves Infected with Pseudomonas syringae pv. tabaci

    PubMed Central

    Cheng, Dan-Dan; Liu, Mei-Jun; Sun, Xing-Bin; Zhao, Min; Chow, Wah S.; Sun, Guang-Yu; Zhang, Zi-Shan; Hu, Yan-Bo

    2016-01-01

    Pseudomonas syringae pv. tabaci (Pst) is a hemibiotrophic bacterial pathogen responsible for tobacco wildfire disease. Although considerable research has been conducted on the tobacco plant’s tolerance to Pst, the role of light in the responses of the photosystems to Pst infection is poorly understood. This study aimed to elucidate the underlying mechanisms of the reduced photosystem damage in tobacco leaves due to Pst infection under light conditions. Compared to dark conditions, Pst infection under light conditions resulted in less chlorophyll degradation and a smaller decline in photosynthetic function. Although the maximal quantum yield of photosystem II (PSII) and the activity of the photosystem I (PSI) complex decreased as Pst infection progressed, damage to PSI and PSII after infection was reduced under light conditions compared to dark conditions. Pst was 17-fold more abundant in tobacco leaves under dark compared to light conditions at 3 days post inoculation (dpi). Additionally, H2O2 accumulated to a high level in tobacco leaves after Pst infection under light conditions; although to a lesser extent, H2O2 accumulation was also significant under dark conditions. Pretreatment with H2O2 alleviated chlorotic lesions and decreased Pst abundance in tobacco leaves at 3 dpi under dark conditions. MV pretreatment had the same effects under light conditions, whereas 3-(3,4-dichlorophenyl)-1,1-dimethylurea pretreatment aggravated chlorotic lesions and increased the Pst population. These results indicate that chlorotic symptoms and the size of the bacterial population are each negatively correlated with H2O2 accumulation. In other words, light appears to suppress the Pst population in tobacco leaves through the accumulation of H2O2 during infection. PMID:27148334

  5. A bio-cultural approach to the study of food choice: The contribution of taste genetics, population and culture.

    PubMed

    Risso, Davide S; Giuliani, Cristina; Antinucci, Marco; Morini, Gabriella; Garagnani, Paolo; Tofanelli, Sergio; Luiselli, Donata

    2017-03-31

    The study of food choice, one of the most complex human traits, requires an integrated approach that takes into account environmental, socio-cultural and biological diversity. We recruited 183 volunteers from four geo-linguistic groups and highly diversified in terms of both genetic background and food habits from whom we collected genotypes and phenotypes tightly linked to taste perception. We confirmed previous genetic associations, in particular with stevioside perception, and noted significant differences in food consumption: in particular, broccoli, mustard and beer consumption scores were significantly higher (Adjusted P = 0.02, Adjusted P < 0.0001 and Adjusted P = 0.01, respectively) in North Europeans, when compared to the other groups. Licorice and Parmesan cheese showed lower consumption and liking scores in the Sri Lankan group (Adjusted P = 0.001 and Adjusted P < 0.001, respectively). We also highlighted how rs860170 (TAS2R16) strongly differentiated populations and was associated to salicin bitterness perception. Identifying genetic variants on chemosensory receptors that vary across populations and show associations with taste perception and food habits represents a step towards a better comprehension of this complex trait, aimed at improving the individual health status. This is the first study that concurrently explores the contribution of genetics, population diversity and cultural aspects in taste perception and food consumption.

  6. Effects of bacterial contamination of media on the diagnosis of Tritrichomonas foetus by culture and real-time PCR.

    PubMed

    Clothier, Kristin A; Villanueva, Michelle; Torain, Andrea; Hult, Cynthia; Wallace, Rachel

    2015-03-15

    The venereal pathogen Tritrichomonas foetus causes early embryonic death and abortion in cattle. With no approved treatment, control involves detection of infected animals and their removal from the herd. Culture is the traditional diagnostic method; standard media are formulated to support protozoal growth while suppressing competing organisms which may prevent microscopic recognition of T. foetus. Real-time PCR increases diagnostic sensitivity and specificity over culture but requires intact T. foetus DNA for detection. The purposes of this study were 1) to evaluate the effects of resident preputial bacteria that are not suppressed by antimicrobials in a commercial culture medium (InPouch™) on T. foetus detection by culture and PCR, and 2) to determine the performance of a laboratory-prepared culture medium on T. foetus detection by culture and PCR in samples with and without this bacterial contamination. A known concentration of one of three different strains of T. foetus inoculated into InPouch™ (IP) or modified Diamonds-Plastridge media (DPM) were co-incubated with a smegma culture media (CONTAM) for 24h and examined microscopically for the presence of identifiable T. foetus. PCR was performed on IP samples to determine if CONTAM also affected T. foetus DNA detection. A PCR protocol was then validated in DPM that performed similarly to the established IP PCR method. IP and DPM with CONTAM were spiked with serial dilutions that mimic field infections of one of four T. foetus strains and evaluated by real-time PCR; cycles to threshold (Ct) values and "positive" classification were compared between media. T. foetus motility and morphology as well as media pH were severely altered in IP samples with CONTAM compared to those without as well as to DPM medium with and without CONTAM (P<0.0001). PCR testing demonstrated significantly greater Ct values were for T. foetus DNA (P<0.001) in IP contaminated with smegma bacteria compared to those without. When using T

  7. RNA-stable-isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel.

    PubMed

    Tannock, Gerald W; Lawley, Blair; Munro, Karen; Sims, Ian M; Lee, Julian; Butts, Christine A; Roy, Nicole

    2014-04-01

    Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope ((13)C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [(13)C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect (13)C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the (13)C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA-stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism.

  8. eSalud: Designing and Implementing Culturally Competent eHealth Research With Latino Patient Populations

    PubMed Central

    Banas, Jennifer; Smith, Jeremiah; Languido, Lauren; Shen, Elaine; Gutierrez, Sandra; Cordero, Evelyn; Flores, Lucia

    2014-01-01

    eHealth is characterized by technology-enabled processes, systems, and applications that expedite accurate, real-time health information, feedback, and skill development to advance patient-centered care. When designed and applied in a culturally competent manner, eHealth tools can be particularly beneficial for traditionally marginalized ethnic minority groups, such as Latinos, a group that has been identified as being at the forefront of emerging technology use in the United States. In this analytic overview, we describe current eHealth research that has been conducted with Latino patient populations. In addition, we highlight cultural and linguistic factors that should be considered during the design and implementation of eHealth interventions with this population. With increasing disparities in preventive care information, behaviors, and services, as well as health care access in general, culturally competent eHealth tools hold great promise to help narrow this gap and empower communities. PMID:25320901

  9. The population structure of antibiotic-producing bacterial symbionts of Apterostigma dentigerum ants: impacts of coevolution and multipartite symbiosis.

    PubMed

    Caldera, Eric J; Currie, Cameron R

    2012-11-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured ([Formula: see text]) and dispersal-limited (i.e., significant isolation by distance; [Formula: see text], [Formula: see text]) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., [Formula: see text] in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species ([Formula: see text], [Formula: see text]), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a

  10. Improving protein delivery of fibroblast growth factor-2 from bacterial inclusion bodies used as cell culture substrates.

    PubMed

    Seras-Franzoso, Joaquin; Peebo, Karl; García-Fruitós, Elena; Vázquez, Esther; Rinas, Ursula; Villaverde, Antonio

    2014-03-01

    Bacterial inclusion bodies (IBs) have recently been used to generate biocompatible cell culture interfaces, with diverse effects on cultured cells such as cell adhesion enhancement, stimulation of cell growth or induction of mesenchymal stem cell differentiation. Additionally, novel applications of IBs as sustained protein delivery systems with potential applications in regenerative medicine have been successfully explored. In this scenario, with IBs gaining significance in the biomedical field, the fine tuning of this functional biomaterial is crucial. In this work, the effect of temperature on fibroblast growth factor-2 (FGF-2) IB production and performance has been evaluated. FGF-2 was overexpressed in Escherichia coli at 25 and 37 °C, producing IBs with differences in size, particle structure and biological activity. Cell culture topographies made with FGF-2 IBs biofabricated at 25 °C showed higher levels of biological activity as well as a looser supramolecular structure, enabling a higher protein release from the particles. In addition, the controlled use of FGF-2 protein particles enabled the generation of functional topographies with multiple biological activities being effective on diverse cell types.

  11. Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

    NASA Astrophysics Data System (ADS)

    González-Toril, E.; Amils, R.; Delmas, R. J.; Petit, J.-R.; Komárek, J.; Elster, J.

    2009-01-01

    Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas), in a minimal mineral (oligotrophic) media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the marine Antarctic soil the poorest (only one). Snow samples from Col du Midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone). The only microorganism identified in the Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.

  12. Defined bacterial culture development for methane generation from lactose. [Streptococcus lactis; Clostridium formicoaceticum; Methanococcus mazei

    SciTech Connect

    Yang, S.T.; Tang, I.C.; Okos, M.R.

    1988-06-20

    The defined microbial cultures for methane generation from lactose were investigated. A mixed culture consisting of homolactic (Streptococcus lactis), homoacetic (Clostridium formicoaceticum), and acetate-utilizing methanogenic (Methanococcus mazei) bacteria was used to convert lactose and whey permeate to methane at mesophilic temperatures (35-37/sup 0/C) and a pH around 7.0. Lactose was first converted to lactic acid by S. lactis, then to acetic acid by C. formicoaceticum, and finally to methane and CO/sub 2/ by M. mazei. About 5.3 mol methane were obtained from each mole of lactose consumed, and the conversion of acetate to methane was the rate-limiting step for this mixed-culture fermentation.

  13. A heterogeneous population model for the analysis of bacterial growth kinetics.

    PubMed

    McKellar, R C

    1997-05-20

    A two-compartment, heterogeneous population model (HPM) was derived using the simulation software SB ModelMaker to describe the growth of Listeria monocytogenes in bacteriological media at 5-35 degrees C. The model assumed that, at time t = 0, the inoculum was distributed between two distinct compartments, Non-Growing and Growing, and that growth could be described by four parameters: initial total cell population (N0), final maximum cell population (Nmax), maximum specific growth rate (mu(max)), and initial cell population in the Growing compartment (G0). The model was fitted to the data by optimizing the four parameters, and lag phase duration (lambda) was calculated. The resulting values of mu(max) and lambda were similar to those determined using the modified Gompertz equation. A new parameter, w0, was defined which relates to the proportion of the initial cell population capable of growth, and is a measure of the initial physiological state of the cells. A modified model in which mu(max) was replaced with a temperature function, and w0 replaced G0, was used to predict the effect of temperature on the growth of L. monocytogenes. The results of this study raise questions concerning the current definition of the lag phase.

  14. Antibiotic resistance among cultured bacterial isolates from bioethanol fermentation facilities across the United States.

    PubMed

    Murphree, Colin A; Heist, E Patrick; Moe, Luke A

    2014-09-01

    Bacterial contamination of fuel ethanol fermentations by lactic acid bacteria (LAB) can have crippling effects on bioethanol production. Producers have had success controlling bacterial growth through prophylactic addition of antibiotics to fermentors, yet concerns have arisen about antibiotic resistance among the LAB. Here, we report on mechanisms used by 32 LAB isolates from eight different US bioethanol facilities to persist under conditions of antibiotic stress. Minimum inhibitory concentration assays with penicillin, erythromycin, and virginiamycin revealed broad resistance to each of the antibiotics as well as high levels of resistance to individual antibiotics. Phenotypic assays revealed that antibiotic inactivation mechanisms contributed to the high levels of individual resistances among the isolates, especially to erythromycin and virginiamycin, yet none of the isolates appeared to use a β-lactamase. Biofilm formation was noted among the majority of the isolates and may contribute to persistence under low levels of antibiotics. Nearly all of the isolates carried at least one canonical antibiotic resistance gene and many carried more than one. The erythromycin ribosomal methyltransferase (erm) gene class was found in 19 of 32 isolates, yet a number of these isolates exhibit little to no resistance to erythromycin. The erm genes were present in 15 isolates that encoded more than one antibiotic resistance mechanism, suggestive of potential genetic linkages.

  15. Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants.

    PubMed

    Araújo, Welington L; Marcon, Joelma; Maccheroni, Walter; Van Elsas, Jan Dirk; Van Vuurde, Jim W L; Azevedo, João Lúcio

    2002-10-01

    Citrus variegated chlorosis (CVC) is caused by Xylella fastidiosa, a phytopathogenic bacterium that can infect all Citrus sinensis cultivars. The endophytic bacterial communities of healthy, resistant, and CVC-affected citrus plants were studied by using cultivation as well as cultivation-independent techniques. The endophytic communities were assessed in surface-disinfected citrus branches by plating and denaturing gradient gel electrophoresis (DGGE). Dominant isolates were characterized by fatty-acid methyl ester analysis as Bacillus pumilus, Curtobacterium flaccumfaciens, Enterobacter cloacae, Methylobacterium spp. (including Methylobacterium extorquens, M. fujisawaense, M. mesophilicum, M. radiotolerans, and M. zatmanii), Nocardia sp., Pantoea agglomerans, and Xanthomonas campestris. We observed a relationship between CVC symptoms and the frequency of isolation of species of Methylobacterium, the genus that we most frequently isolated from symptomatic plants. In contrast, we isolated C. flaccumfaciens significantly more frequently from asymptomatic plants than from those with symptoms of CVC while P. agglomerans was frequently isolated from tangerine (Citrus reticulata) and sweet-orange (C. sinensis) plants, irrespective of whether the plants were symptomatic or asymptomatic or showed symptoms of CVC. DGGE analysis of 16S rRNA gene fragments amplified from total plant DNA resulted in several bands that matched those from the bacterial isolates, indicating that DGGE profiles can be used to detect some endophytic bacteria of citrus plants. However, some bands had no match with any isolate, suggesting the occurrence of other, nonculturable or as yet uncultured, endophytic bacteria. A specific band with a high G+C ratio was observed only in asymptomatic plants. The higher frequency of C. flaccumfaciens in asymptomatic plants suggests a role for this organism in the resistance of plants to CVC.

  16. Synchrony in human, mouse and bacterial cell cultures--a comparison

    NASA Technical Reports Server (NTRS)

    Helmstetter, Charles E.; Thornton, Maureen; Romero, Ana; Eward, K. Leigh

    2003-01-01

    Growth characteristics of synchronous human MOLT-4, human U-937 and mouse L1210 cultures produced with a new minimally-disturbing technology were compared to each other and to synchronous Escherichia coli B/r. Based on measurements of cell concentrations during synchronous growth, synchrony persisted in similar fashion for all cells. Cell size and DNA distributions in the mammalian cultures also progressed synchronously and reproducibly for multiple cell cycles. The results demonstrate that unambiguous multi-cycle synchrony, critical for verifying the absence of significant growth imbalances induced by the synchronization procedure, is feasible with these cell lines, and possibly others.

  17. Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices

    PubMed Central

    Xia, Ye; DeBolt, Seth; Dreyer, Jamin; Scott, Delia; Williams, Mark A.

    2015-01-01

    Plants have a diverse internal microbial biota that has been shown to have an important influence on a range of plant health attributes. Although these endophytes have been found to be widely occurring, few studies have correlated agricultural production practices with endophyte community structure and function. One agricultural system that focuses on preserving and enhancing soil microbial abundance and biodiversity is organic farming, and numerous studies have shown that organically managed system have increased microbial community characteristics. Herein, the diversity and specificity of culturable bacterial endophytes were evaluated in four vegetable crops: corn, tomato, melon, and pepper grown under organic or conventional practices. Endophytic bacteria were isolated from surface-sterilized shoot, root, and seed tissues and sequence identified. A total of 336 bacterial isolates were identified, and grouped into 32 species and five phyla. Among these, 239 isolates were from organically grown plants and 97 from those grown conventionally. Although a diverse range of bacteria were documented, 186 were from the Phylum Firmicutes, representing 55% of all isolates. Using the Shannon diversity index, we observed a gradation of diversity in tissues, with shoots and roots having a similar value, and seeds having the least diversity. Importantly, endophytic microbial species abundance and diversity was significantly higher in the organically grown plants compared to those grown using conventional practices, potentially indicating that organic management practices may increase endophyte presence and diversity. The impact that these endophytes could have on plant growth and yield was evaluated by reintroducing them into tomato plants in a greenhouse environment. Of the bacterial isolates tested, 61% were found to promote tomato plant growth and 50–64% were shown to enhance biomass accumulation, illustrating their potential agroecosystem application. PMID:26217348

  18. a Paradox in Life Thermodynamics:. the Long-Term Survival of Bacterial Populations

    NASA Astrophysics Data System (ADS)

    Carnazza, S.; Guglielmino, S.; Nicolò, M.; Santoro, F.; Oliveri, F.

    2008-04-01

    Pseudomonas aeruginosa is an ubiquitous bacterium that, due to its high metabolic versatility, is able to persist for prolonged periods of time. It is the ethiological agent of cystic fibrosis and is involved in urinary infections, conjunctivitis, otitis and pneumonia. We present the results of a batch culture of P. aeruginosa inoculated in LB medium and monitored weekly for a period of 24 months during which no more nutrients are added. A mathematical model suitable to describe the experimental viability data is given.

  19. Enumerating Virus-Like Particles and Bacterial Populations in the Sinuses of Chronic Rhinosinusitis Patients Using Flow Cytometry

    PubMed Central

    Carlson-Jones, Jessica A. P.; Paterson, James S.; Newton, Kelly; Smith, Renee J.; Dann, Lisa M.; Speck, Peter; Mitchell, James G.; Wormald, Peter-John

    2016-01-01

    There is increasing evidence to suggest that the sinus microbiome plays a role in the pathogenesis of chronic rhinosinusitis (CRS). However, the concentration of these microorganisms within the sinuses is still unknown. We show that flow cytometry can be used to enumerate bacteria and virus-like particles (VLPs) in sinus flush samples of CRS patients. This was achieved through trialling 5 sample preparation techniques for flow cytometry. We found high concentrations of bacteria and VLPs in these samples. Untreated samples produced the highest average bacterial and VLP counts with 3.3 ± 0.74 x 107 bacteria ml-1 and 2.4 ± 1.23 x 109 VLP ml-1 of sinus flush (n = 9). These counts were significantly higher than most of the treated samples (p < 0.05). Results showed 103 and 104 times inter-patient variation for bacteria and VLP concentrations. This wide variation suggests that diagnosis and treatment need to be personalised and that utilising flow cytometry is useful and efficient for this. This study is the first to enumerate bacterial and VLP populations in the maxillary sinus of CRS patients. The relevance of enumeration is that with increasing antimicrobial resistance, antibiotics are becoming less effective at treating bacterial infections of the sinuses, so alternative therapies are needed. Phage therapy has been proposed as one such alternative, but for dosing, the abundance of bacteria is required. Knowledge of whether phages are normally present in the sinuses will assist in gauging the safety of applying phage therapy to sinuses. Our finding, that large numbers of VLP are frequently present in sinuses, indicates that phage therapy may represent a minimally disruptive intervention towards the nasal microbiome. We propose that flow cytometry can be used as a tool to assess microbial biomass dynamics in sinuses and other anatomical locations where infection can cause disease. PMID:27171169

  20. Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil.

    PubMed

    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.

  1. Hierarchical nested trial design (HNTD) for demonstrating treatment efficacy of new antibacterial drugs in patient populations with emerging bacterial resistance.

    PubMed

    Huque, Mohammad F; Valappil, Thamban; Soon, Guoxing Greg

    2014-11-10

    In the last decade or so, pharmaceutical drug development activities in the area of new antibacterial drugs for treating serious bacterial diseases have declined, and at the same time, there are worries that the increased prevalence of antibiotic-resistant bacterial infections, especially the increase in drug-resistant Gram-negative infections, limits available treatment options . A recent CDC report, 'Antibiotic Resistance Threats in the United States', indicates that antimicrobial resistance is one of our most serious health threats. However, recently, new ideas have been proposed to change this situation. An idea proposed in this regard is to conduct randomized clinical trials in which some patients, on the basis of a diagnostic test, may show presence of bacterial pathogens that are resistant to the control treatment, whereas remaining patients would show pathogens that are susceptible to the control. The control treatment in such trials can be the standard of care or the best available therapy approved for the disease. Patients in the control arm with resistant pathogens can have the option for rescue therapies if their clinical signs and symptoms worsen. A statistical proposal for such patient populations is to use a hierarchical noninferiority-superiority nested trial design that is informative and allows for treatment-to-control comparisons for the two subpopulations without any statistical penalty. This design can achieve in the same trial dual objectives: (i) to show that the new drug is effective for patients with susceptible pathogens on the basis of a noninferiority test and (ii) to show that it is superior to the control in patients with resistant pathogens. This paper addresses statistical considerations and methods for achieving these two objectives for this design. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

  2. Hydroxytyrosol from tyrosol using hydroxyphenylacetic acid-induced bacterial cultures and evidence of the role of 4-HPA 3-hydroxylase.

    PubMed

    Liebgott, Pierre-Pol; Amouric, Agnès; Comte, Alexia; Tholozan, Jean-Luc; Lorquin, Jean

    2009-12-01

    Hydroxytyrosol (HTyr) is a potent natural antioxidant found in olive mill wastewaters. Bacterial conversion of 4-tyrosol (2-(4-hydroxyphenyl)-ethanol) to HTyr was reported in a limited number of bacterial species including Pseudomonas aeruginosa. In this work, we studied this conversion, taking as a model the newly isolated Halomonas sp. strain HTB24. It was first hypothesized that the enzyme responsible for 4-tyrosol hydroxylation in HTyr was a 4-hydroxyphenylacetic acid 3-hydroxylase (HPAH, EC 1.14.13.3), previously known to convert 4-hydroxyphenylacetic acid (4-HPA) into 3,4-dihydroxyphenylacetic acid (3,4-DHPA) in P. aeruginosa. Cloning and expression of hpaB (oxygenase component) and hpaC (reductase component) genes from P. aeruginosa confirmed this hypothesis. Furthermore, using cultures of HTB24 containing 4-tyrosol, it was shown that 4-HPA accumulation preceded 4-tyrosol hydroxylation. We further demonstrated that the synthesis of HPAH activity was induced by 4-HPA, with the latter compound being formed from 4-tyrosol oxidation by aryl-dehydrogenases. Interestingly, similar results were obtained with other 4-HPA-induced bacteria, including P. aeruginosa, Serratia marcescens, Escherichia coli, Micrococcus luteus and other Halomonas, thus demonstrating general hydroxylating activity of 4-tyrosol by the HPAH enzyme. E. coli W did not have aryl-dehydrogenase activity and hence were unable to oxidize 4-tyrosol to 4-HPA and HTyr to 3,4-DHPA, making this bacterium a good candidate for achieving better HTyr production.

  3. A Diverse Soil Microbiome Degrades More Crude Oil than Specialized Bacterial Assemblages Obtained in Culture

    PubMed Central

    Stefani, Franck O. P.; Abram, Katrina; Champagne, Julie; Yergeau, Etienne; Hijri, Mohamed

    2016-01-01

    ABSTRACT Soil microbiome modification may alter system function, which may enhance processes like bioremediation. In this study, we filled microcosms with gamma-irradiated soil that was reinoculated with the initial soil or cultivated bacterial subsets obtained on regular media (REG-M) or media containing crude oil (CO-M). We allowed 8 weeks for microbiome stabilization, added crude oil and monoammonium phosphate, incubated the microcosms for another 6 weeks, and then measured the biodegradation of crude oil components, bacterial taxonomy, and functional gene composition. We hypothesized that the biodegradation of targeted crude oil components would be enhanced by limiting the microbial taxa competing for resources and by specifically selecting bacteria involved in crude oil biodegradation (i.e., CO-M). Postincubation, large differences in taxonomy and functional gene composition between the three microbiome types remained, indicating that purposeful soil microbiome structuring is feasible. Although phylum-level bacterial taxonomy was constrained, operational taxonomic unit composition varied between microbiome types. Contrary to our hypothesis, the biodegradation of C10 to C50 hydrocarbons was highest when the original microbiome was reinoculated, despite a higher relative abundance of alkane hydroxylase genes in the CO-M microbiomes and of carbon-processing genes in the REG-M microbiomes. Despite increases in the relative abundances of genes potentially linked to hydrocarbon processing in cultivated subsets of the microbiome, reinoculation of the initial microbiome led to maximum biodegradation. IMPORTANCE In this study, we show that it is possible to sustainably modify microbial assemblages in soil. This has implications for biotechnology, as modification of gut microbial assemblages has led to improved treatments for diseases like Clostridium difficile infection. Although the soil environment determined which major phylogenetic groups of bacteria would dominate

  4. Genetic relationship between cultured populations of Pacific oyster revealed by RAPD analysis.

    PubMed

    Aranishi, Futoshi; Okimoto, Takane

    2004-01-01

    We developed random amplified polymorphic DNA (RAPD) analysis for the assessment of the genetic relationship between cultured populations of the Pacific oyster Crassostrea gigas Thunberg in Hiroshima and Goseong, the largest oyster farming areas in Japan and Korea, respectively. Of 25 arbitrary primers comprising decamer nucleotides of random sequences, polymerase chain reaction amplifications with 5 different primers gave reproducible electrophoretic patterns. A total of 49 RAPD markers were clearly identified for the Hiroshima and Goseong populations, and 46 markers were polymorphic presenting mean polymorphism rates of the respective populations at 92.29% and 93.32%. Pairwise genetic distances of each 20 individuals from these populations served to produce a UPGMA dendrogram. The dendrogram comprised two main clusters, one of which was a nested cluster including all individuals of the Hiroshima population along with 12 individuals of the Goseong population, and the other cluster included the remaining individuals of the Goseong population. Results indicate that RAPD markers are useful for the assessment of the genetic relationships between populations of the Pacific oyster and further that a significant portion of oysters imported from Korea could be genetically related to the Hiroshima population.

  5. BACTERIAL POPULATION SHIFTS IN THE RUMEN OF LACTATING DAIRY COWS WITHIN AND ACROSS FEEDING CYCLES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While species composition of the ruminal microflora is thought to change during the feeding cycle due to variations in feed intake and ruminal environmental conditions, no studies have systematically characterized these purported population shifts. We used PCR amplification and automated ribosomal ...

  6. Bacterial populations within copper mine tailings: long-term effects of amendment with Class A biosolids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study evaluates the effect of surface application of dried Class A biosolids on microbial populations within copper mine tailings. Methods and Results: Mine tailing sites were established at ASARCO Mission Mine close to Sahuarita, Arizona. Site 1 (Dec. 1998) was amended with 248 tons ha-1 of C...

  7. Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices.

    PubMed

    Battini, Fabio; Cristani, Caterina; Giovannetti, Manuela; Agnolucci, Monica

    2016-02-01

    Arbuscular Mycorrhizal Fungi (AMF) live in symbiosis with most crop plants and represent essential elements of soil fertility and plant nutrition and productivity, facilitating soil mineral nutrient uptake and protecting plants from biotic and abiotic stresses. These beneficial services may be mediated by the dense and active spore-associated bacterial communities, which sustain diverse functions, such as the promotion of mycorrhizal activity, biological control of soilborne diseases, nitrogen fixation, and the supply of nutrients and growth factors. In this work, we utilised culture-dependent methods to isolate and functionally characterize the microbiota strictly associated to Rhizophagus intraradices spores, and molecularly identified the strains with best potential plant growth promoting (PGP) activities by 16S rDNA sequence analysis. We isolated in pure culture 374 bacterial strains belonging to different functional groups-actinobacteria, spore-forming, chitinolytic and N2-fixing bacteria-and screened 122 strains for their potential PGP activities. The most common PGP trait was represented by P solubilization from phytate (69.7%), followed by siderophore production (65.6%), mineral P solubilization (49.2%) and IAA production (42.6%). About 76% of actinobacteria and 65% of chitinolytic bacteria displayed multiple PGP activities. Nineteen strains with best potential PGP activities, assigned to Sinorhizobium meliloti, Streptomyces spp., Arthrobacter phenanthrenivorans, Nocardiodes albus, Bacillus sp. pumilus group, Fictibacillus barbaricus and Lysinibacillus fusiformis, showed the ability to produce IAA and siderophores and to solubilize P from mineral phosphate and phytate, representing suitable candidates as biocontrol agents, biofertilisers and bioenhancers, in the perspective of targeted management of beneficial symbionts and their associated bacteria in sustainable food production systems.

  8. Carbon transformations by attached bacterial populations in granitic groundwater from deep crystalline bed-rock of the Stripa research mine.

    PubMed

    Ekendahl, S; Pedersen, K

    1994-07-01

    This paper presents and compares the assimilation rates of CO2 and lactate, and the lactate respiration rates, of attached bacterial populations growing in slowly flowing groundwater (1-3 mm s-1) from deep crystalline bed-rock of the Stripa research mine, Sweden. The bacteria studied grew in anoxic, high-pH (9-10) and low-redox artesian groundwater flowing up through tubing from two levels of a borehole designated V2, 812-820 m and 970-1240 m below ground. Bacteria were allowed to attach to and grow on sterile glass microscope slides in laminar-flow reactors connected to the flowing groundwater. Total numbers of bacteria were counted by acridine orange direct counts. The bacteria grew slowly, with doubling times of 34 d at 10 degrees C for the 812-820 m population, 23 d for the 970-1240 m population at 10 degrees C and 16 d for this population at 20 degrees C. Numbers of attached bacteria reached between 10(6) and 10(7) bacteria cm-2. The populations at the two levels of the borehole were different in physiology as well as in phylogeny and reflected the heterogeneity between the sampling levels. The earlier proposed presence of sulphate-reducing bacteria could not be confirmed. This is discussed in relation to results from 16S rRNA gene sequencing studies. The CO2 assimilation rates (as mol CO2 cm-2 h-1, using liquid scintillation techniques) increased with depth and temperature.(ABSTRACT TRUNCATED AT 250 WORDS)

  9. Culture-independent study of bacterial communities in tropical river sediment.

    PubMed

    Thoetkiattikul, Honglada; Mhuantong, Wuttichai; Pinyakong, Onruthai; Wisawapipat, Worachart; Yamazoe, Atsushi; Fujita, Nobuyuki; Eurwilaichitr, Lily; Champreda, Verawat

    2017-01-01

    Ubiquitous microbial communities in river sediments actively govern organic matter decomposition, nutrient recycling, and remediation of toxic compounds. In this study, prokaryotic diversity in two major rivers in central Thailand, the Chao Phraya (CP) and the Tha Chin (TC) distributary was investigated. Significant differences in sediment physicochemical properties, particularly silt content, were noted between the two rivers. Tagged 16S rRNA sequencing on a 454 platform showed that the sediment microbiomes were dominated by Gammaproteobacteria and sulfur/sulfate reducing Deltaproteobacteria, represented by orders Desulfobacteriales and Desulfluromonadales together with organic degraders Betaproteobacteria (orders Burkholderiales and Rhodocyclales) together with the co-existence of Bacteroidetes predominated by Sphingobacteriales. Enrichment of specific bacterial orders was found in the clayey CP and silt-rich TC sediments, including various genera with known metabolic capability on decomposition of organic matter and xenobiotic compounds. The data represent one of the pioneered works revealing heterogeneity of bacteria in river sediments in the tropics.

  10. Comparative assessment of the efficacy of bacterial and cyanobacterial phytohormones in plant tissue culture.

    PubMed

    Hussain, Anwar; Hasnain, Shahida

    2012-04-01

    Efficient callus and explant regeneration medium, using microbial extract (SPE purified) or supernatant has been formulated for Brassica oleracea L. var. capitata. Two cyanobacterial strains (Anabaena sp. Ck1 and Chroococcidiopsis sp. Ck4) and two bacterial strains, (Pseudomonas spp. Am3 and Am4) known to produce a number of cytokinins, tZ, cZ, ZR, DHZR and IAA were selected for the media formulation. Supernatant from strains with high cytokinin to IAA ratio, including Pseudomonas aeruginosa Am3 (2.08) and Chroococcidiopsis sp. Ck4 (0.8) efficiently induced compact calli which were turned green upon exposure to light. The strains producing lower cytokinins to IAA ratio (0.11-0.13) on the other hand induced friable callus which were unable to regenerate on the selected media combinations. Leaf, stem and root explants of Brassica oleracea L. regenerated on MS medium supplemented with phytohormones from microbial origin with efficiency comparable to standard cytokinins and IAA. Supplements from cyanobacterial origin proved to be the best for induction of adventitious roots and shoots on internodal and petiolar segments. Hypocotyl explants however, responded well on MS supplemented with bacterial metabolites. Induction of adventitious shoots on root explants was supported by phytohormones from both origin equally well. Callus induction on the seeds and regeneration of shoots on calli was also observed. Cyanobacteria based media were more efficient to induce calli capable of regeneration upon exposure to light. Internodal explants were highly amenable to regenerate shoot and roots simultaneously. Root explants were the less successful to regenerate shoots.

  11. Bartonellae in domestic and stray cats from Israel: comparison of bacterial cultures and high-resolution melt real-time PCR as diagnostic methods.

    PubMed

    Gutiérrez, Ricardo; Morick, Danny; Gross, Ifat; Winkler, Ronen; Abdeen, Ziad; Harrus, Shimon

    2013-12-01

    To determine the occurrence of feline bartonellosis in Israel, blood samples were collected from 179 stray and 155 domestic cats from 18 cities or villages in central and northcentral Israel. Samples were screened for Bartonella infection by culture isolation and molecular detection using high-resolution melt (HRM) real-time PCR assay targeting the 16S-23S rRNA internal transcribed spacer (ITS). All positive samples were confirmed by two additional HRM real-time PCR assays targeting two fragments of the β-subunit of RNA polymerase (rpoB) and the 16S rRNA genes. The prevalence of Bartonella spp. infection in the general tested population was 25.1% (84/334). A higher prevalence was detected in the stray (30.7%; 55/179) than the domestic cats (18.7%; 29/155). Bartonella henselae, Bartonella clarridgeiae, and Bartonella koehlerae were highly prevalent in both cat populations, however their distribution among the two populations varied significantly (p=0.016). B. clarridgeiae and B. koehlerae were found to be more prevalent in stray than domestic cats, whereas B. henselae was evenly distributed. Co-infection with two or more different Bartonella spp. was determined in 2.1% (7) of the cats. The ITS HRM real-time PCR assay used in this study was shown to have a greater screening power than bacterial isolation, detecting 94.0% (79/84) compared to 35.7% (30/84), respectively, of all positive samples. The high prevalence of these zoonotic Bartonella species, coupled with the overpopulation of stray cats, and increased numbers of domestic cats in the major urban centers in Israel represent a significant threat for the public health in this country.

  12. The effect of polymer addition on granulation in an anaerobic baffled reactor (ABR). Part II: compartmentalization of bacterial populations.

    PubMed

    Uyanik, S; Sallis, P J; Anderson, G K

    2002-02-01

    The microbial ecology of wastewater treatment plants remains one of the least understood aspects in both aerobic and anaerobic systems, despite the fact that both processes are ultimately dependent on an active biomass for operational efficiency. Ultimately, future developments in anaerobic treatment processes will require a much greater understanding of the fundamental relationships between bacterial populations within the biomass if optimum process efficiency is to be fully realised. This study assesses the influence of polymer addition on granule formation within an ABR and compares the ecology of the biomass in each compartment of two ABRs treating ice-cream wastewater. To our knowledge, this is the first reported characterisation of the microbiology of acidogenic and methanogenic bacteria in the individual compartments of an ABR. The polymer-amended reactor contained sludge that had a greater density of anaerobic bacteria and larger and denser granules than the control reactor, indicating that polymer addition possibly contributed to the retention of active biomass within the ABR. The average fraction of autofluorescent methanogens was lower, with 1.5% being in the initial compartments of the ABRs, compared to the last compartment which had 15%, showing that each compartment of an ABR had a unique microbial composition. Partial spatial separation of anaerobic bacteria appeared to have taken place with acidogenic bacteria predominating in the initial compartments and methanogenic bacteria predominating in the final compartments. Scanning electron micrographs have revealed that the dominant bacteria in the initial compartments of the ABR (Compartments 1 and 2) were those which could consume H2/CO2 and formate as substrate, i.e. Methanobrevibacter, Methanococcus, with populations shifting to acetate utilisers, i.e. Methanosaeta, Methanosarcina, in the final compartments (Compartments 3 and 4). In addition, there appeared to be a stratified structure to the

  13. Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

    PubMed Central

    Hernández, Marcela; Yuan, Quan; Conrad, Ralf

    2015-01-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with 13CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with 13C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the “Spartobacteria” and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. PMID:25616793

  14. Collective Bacterial Dynamics Revealed Using a Three-Dimensional Population-Scale Defocused Particle Tracking Technique

    PubMed Central

    Wu, Mingming; Roberts, John W.; Kim, Sue; Koch, Donald L.; DeLisa, Matthew P.

    2006-01-01

    An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming Escherichia coli cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type Escherichia coli strain RP437 as well as for isogenic derivatives that display smooth swimming due to a cheA deletion (strain RP9535) or incessant tumbling behavior due to a cheZ deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria. PMID:16820497

  15. Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

    NASA Technical Reports Server (NTRS)

    Ortega, Maya C.

    2011-01-01

    Stromatolites are layered sedimentary structures resulting from microbial mat communities that remove carbon dioxide from their environment and biomineralize it as calcium carbonate. Although prevalent in the fossil record, stromatolites are rare in the modem world and are only found in a few locations including Highbome Cay in the Bahamas. The stromatolites found at this shallow marine site are analogs to ancient microbial mat ecosystems abundant in the Precambrian period on ancient Earth. To understand how stromatolites form and develop, it is important to identify what microorganisms are present in these mats, and how these microbes contribute to geological structure. These results will provide insight into the molecular and geochemical processes of microbial communities that prevailed on ancient Earth. Since stromatolites are formed by lithifying microbial mats that are able to mineralize calcium carbonate, understanding the biological mechanisms involved may lead to the development of carbon sequestration technologies that will be applicable in human spaceflight, as well as improve our understanding of global climate and its sustainability. The objective of my project was to analyze the archaeal and bacterial dIversity in stromatolites from Highborn Cay in the Bahamas. The first step in studying the molecular processes that the microorganisms carry out is to ascertain the microbial complexity within the mats, which includes identifying and estimating the numbers of different microbes that comprise these mats.

  16. Bacterial and fungal DNA extraction from positive blood culture bottles: a manual and an automated protocol.

    PubMed

    Mäki, Minna

    2015-01-01

    When adapting a gene amplification-based method in a routine sepsis diagnostics using a blood culture sample as a specimen type, a prerequisite for a successful and sensitive downstream analysis is the efficient DNA extraction step. In recent years, a number of in-house and commercial DNA extraction solutions have become available. Careful evaluation in respect to cell wall disruption of various microbes and subsequent recovery of microbial DNA without putative gene amplification inhibitors should be conducted prior selecting the most feasible DNA extraction solution for the downstream analysis used. Since gene amplification technologies have been developed to be highly sensitive for a broad range of microbial species, it is also important to confirm that the used sample preparation reagents and materials are bioburden-free to avoid any risks for false-positive result reporting or interference of the diagnostic process. Here, one manual and one automated DNA extraction system feasible for blood culture samples are described.

  17. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

    PubMed

    Johnston, Eric R; Rodriguez-R, Luis M; Luo, Chengwei; Yuan, Mengting M; Wu, Liyou; He, Zhili; Schuur, Edward A G; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong; Konstantinidis, Konstantinos T

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  18. Diverse UV-B resistance of culturable bacterial community from high-altitude wetland water.

    PubMed

    Zenoff, Veronica Fernández; Heredia, Judith; Ferrero, Marcela; Siñeriz, Faustino; Farías, María Eugenia

    2006-05-01

    Isolation of most ultraviolet B (UV-B)-resistant culturable bacteria that occur in the habitat of Laguna Azul, a high-altitude wetland [4554 m above sea level (asl)] from the Northwestern Argentinean Andes, was carried out by culture-based methods. Water from this environment was exposed to UV-B radiation under laboratory conditions during 36 h, at an irradiance of 4.94 W/m2. It was found that the total number of bacteria in water samples decreased; however, most of the community survived long-term irradiation (312 nm) (53.3 kJ/m2). The percentage of bacteria belonging to dominant species did not vary significantly, depending on the number of UV irradiation doses. The most resistant microbes in the culturable community were Gram-positive pigmented species (Bacillus megaterium [endospores and/or vegetative cells], Staphylococcus saprophyticus, and Nocardia sp.). Only one Gram-negative bacterium could be cultivated (Acinetobacter johnsonii). Nocardia sp. that survived doses of 3201 kJ/m2 were the most resistant bacteria to UV-B treatment. This study is the first report on UV-B resistance of a microbial community isolated from high-altitude extreme environments, and proposes a method for direct isolation of UV-B-resistant bacteria from extreme irradiated environments.

  19. Propionibacterium acnes: Time-to-Positivity in Standard Bacterial Culture From Different Anatomical Sites

    PubMed Central

    Abdulmassih, Rasha; Makadia, Jina; Como, James; Paulson, Michelle; Min, Zaw; Bhanot, Nitin

    2016-01-01

    Background Propionibacterium acnes infections are likely under-recognized and underreported. This is partly because of low clinical suspicion, perceived non-pathogenicity, or lack of adequate culture incubation time. We conducted a study to assess t