Science.gov

Sample records for efficient bacterial association

  1. Heterotrophic bacterial production, respiration, and growth efficiency associated with upwelling intensity in the Ulleung Basin, East Sea

    NASA Astrophysics Data System (ADS)

    Kim, Bomina; Kim, Sung-Han; Kwak, Jung Hyun; Kang, Chang-Keun; Lee, Sang Heon; Hyun, Jung-Ho

    2017-09-01

    We investigated bacterial production (BP) and respiration (BR), as well as the physico-chemical properties of the water column, to elucidate the effect of upwelling on heterotrophic bacterial metabolic activities and growth efficiency (BGE) in July 2012 and May 2013 in the Ulleung Basin (UB), East/Japan Sea. The upwelled conditions were characterized by higher chlorophyll-a (Chl-a) concentrations resulting from the upward shift of the nitracline compared to that of the non-upwelled condition. Analyses of the size fractions of Chl-a and pigment composition revealed that large size phytoplankton (> 20 μm), mainly consisting of diatoms, appeared to be the major phytoplankton component. BP and BR were significantly correlated with Chl-a (P < 0.001), but the correlations with temperature were not significant (P > 0.05). These results suggest that bacterial metabolic activities are stimulated by the availability of organic resources enhanced by upwelling in the UB. Further statistical analysis showed that the difference in BP and BGE with variations in upwelling intensity were significant (P = 0.018 for BP, P = 0.035 for BGE), but the difference in BR was not significant (P = 0.321). These results suggest that metabolic energy is partitioned more for BP under a strong upwelling condition, i.e. high nutrient and Chl-a conditions. In contrast, the energy generated via respiration was partitioned more for maintaining metabolism rather than for biomass production under weakly or non-upwelled conditions, i.e. stratified and low Chl-a conditions. Overall, our results suggest that any changes in upwelling intensity would significantly affect the carbon cycle associated with the fate of primary production, and the role of the microbial loop in the UB where changes in the intensity and frequency of upwelling associated with climatic changes are in progress.

  2. Transfusion-associated bacterial sepsis.

    PubMed Central

    Wagner, S J; Friedman, L I; Dodd, R Y

    1994-01-01

    The incidence of sepsis caused by transfusion of bacterially contaminated blood components is similar to or less than that of transfusion-transmitted hepatitis C virus infection, yet significantly exceeds those currently estimated for transfusion-associated human immunodeficiency and hepatitis B viruses. Outcomes are serious and may be fatal. In addition, transfusion of sterile allogenic blood can have generalized immunosuppressive effects on recipients, resulting in increased susceptibility to postoperative infection. This review examines the frequency of occurrence of transfusion-associated sepsis, the organisms implicated, and potential sources of bacteria. Approaches to minimize the frequency of sepsis are discussed, including the benefits and disadvantages of altering the storage conditions for blood. In addition, the impact of high levels of bacteria on the gross characteristics of erythrocyte and platelet concentrates is described. The potentials and limitations of current tests for detecting bacteria in blood are also discussed. PMID:7923050

  3. Bacterial and viral infections associated with influenza.

    PubMed

    Joseph, Carol; Togawa, Yu; Shindo, Nahoko

    2013-09-01

    Influenza-associated bacterial and viral infections are responsible for high levels of morbidity and death during pandemic and seasonal influenza episodes. A review was undertaken to assess and evaluate the incidence, epidemiology, aetiology, clinical importance and impact of bacterial and viral co-infection and secondary infection associated with influenza. A review was carried out of published articles covering bacterial and viral infections associated with pandemic and seasonal influenza between 1918 and 2009 (and published through December 2011) to include both pulmonary and extra-pulmonary infections. While pneumococcal infection remains the predominant cause of bacterial pneumonia, the review highlights the importance of other co- and secondary bacterial and viral infections associated with influenza, and the emergence of newly identified dual infections associated with the 2009 H1N1 pandemic strain. Severe influenza-associated pneumonia is often bacterial and will necessitate antibiotic treatment. In addition to the well-known bacterial causes, less common bacteria such as Legionella pneumophila may also be associated with influenza when new influenza strains emerge. This review should provide clinicians with an overview of the range of bacterial and viral co- or secondary infections that could present with influenza illness.

  4. Change of Collision Efficiency with Distance in Bacterial Transport Experiements

    SciTech Connect

    Dong, Hailiang; Scheibe, Timothy D.; Johnson, William P.; Monkman, Crystal; Fuller, Mark E.

    2006-05-01

    Previous bacterial transport studies have shown decreased bacterial adhesion with transport distance, largely based on laboratory core experiments. An inferred effect of microbial population variability is invoked to interpret experimental data, but there lacks direct measurement at field-scale, especially in correlation of transport distance with change of bacterial surface properties. This study was undertaken to determine change of collision efficiency with transport distance, taking advantage of the bacterial transport experiment in Oyster, VA in the summer of 2001. Upon injection of an adhesion deficient strain, Comamonas sp. DA001 into a up-gradient well, bacterial samples were taken from multi-level samplers along the flow path, and were injected into cores of 40 cm in length and 7.5 cm in diameter packed with homogenized sediment from the same site, South Oyster focus area (SOFA). Bacterial suspension samples were also measured for bacterial electrophoretic mobility distribution. Using filtration theory, collision efficiency, the probability of bacterial attachment to the grain surfaces upon collision and a quantitative measure of bacterial adhesion, was determined using CXTFIT model fitted attachment rate, measured grain size (10th percentile), porosity, flow velocity, and collector efficiency. Collision efficiency was also determined based on the fraction of retention in the cores. Contrary to previous results and interpretation of field-scale breakthrough curves, our experimentally determined collision efficiency increases with transport distance in the core experiments, which correlates with increasingly negative surface charge of the injected bacteria. Therefore we conclude that the apparent decrease in adhesion with transport distance in the field is strongly controlled by field-scale heterogeneity in physical and chemical aquifer properties and not by microbial population heterogeneity.

  5. Bacterial communities associated with the lichen symbiosis.

    PubMed

    Bates, Scott T; Cropsey, Garrett W G; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2011-02-01

    Lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N(2) fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N(2) fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.

  6. Condom use and its association with bacterial vaginosis and bacterial vaginosis-associated vaginal microflora.

    PubMed

    Hutchinson, Katherine B; Kip, Kevin E; Ness, Roberta B

    2007-11-01

    Previous studies have been inconsistent with regard to whether condom use is associated with bacterial vaginosis. We evaluated this association using case-crossover analyses. A total of 871 women at high risk for sexually transmitted diseases were followed for a median of 3 years. At baseline and at 6, 12, 24, and 36 months thereafter, vaginal swabs were obtained for gram stain diagnosis of bacterial vaginosis, culture of microflora, and DNA amplification of Neisseria gonorrhoeae and Chlamydia trachomatis. Case-crossover analyses using incident and recurrent incident case periods were used to assess the associations among condom use, bacterial vaginosis, and vaginal microflora. Consistent condom use (10 out of 10 sexual encounters) was associated with a decreased frequency of bacterial vaginosis (adjusted odds ratio = 0.55 [95% confidence interval 0.35-0.88]). When we excluded women with intermediate flora, consistent condom use was even more strongly protective against bacterial vaginosis (0.37 [0.20-0.70]). Consistent condom use was similarly protective against carriage of anaerobic gram-negative pigmented rods (0.58 [0.36-0.94]). Results were similar when analyses were repeated to capture only first occurrences of outcomes among women without bacterial vaginosis at baseline, suggesting a protective effect against the acquisition of bacterial vaginosis. Consistent condom use was associated with a decrease in the risk for bacterial vaginosis and associated vaginal microflora.

  7. Bacterial vaginosis: association with adverse pregnancy outcome.

    PubMed

    Kimberlin, D F; Andrews, W W

    1998-08-01

    Bacterial vaginosis is the most common lower genital tract infection encountered among women of reproductive age. This condition can best be considered as a vaginal syndrome associated with an alteration of the normal vaginal flora rather than an infection specific to any one microorganism. Bacterial vaginosis is a clinical condition with a complex microbiology that is characterized by a reduced concentration of a normally abundant Lactobacillus species along with high concentrations of gram-negative and anaerobic bacteria, particularly, Gardnerella vaginalis and Mobiluncus, Bacteroides, Prevotella, and Mycoplasma species. The exact make up of the microorganisms and their relative concentration vary among women who have this condition. Although it was previously regarded as a harmless condition, recent work has linked bacterial vaginosis to numerous upper genital tract complications such as preterm labor and preterm delivery, preterm premature rupture of the membranes, chorioamnionitis, and postpartum endometritis. The findings from recent prospective randomized trials suggest that treatment of bacterial vaginosis in certain women who are at high risk for preterm delivery decreases the rate of preterm birth.

  8. Bacterial Pathogens Associated with Hidradenitis Suppurativa, France

    PubMed Central

    Coignard-Biehler, Hélène; Jais, Jean-Philippe; Quesne, Gilles; Frapy, Eric; Poirée, Sylvain; Le Guern, Anne-Sophie; Le Flèche-Matéos, Anne; Hovnanian, Alain; Consigny, Paul-Henry; Lortholary, Olivier; Nassif, Xavier; Nassif, Aude; Join-Lambert, Olivier

    2014-01-01

    Hidradenitis suppurativa (HS) is a skin disease characterized by recurrent nodules or abscesses and chronic suppurating lesions. In the absence of clear pathophysiology, HS is considered to be an inflammatory disease and has no satisfactory medical treatment. Recently, prolonged antimicrobial treatments were shown to improve or resolve HS lesions. We prospectively studied the microbiology of 102 HS lesions sampled from 82 patients using prolonged bacterial cultures and bacterial metagenomics on 6 samples. Staphylococcus lugdunensis was cultured as a unique or predominant isolate from 58% of HS nodules and abscesses, and a polymicrobial anaerobic microflora comprising strict anaerobes, milleri group streptococci, and actinomycetes was found in 24% of abscesses or nodules and in 87% of chronic suppurating lesions. These data show that bacteria known to cause soft tissue and skin infections are associated with HS lesions. Whether these pathogens are the cause of the lesions or are secondary infectious agents, these findings support targeted antimicrobial treatment of HS. PMID:25418454

  9. 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

  10. Bacterial Populations Associated with Smokeless Tobacco Products.

    PubMed

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

    2016-10-15

    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 × 10(6) CFU/g STP) and diversity of bacterial populations than snus (average of 8.33 × 10(1) CFU/g STP) and some chewing tobacco products (average of 2.54 × 10(5) 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. 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 potential

  11. A novel lignin degradation bacterial consortium for efficient pulping.

    PubMed

    Wang, Yanxia; Liu, Quan; Yan, Lei; Gao, Yamei; Wang, Yanjie; Wang, Weidong

    2013-07-01

    A lignin degradation bacterial consortium named LDC was screened from the sludge of a reeds pond by a restricted subculture. It could break down 60.9% lignin in reeds at 30°C under conditions of static culture within 15 days. In order to analyze the diversity of LDC, plate isolation, 16S rDNA clone library and ARDRA (Amplified Ribosomal DNA Restriction Analysis) were performed. Six bacterial strains were isolated from LDC and eighteen DNA phylotypes were identified from 230 bacterial analyzed clones. They were classified into Clostridiales(9.1%), Geovibrio thiophilus (5.1%), Desulfomicrobium (10.9%), Pseudomonas sp. (25.2%), Azoarcus sp. (5.1%), Thauera (5.1%), Paenibacillus sp. (5.1%), Cohnella sp. (2.2%), Acinetobacter sp. (3.1%), Microbacterium (7.8%), and uncultured bacterium (21.3%). In addition, physical characteristics of paper hand-sheets between biological pretreatment and chemical pretreatment were compared. The results showed that LDC had the capability of lignin degradation and was efficient for pulping, which would provide a new choice for biopulping.

  12. Bacterial growth laws reflect the evolutionary importance of energy efficiency.

    PubMed

    Maitra, Arijit; Dill, Ken A

    2015-01-13

    We are interested in the balance of energy and protein synthesis in bacterial growth. How has evolution optimized this balance? We describe an analytical model that leverages extensive literature data on growth laws to infer the underlying fitness landscape and to draw inferences about what evolution has optimized in Escherichia coli. Is E. coli optimized for growth speed, energy efficiency, or some other property? Experimental data show that at its replication speed limit, E. coli produces about four mass equivalents of nonribosomal proteins for every mass equivalent of ribosomes. This ratio can be explained if the cell's fitness function is the the energy efficiency of cells under fast growth conditions, indicating a tradeoff between the high energy costs of ribosomes under fast growth and the high energy costs of turning over nonribosomal proteins under slow growth. This model gives insight into some of the complex nonlinear relationships between energy utilization and ribosomal and nonribosomal production as a function of cell growth conditions.

  13. Bacterial infections associated with allogenic bone transplantation.

    PubMed

    Stepanović, Željko Lj; Ristić, Branko M

    2015-05-01

    Bone allografts are frequently used in orthopedic reconstructive procedures carrying a high risk for recipients. To assess the nature and frequency of allograft contamination and associated surgical infection the case records from our institutional bone bank were reviewed. We retrospectively analyzed the microbiology of discarded bone allografts and the surgical site of the recipients. A case series of patients who acquired surgical site infection after allogenic bone transplantation was presented. Swab culturing was conducted on 309 femoral heads from living donors who underwent partial and total hip arthroplasty between January 2007 and December 2013. To prevent potential bone allograft contamination we used saline solution of 2.0 mg/ml of amikacin during thawing. The overall infection rate was analyzed in 197 recipients. Of the 309 donated femoral heads, 37 were discarded due to bacterial contamination, giving the overall contamination rate of 11.97%. The postoperative survey of 213 bone allotransplantations among 197 recipients showed the infection rate of 2.03%. The coagulase-negative Staphylococcus was the most commonly identified contaminant of bone allografts and recipient surgical sites. The allograft contamination rate and the infection rate among recipients in our institution are in accordance with the international standards. The coagulase-negative Staphylococcus was the most commonly identified contaminant of bone allografts,and recipient surgical sites. There is no strong evidence that surgical site infections were associated with bone allograft utilization. We plan further improvements in allograft handling and decontamination with highly concentrated antibiotic solutions in order to reduce infection risk for recipients.

  14. Bacterial growth laws reflect the evolutionary importance of energy efficiency

    PubMed Central

    Maitra, Arijit; Dill, Ken A.

    2015-01-01

    We are interested in the balance of energy and protein synthesis in bacterial growth. How has evolution optimized this balance? We describe an analytical model that leverages extensive literature data on growth laws to infer the underlying fitness landscape and to draw inferences about what evolution has optimized in Escherichia coli. Is E. coli optimized for growth speed, energy efficiency, or some other property? Experimental data show that at its replication speed limit, E. coli produces about four mass equivalents of nonribosomal proteins for every mass equivalent of ribosomes. This ratio can be explained if the cell’s fitness function is the the energy efficiency of cells under fast growth conditions, indicating a tradeoff between the high energy costs of ribosomes under fast growth and the high energy costs of turning over nonribosomal proteins under slow growth. This model gives insight into some of the complex nonlinear relationships between energy utilization and ribosomal and nonribosomal production as a function of cell growth conditions. PMID:25548180

  15. Bacterial Exposures and Associations with Atopy and Asthma in Children

    PubMed Central

    Valkonen, Maria; Wouters, Inge M.; Täubel, Martin; Rintala, Helena; Lenters, Virissa; Vasara, Ritva; Genuneit, Jon; Braun-Fahrländer, Charlotte; Piarroux, Renaud; von Mutius, Erika; Heederik, Dick; Hyvärinen, Anne

    2015-01-01

    Background The increase in prevalence of asthma and atopic diseases in Western countries has been linked to aspects of microbial exposure patterns of people. It remains unclear which microbial aspects contribute to the protective farm effect. Objective The objective of this study was to identify bacterial groups associated with prevalence of asthma and atopy, and to quantify indoor exposure to some of these bacterial groups. Methods A DNA fingerprinting technique, denaturing gradient gel electrophoresis (DGGE), was applied to mattress dust samples of farm children and control children in the context of the GABRIEL Advanced study. Associations between signals in DGGE and atopy, asthma and other allergic health outcomes were analyzed. Quantitative DNA based assays (qPCR) for four bacterial groups were applied on the dust samples to seek quantitative confirmation of associations indicated in DNA fingerprinting. Results Several statistically significant associations between individual bacterial signals and also bacterial diversity in DGGE and health outcomes in children were observed. The majority of these associations showed inverse relationships with atopy, less so with asthma. Also, in a subsequent confirmation study using a quantitative method (qPCR), higher mattress levels of specifically targeted bacterial groups - Mycobacterium spp., Bifidobacteriaceae spp. and two different clusters of Clostridium spp. - were associated with a lower prevalence of atopy. Conclusion DNA fingerprinting proved useful in identifying bacterial signals that were associated with atopy in particular. These findings were quantitatively confirmed for selected bacterial groups with a second method. High correlations between the different bacterial exposures impede a clear attribution of protective effects to one specific bacterial group. More diverse bacterial flora in mattress dust may link to microbial exposure patterns that protect against development of atopic diseases. PMID:26121165

  16. Viral-bacterial associations in acute apical abscesses.

    PubMed

    Ferreira, Dennis C; Rôças, Isabela N; Paiva, Simone S M; Carmo, Flávia L; Cavalcante, Fernanda S; Rosado, Alexandre S; Santos, Kátia R N; Siqueira, José F

    2011-08-01

    Viral-bacterial and bacterial synergism have been suggested to contribute to the pathogenesis of several human diseases. This study sought to investigate the possible associations between 9 candidate endodontic bacterial pathogens and 9 human viruses in samples from acute apical abscesses. DNA extracts from purulent exudate aspirates of 33 cases of acute apical abscess were surveyed for the presence of 9 selected bacterial species using a 16S ribosomal RNA gene-based nested polymerase chain reaction (PCR) approach. Single or nested PCR assays were used for detection of the human papillomavirus (HPV) and herpesviruses types 1 to 8. Two-thirds of the abscess samples were positive for at least one of the target viruses. Specifically, the most frequently detected viruses were HHV-8 (54.5%); HPV (9%); and varicella zoster virus (VZV), Epstein-Barr virus (EBV), and HHV-6 (6%). Bacterial DNA was present in all cases and the most prevalent bacterial species were Treponema denticola (70%), Tannerella forsythia (67%), Porphyromonas endodontalis (67%), Dialister invisus (61%), and Dialister pneumosintes (57.5%). HHV-8 was positively associated with 7 of the target bacterial species and HPV with 4, but all these associations were weak. Several bacterial pairs showed a moderate positive association. Viral coinfection was found in 6 abscess cases, but no significant viral association could be determined. Findings demonstrated that bacterial and viral DNA occurred concomitantly in two-thirds of the samples from endodontic abscesses. Although this may suggest a role for viruses in the etiology of apical abscesses, the possibility also exists that the presence of viruses in abscess samples is merely a consequence of the bacterially induced disease process. Further studies are necessary to clarify the role of these viral-bacterial interactions, if any, in the pathogenesis of acute apical abscesses. Copyright © 2011 Mosby, Inc. All rights reserved.

  17. [Viral-bacterial-fungal associations in chronic tonsillitis in children].

    PubMed

    Gudima, I A; Vasil'eva, L I; Bragina, L E; Suchkov, I Iu

    2001-01-01

    The microflora of palatal tonsils was studied in 84 children with chronic tonsillitis in comparison with that in the control group of 38 healthy children. In most of the sick children viral-bacterial and less frequently viral-bacterial-fungal associations were detected with the prevalence of reo- and adenoviruses, Epstein-Barr viruses, coagulase negative staphylococci and Staphylococcus aureus, as well as peptostreptococci. Adhesive activity and persistence factors among the main bacterial pathogens were shown to be widely prevalent. The depth of the lesion of tonsillar tissue by the infective agents of bacterial and fungal nature, as well as their persistence potential, depended on the taxonomic position of these microorganisms.

  18. The Role of Bacterial Biofilms and Surface Components in Plant-Bacterial Associations

    PubMed Central

    Bogino, Pablo C.; de las Mercedes Oliva, María; Sorroche, Fernando G.; Giordano, Walter

    2013-01-01

    The role of bacterial surface components in combination with bacterial functional signals in the process of biofilm formation has been increasingly studied in recent years. Plants support a diverse array of bacteria on or in their roots, transport vessels, stems, and leaves. These plant-associated bacteria have important effects on plant health and productivity. Biofilm formation on plants is associated with symbiotic and pathogenic responses, but how plants regulate such associations is unclear. Certain bacteria in biofilm matrices have been found to induce plant growth and to protect plants from phytopathogens (a process termed biocontrol), whereas others are involved in pathogenesis. In this review, we systematically describe the various components and mechanisms involved in bacterial biofilm formation and attachment to plant surfaces and the relationships of these mechanisms to bacterial activity and survival. PMID:23903045

  19. An efficient depyrogenation method for recombinant bacterial outer membrane lipoproteins.

    PubMed

    Basto, Afonso P; Morais, Joana; Marcelino, Eduardo; Leitão, Alexandre; Santos, Dulce M

    2014-06-01

    Bacterial outer membrane lipoproteins are anchored in the outer membrane lipid layer in close association with lipopolysaccharides (LPS) and with other hydrophobic membrane proteins, making their purification technically challenging. We have previously shown that a thorough delipidation of outer membrane preparations from the Escherichia coli expression host is an important step to eliminate contaminant proteins when purifying recombinant antigens expressed in fusion with the Pseudomonas aeruginosa OprI lipoprotein. Here we report the cloning and expression of three antigens in fusion with OprI (ovalbumin, eGFP and BbPDI) and our efforts to deal with the variable LPS contamination levels observed in different batches of purified lipoproteins. The use of polymyxin B columns or endotoxin removal polycationic magnetic beads for depyrogenation of purified lipoproteins resulted in high protein losses and the use of Triton X-114 or sodium deoxycholate during the course of affinity chromatography showed to be ineffective to reduce LPS contamination. Instead, performing a hot phenol/water LPS extraction from outer membrane preparations prior to metal affinity chromatography allowed the purification of the recombinant fusion lipoproteins with LPS contents below 0.02EU/μg of protein. The purified recombinant lipoproteins retain their capacity to stimulate bone marrow-derived dendritic cells allowing for the study of their immunomodulatory properties through TLR2/1. This is a simple and easy to scale up method that can also be considered for the purification of other outer membrane lipoproteins.

  20. In Vitro Studies of Bacterial Cellulose and Magnetic Nanoparticles Smart Nanocomposites for Efficient Chronic Wounds Healing

    PubMed Central

    Bunea, Mihaela-Cristina; Stanescu, Paul; Casarica, Angela; Iovu, Horia; Zaharia, Catalin

    2015-01-01

    The quality of life of patients with chronic wounds can be extremely poor and, therefore, over the past decades, great efforts have been made to develop efficient strategies to improve the healing process and the social impact associated with these conditions. Cell based therapy, as a modern tissue engineering strategy, involves the design of 3D cell-scaffold bioconstructs obtained by preseeding drug loaded scaffolds with undifferentiated cells in order to achieve in situ functional de novo tissue. This paper reports on the development of bionanocomposites based on bacterial cellulose and magnetic nanoparticles (magnetite) for efficient chronic wounds healing. Composites were obtained directly in the cellulose bacterial culture medium by dispersing various amounts of magnetite nanoparticles during the biosynthesis process. After purification and drying, the membranes were characterized by Raman spectroscopy and X-ray diffraction to reveal the presence of magnetite within the bacterial cellulose matrix. Morphological investigation was employed through SEM and TEM analyses on bionanocomposites. The biocompatibility of these innovative materials was studied in relation to human adipose derived stem cells in terms of cellular morphology, viability, and proliferation as well as scaffolds cytotoxic potential. PMID:26106420

  1. Unconventional bacterial association for dough leavening.

    PubMed

    Musatti, Alida; Mapelli, Chiara; Foschino, Roberto; Picozzi, Claudia; Rollini, Manuela

    2016-11-21

    The purpose of the research was to obtain innovative yeast-free doughs leavened by Zymomonas mobilis and Lactobacillus sanfranciscensis. Z. mobilis, as well as Saccharomyces cerevisiae, produces an equimolar mixture of ethanol and CO2 through glucose, fructose or sucrose fermentation. In the present work, the inability of Z. mobilis to metabolize maltose has been circumvented by the addition of L. sanfranciscensis in the formulation. Indeed, L. sanfranciscensis, a heterofermentative lactic acid bacterium (LAB) typical of sourdough environment, hydrolyzes maltose releasing glucose which can be used by Z. mobilis for its metabolism. Biomass samples of Z. mobilis subs. mobilis DSM 424 and L. sanfranciscensis DSM 20663 were grown separately in liquid media and then associated in a model dough. Leavening trials set up by using three different microbial combinations (Lactobacillus:Zymomonas 80+80mg, 15+145mg and 145+15mg biomass, i.e. 1:1, 1:10 and 10:1 respectively on cell dry weight basis) evidenced CO2 production levels (mL) higher than the mathematical sum of CO2 produced by the single bacteria. In particular, when the biomass combination of L. sanfranciscensis and Z. mobilis was 1:1 (80+80mg cdw) and 10:1 (145+15mg cdw) a CO2 production of 46.3-41.4mL versus 26.7-28.5mL was achieved. The calculated productivity gain showed positive performances of the microbial combination up to 180-240min leavening. The subsequent efficiency loss may be due several factors, above all glucose shortage for Z. mobilis, as well as decrease of dough pH that can negatively affect both Lactobacillus and Zymomonas metabolism. As in traditional sourdoughs, L. sanfranciscensis was responsible for the souring activity with positive effects on both dough tasting and reduction of spoilage microbiota; Z. mobilis was instead responsible for most of the CO2 production. A bakery product leavened with the unconventional association Z. mobilis - L. sanfranciscensis will be addressed to people having

  2. Secondary Bacterial Infections Associated with Influenza Pandemics

    PubMed Central

    Morris, Denise E.; Cleary, David W.; Clarke, Stuart C.

    2017-01-01

    Lower and upper respiratory infections are the fourth highest cause of global mortality (Lozano et al., 2012). Epidemic and pandemic outbreaks of respiratory infection are a major medical concern, often causing considerable disease and a high death toll, typically over a relatively short period of time. Influenza is a major cause of epidemic and pandemic infection. Bacterial co/secondary infection further increases morbidity and mortality of influenza infection, with Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus reported as the most common causes. With increased antibiotic resistance and vaccine evasion it is important to monitor the epidemiology of pathogens in circulation to inform clinical treatment and development, particularly in the setting of an influenza epidemic/pandemic. PMID:28690590

  3. Association between periodontal disease, bacterial vaginosis, and sexual risk behaviors

    PubMed Central

    Zabor, Emily Craig; Klebanoff, Mark; Yu, Kai; Zhang, Jun; Nansel, Tonja; Andrews, William; Schwebke, Jane; Jeffcoat, Marjorie

    2010-01-01

    Background Both periodontal disease and bacterial vaginosis may cause adverse pregnancy outcomes. This study evaluated the association between periodontal disease and bacterial vaginosis. Methods Data from 3569 women enrolled in the Longitudinal Study of Vaginal Flora was used. Periodontal disease, defined as >3 sites with ≥4mm attachment loss, was assessed by specially-calibrated hygienists at baseline. Positive bacterial vaginosis status was based on a Nugent Gram stain score ≥7. Pairs of independent variables were compared with Pearson's chi-square and risk ratios were calculated through log-binomial regression. Results 28% of women with bacterial vaginosis had periodontal disease compared to 22% without, corresponding to 1.29 (95% CI: 1.13, 1.47) times greater risk of periodontal disease among women with bacterial vaginosis. In adjusted analysis the risk ratio dropped to 1.23 (95% CI: 1.08, 1.40). Receptive oral sex with an uncircumcised partner was associated with 1.28 times (95% CI: 0.97, 1.69) the risk for periodontal disease compared to receptive oral sex with a circumcised partner, though the association is not statistically significant. Conclusions In this population, there is a small but significant association between periodontal disease and bacterial vaginosis and a possible trend between receptive oral sex with an uncircumcised partner and periodontal disease. PMID:20636412

  4. Association between periodontal disease, bacterial vaginosis, and sexual risk behaviours.

    PubMed

    Zabor, Emily Craig; Klebanoff, Mark; Yu, Kai; Zhang, Jun; Nansel, Tonja; Andrews, William; Schwebke, Jane; Jeffcoat, Marjorie

    2010-10-01

    Both periodontal disease and bacterial vaginosis may cause adverse pregnancy outcomes. This study evaluated the association between periodontal disease and bacterial vaginosis. Data from 3569 women enrolled in the Longitudinal Study of Vaginal Flora were used. Periodontal disease, defined as greater than three sites with ≥4 mm attachment loss, was assessed by specially calibrated hygienists at baseline. Positive bacterial vaginosis status was based on a Nugent Gram stain score ≥7. Pairs of independent variables were compared with Pearson's χ(2) and risk ratios were calculated through log-binomial regression. Twenty-eight per cent of women with bacterial vaginosis had periodontal disease compared with 22% without , corresponding to 1.29 (95% CI: 1.13, 1.47) times greater risk of periodontal disease among women with bacterial vaginosis. In adjusted analysis the risk ratio dropped to 1.23 (95% CI: 1.08, 1.40). Receptive oral sex with an uncircumcised partner was associated with 1.28 times (95% CI: 0.97, 1.69) the risk for periodontal disease compared with receptive oral sex with a circumcised partner, though the association is not statistically significant. In this population, there is a small but significant association between periodontal disease and bacterial vaginosis and a possible trend between receptive oral sex with an uncircumcised partner and periodontal disease. © 2010 John Wiley & Sons A/S.

  5. Impact of Feed Efficiency and Diet on Adaptive Variations in the Bacterial Community in the Rumen Fluid of Cattle

    PubMed Central

    Hernandez-Sanabria, Emma; Goonewardene, Laksiri A.; Wang, Zhiquan; Durunna, Obioha N.; Moore, Stephen S.

    2012-01-01

    Limited knowledge of the structure and activities of the ruminal bacterial community prevents the understanding of the effect of population dynamics on functional bacterial groups and on host productivity. This study aimed to identify particular bacteria associated with host feed efficiency in steers with differing diets and residual feed intake (RFI) using culture-independent methods: PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis. PCR-DGGE profiles were generated from the ruminal fluid of 55 steers fed a low-energy-density diet and then switched to a high-energy-density diet. Bacterial profile comparisons by multivariate statistical analysis showed a trend only for RFI-related clusters on the high-energy diet. When steers (n = 19) belonging to the same RFI group under both diets were used to identify specific bacterial phylotypes related to feed efficiency traits, correlations were detected between dry matter intake, average daily gain, and copy numbers of the 16S rRNA gene of Succinivibrio sp. in low-RFI (efficient) steers, whereas correlations between Robinsoniella sp. and RFI (P < 0.05) were observed for high-RFI (inefficient) animals. Eubacterium sp. differed significantly (P < 0.05) between RFI groups that were only on the high-energy diet. Our work provides a comprehensive framework to understand how particular bacterial phylotypes contribute to differences in feed efficiency and ultimately influence host productivity, which may either depend on or be independent from diet factors. PMID:22156428

  6. A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

    PubMed Central

    Maboni, Grazieli; Blanchard, Adam; Frosth, Sara; Stewart, Ceri; Emes, Richard; Tötemeyer, Sabine

    2017-01-01

    Ovine footrot is a highly prevalent bacterial disease caused by Dichelobacter nodosus and characterised by the separation of the hoof horn from the underlying skin. The role of innate immune molecules and other bacterial communities in the development of footrot lesions remains unclear. This study shows a significant association between the high expression of IL1β and high D. nodosus load in footrot samples. Investigation of the microbial population identified distinct bacterial populations in the different disease stages and also depending on the level of inflammation. Treponema (34%), Mycoplasma (29%) and Porphyromonas (15%) were the most abundant genera associated with high levels of inflammation in footrot. In contrast, Acinetobacter (25%), Corynebacteria (17%) and Flavobacterium (17%) were the most abundant genera associated with high levels of inflammation in healthy feet. This demonstrates for the first time there is a distinct microbial community associated with footrot and high cytokine expression. PMID:28338081

  7. A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

    NASA Astrophysics Data System (ADS)

    Maboni, Grazieli; Blanchard, Adam; Frosth, Sara; Stewart, Ceri; Emes, Richard; Tötemeyer, Sabine

    2017-03-01

    Ovine footrot is a highly prevalent bacterial disease caused by Dichelobacter nodosus and characterised by the separation of the hoof horn from the underlying skin. The role of innate immune molecules and other bacterial communities in the development of footrot lesions remains unclear. This study shows a significant association between the high expression of IL1β and high D. nodosus load in footrot samples. Investigation of the microbial population identified distinct bacterial populations in the different disease stages and also depending on the level of inflammation. Treponema (34%), Mycoplasma (29%) and Porphyromonas (15%) were the most abundant genera associated with high levels of inflammation in footrot. In contrast, Acinetobacter (25%), Corynebacteria (17%) and Flavobacterium (17%) were the most abundant genera associated with high levels of inflammation in healthy feet. This demonstrates for the first time there is a distinct microbial community associated with footrot and high cytokine expression.

  8. 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.

  9. The combination of different carbon sources enhances bacterial growth efficiency in aquatic ecosystems.

    PubMed

    Fonte, Ellen S; Amado, André M; Meirelles-Pereira, Frederico; Esteves, Francisco A; Rosado, Alexandre S; Farjalla, Vinicius F

    2013-11-01

    The dissolved organic carbon (DOC) pool is composed of several organic carbon compounds from different carbon sources. Each of these sources may support different bacterial growth rates, but few studies have specifically analyzed the effects of the combination of different carbon sources on bacterial metabolism. In this study, we evaluated the response of several metabolic parameters, including bacterial biomass production (BP), bacterial respiration (BR), bacterial growth efficiency (BGE), and bacterial community structure, on the presence of three DOC sources alone and in combination. We hypothesized that the mixture of different DOC sources would increase the efficiency of carbon use by bacteria (BGE). We established a full-factorial substitutive design (seven treatments) in which the effects of the number and identity of DOC sources on bacterial metabolism were evaluated. We calculated the expected metabolic rates of the combined DOC treatments based on the single-DOC treatments and observed a positive interaction on BP, a negative interaction on BR, and, consequently, a positive interaction on BGE for the combinations. The bacterial community composition appeared to have a minor impact on differences in bacterial metabolism among the treatments. Our data indicate that mixtures of DOC sources result in a more efficient biological use of carbon. This study provides strong evidence that the mixture of different DOC sources is a key factor affecting the role of bacteria in the carbon flux of aquatic ecosystems.

  10. Metamorphosis of a Butterfly-Associated Bacterial Community

    PubMed Central

    Hammer, Tobin J.; McMillan, W. Owen; Fierer, Noah

    2014-01-01

    Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies. PMID:24466308

  11. Metamorphosis of a butterfly-associated bacterial community.

    PubMed

    Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

    2014-01-01

    Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

  12. Bacterial diversity associated with the Caribbean tunicate Ecteinascidia turbinata.

    PubMed

    Pérez-Matos, Ana E; Rosado, William; Govind, Nadathur S

    2007-08-01

    The Caribbean tunicate, Ecteinascidia turbinata produces the anti-cancer agent ET-743 that could well be a metabolite of an associated bacterial strain. This current study aims at the analysis of bacteria that are persistently and specifically associated with this invertebrate. Utilizing techniques such as denaturing gradient gel electrophoresis, DNA sequencing and phylogenetic analysis of bacteria from E. turbinata collected from different locations in the Caribbean Sea, we report here the identification of five possible persistently associated bacteria. Of these, only one organism, Candidatus Endoecteinascidia frumentensis, was found specifically associated to E. turbinata from the Caribbean and has also been found to be associated with E. turbinata from the Mediterranean. These experiments suggest that assessment of bacterial diversity associated with invertebrates from different geographical sites might be an effective way of identifying persistently and specifically associated bacteria.

  13. Bacterial associations with decaying wood : a review

    Treesearch

    C. A. Clausen

    1996-01-01

    Wood-inhabiting bacteria are associated with wood decay and may have an indirect influence on the decay process. Bacteria are able to affect wood permeability, attack wood structure, or work synergistically with other bacteria and soft-rot fungi to predispose wood to fungal attack. Bacteria that can inhabit chemically treated wood are recognized. The natural ability of...

  14. Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers

    PubMed Central

    Jiang, Tieshan; Mandal, Rabindra K.; Wideman, Robert F.; Khatiwara, Anita; Pevzner, Igal; Min Kwon, Young

    2015-01-01

    Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in

  15. The impact of deposition site on vaccination efficiency of a live bacterial poultry vaccine.

    PubMed

    Evans, J D; Leigh, S A; Purswell, J L; Collier, S D; Kim, E J; Boykin, D L; Branton, S L

    2015-08-01

    Vaccines are utilized within the poultry industry to minimize disease-associated losses and spray vaccination is a commonly utilized means for the mass application of poultry vaccines. During this process, vaccine-laden particles are deposited upon target areas (e.g., eyes, nares, and oral cavity) resulting in the direct internalization of the vaccine. However, particles are also deposited on nontarget areas such as the exterior of the subject and its surrounding environment. To better determine the fate of particles deposited upon nontarget areas and the impact of deposition site on the efficiency of vaccine application, a live bacterial poultry vaccine (AviPro(®) MG F) was applied via spray using a spray cabinet with a slotted partition allowing for head-only, body-only, and whole-bird spray application. At 11 wk age, Hy-Line(®) W-36 pullets (n = 280) were allocated equally among 7 treatments including: nonvaccinated controls, pullets spray-vaccinated at the manufacturer's recommended dose (1X) in a site-specific manner (head-only, body-only, and whole-bird), pullets spray-vaccinated at 5X the recommended level (body-only), pullets vaccinated by manual eye-drop application (1X), and pullets eye-drop vaccinated at a level approximating that achieved during the spray vaccination process (1/700X). At 6 to 7 wk postvaccination, vaccination efficiency was assessed via serological-based assays [serum plate agglutination (SPA) and ELISA] and the detection of vaccine-derived in vivo populations. Results indicate an additive contribution of the vaccine deposited on the body to the overall vaccination efficiency of this live bacterial live poultry vaccine. © 2015 Poultry Science Association Inc.

  16. Soil bacterial communities associated with natural and commercial Cyclopia spp.

    PubMed

    Postma, Anneke; Slabbert, Etienne; Postma, Ferdinand; Jacobs, Karin

    2016-03-01

    The commercially important plants in the genus Cyclopia spp. are indigenous to the Cape Floristic Region of South Africa and are used to manufacture an herbal tea known as honeybush tea. Growing in the low nutrient fynbos soils, these plants are highly dependent on symbiotic interactions with soil microorganisms for nutrient acquisition. The aim of this study was to investigate the soil bacterial communities associated with two commercially important Cyclopia species, namely C. subternata and C. longifolia. Specific interest was the differences between rhizosphere and bulk soil collected from natural sites and commercially grown plants. Samples were collected on two occasions to include a dry summer and wet winter season. Results showed that the dominant bacterial taxa associated with these plants included Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria. Commercial and natural as well as rhizosphere and bulk soil samples were highly similar in bacterial diversity and species richness. Significant differences were detected in bacterial community structures and co-occurrence patterns between the wet and dry seasons. The results of this study improved our knowledge on what effect commercial Cyclopia plantations and seasonal changes can have on soil bacterial communities within the endemic fynbos biome.

  17. Chemical Properties Associated with Bacterial Wetwood in Red Oaks

    Treesearch

    Zicai Xu; Theodor D. Leininger; Andy W.C. Lee; Frank H. Tainter

    2001-01-01

    Bacterial wetwood is a major cause of value loss in the red oak lumber industry in the United States. Red oak trees in Mississippi, South Carolina, and Florida were sampled and evaluated for certain chemical properties possibly associated with the wetwood condition. Specific variables investigated were pH and concentmtions of methane, cations (Na+. Ca++, K+, and Mg...

  18. Effects of nicotine on bacterial toxins associated with cot death.

    PubMed Central

    Sayers, N M; Drucker, D B; Telford, D R; Morris, J A

    1995-01-01

    Toxins produced by staphylococci and enterobacteria isolated from the nasopharynx of cases of sudden infant death syndrome (SIDS) have a lethal effect when injected into chick embryos. If the toxins are progressively diluted the lethal effect disappears, but certain combinations of toxins show synergy so that if sublethal doses are mixed a highly lethal effect is produced. In this paper it is shown that nicotine at very low concentrations (less than that produced in man by 0.05 cigarettes) potentiates the lethal action of certain SIDS associated bacterial toxins and markedly potentiates the lethal action of synergistic combinations of bacterial toxins. These results could explain, at least in part, why parental smoking increases the risk of SIDS. They also provide further support for the common bacterial toxin hypothesis of cot death. PMID:8546517

  19. 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

  20. [Factors associated with emergency department revisits for acute bacterial prostatitis].

    PubMed

    Ferré Losa, Carles; Llopis Roca, Ferran; Jacob Rodríguez, Javier; Cabello Zamora, Irene; Martínez Muñoz, Concepción; Bardés Robles, Ignasi

    2017-01-01

    To analyze factors associated with revisits by patients with acute bacterial prostatitis treated in a hospital emergency department. Descriptive analysis and prospective follow-up of a cohort of patients with acute bacterial prostatitis treated in an emergency department. We included 241 episodes of acute bacterial prostatitis. The mean (SD) age was 63 (16) years. Seventy-three percent reported dysuria, 64% had fever, and between 15.4% and 22.4% had medical histories of cancer, urethral/bladder catheterization, or prostate adenoma. Positive urine cultures were obtained for 48.1% and positive blood cultures for 17.6%. Escherichia coli was the bacterium isolated most often, and 27.7% of the cultures showed resistance to ciprofloxacin and amoxicillin-clavulanic acid. Twenty-nine patients (12%) revisited within 30 days. The only factors associated with revisiting were performance of a rectal examination (odds ratio [OR], 9.23; 95% CI, 1.12-75.82) and bacteremia (OR, 3.81; 95% CI, 1.31-11.04) (P<.05). Factors associated with revisiting for acute bacterial prostatitis were bacteremia and performance of a rectal examination.

  1. Impact of heat shock step on bacterial transformation efficiency.

    PubMed

    Rahimzadeh, Maral; Sadeghizadeh, Majid; Najafi, Farhood; Arab, Seyed; Mobasheri, Hamid

    2016-12-01

    CaCl2 treatment followed by heat shock is the most common method for artificial transformation. Here, the cells were transformed using CaCl2 treatment either with heat shock (standard protocol) or without heat shock (lab protocol) to comprehend the difference in transformation efficiency. The BL21 strain of Escherichia coli (E. coli) was being susceptible using CaCl2 treatment. Some Cells were kept at -80 (o)C while the others were kept at 4 ˚C. Afterwards the susceptible cells were transformed using either standard or lab protocol. The transformation efficiency between cells experienced heat shock and those were not influenced by heat shock was almost the same. Moreover, regardless of transformation protocol, the cells kept at 4 ˚C were transformed more efficiently in compared to those were kept at -80 (o)C.

  2. Impact of heat shock step on bacterial transformation efficiency

    PubMed Central

    Rahimzadeh, Maral; Sadeghizadeh, Majid; Najafi, Farhood; Arab, Seyed; Mobasheri, Hamid

    2016-01-01

    CaCl2 treatment followed by heat shock is the most common method for artificial transformation. Here, the cells were transformed using CaCl2 treatment either with heat shock (standard protocol) or without heat shock (lab protocol) to comprehend the difference in transformation efficiency. The BL21 strain of Escherichia coli (E. coli) was being susceptible using CaCl2 treatment. Some Cells were kept at -80 oC while the others were kept at 4 ˚C. Afterwards the susceptible cells were transformed using either standard or lab protocol. The transformation efficiency between cells experienced heat shock and those were not influenced by heat shock was almost the same. Moreover, regardless of transformation protocol, the cells kept at 4 ˚C were transformed more efficiently in compared to those were kept at -80 oC. PMID:28261629

  3. Bacterial communities associated with apical periodontitis and dental implant failure

    PubMed Central

    Dingsdag, Simon; Nelson, Stephen; Coleman, Nicholas V.

    2016-01-01

    Background Previously, we demonstrated that bacteria reside in apparently healed alveolar bone, using culture and Sanger sequencing techniques. Bacteria in apparently healed alveolar bone may have a role in peri-implantitis and dental implant failure. Objective To compare bacterial communities associated with apical periodontitis, those colonising a failed implant and alveolar bone with reference biofilm samples from healthy teeth. Methods and results The study consisted of 196 samples collected from 40 patients undergoing routine dental implant insertion or rehabilitation. The bacterial 16S ribosomal DNA sequences were amplified. Samples yielding sufficient polymerase chain reaction product for further molecular analyses were subjected to terminal restriction fragment length polymorphism (T-RFLP; 31 samples) and next generation DNA sequencing (454 GS FLX Titanium; 8 samples). T-RFLP analysis revealed that the bacterial communities in diseased tissues were more similar to each other (p<0.049) than those from the healthy reference samples. Next generation sequencing detected 13 bacterial phyla and 373 putative bacterial species, revealing an increased abundance of Gram-negative [Prevotella, Fusobacterium (p<0.004), Treponema, Veillonellaceae, TG5 (Synergistetes)] bacteria and a decreased abundance of Gram-positive [(Actinomyces, Corynebacterium (p<0.008)] bacteria in the diseased tissue samples (n=5) relative to reference supragingival healthy samples (n=3). Conclusion Increased abundances of Prevotella, Fusobacterium and TG5 (Synergistetes) were associated with apical periodontitis and a failed implant. A larger sample set is needed to confirm these trends and to better define the processes of bacterial pathogenesis in implant failure and apical periodontitis. The application of combined culture-based, microscopic and molecular technique-based approaches is suggested for future studies. PMID:27834171

  4. Dynamics of bacterial and fungal communities associated with eggshells during incubation

    PubMed Central

    Grizard, Stéphanie; Dini-Andreote, Francisco; Tieleman, B Irene; Salles, Joana F

    2014-01-01

    Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and internal transcribed spacer (ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival. We aimed to describe the dynamics of bacterial and fungal communities on homing pigeon eggshell surfaces. We investigated these communities at early and late incubation stages. PMID:24772289

  5. Salt marsh sediment characteristics as key regulators on the efficiency of hydrocarbons bioremediation by Juncus maritimus rhizospheric bacterial community.

    PubMed

    Ribeiro, Hugo; Almeida, C Marisa R; Magalhães, Catarina; Bordalo, Adriano A; Mucha, Ana P

    2015-01-01

    Mitigation of petroleum hydrocarbons was investigated during a 5-month greenhouse experiment, to assess the rhizoremediation (RR) potential in sediments with different characteristics colonized by Juncus maritimus, a salt marsh plant commonly found in temperate estuaries. Furthermore, the efficiency of two bioremediation treatments namely biostimulation (BS) by the addition of nutrients, and bioaugmentation (BA) by addition of indigenous microorganisms, was tested in combination with RR. The effect of the distinct treatments on hydrocarbon degradation, root biomass weight, and bacterial community structure was assessed. Our result showed higher potential for hydrocarbon degradation (evaluated by total petroleum hydrocarbon analysis) in coarse rhizosediments with low organic matter (OM), than rhizosediments with high OM, and small size particles. Moreover, the bacterial community structure was shaped according to the rhizosediment characteristics, highlighting the importance of specific microbe-particle associations to define the structure of rhizospheric bacterial communities, rather than external factors, such as hydrocarbon contamination or the applied treatments. The potential for hydrocarbon RR seems to depend on root system development and bacterial diversity, since biodegradation efficiencies were positively related with these two parameters. Treatments with higher root biomass, and concomitantly with higher bacterial diversity yielded higher hydrocarbon degradation. Moreover, BS and BA did not enhance hydrocarbons RR. In fact, it was observed that higher nutrient availability might interfere with root growth and negatively influence hydrocarbon degradation performance. Therefore, our results suggested that to conduct appropriate hydrocarbon bioremediation strategies, the effect of sediment characteristics on root growth/exploration should be taken into consideration, a feature not explored in previous studies. Furthermore, strategies aiming for the recovery

  6. Heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations.

    PubMed

    Eiler, Alexander; Langenheder, Silke; Bertilsson, Stefan; Tranvik, Lars J

    2003-07-01

    Batch cultures of aquatic bacteria and dissolved organic matter were used to examine the impact of carbon source concentration on bacterial growth, biomass, growth efficiency, and community composition. An aged concentrate of dissolved organic matter from a humic lake was diluted with organic compound-free artificial lake water to obtain concentrations of dissolved organic carbon (DOC) ranging from 0.04 to 2.53 mM. The bacterial biomass produced in the cultures increased linearly with the DOC concentration, indicating that bacterial biomass production was limited by the supply of carbon. The bacterial growth rate in the exponential growth phase exhibited a hyperbolic response to the DOC concentration, suggesting that the maximum growth rate was constrained by the substrate concentration at low DOC concentrations. Likewise, the bacterial growth efficiency calculated from the production of biomass and CO(2) increased asymptotically from 0.4 to 10.4% with increasing DOC concentration. The compositions of the microbial communities that emerged in the cultures were assessed by separation of PCR-amplified 16S rRNA fragments by denaturing gradient gel electrophoresis. Nonmetric multidimensional scaling of the gel profiles showed that there was a gradual change in the community composition along the DOC gradient; members of the beta subclass of the class Proteobacteria and members of the Cytophaga-Flavobacterium group were well represented at all concentrations, whereas members of the alpha subclass of the Proteobacteria were found exclusively at the lowest carbon concentration. The shift in community composition along the DOC gradient was similar to the patterns of growth efficiency and growth rate. The results suggest that the bacterial growth efficiencies, the rates of bacterial growth, and the compositions of bacterial communities are not constrained by substrate concentrations in most natural waters, with the possible exception of the most oligotrophic environments.

  7. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis.

    PubMed

    Oakley, Brian B; Fiedler, Tina L; Marrazzo, Jeanne M; Fredricks, David N

    2008-08-01

    Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 +/- 0.7 versus 5.2 +/- 0.75 (mean +/- standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the Prevotella species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level, Actinobacteria and Bacteroidetes were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities.

  8. Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis▿ †

    PubMed Central

    Oakley, Brian B.; Fiedler, Tina L.; Marrazzo, Jeanne M.; Fredricks, David N.

    2008-01-01

    Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 ± 0.7 versus 5.2 ± 0.75 (mean ± standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the Prevotella species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level, Actinobacteria and Bacteroidetes were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities. PMID:18487399

  9. Bacterial Community Associated with Black Band Disease in Corals

    PubMed Central

    Frias-Lopez, Jorge; Klaus, James S.; Bonheyo, George T.; Fouke, Bruce W.

    2004-01-01

    Black band disease (BBD) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. While it has been well established that the BBD bacterial mat is dominated by a cyanobacterium, the quantitative composition of the BBD bacterial mat community has not described previously. Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to characterize the infectious bacterial community of the bacterial mat causing BBD. These analyses revealed that the bacterial composition of the BBD mat does not vary between different coral species but does vary when different species of cyanobacteria are dominant within the mat. On the basis of the results of a new method developed to identify organisms detected by T-RFLP analysis, our data show that besides the cyanobacterium, five species of the division Firmicutes, two species of the Cytophaga-Flexibacter-Bacteroides (CFB) group, and one species of δ-proteobacteria are also consistently abundant within the infectious mat. Of these dominant taxa, six were consistently detected in healthy corals. However, four of the six were found in much higher numbers in BBD mats than in healthy corals. One species of the CFB group and one species of Firmicutes were not always associated with the bacterial communities present in healthy corals. Of the eight dominant bacteria identified, two species were previously found in clone libraries obtained from BBD samples; however, these were not previously recognized as important. Furthermore, despite having been described as an important component of the pathogenetic mat, a Beggiatoa species was not detected in any of the samples analyzed. These results will permit the dominant BBD bacteria to be targeted for isolation and culturing experiments aimed at deciphering the disease etiology. PMID:15466538

  10. Bacterial protein signals are associated with Crohn’s disease

    PubMed Central

    Juste, Catherine; Kreil, David P; Beauvallet, Christian; Guillot, Alain; Vaca, Sebastian; Carapito, Christine; Mondot, Stanislas; Sykacek, Peter; Sokol, Harry; Blon, Florence; Lepercq, Pascale; Levenez, Florence; Valot, Benoît; Carré, Wilfrid; Loux, Valentin; Pons, Nicolas; David, Olivier; Schaeffer, Brigitte; Lepage, Patricia; Martin, Patrice; Monnet, Véronique; Seksik, Philippe; Beaugerie, Laurent; Ehrlich, S Dusko; Gibrat, Jean-François; Van Dorsselaer, Alain; Doré, Joël

    2014-01-01

    Objective No Crohn’s disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. Here we explore the feasibility of extracting bacterial protein signals relevant to CD, by interrogating myriads of intestinal bacterial proteomes from a small number of patients and healthy controls. Design We first developed and validated a workflow—including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS—to discover protein signals from CD-associated gut microbial communities. Then we used selected reaction monitoring (SRM) to confirm a set of candidates. In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions. Results Our 2D-DIGE-based discovery approach revealed an imbalance of intestinal bacterial functions in CD. Many proteins, largely derived from Bacteroides species, were over-represented, while under-represented proteins were mostly from Firmicutes and some Prevotella members. Most overabundant proteins could be confirmed using SRM. They correspond to functions allowing opportunistic pathogens to colonise the mucus layers, breach the host barriers and invade the mucosae, which could still be aggravated by decreased host-derived pancreatic zymogen granule membrane protein GP2 in CD patients. Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins. Conclusions This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis. PMID:24436141

  11. Bacterial protein signals are associated with Crohn's disease.

    PubMed

    Juste, Catherine; Kreil, David P; Beauvallet, Christian; Guillot, Alain; Vaca, Sebastian; Carapito, Christine; Mondot, Stanislas; Sykacek, Peter; Sokol, Harry; Blon, Florence; Lepercq, Pascale; Levenez, Florence; Valot, Benoît; Carré, Wilfrid; Loux, Valentin; Pons, Nicolas; David, Olivier; Schaeffer, Brigitte; Lepage, Patricia; Martin, Patrice; Monnet, Véronique; Seksik, Philippe; Beaugerie, Laurent; Ehrlich, S Dusko; Gibrat, Jean-François; Van Dorsselaer, Alain; Doré, Joël

    2014-10-01

    No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. Here we explore the feasibility of extracting bacterial protein signals relevant to CD, by interrogating myriads of intestinal bacterial proteomes from a small number of patients and healthy controls. We first developed and validated a workflow-including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS-to discover protein signals from CD-associated gut microbial communities. Then we used selected reaction monitoring (SRM) to confirm a set of candidates. In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions. Our 2D-DIGE-based discovery approach revealed an imbalance of intestinal bacterial functions in CD. Many proteins, largely derived from Bacteroides species, were over-represented, while under-represented proteins were mostly from Firmicutes and some Prevotella members. Most overabundant proteins could be confirmed using SRM. They correspond to functions allowing opportunistic pathogens to colonise the mucus layers, breach the host barriers and invade the mucosae, which could still be aggravated by decreased host-derived pancreatic zymogen granule membrane protein GP2 in CD patients. Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins. This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  12. Soil bacterial community shifts associated with sugarcane straw removal

    NASA Astrophysics Data System (ADS)

    Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

    2017-04-01

    driver of bacterial community variation in sugarcane areas with straw removal and the bacterial community showed clusters according to the sampling date: early sampling (0 and 4 months) and late sampling (8 and 12 months). Alterations on the straw composition over the decomposition process is associated with these shifts on material community among the sampling date. Moreover, the rates of straw removal separated the bacterial community in two groups: high (75 and 100% of straw removal) and low (50% and no straw removal) rates of straw removal. This pattern could be attributed to differences in the soil environment (humidity and temperature), a strong driver of shifts on bacterial community. In conclusion, the bacterial community was affected by the time since the straw removal and by the rates of straw removal. Finally, both straw removal management and soil quality should be carefully evaluated, in order to maintain the sustainability of 2G sugarcane ethanol production in Brazil.

  13. Assessing the diversity of bacterial communities associated with plants

    PubMed Central

    Andreote, Fernando Dini; Azevedo, João Lúcio; Araújo, Welington Luiz

    2009-01-01

    Plant–bacteria interactions result from reciprocal recognition between both species. These interactions are responsible for essential biological processes in plant development and health status. Here, we present a review of the methodologies applied to investigate shifts in bacterial communities associated with plants. A description of techniques is made from initial isolations to culture-independent approaches focusing on quantitative Polymerase Chain Reaction in real time (qPCR), Denaturing Gradient Gel Electrophoresis (DGGE), clone library construction and analysis, the application of multivariate analyses to microbial ecology data and the upcoming high throughput methodologies such as microarrays and pyrosequencing. This review supplies information about the development of traditional methods and a general overview about the new insights into bacterial communities associated with plants. PMID:24031382

  14. Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

    PubMed Central

    Sarria-Guzmán, Yohanna; Chávez-Romero, Yosef; Gómez-Acata, Selene; Montes-Molina, Joaquín Adolfo; Morales-Salazar, Eleacin; Dendooven, Luc; Navarro-Noya, Yendi E.

    2016-01-01

    Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health. PMID:27524305

  15. Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues.

    PubMed

    Sarria-Guzmán, Yohanna; Chávez-Romero, Yosef; Gómez-Acata, Selene; Montes-Molina, Joaquín Adolfo; Morales-Salazar, Eleacin; Dendooven, Luc; Navarro-Noya, Yendi E

    2016-09-29

    Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health.

  16. Bacterial proteostasis balances energy and chaperone utilization efficiently

    PubMed Central

    Santra, Mantu; Farrell, Daniel W.; Dill, Ken A.

    2017-01-01

    Chaperones are protein complexes that help to fold and disaggregate a cell’s proteins. It is not understood how four major chaperone systems of Escherichia coli work together in proteostasis: the recognition, sorting, folding, and disaggregating of the cell’s many different proteins. Here, we model this machine. We combine extensive data on chaperoning, folding, and aggregation rates with expression levels of proteins and chaperones measured at different growth rates. We find that the proteostasis machine recognizes and sorts a client protein based on two biophysical properties of the client’s misfolded state (M state): its stability and its kinetic accessibility from its unfolded state (U state). The machine is energy-efficient (the sickest proteins use the most ATP-expensive chaperones), comprehensive (it can handle any type of protein), and economical (the chaperone concentrations are just high enough to keep the whole proteome folded and disaggregated but no higher). The cell needs higher chaperone levels in two situations: fast growth (when protein production rates are high) and very slow growth (to mitigate the effects of protein degradation). This type of model complements experimental knowledge by showing how the various chaperones work together to achieve the broad folding and disaggregation needs of the cell. PMID:28292901

  17. Bacterial proteostasis balances energy and chaperone utilization efficiently.

    PubMed

    Santra, Mantu; Farrell, Daniel W; Dill, Ken A

    2017-03-28

    Chaperones are protein complexes that help to fold and disaggregate a cell's proteins. It is not understood how four major chaperone systems of Escherichia coli work together in proteostasis: the recognition, sorting, folding, and disaggregating of the cell's many different proteins. Here, we model this machine. We combine extensive data on chaperoning, folding, and aggregation rates with expression levels of proteins and chaperones measured at different growth rates. We find that the proteostasis machine recognizes and sorts a client protein based on two biophysical properties of the client's misfolded state (M state): its stability and its kinetic accessibility from its unfolded state (U state). The machine is energy-efficient (the sickest proteins use the most ATP-expensive chaperones), comprehensive (it can handle any type of protein), and economical (the chaperone concentrations are just high enough to keep the whole proteome folded and disaggregated but no higher). The cell needs higher chaperone levels in two situations: fast growth (when protein production rates are high) and very slow growth (to mitigate the effects of protein degradation). This type of model complements experimental knowledge by showing how the various chaperones work together to achieve the broad folding and disaggregation needs of the cell.

  18. Effect of turbidity on chlorination efficiency and bacterial persistence in drinking water.

    PubMed

    LeChevallier, M W; Evans, T M; Seidler, R J

    1981-07-01

    To define interrelationships between elevated turbidities and the efficiency of chlorination in drinking water, experiments were performed to measure bacterial survival, chlorine demand, and interference with microbiological determinations. Experiments were conducted on the surface water supplies for communities which practice chlorination as the only treatment. Therefore, the conclusions of this study apply only to such systems. Results indicated that disinfection efficiency (log10 of the decrease in coliform numbers) was negatively correlated with turbidity and was influenced by season, chlorine demand of the samples, and the initial coliform level. Total organic carbon was found to be associated with turbidity and was shown to interfere with maintenance of a free chlorine residual by creating a chlorine demand. Interference with coliform detection in turbid waters could be demonstrated by the recovery of typical coliforms from apparently negative filters. The incidence of coliform masking in the membrane filter technique was found to increase as the turbidity of the chlorinated samples increased. the magnitude of coliform masking in the membrane filter technique increased from less than 1 coliform per 100 ml in water samples of less than 5 nephelometric turbidity units to greater than 1 coliform per 100 ml in water samples of greater than 5 nephelometric turbidity units. Statistical models were developed to predict the impact of turbidity on drinking water quality. The results justify maximum contaminant levels for turbidity in water entering a distribution system as stated in the National Primary Drinking Water Regulations of the Safe Drinking Water Act.

  19. Effect of turbidity on chlorination efficiency and bacterial persistence in drinking water.

    PubMed Central

    LeChevallier, M W; Evans, T M; Seidler, R J

    1981-01-01

    To define interrelationships between elevated turbidities and the efficiency of chlorination in drinking water, experiments were performed to measure bacterial survival, chlorine demand, and interference with microbiological determinations. Experiments were conducted on the surface water supplies for communities which practice chlorination as the only treatment. Therefore, the conclusions of this study apply only to such systems. Results indicated that disinfection efficiency (log10 of the decrease in coliform numbers) was negatively correlated with turbidity and was influenced by season, chlorine demand of the samples, and the initial coliform level. Total organic carbon was found to be associated with turbidity and was shown to interfere with maintenance of a free chlorine residual by creating a chlorine demand. Interference with coliform detection in turbid waters could be demonstrated by the recovery of typical coliforms from apparently negative filters. The incidence of coliform masking in the membrane filter technique was found to increase as the turbidity of the chlorinated samples increased. the magnitude of coliform masking in the membrane filter technique increased from less than 1 coliform per 100 ml in water samples of less than 5 nephelometric turbidity units to greater than 1 coliform per 100 ml in water samples of greater than 5 nephelometric turbidity units. Statistical models were developed to predict the impact of turbidity on drinking water quality. The results justify maximum contaminant levels for turbidity in water entering a distribution system as stated in the National Primary Drinking Water Regulations of the Safe Drinking Water Act. Images PMID:7259162

  20. Predicting bacterial fitness cost associated with drug resistance.

    PubMed

    Guo, Beining; Abdelraouf, Kamilia; Ledesma, Kimberly R; Nikolaou, Michael; Tam, Vincent H

    2012-04-01

    It has been proposed that antimicrobial resistance could be associated with a fitness cost in bacteria, which is often determined by competition experiments between isogenic strains (wild-type and mutant). However, this conventional approach is time consuming and labour intensive. An alternative method was developed to assess the fitness cost in drug-resistant bacteria. Time-growth studies were performed with approximately 1 × 10(5) cfu/mL of Acinetobacter baumannii or Pseudomonas aeruginosa at baseline. Serial samples were obtained to quantify the bacterial burden over 24 h. The growth rates (K(g)) of isogenic strains (antibiotic susceptible and resistant) were determined individually and used to predict their relative abundance in a co-culture over an extended period of time. The predicted difference between the two strains was subsequently validated by in vitro growth competition experiments. The growth rates of A. baumannii were not significantly different in different strengths of growth medium. The difference in bacterial burden observed in competition studies was in general agreement with the predicted difference based on K(g) values, suggesting good predicting ability of the mathematical model. The proposed mathematical model was found to be reasonable in characterizing bacterial growth and predicting the fitness cost of resistance. This simple method appears robust in the assessment of fitness cost associated with drug resistance and warrants further investigations.

  1. Bacterial Diversity Associated with the Coccolithophorid Algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii

    PubMed Central

    Green, David H.; Echavarri-Bravo, Virginia; Brennan, Debra; Hart, Mark C.

    2015-01-01

    Coccolithophores are unicellular calcifying marine phytoplankton that can form large and conspicuous blooms in the oceans and make significant contributions to oceanic carbon cycling and atmospheric CO2 regulation. Despite their importance, the bacterial diversity associated with these algae has not been explored for ecological or biotechnological reasons. Bacterial membership of Emiliania huxleyi and Coccolithus pelagicus f. braarudii cultures was assessed using cultivation and cultivation-independent methods. The communities were species rich compared to other phytoplankton cultures. Community analysis identified specific taxa which cooccur in all cultures (Marinobacter and Marivita). Hydrocarbon-degrading bacteria were found in all cultures. The presence of Acidobacteria, Acidimicrobidae, Schlegelella, and Thermomonas was unprecedented but were potentially explained by calcification associated with coccolith production. One strain of Acidobacteria was cultivated and is closely related to a marine Acidobacteria isolated from a sponge. From this assessment of the bacterial diversity of coccolithophores, a number of biotechnological opportunities are evident, from bioprospecting for novel taxa such as Acidobacteria to helping understand the relationship between obligate hydrocarbonoclastic bacteria occurrence with phytoplankton and to revealing bacterial taxa that have a specific association with algae and may be suitable candidates as a means to improve the efficiency of mass algal cultivation. PMID:26273594

  2. Association between Bacterial Infection and Peripheral Vascular Disease: A Review

    PubMed Central

    Budzyński, Jacek; Wiśniewska, Joanna; Ciecierski, Marek; Kędzia, Anna

    2015-01-01

    There are an increasing number of data showing a clinically important association between bacterial infection and peripheral artery disease (PAD). Bacteria suspected of being involved in PAD pathogenesis are: periodontal bacteria, gut microbiota, Helicobacter pylori, and Chlamydia pneumoniae. Infectious agents may be involved in the pathogenesis of atherosclerosis via activation of a systemic or local host immunological response to contamination of extravascular tissues or the vascular wall, respectively. A systemic immunological reaction may damage vascular walls in the course of autoimmunological cross-reactions between anti-pathogen antibodies and host vascular antigens (immunological mimicry), pathogen burden mechanisms (nonspecific activation of inflammatory processes in the vascular wall), and neuroendocrine-immune cross-talk. Besides activating the inflammatory pathway, bacterial infection may trigger PAD progression or exacerbation by enhancement of platelet reactivity, by a stimulatory effect on von Willebrand factor binding, factor VIII, fibrinogen, P-selectin activation, disturbances in plasma lipids, increase in oxidative stress, and resistance to insulin. Local inflammatory host reaction and induction of atherosclerotic plaque progression and/or instability result mainly from atherosclerotic plaque colonization by microorganisms. Despite these premises, the role of bacterial infection in PAD pathogenesis should still be recognized as controversial, and randomized, controlled trials are required to evaluate the outcome of periodontal or gut bacteria modification (through diet, prebiotics, and probiotics) or eradication (using antibiotics) in hard and surrogate cardiovascular endpoints. PMID:26900306

  3. Mucosa-associated bacterial diversity in necrotizing enterocolitis.

    PubMed

    Brower-Sinning, Rachel; Zhong, Diana; Good, Misty; Firek, Brian; Baker, Robyn; Sodhi, Chhinder P; Hackam, David J; Morowitz, Michael J

    2014-01-01

    Previous studies of infant fecal samples have failed to clarify the role of gut bacteria in the pathogenesis of NEC. We sought to characterize bacterial communities within intestinal tissue resected from infants with and without NEC. 26 intestinal samples were resected from 19 infants, including 16 NEC samples and 10 non-NEC samples. Bacterial 16S rRNA gene sequences were amplified and sequenced. Analysis allowed for taxonomic identification, and quantitative PCR was used to quantify the bacterial load within samples. NEC samples generally contained an increased total burden of bacteria. NEC and non-NEC sample sets were both marked by high inter-individual variability and an abundance of opportunistic pathogens. There was no statistically significant distinction between the composition of NEC and non-NEC microbial communities. K-means clustering enabled us to identify several stable clusters, including clusters of NEC and midgut volvulus samples enriched with Clostridium and Bacteroides. Another cluster containing both NEC and non-NEC samples was marked by an abundance of Enterobacteriaceae and decreased diversity among NEC samples. The results indicate that NEC is a disease without a uniform pattern of microbial colonization, but that NEC is associated with an abundance of strict anaerobes and a decrease in community diversity.

  4. Mucosa-Associated Bacterial Diversity in Necrotizing Enterocolitis

    PubMed Central

    Brower-Sinning, Rachel; Zhong, Diana; Good, Misty; Firek, Brian; Baker, Robyn; Sodhi, Chhinder P.; Hackam, David J.; Morowitz, Michael J.

    2014-01-01

    Background Previous studies of infant fecal samples have failed to clarify the role of gut bacteria in the pathogenesis of NEC. We sought to characterize bacterial communities within intestinal tissue resected from infants with and without NEC. Methods 26 intestinal samples were resected from 19 infants, including 16 NEC samples and 10 non-NEC samples. Bacterial 16S rRNA gene sequences were amplified and sequenced. Analysis allowed for taxonomic identification, and quantitative PCR was used to quantify the bacterial load within samples. Results NEC samples generally contained an increased total burden of bacteria. NEC and non-NEC sample sets were both marked by high inter-individual variability and an abundance of opportunistic pathogens. There was no statistically significant distinction between the composition of NEC and non-NEC microbial communities. K-means clustering enabled us to identify several stable clusters, including clusters of NEC and midgut volvulus samples enriched with Clostridium and Bacteroides. Another cluster containing both NEC and non-NEC samples was marked by an abundance of Enterobacteriaceae and decreased diversity among NEC samples. Conclusions The results indicate that NEC is a disease without a uniform pattern of microbial colonization, but that NEC is associated with an abundance of strict anaerobes and a decrease in community diversity. PMID:25203729

  5. Bacterial associates of seed-parasitic wasps (Hymenoptera: Megastigmus).

    PubMed

    Paulson, Amber R; von Aderkas, Patrick; Perlman, Steve J

    2014-09-25

    The success of herbivorous insects has been shaped largely by their association with microbes. Seed parasitism is an insect feeding strategy involving intimate contact and manipulation of a plant host. Little is known about the microbial associates of seed-parasitic insects. We characterized the bacterial symbionts of Megastigmus (Hymenoptera: Torymidae), a lineage of seed-parasitic chalcid wasps, with the goal of identifying microbes that might play an important role in aiding development within seeds, including supplementing insect nutrition or manipulating host trees. We screened multiple populations of seven species for common facultative inherited symbionts. We also performed culture independent surveys of larvae, pupae, and adults of M. spermotrophus using 454 pyrosequencing. This major pest of Douglas-fir is the best-studied Megastigmus, and was previously shown to manipulate its tree host into redirecting resources towards unfertilized ovules. Douglas-fir ovules and the parasitoid Eurytoma sp. were also surveyed using pyrosequencing to help elucidate possible transmission mechanisms of the microbial associates of M. spermotrophus. Three wasp species harboured Rickettsia; two of these also harboured Wolbachia. Males and females were infected at similar frequencies, suggesting that these bacteria do not distort sex ratios. The M. spermotrophus microbiome is dominated by five bacterial OTUs, including lineages commonly found in other insect microbiomes and in environmental samples. The bacterial community associated with M. spermotrophus remained constant throughout wasp development and was dominated by a single OTU - a strain of Ralstonia, in the Betaproteobacteria, comprising over 55% of all bacterial OTUs from Megastigmus samples. This strain was also present in unparasitized ovules. This is the first report of Ralstonia being an abundant and potentially important member of an insect microbiome, although other closely-related Betaproteobacteria, such as

  6. Room temperature electrocompetent bacterial cells improve DNA transformation and recombineering efficiency

    PubMed Central

    Tu, Qiang; Yin, Jia; Fu, Jun; Herrmann, Jennifer; Li, Yuezhong; Yin, Yulong; Stewart, A. Francis; Müller, Rolf; Zhang, Youming

    2016-01-01

    Bacterial competent cells are essential for cloning, construction of DNA libraries, and mutagenesis in every molecular biology laboratory. Among various transformation methods, electroporation is found to own the best transformation efficiency. Previous electroporation methods are based on washing and electroporating the bacterial cells in ice-cold condition that make them fragile and prone to death. Here we present simple temperature shift based methods that improve DNA transformation and recombineering efficiency in E. coli and several other gram-negative bacteria thereby economizing time and cost. Increased transformation efficiency of large DNA molecules is a significant advantage that might facilitate the cloning of large fragments from genomic DNA preparations and metagenomics samples. PMID:27095488

  7. The bacterial ribonuclease P holoenzyme requires specific, conserved residues for efficient catalysis and substrate positioning.

    PubMed

    Reiter, Nicholas J; Osterman, Amy K; Mondragón, Alfonso

    2012-11-01

    RNase P is an RNA-based enzyme primarily responsible for 5'-end pre-tRNA processing. A structure of the bacterial RNase P holoenzyme in complex with tRNAPhe revealed the structural basis for substrate recognition, identified the active site location, and showed how the protein component increases functionality. The active site includes at least two metal ions, a universal uridine (U52), and P RNA backbone moieties, but it is unclear whether an adjacent, bacterially conserved protein loop (residues 52-57) participates in catalysis. Here, mutagenesis combined with single-turnover reaction kinetics demonstrate that point mutations in this loop have either no or modest effects on catalytic efficiency. Similarly, amino acid changes in the 'RNR' region, which represent the most conserved region of bacterial RNase P proteins, exhibit negligible changes in catalytic efficiency. However, U52 and two bacterially conserved protein residues (F17 and R89) are essential for efficient Thermotoga maritima RNase P activity. The U52 nucleotide binds a metal ion at the active site, whereas F17 and R89 are positioned >20 Å from the cleavage site, probably making contacts with N(-4) and N(-5) nucleotides of the pre-tRNA 5'-leader. This suggests a synergistic coupling between transition state formation and substrate positioning via interactions with the leader.

  8. Efficient quantification and characterization of bacterial outer membrane derived nano-particles with flow cytometric analysis.

    PubMed

    Wieser, Andreas; Storz, Enno; Liegl, Gabriele; Peter, Annabell; Pritsch, Michael; Shock, Jonathan; Wai, Sun Nyunt; Schubert, Sören

    2014-11-01

    There currently exists no efficient and easy method for size profiling and counting of membranous nano-scale particles, such as bacterial outer membrane vesicles (OMVs). We present here a cost-effective and fast method capable of profiling and counting small sample volumes of nano-scale membranous vesicles with standard laboratory equipment without the need for any washing steps. OMV populations of different bacterial species are compared and even subpopulations of OMVs can be identified after a simple labelling procedure. Counting is possible over three orders of magnitude without any changes to the protocol. Protein contaminations do not alter the described measurements.

  9. High efficiency binding aptamers for a wide range of sepsis bacterial agents.

    PubMed

    Graziani, Ana Cláudia; Stets, Maria Isabel; Lopes, Ana Luisa Kalb; Schluga, Pedro Henrique Caires; Marton, Soledad; Mendes, Ieda Ferreira; Andrade, Antero Silva Ribeiro de; Krieger, Marco Aurélio; Cardoso, Josiane

    2017-01-24

    Sepsis is a major health problem worldwide, with an extremely high rate of morbidity and mortality, partly due to delayed diagnosis during early disease. Currently, sepsis diagnosis requires bacterial culturing of blood samples over several days, while PCR-based molecular diagnosis methods are faster, but lack sensitivity. The use of biosensors containing nucleic acid aptamers that bind targets with high affinity and specificity could accelerate sepsis diagnosis. Previously, we used Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to develop the aptamers Antibac1 and Antibac2, targeting the ubiquitous bacterial peptidoglycan. Here, we show that these aptamers bind to four Gram-positive and seven Gram-negative bacterial sepsis agents with high binding efficiency. Thus, these aptamers could be used in combination as biological recognition elements in the development of biosensors that are an alternative to rapid bacteria detection, since they could provide culture and amplification-free tests for rapid clinical sepsis diagnosis.

  10. Bacterial growth efficiency in a partly eutrophicated bay of South China Sea: Implication for anthropogenic impacts and potential hypoxia events.

    PubMed

    Song, Xing-Yu; Liu, Hua-Xue; Zhong, Yu; Tan, Ye-Hui; Qin, Geng; Li, Kai-Zhi; Shen, Ping-Ping; Huang, Liang-Min; Wang, You-Shao

    2015-10-01

    Bacterial metabolism plays a dual role [bacterial production (BP) and bacterial respiration (BR)] in the aquatic ecosystem and potentially leads to hypoxia in the coastal eutrophic area. Bacterial growth efficiency (BGE) is an important index showing the contribution of bacterial metabolism to marine biological production and carbon budget in the pelagic ecosystem. In this study, the spatial and seasonal variety as well as diurnal variation dynamics of BGE and associated ecological characteristics were investigated in a partly eutrophicated subtropical bay (the Daya Bay) located in the northern South China Sea. Furthermore, the relationship between bacterial metabolism and potential hypoxia event was analyzed. The average BGE was 0.14 and 0.22 in summer and winter, respectively, which was lower than the mean value ever reported in other coastal and estuarine waters. The diurnal variations of BGE and BP were widely fluctuated in the Daya Bay, with approximately 3-8 fold variation of BP and 2-3 fold variation of BR in different seasons, suggesting the importance of short-term ecological dynamics on evaluating the long-term ecological processes in the coastal waters. BR was the predominant contributor to the bacterial carbon demand; however, the variation of BGE was controlled by BP in both seasons. BGE was always high in the near-shore waters with higher eutrophic level and more active BP and BR. The bacterial metabolism could deplete dissolved oxygen (DO) in the Daya bay within about 9 days when the water body was enclosed and photosynthesis was prohibited. Therefore, low DO concentration and potential hypoxia was more likely to be found in the near-shore waters of the Daya Bay in summer, since the water was stratified and enclosed with poor water exchange capacity in this area. While in winter, hypoxia seldom occurred due to vertical mixing throughout the water column. Further biological-physical coupling research is recommended to find out the detailed formation

  11. Prokaryotic RNA Associated to Bacterial Viability Induces Polymorphonuclear Neutrophil Activation.

    PubMed

    Rodriguez-Rodrigues, Nahuel; Castillo, Luis A; Landoni, Verónica I; Martire-Greco, Daiana; Milillo, M Ayelén; Barrionuevo, Paula; Fernández, Gabriela C

    2017-01-01

    Polymorphonuclear neutrophils (PMN) are the first cellular line of antibacterial host defense. They sense pathogens through recognition of pathogen-associated molecular patterns (PAMPs) by innate pattern recognition receptors, such as Toll-like receptors (TLR). The aim of this study was to investigate whether PMN sense bacterial viability and explore which viability factor could be involved in this phenomenon. For this purpose, different functions were evaluated in isolated human PMN using live Escherichia coli (Ec) and heat-killed Ec (HK-Ec). We found that bacterial viability was indispensable to induce PMN activation, as measured by forward-scatter (FSC) increase, CD11b surface expression, chemotaxis, reactive oxygen species (ROS) generation and neutrophil extracellular trap (NET) formation. As uncapped non-polyadenylated prokaryotic mRNA has been recognized as a PAMP associated to bacterial viability by macrophages and dendritic cells, total prokaryotic RNA (pRNA) from live Ec was purified and used as a stimulus for PMN. pRNA triggered similar responses to those observed with live bacteria. No RNA could be isolated from HK-Ec, explaining the lack of effect of dead bacteria. Moreover, the supernatant of dead bacteria was able to induce PMN activation, and this was associated with the presence of pRNA in this supernatant, which is released in the killing process. The induction of bactericidal functions (ROS and NETosis) by pRNA were abolished when the supernatant of dead bacteria or isolated pRNA were treated with RNAse. Moreover, endocytosis was necessary for pRNA-induced ROS generation and NETosis, and priming was required for the induction of pRNA-induced ROS in whole blood. However, responses related to movement and degranulation (FSC increase, CD11b up-regulation, and chemotaxis) were still triggered when pRNA was digested with RNase, and were not dependent on pRNA endocytosis or PMN priming. In conclusion, our results indicate that PMN sense live bacteria

  12. Prokaryotic RNA Associated to Bacterial Viability Induces Polymorphonuclear Neutrophil Activation

    PubMed Central

    Rodriguez-Rodrigues, Nahuel; Castillo, Luis A.; Landoni, Verónica I.; Martire-Greco, Daiana; Milillo, M. Ayelén; Barrionuevo, Paula; Fernández, Gabriela C.

    2017-01-01

    Polymorphonuclear neutrophils (PMN) are the first cellular line of antibacterial host defense. They sense pathogens through recognition of pathogen-associated molecular patterns (PAMPs) by innate pattern recognition receptors, such as Toll-like receptors (TLR). The aim of this study was to investigate whether PMN sense bacterial viability and explore which viability factor could be involved in this phenomenon. For this purpose, different functions were evaluated in isolated human PMN using live Escherichia coli (Ec) and heat-killed Ec (HK-Ec). We found that bacterial viability was indispensable to induce PMN activation, as measured by forward-scatter (FSC) increase, CD11b surface expression, chemotaxis, reactive oxygen species (ROS) generation and neutrophil extracellular trap (NET) formation. As uncapped non-polyadenylated prokaryotic mRNA has been recognized as a PAMP associated to bacterial viability by macrophages and dendritic cells, total prokaryotic RNA (pRNA) from live Ec was purified and used as a stimulus for PMN. pRNA triggered similar responses to those observed with live bacteria. No RNA could be isolated from HK-Ec, explaining the lack of effect of dead bacteria. Moreover, the supernatant of dead bacteria was able to induce PMN activation, and this was associated with the presence of pRNA in this supernatant, which is released in the killing process. The induction of bactericidal functions (ROS and NETosis) by pRNA were abolished when the supernatant of dead bacteria or isolated pRNA were treated with RNAse. Moreover, endocytosis was necessary for pRNA-induced ROS generation and NETosis, and priming was required for the induction of pRNA-induced ROS in whole blood. However, responses related to movement and degranulation (FSC increase, CD11b up-regulation, and chemotaxis) were still triggered when pRNA was digested with RNase, and were not dependent on pRNA endocytosis or PMN priming. In conclusion, our results indicate that PMN sense live bacteria

  13. Bacterial communities in commercial aircraft high-efficiency particulate air (HEPA) filters assessed by PhyloChip analysis.

    PubMed

    Korves, T M; Piceno, Y M; Tom, L M; Desantis, T Z; Jones, B W; Andersen, G L; Hwang, G M

    2013-02-01

    Air travel can rapidly transport infectious diseases globally. To facilitate the design of biosensors for infectious organisms in commercial aircraft, we characterized bacterial diversity in aircraft air. Samples from 61 aircraft high-efficiency particulate air (HEPA) filters were analyzed with a custom microarray of 16S rRNA gene sequences (PhyloChip), representing bacterial lineages. A total of 606 subfamilies from 41 phyla were detected. The most abundant bacterial subfamilies included bacteria associated with humans, especially skin, gastrointestinal and respiratory tracts, and with water and soil habitats. Operational taxonomic units that contain important human pathogens as well as their close, more benign relatives were detected. When compared to 43 samples of urban outdoor air, aircraft samples differed in composition, with higher relative abundance of Firmicutes and Gammaproteobacteria lineages in aircraft samples, and higher relative abundance of Actinobacteria and Betaproteobacteria lineages in outdoor air samples. In addition, aircraft and outdoor air samples differed in the incidence of taxa containing human pathogens. Overall, these results demonstrate that HEPA filter samples can be used to deeply characterize bacterial diversity in aircraft air and suggest that the presence of close relatives of certain pathogens must be taken into account in probe design for aircraft biosensors. A biosensor that could be deployed in commercial aircraft would be required to function at an extremely low false alarm rate, making an understanding of microbial background important. This study reveals a diverse bacterial background present on aircraft, including bacteria closely related to pathogens of public health concern. Furthermore, this aircraft background is different from outdoor air, suggesting different probes may be needed to detect airborne contaminants to achieve minimal false alarm rates. This study also indicates that aircraft HEPA filters could be used

  14. Tropical freshwater ecosystems have lower bacterial growth efficiency than temperate ones

    PubMed Central

    Amado, André M.; Meirelles-Pereira, Frederico; Vidal, Luciana O.; Sarmento, Hugo; Suhett, Albert L.; Farjalla, Vinicius F.; Cotner, James B.; Roland, Fabio

    2013-01-01

    Current models and observations indicate that bacterial respiration should increase and growth efficiency (BGE) should decrease with increasing temperatures. However, these models and observations are mostly derived from data collected in temperate regions, and the tropics are under-represented. The aim of this work was to compare bacterial metabolism, namely bacterial production (BP) and respiration (BR), bacterial growth efficiency (BGE) and bacterial carbon demand (BCD) between tropical and temperate ecosystems via a literature review and using unpublished data. We hypothesized that (1) tropical ecosystems have higher metabolism than temperate ones and, (2) that BGE is lower in tropical relative to temperate ecosystems. We collected a total of 498 coupled BP and BR observations (Ntotal = 498; Ntemperate = 301; Ntropical = 197), calculated BGE (BP/(BP+BR)) and BCD (BP+BR) for each case and examined patterns using a model II regression analysis and compared each parameter between the two regions using non-parametric Mann–Whitney U test. We observed a significant positive linear regression between BR and BP for the whole dataset, and also for tropical and temperate data separately. We found that BP, BR and BCD were higher in the tropics, but BGE was lower compared to temperate regions. Also, BR rates per BP unit were at least two fold higher in the tropics than in temperate ecosystems. We argue that higher temperature, nutrient limitation, and light exposure all contribute to lower BGE in the tropics, mediated through effects on thermodynamics, substrate stoichiometry, nutrient availability and interactions with photochemically produced compounds. More efforts are needed in this study area in the tropics, but our work indicates that bottom-up (nutrient availability and resource stoichiometry) and top-down (grazer pressure) processes, coupled with thermodynamic constraints, might contribute to the lower BGE in the tropics relative to temperate regions. PMID

  15. Associations between bacterial communities of house dust and infant gut

    SciTech Connect

    Konya, T.; Koster, B.; Maughan, H.; Escobar, M.; Azad, M.B.; Guttman, D.S.; Sears, M.R.; Becker, A.B.; Brook, J.R.; Takaro, T.K.; Kozyrskyj, A.L.; Scott, J.A.

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  16. Associations between bacterial communities of house dust and infant gut.

    PubMed

    Konya, T; Koster, B; Maughan, H; Escobar, M; Azad, M B; Guttman, D S; Sears, M R; Becker, A B; Brook, J R; Takaro, T K; Kozyrskyj, A L; Scott, J A

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust-stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  17. Effects of viral enrichment on bacterial production, respiration and growth efficiency

    NASA Astrophysics Data System (ADS)

    Bonilla-Findji, O.; Rochelle-Newall, E.; Weinbauer, M. G.; Gattuso, J.-P.

    2003-04-01

    Viruses are the most common biological agents in the sea. They can influence many ecological processes such as nutrient and carbon cycling, particle size distribution, algal bloom control, species diversity and gene transfer. As they are mainly bacteriophages they not only influence bacterial abundances but also potentially, the bacterial respiration and production, as has been suggested in by Fuhrman’s model in 1992 and a few recent experimental studies. Through their lytic action viruses can influence biogeochemical cycles and so affect the functioning of the whole marine ecosystem. In order to explore this hypothesis and provide some quantitative data we: (1) studied the effects of viruses on bacterial respiration (BR), production (BP) and growth efficiency (BGE) and (2) investigated whether these effects change over time. A viral enrichment experiment was performed in April and May 2002, where the bacterial community isolated from the Bay of Villefranche was exposed to three treatments: Vo (no viral addition), Vm (enrichment of 1-1.5 fold inactivated viruses) and V+ (enrichment of 1-1.5 fold active viruses). No virally induced effects on bacterial metabolism were observed in April but in May after 24 h of incubation, BR was stimulated by ca. 39% in V+ compared to Vo and by 20% relative to Vm. In the presence of active viruses, BP was repressed by ca. 40% compared to Vo and BGE was reduced by 48%. In May, viruses increased the total bacterial carbon demand (17% in V+ compared to Vo, and by 11% relative to Vm). Our results suggest that viruses seem to induce a shift in the specific role of bacterioplankton by reducing the carbon flow to the higher trophic levels and by stimulating the DOM ‡ bacteria ‡ CO2, N, P, Fe pathway.

  18. Gram-negative bacterial molecules associate with Alzheimer disease pathology

    PubMed Central

    Stamova, Boryana; Jin, Lee-Way; DeCarli, Charles; Phinney, Brett; Sharp, Frank R.

    2016-01-01

    Objective: We determined whether Gram-negative bacterial molecules are associated with Alzheimer disease (AD) neuropathology given that previous studies demonstrate Gram-negative Escherichia coli bacteria can form extracellular amyloid and Gram-negative bacteria have been reported as the predominant bacteria found in normal human brains. Methods: Brain samples from gray and white matter were studied from patients with AD (n = 24) and age-matched controls (n = 18). Lipopolysaccharide (LPS) and E coli K99 pili protein were evaluated by Western blots and immunocytochemistry. Human brain samples were assessed for E coli DNA followed by DNA sequencing. Results: LPS and E coli K99 were detected immunocytochemically in brain parenchyma and vessels in all AD and control brains. K99 levels measured using Western blots were greater in AD compared to control brains (p < 0.01) and K99 was localized to neuron-like cells in AD but not control brains. LPS levels were also greater in AD compared to control brain. LPS colocalized with Aβ1-40/42 in amyloid plaques and with Aβ1-40/42 around vessels in AD brains. DNA sequencing confirmed E coli DNA in human control and AD brains. Conclusions: E coli K99 and LPS levels were greater in AD compared to control brains. LPS colocalized with Aβ1-40/42 in amyloid plaques and around vessels in AD brain. The data show that Gram-negative bacterial molecules are associated with AD neuropathology. They are consistent with our LPS-ischemia-hypoxia rat model that produces myelin aggregates that colocalize with Aβ and resemble amyloid-like plaques. PMID:27784770

  19. Association between bacterial infection and radiologically confirmed pneumonia among children.

    PubMed

    Nascimento-Carvalho, Cristiana M; Araújo-Neto, César A; Ruuskanen, Olli

    2015-05-01

    The role of chest radiograph (CXR) among children with community-acquired pneumonia is controversial. We aimed to assess if there is association between a specific etiology and radiologically confirmed pneumonia. This was a prospective cross-sectional study. Based on report of respiratory complaints and fever/difficulty breathing plus the detection of pulmonary infiltrate/pleural effusion on the CXR taken upon admission read by the pediatrician on duty, children <5-year-old hospitalized with community-acquired pneumonia were enrolled. On admission, clinical data and biological samples were collected to investigate 19 etiological agents (11 viruses and 8 bacteria). CXR taken upon admission was independently read by a pediatric radiologist blinded to clinical data. The study group comprised 209 cases with evaluated CXR and establishment of a probable etiology. Radiologically confirmed pneumonia, normal CXR and other radiographic diagnoses were described for 165 (79.0%), 36 (17.2%) and 8 (3.8%) patients, respectively. Viral infection was significantly more common among patients without radiologically confirmed pneumonia (68.2% vs. 47.9%; P = 0.02), particularly among those with normal CXR (66.7% vs. 47.9%; P = 0.04) when compared with patients with radiologically confirmed pneumonia. Bacterial infection was more frequent among cases with radiologically confirmed pneumonia (52.1% vs. 31.8%; P = 0.02). Likewise, pneumococcal infection was more frequently detected among children with radiologically confirmed pneumonia in regard to children with normal CXR (24.2% vs. 8.3%; P = 0.04). Sensitivity (95% confidence interval) of radiologically confirmed pneumonia for pneumococcal infection was 93% (80-98%), and negative predictive value (95% confidence interval) of normal CXR for pneumococcal infection was 92% (77-98%). Bacterial infection, especially pneumococcal one, is associated with radiologically confirmed pneumonia.

  20. Gram-negative bacterial molecules associate with Alzheimer disease pathology.

    PubMed

    Zhan, Xinhua; Stamova, Boryana; Jin, Lee-Way; DeCarli, Charles; Phinney, Brett; Sharp, Frank R

    2016-11-29

    We determined whether Gram-negative bacterial molecules are associated with Alzheimer disease (AD) neuropathology given that previous studies demonstrate Gram-negative Escherichia coli bacteria can form extracellular amyloid and Gram-negative bacteria have been reported as the predominant bacteria found in normal human brains. Brain samples from gray and white matter were studied from patients with AD (n = 24) and age-matched controls (n = 18). Lipopolysaccharide (LPS) and E coli K99 pili protein were evaluated by Western blots and immunocytochemistry. Human brain samples were assessed for E coli DNA followed by DNA sequencing. LPS and E coli K99 were detected immunocytochemically in brain parenchyma and vessels in all AD and control brains. K99 levels measured using Western blots were greater in AD compared to control brains (p < 0.01) and K99 was localized to neuron-like cells in AD but not control brains. LPS levels were also greater in AD compared to control brain. LPS colocalized with Aβ1-40/42 in amyloid plaques and with Aβ1-40/42 around vessels in AD brains. DNA sequencing confirmed E coli DNA in human control and AD brains. E coli K99 and LPS levels were greater in AD compared to control brains. LPS colocalized with Aβ1-40/42 in amyloid plaques and around vessels in AD brain. The data show that Gram-negative bacterial molecules are associated with AD neuropathology. They are consistent with our LPS-ischemia-hypoxia rat model that produces myelin aggregates that colocalize with Aβ and resemble amyloid-like plaques. © 2016 American Academy of Neurology.

  1. Isolation and identification of efficient Egyptian malathion-degrading bacterial isolates.

    PubMed

    Hamouda, S A; Marzouk, M A; Abbassy, M A; Abd-El-Haleem, D A; Shamseldin, Abdelaal

    2015-03-01

    Bacterial isolates degrading malathion were isolated from the soil and agricultural waste water due to their ability to grow on minimal salt media amended with malathion as a sole carbon source. Efficiencies of native Egyptian bacterial malathion-degrading isolates were investigated and the study generated nine highly effective malathion-degrading bacterial strains among 40. Strains were identified by partial sequencing of 16S rDNA analysis. Comparative analysis of 16S rDNA sequences revealed that these bacteria are similar with the genus Acinetobacter and Bacillus spp. and RFLP based PCR of 16S rDNA gave four different RFLP patterns among strains with enzyme HinfI while with enzyme HaeI they gave two RFLP profiles. The degradation rate of malathion in liquid culture was estimated using gas chromatography. Bacterial strains could degrade more than 90% of the initial malathion concentration (1000 ppm) within 4 days. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Bacterial colonization and associated factors in patients with bronchiectasis.

    PubMed

    Borekci, Sermin; Halis, Ayse Nigar; Aygun, Gokhan; Musellim, Benan

    2016-01-01

    To evaluate the bacterial colonization and associated risk factors in patients with bronchiectasis. A total of 121 patients followed at the Bronchiectasis Unit, between 1996 and 2013 and diagnosed as having noncystic fibrosis bronchiectasis with high resolution computed tomography or multi-slice computed tomography were included in this retrospective study. The following definition of colonization was used for study purposes: Detection of at least two isolates of an organism separated by at least 3 months in a year. Of these 121 patients, 65 (54%) were female and 56 (46%) were male. Mean age was 50.6 ± 16.1 years. Mean duration of illness was 20.3 ± 15.5 years. 43 (35.5%) cases had colonization. The major pathogens responsible for colonization were Pseudomonas aeruginosa (n = 25; 20.6%) and Haemophilus influenzae (n = 14, 11.5%). The stepwise logistic regression analysis showed a significant association between colonization and a low percentage of forced vital capacity (FVC%) and the presence of cystic bronchiectasis (P < 0.05). The following factors have been found to be associated with colonization in patients with bronchiectasis: Low FVC% and the presence of cystic bronchiectasis.

  3. Bacterial activity and bacterioplankton diversity in the eutrophic River Warnow--direct measurement of bacterial growth efficiency and its effect on carbon utilization.

    PubMed

    Warkentin, Mareike; Freese, Heike M; Schumann, Rhena

    2011-01-01

    The influence of bacterial activity and diversity on bacterial growth efficiency was investigated in a flatland river. Eutrophic River Warnow drains predominantly agricultural land and is heavily loaded with nutrients, dissolved and particulate organic matter (DOM and POM), especially humic substances. Although the water column bacterial community consists of many inactive or damaged cells, bacterioplankton sustained a high bacterial secondary production of 0.2-14.5 μg C L(-1) h(-1) and a high DNA synthesis (thymidine uptake) of 6.1-15.5 μg C L(-1) h(-1). The direct and short-term measurement of bacterial respiration (by optodes) revealed high respiration rates especially in summer leading to directly estimated bacterial growth efficiencies (BGE) of 2-28%. These values are compared to calculations based only on bacterial production, which considerably overestimated BGEs. From all these data, River Warnow can be characterized as a strongly remineralizing system. River Warnow was dominated among others by Cytophaga/Flavobacteria and Actinobacteria which are typical for organic rich waters because of their ability to degrade high molecular weight compounds. However, community composition did not significantly affect BGE.

  4. Bacterial capture efficiency and antimicrobial activity of phage-functionalized model surfaces.

    PubMed

    Hosseinidoust, Zeinab; Van de Ven, Theo G M; Tufenkji, Nathalie

    2011-05-03

    The rise of antibiotic-resistant bacteria has directed substantial attention toward the use of bacteriophages as a means to control bacterial populations. It has been proposed that bacteriophages can be applied as a coating on surfaces in healthcare settings or on indwelling medical devices to create an antimicrobial surface. In this study, antimicrobial model surfaces functionalized with five different types of bacteriophage were prepared and characterized with X-ray photoelectron spectroscopy and atomic force microscopy. The bacterial capture efficiency of these functionalized surfaces was studied for two common bacteria, Escherichia coli and Salmonella typhimurium. Binding of the phages to a solid surface affected their biofunctionality as expressed by the capture efficiency and rate of host membrane disruption. Moreover, the size and shape of the bacteriophage and positioning of its specific binding proteins significantly affected its bacterial capture capability in the immobilized state. Symmetric bacteriophages were found to be a better choice for antibacterial surfaces compared to more asymmetric tailed bacteriophages. Immobilized phages were found to disrupt the membranes of attached bacteria and are thus proposed as a candidate for antimicrobial surfaces.

  5. Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency.

    PubMed

    Jewell, Kelsea A; McCormick, Caroline A; Odt, Christine L; Weimer, Paul J; Suen, Garret

    2015-07-01

    Fourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows were Bacteroidetes (49.42%), Firmicutes (39.32%), Proteobacteria (5.67%), and Tenericutes (2.17%), and the most abundant genera included Prevotella (40.15%), Butyrivibrio (2.38%), Ruminococcus (2.35%), Coprococcus (2.29%), and Succiniclasticum (2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles.

  6. Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

    PubMed Central

    Jewell, Kelsea A.; McCormick, Caroline A.; Odt, Christine L.; Weimer, Paul J.

    2015-01-01

    Fourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows were Bacteroidetes (49.42%), Firmicutes (39.32%), Proteobacteria (5.67%), and Tenericutes (2.17%), and the most abundant genera included Prevotella (40.15%), Butyrivibrio (2.38%), Ruminococcus (2.35%), Coprococcus (2.29%), and Succiniclasticum (2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles. PMID:25934629

  7. Bacterial communities associated with flea vectors of plague.

    PubMed

    Erickson, David L; Anderson, Nathan E; Cromar, Lauren M; Jolley, Andrea

    2009-11-01

    The microbial flora associated with fleas may affect their ability to transmit specific pathogens, including Yersinia pestis, and also could be used to develop paratransgenesis-based approaches to interfere with transmission. To begin addressing this hypothesis, the microbial flora associated with the relatively efficient Y. pestis vectors Xenopsylla cheopis (Rothschild) (Siphonaptera: Pulicidae) and Oropsyllamontana (Baker) (Siphonaptera: Ceratophyllidae), and the inefficient vector Ctenocephalides felis felis (Bouché) (Siphonaptera: Pulicidae) were investigated using polymerase chain reaction amplification of 16S rDNA genes. DNA sequencing revealed that these species harbor distinct communities of microbial flora and suggest that Acinetobacter sp. might be used in developing anti-transmission strategies.

  8. Clinical surface modification process using the nitrogen plasma and its anti-bacterial efficiency.

    PubMed

    Ghoranneviss, M; Shahidi, S; Elahi, A Salar

    2016-11-22

    In this research, the cotton fabrics were treated with nitrogen plasma for the clinical and anti-bacterial purposes. Turmeric was used a as a natural dye. Some part of both untreated and plasma treated samples was immersed in silver nitrate as a mordant before dyeing. Effect of plasma and silver nitrate on dye ability of cotton samples was compared and studied. Samples were analyzed with different experimental methods, such as scanning electron microscopy (SEM), Reflection spectro-photometry and antibacterial test. Results showed that, turmeric dye have anti-bacterial efficiency and good antibacterial activity achieved by plasma treatment of fabrics. In case of AgNO3 treatment, samples showed 100% antibacterial activity. It also concluded that, nitrogen plasma has synergic effect on antibacterial activity of turmeric as natural dye on cotton fabrics.

  9. Simultaneous selection of soil electroactive bacterial communities associated to anode and cathode in a two-chamber Microbial Fuel Cell

    NASA Astrophysics Data System (ADS)

    Chiellini, Carolina; Bacci, Giovanni; Fani, Renato; Mocali, Stefano

    2016-04-01

    Different bacteria have evolved strategies to transfer electrons over their cell surface to (or from) their extracellular environment. This electron transfer enables the use of these bacteria in bioelectrochemical systems (BES) such as Microbial Fuel Cells (MFCs). In MFC research the biological reactions at the cathode have long been a secondary point of interest. However, bacterial biocathodes in MFCs represent a potential advantage compared to traditional cathodes, for both their low costs and their low impact on the environment. The main challenge in biocathode set-up is represented by the selection of a bacterial community able to efficiently accept electrons from the electrode, starting from an environmental matrix. In this work, a constant voltage was supplied on a two-chamber MFC filled up with soil over three weeks in order to simultaneously select an electron donor bacterial biomass on the anode and an electron acceptor biomass on the cathode, starting from the same soil. Next Generation Sequencing (NGS) analysis was performed to characterize the bacterial community of the initial soil, in the anode, in the cathode and in the control chamber not supplied with any voltage. Results highlighted that both the MFC conditions and the voltage supply affected the soil bacterial communities, providing a selection of different bacterial groups preferentially associated to the anode (Betaproteobacteria, Bacilli and Clostridia) and to the cathode (Actinobacteria and Alphaproteobacteria). These results confirmed that several electroactive bacteria are naturally present within a top soil and, moreover, different soil bacterial genera could provide different electrical properties.

  10. Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments

    PubMed Central

    Zarzycki, Jan; Erbilgin, Onur

    2015-01-01

    Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde. Recently, it was shown that the most prevalent signature enzymes encoded by BMC loci are glycyl radical enzymes, yet little is known about the function of these BMCs. Here we characterize the glycyl radical enzyme-associated microcompartment (GRM) loci using a combination of bioinformatic analyses and active-site and structural modeling to show that the GRMs comprise five subtypes. We predict distinct functions for the GRMs, including the degradation of choline, propanediol, and fuculose phosphate. This is the first family of BMCs for which identification of the signature enzyme is insufficient for predicting function. The distinct GRM functions are also reflected in differences in shell composition and apparently different assembly pathways. The GRMs are the counterparts of the vitamin B12-dependent propanediol- and ethanolamine-utilizing BMCs, which are frequently associated with virulence. This study provides a comprehensive foundation for experimental investigations of the diverse roles of GRMs. Understanding this plasticity of function within a single BMC family, including characterization of differences in permeability and assembly, can inform approaches to BMC bioengineering and the design of therapeutics. PMID:26407889

  11. Bacterial pathogens associated with bloody diarrhea in Uruguayan children.

    PubMed

    Mota, M I; Gadea, M P; González, S; González, G; Pardo, L; Sirok, A; Rivas, M; Algorta, G; Schelotto, F; Varela, G

    2010-01-01

    Diarrheal disease continues to be a serious health problem, especially in developing countries. Bloody diarrhea represents approximately 20-30% of all cases and has higher morbidity and mortality. Treatment with antibiotics is beneficial in cases of Shigella, Campylobacter, Yersinia and Salmonella infection, principally in those children with a higher risk of invasive disease. The aims of this study were to detect the bacterial agents associated with bloody diarrhea in children and to determine their antimicrobial susceptibility patterns. Between June 2001 and January 2008, 249 children with bloody diarrhea were studied. Shigella and Shiga toxin-producing Escherichia coli (STEC) were recovered from 48 (19.3%) and 3 (1.2%) of the total of cases, respectively. In 49 out of 249 children, in whom other enteropathogens were investigated, we recovered Campylobacter jejuni from 7 children (14.3%), Salmonella spp. from 2 (4.1%) and Aeromonas spp. from 1 (2%) in addition to Shigella from 7 children (14.3%). Thirty-four (70%) Shigella isolates showed resistance to ampicillin and 13 (27%) to trimethoprim-sulfamethoxazole. All Shigella isolates were susceptible to nalidixic acid, ciprofloxacin and ceftriaxone. Salmonella and STEC isolates were susceptible to all antibiotics assayed. Thus, the use of trimethoprim-sulfamethoxazole or ampicillin would not be appropriate for the empirical treatment of Shigella - associated diarrhea.

  12. Influence of forest trees on the distribution of mineral weathering-associated bacterial communities of the Scleroderma citrinum mycorrhizosphere.

    PubMed

    Calvaruso, Christophe; Turpault, Marie-Pierre; Leclerc, Elisabeth; Ranger, Jacques; Garbaye, Jean; Uroz, Stéphane; Frey-Klett, Pascale

    2010-07-01

    In acidic forest soils, availability of inorganic nutrients is a tree-growth-limiting factor. A hypothesis to explain sustainable forest development proposes that tree roots select soil microbes involved in central biogeochemical processes, such as mineral weathering, that may contribute to nutrient mobilization and tree nutrition. Here we showed, by combining soil analyses with cultivation-dependent analyses of the culturable bacterial communities associated with the widespread mycorrhizal fungus Scleroderma citrinum, a significant enrichment of bacterial isolates with efficient mineral weathering potentials around the oak and beech mycorrhizal roots compared to bulk soil. Such a difference did not exist in the rhizosphere of Norway spruce. The mineral weathering ability of the bacterial isolates was assessed using a microplaque assay that measures the pH and the amount of iron released from biotite. Using this microplate assay, we demonstrated that the bacterial isolates harboring the most efficient mineral weathering potential belonged to the Burkholderia genus. Notably, previous work revealed that oak and beech harbored very similar pHs in the 5- to 10-cm horizon in both rhizosphere and bulk soil environments. In the spruce rhizosphere, in contrast, the pH was significantly lower than that in bulk soil. Because the production of protons is one of the main mechanisms responsible for mineral weathering, our results suggest that certain tree species have developed indirect strategies for mineral weathering in nutrient-poor soils, which lie in the selection of bacterial communities with efficient mineral weathering potentials.

  13. Association of Recent Bacterial Vaginosis With Acquisition of Mycoplasma genitalium.

    PubMed

    Lokken, Erica M; Balkus, Jennifer E; Kiarie, James; Hughes, James P; Jaoko, Walter; Totten, Patricia A; McClelland, R Scott; Manhart, Lisa E

    2017-07-15

    We assessed the association between recent bacterial vaginosis (BV) and incident Mycoplasma genitalium, a sexually transmitted bacterium associated with adverse female reproductive health outcomes. Female sex workers in Mombasa, Kenya, completed a monthly sexual behavior interview and clinical examination. During February 2005-February 2006, vaginal fluid specimens collected from women every other month were tested for M. genitalium by nucleic acid amplification testing. Vaginal microbiota were assessed monthly and categorized by Nugent score (0-3 = normal microbiota, 4-6 = intermediate microbiota disruption, and 7-10 = BV). A discrete failure time analysis for multiple events using logistic regression was employed to estimate the odds of incident M. genitalium infection at follow-up visits among women with BV (vs. normal microbiota) at the preceding visit. Among the 280 women, 54.3% were positive for human immunodeficiency virus. At baseline, 16.1% had prevalent M. genitalium infection and 40.4% had prevalent BV. There were 59 incident M. genitalium infections among 50 women, for an incidence rate of 34.6 cases per 100 person-years. Following adjustment for age, human immunodeficiency virus status, and time, prior BV was associated with a 3.5-fold increase in odds of incident M. genitalium (adjusted odds ratio = 3.49, 95% confidence interval: 1.86, 6.56). This strong association suggests that BV may enhance susceptibility to M. genitalium infection. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Gardnerella vaginalis-associated bacterial vaginosis in Bulgarian women.

    PubMed

    Gergova, Raina T; Strateva, Tanya V; Mitov, Ivan G

    2013-01-01

    Bacterial vaginosis (BV) is the most common cause of vaginal discharge in women of reproductive age. The purpose of this study was to determine the frequency of BV in Bulgarian pregnant and nonpregnant women from several age ranges and to compare three different laboratory methods for Gardnerella vaginalis detection in patents suffering from BV. Between September 2011 and June 2012, 809 women of 16-40 years of age separated in two major groups: nonpregnant - 469 (355 with and 114 without symptoms) and pregnant - 340 (213 and 127 respectively) were enrolled for the study. The women underwent three different laboratory tests simultaneously: scoring of Gram staining of vaginal smear, culture, and polymerase chain reaction (PCR) assay for G. vaginalis. The microscopic method detected high frequency of BV in symptomatic (57%) whereas only a minority of asymptomatic subjects (14%) were detected. G. vaginalis-associated BV was diagnosed in approximately equal proportions when evaluated with PCR and microscopic method for both pregnant and nonpregnant women. The comparative analysis of microscopic evaluation, culture and PCR assays demonstrated greater concurrence (about 90%) between Gram staining and PCR detection for BV, than both methods compared to culture. The combination of microscopy and PCR turned out to be very reliable and repeatable for detecting G. vaginalis-associated BV. This is the first comparative investigation on the epidemiology of G. vaginalis-associated BV in Bulgaria. The established highest frequency in the young Bulgarian women (21-30 years) is alarming and should be considered in prophylaxis and reproductive programmes. Copyright © 2013 Elsevier Editora Ltda. All rights reserved.

  15. Association between small intestinal bacterial overgrowth and deep vein thrombosis

    PubMed Central

    Fialho, Andre; Fialho, Andrea; Schenone, Aldo; Thota, Prashanthi; McCullough, Arthur; Shen, Bo

    2016-01-01

    Objective: Small intestinal bacterial overgrowth (SIBO) has been associated with several diseases. The association between SIBO and deep vein thrombosis (DVT) has not been investigated. This study was aimed to investigate the frequency and risk factors for the development of DVT in patients tested for SIBO. Methods: All 321 eligible patients were included from the Cleveland Clinic Gastrointestinal Motility Lab databank from January 2008 to January 2014. Patients who were evaluated with glucose hydrogen/methane breath test as well as Doppler ultrasonography for suspected DVT were included. Patients with catheter-related DVT were excluded. The primary outcomes were the frequency and risk factors (including SIBO) for DVT in this patient population. Results: Of the 321-case cohort, 144 patients (44.9%) tested positive for SIBO, and 53 (16.5%) had ultrasonographic findings of DVT. SIBO evaluation before the evaluation of DVT occurred in 201 patients (median time from the breath test to ultrasonography: 27 months; interquartile range [IQR]: 11.0–45.0 months), and SIBO evaluation after evaluation for DVT occurred in 120 patients (median time from ultrasonography to the breath test: 30 months; IQR: 11.8–54.3 months). In the univariate analysis, DVT was associated with family history of thromboembolic events (35.8% vs 16.0%, P=0.001), chronic kidney diseases (CKD; 26.4% vs 13.4%, P=0.019) and the presence of SIBO (69.8% vs 39.9%, P<0.001). In the multivariate analysis, family history of thromboembolic events (odds ratio [OR]: 3.39; 95% confidence interval [CI]: 1.67–6.87; P<0.001), CKD (OR: 2.23; 95%CI: 1.04–4.74; P = 0.037), and the presence of SIBO (OR: 3.27; 95% CI: 1.70–6.32; P < 0.001) remained independently associated with DVT. Conclusion: SIBO was found to be associated with DVT. The nature of this association warrants further investigation. PMID:27044499

  16. Bacterial filtration efficiency of green soy protein based nanofiber air filter.

    PubMed

    Lubasova, D; Netravali, A; Parker, J; Ingel, B

    2014-07-01

    High bacterial filtration efficiency (BFE) filters, based on nanofibers derived from blends of grain proteins and poly-ethylene-oxide (PEO), were produced by an electrospinning process. Specifically, polymer blends consisting of purified soy flour/PEO with a ratio of 7/3 were spun into nanofibers and characterized. A new laboratory based experimental apparatus for testing BFE was designed and used to test BFE of bacterial aerosols consisting of Escherichia coli (E. coli). Performances of soy protein based nanofiber filters with nanofiber mass varying from 1 to 5 g/m2 as well as a nanofiber filters prepared from pure PEO were compared. The results showed that BFE values for filters containing 5 g/m2 protein based nanofibers and PEO nanofiber filter were 100 and 81.5%, respectively. The results also indicated that the BFE increased as the protein content in the nanofiber filter increased. These novel protein based nanofiber filters have demonstrated a clear potential for effective removal and retention of E. coli bacteria during air-filtration. These filters can be effectively deployed in environments such as hospitals and senior residential areas to reduce bacterial infections.

  17. Risk of spontaneous bacterial peritonitis associated with gastric Acid suppression.

    PubMed

    Chang, Shy-Shin; Lai, Chih-Cheng; Lee, Meng-tse Gabriel; Lee, Yu-Chien; Tsai, Yi-Wen; Hsu, Wan-Ting; Lee, Chien-Chang

    2015-06-01

    The primary objective of this study was to determine the association between the use of gastric acid suppressants (GAS) and the risk of developing spontaneous bacterial peritonitis (SBP) in patients with advanced liver cirrhosis (LC). A case-control study nested within a cohort of 480,000 representatives of Taiwan National Health Insurance beneficiaries was carried out. A case was matched with 100 controls on age, gender, and index date of SBP diagnosis. GAS use was identified from the 1-year period before the index date. Conditional logistic regression analysis was used to adjust for various unbalanced covariates between users and nonusers of GAS. A total of 947 cases of SBP were identified among the 86,418 patients with advanced LC. A significant increased risk of developing SBP was found to be associated with current (within 30 days), and recent (within 30-90 day) use of 2 different classes of GAS: proton pump inhibitors (PPIs) and histamine 2 receptor antagonists (H2RAs). The confounder adjusted rate ratio (aRR) for the current use of PPIs was 2.77 (95% CI: 1.90-4.04) and H2RAs was 2.62 (95% CI: 2.00-3.42). The risk of SBP attenuated for the recent use of PPIs (aRR: 2.20, 95%CI: 1.60-3.02) or H2RAs (aRR: 1.72, 95% CI: 1.25-2.37). In addition, sensitivity analysis using hospitalized SBP as the primary outcome showed a similar risk for the current use of PPIs (aRR, 3.24; 95% CI: 2.08-5.05) and H2RAs (aRR 2.43; 95% CI 1.71-3.46). Furthermore, higher cumulative days of gastric acid suppression were associated with a higher risk of SBP (trend P < 0.0001). To conclude, exposure to GAS was associated with an increased risk of SBP in patients with advanced LC. The association was more pronounced in current PPI users compared with nonusers.

  18. Marine bacterial, archaeal and protistan association networks reveal ecological linkages.

    PubMed

    Steele, Joshua A; Countway, Peter D; Xia, Li; Vigil, Patrick D; Beman, J Michael; Kim, Diane Y; Chow, Cheryl-Emiliane T; Sachdeva, Rohan; Jones, Adriane C; Schwalbach, Michael S; Rose, Julie M; Hewson, Ian; Patel, Anand; Sun, Fengzhu; Caron, David A; Fuhrman, Jed A

    2011-09-01

    Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes.

  19. Development of an Efficient Bacterial Consortium for the Potential Remediation of Hydrocarbons from Contaminated Sites

    PubMed Central

    Patowary, Kaustuvmani; Patowary, Rupshikha; Kalita, Mohan C.; Deka, Suresh

    2016-01-01

    The intrinsic biodegradability of hydrocarbons and the distribution of proficient degrading microorganisms in the environment are very crucial for the implementation of bioremediation practices. Among others, one of the most favorable methods that can enhance the effectiveness of bioremediation of hydrocarbon-contaminated environment is the application of biosurfactant producing microbes. In the present study, the biodegradation capacities of native bacterial consortia toward total petroleum hydrocarbons (TPH) with special emphasis to poly aromatic hydrocarbons were determined. The purpose of the study was to isolate TPH degrading bacterial strains from various petroleum contaminated soil of Assam, India and develop a robust bacterial consortium for bioremediation of crude oil of this native land. From a total of 23 bacterial isolates obtained from three different hydrocarbons contaminated samples five isolates, namely KS2, PG1, PG5, R1, and R2 were selected as efficient crude oil degraders with respect to their growth on crude oil enriched samples. Isolates KS2, PG1, and R2 are biosurfactant producers and PG5, R1 are non-producers. Fourteen different consortia were designed involving both biosurfactant producing and non-producing isolates. Consortium 10, which comprises two Bacillus strains namely, Bacillus pumilus KS2 and B. cereus R2 (identified by 16s rRNA sequencing) has shown the best result in the desired degradation of crude oil. The consortium showed degradation up to 84.15% of TPH after 5 weeks of incubation, as revealed from gravimetric analysis. FTIR (Fourier transform infrared) and GCMS (Gas chromatography-mass spectrometer) analyses were correlated with gravimetric data which reveals that the consortium has removed a wide range of petroleum hydrocarbons in comparison with abiotic control including different aliphatic and aromatic hydrocarbons. PMID:27471499

  20. Development of an Efficient Bacterial Consortium for the Potential Remediation of Hydrocarbons from Contaminated Sites.

    PubMed

    Patowary, Kaustuvmani; Patowary, Rupshikha; Kalita, Mohan C; Deka, Suresh

    2016-01-01

    The intrinsic biodegradability of hydrocarbons and the distribution of proficient degrading microorganisms in the environment are very crucial for the implementation of bioremediation practices. Among others, one of the most favorable methods that can enhance the effectiveness of bioremediation of hydrocarbon-contaminated environment is the application of biosurfactant producing microbes. In the present study, the biodegradation capacities of native bacterial consortia toward total petroleum hydrocarbons (TPH) with special emphasis to poly aromatic hydrocarbons were determined. The purpose of the study was to isolate TPH degrading bacterial strains from various petroleum contaminated soil of Assam, India and develop a robust bacterial consortium for bioremediation of crude oil of this native land. From a total of 23 bacterial isolates obtained from three different hydrocarbons contaminated samples five isolates, namely KS2, PG1, PG5, R1, and R2 were selected as efficient crude oil degraders with respect to their growth on crude oil enriched samples. Isolates KS2, PG1, and R2 are biosurfactant producers and PG5, R1 are non-producers. Fourteen different consortia were designed involving both biosurfactant producing and non-producing isolates. Consortium 10, which comprises two Bacillus strains namely, Bacillus pumilus KS2 and B. cereus R2 (identified by 16s rRNA sequencing) has shown the best result in the desired degradation of crude oil. The consortium showed degradation up to 84.15% of TPH after 5 weeks of incubation, as revealed from gravimetric analysis. FTIR (Fourier transform infrared) and GCMS (Gas chromatography-mass spectrometer) analyses were correlated with gravimetric data which reveals that the consortium has removed a wide range of petroleum hydrocarbons in comparison with abiotic control including different aliphatic and aromatic hydrocarbons.

  1. A Plasmid Set for Efficient Bacterial Artificial Chromosome (BAC) Transgenesis in Zebrafish

    PubMed Central

    Fuentes, Fernando; Reynolds, Eric; Lewellis, Stephen W.; Venkiteswaran, Gayatri; Knaut, Holger

    2016-01-01

    Transgenesis of large DNA constructs is essential for gene function analysis. Recently, Tol2 transposase-mediated transgenesis has emerged as a powerful tool to insert bacterial artificial chromosome (BAC) DNA constructs into the genome of zebrafish. For efficient transgenesis, the genomic DNA piece in the BAC construct needs to be flanked by Tol2 transposon sites, and the constructs should contain a transgenesis marker for easy identification of transgenic animals. We report a set of plasmids that contain targeting cassettes that allow the insertion of Tol2 sites and different transgenesis markers into BACs. Using BACs containing these targeting cassettes, we show that transgenesis is as efficient as iTol2, that preselecting for expression of the transgenesis marker increases the transgenesis rate, and that BAC transgenics faithfully recapitulate the endogenous gene expression patterns and allow for the estimation of the endogenous gene expression levels. PMID:26818072

  2. Bacterial community composition in rainwater associated with synoptic weather in an area downwind of the Asian continent.

    PubMed

    Hu, Wei; Murata, Kotaro; Horikawa, Yuka; Naganuma, Ayumi; Zhang, Daizhou

    2017-12-01

    Bacteria are abundant in atmospheric waters and can be disseminated by precipitation to the surface of the Earth, potentially influencing ecosystems, public health and climate. However, data on bacterial communities in rainwater, especially on the association with weather, are very limited. In this study, rainwater was collected at the coastal city Kumamoto, southwestern Japan, in 2015. The bacterial communities in fourteen samples were identified using 16S rRNA sequencing and compared according to the rain types at the synoptic scale, i.e., cyclones, Meiyu and non-Meiyu stationary fronts, and typhoons. Diverse bacterial communities were present in all four types of rainwater and were dominated by the phyla Proteobacteria (37%), Bacteroidetes (16%), Cyanobacteria (14%), Actinobacteria (9%), Acidobacteria (8%) and Firmicutes (5%). Approximately half of the phyla (16 out of 33) were common among the rain types. The operational taxonomic units (OTUs) common among the four types of rainwater represented the majority (averagely 74%) of the sequences, indicating the predominance of common bacterial OTUs regardless of rain type. On the other hand, the synoptic weather systems and the origins of air masses associated with the rain likely resulted in distinct bacterial communities. High fractions of bacterial soil indicator taxa signified the large contribution of bacteria from soils. Genera containing ice nucleation-active bacteria were identified in all samples except one typhoon rain sample. Marine bacterial taxa, e.g., Pseudoalteromonas, Synechococcus and Marinobacter, were detected in several samples, indicating the dispersal of marine bacteria via clouds and rainwater. Fecal indicator bacteria were also detected in all samples. Thus, the bacteria in the four types of rainwater were characterized by largely overlapping communities with some differences in community composition, indicating that rain is an efficient pathway for the dissemination of bacterial communities

  3. Promiscuity in mice is associated with increased vaginal bacterial diversity

    NASA Astrophysics Data System (ADS)

    Macmanes, Matthew David

    2011-11-01

    Differences in the number of sexual partners (i.e., mating system) have the potential to exert a strong influence on the bacterial communities present in reproductive structures like the vagina. Because this structure serves as a conduit for gametes, bacteria present there may have a pronounced, direct effect on host reproductive success. As a first step towards the identification of the relationship between sexual behavior and potentially pathogenic bacterial communities inhabiting vital reproductive structures, as well as their potential effects on fitness, I sought to quantify differences in bacterial diversity in a promiscuous and monogamous mammal species. To accomplish this, I used two sympatric species of Peromyscus rodents— Peromyscus californicus and Peromyscus maniculatus that differ with regard to the number of sexual partners per individual to test the hypothesis that bacterial diversity should be greater in the promiscuous P. maniculatus relative to the monogamous P. californicus. As predicted, phylogenetically controlled and operational taxonomic unit-based indices of bacterial diversity indicated that diversity is greater in the promiscuous species. These results provide important new insights into the effects of mating system on bacterial diversity in free-living vertebrates, and may suggest a potential cost of promiscuity.

  4. Promiscuity in Mice is Associated with Increased Vaginal Bacterial Diversity

    PubMed Central

    MacManes, Matthew D.

    2011-01-01

    Differences in the number of sexual partners (i.e., mating system) have the potential to exert a strong influence on the bacterial communities present in reproductive structures like the vagina. Because this structure serves as a conduit for gametes, bacteria present there may have a pronounced, direct effect on host reproductive success. As a first step towards the identification of the relationship between sexual behavior and potentially pathogenic bacterial communities inhabiting vital reproductive structures—as well as their potential effects on fitness, I sought to quantify differences in bacterial diversity in a promiscuous and monogamous mammal species. To accomplish this, I used 2 sympatric species of Peromyscus rodents—P. californicus and P. maniculatus that differ with regard to numbers of sexual partners per individual to test the hypothesis that bacterial diversity should be greater in the promiscuous P. maniculatus relative to the monogamous P. californicus. As predicted, phylogenetically controlled and operational taxonomic unit-based indices of bacterial diversity indicated that diversity is greater in the promiscuous species. These results provide important new insights into the effects of mating system on bacterial diversity in free-living vertebrates, and may suggest a potential cost of promiscuity. PMID:21964973

  5. Bacterial community associated with ensilage process of wilted guinea grass.

    PubMed

    Parvin, S; Nishino, N

    2009-12-01

    To determine the effects of wilting, storage period and bacterial inoculant on the bacterial community and ensiling fermentation of guinea grass silage. Fermentation products, colony counts and denaturing gradient gel electrophoresis (DGGE) profiles were determined. There was more lactic acid than acetic acid in all silages, but the lactic acid to acetic acid ratio decreased with storage time. This shift from lactic to acetic acid was not prevented even with a combination of wilting and bacterial inoculant. The DGGE analyses suggest that facultatively heterofermentative lactic acid bacteria (Lactobacillus plantarum, Lactobacillus brevis and Lactobacillus pentosus) were involved in the shift to acetic acid fermentation. Lactic acid can dominate the fermentation in tropical grass silage with sufficient wilting prior to ensiling. Prolonged storage may lead to high levels of acetic acid without distinctive changes in the bacterial community. The bacterial community looks stable compared to fermentation products over the course of long storage periods in tropical grass silage. Acetic acid fermentation in tropical grass silage can be a result of the changes in bacterial metabolism rather than community structure.

  6. First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific.

    PubMed

    Hernández-Zulueta, Joicye; Araya, Rubén; Vargas-Ponce, Ofelia; Díaz-Pérez, Leopoldo; Rodríguez-Troncoso, Alma P; Ceh, Janja; Ríos-Jara, Eduardo; Rodríguez-Zaragoza, Fabián A

    2016-12-01

    Bacterial assemblages associated with the hermatypic corals Pocillopora damicornis and P. verrucosa, the surrounding seawater and the sediment at six coral reef sites in the north section of the Tropical Eastern Pacific were assessed using MiSeq Illumina sequencing of the V4 region of the 16S rDNA. The bacterial microbiota in both coral species, seawater and sediment were stable to seasonal variations. Bacterial assemblages between the same substrates were not significantly different from each other in the six sites sampled. Interestingly, the bacterial composition between substrates within the same site was significantly different, or not, depending on the conservation status of the site. Moreover, we found species-specific bacterial OTUs in both coral species. Analyzing the relationship between bacterial composition and environmental variables revealed a positive correlation between bacterial assemblages and dissolved oxygen, ammonium and silicate.

  7. Same, same but different: symbiotic bacterial associations in GBR sponges.

    PubMed

    Webster, N S; Luter, H M; Soo, R M; Botté, E S; Simister, R L; Abdo, D; Whalan, S

    2012-01-01

    Symbioses in marine sponges involve diverse consortia of microorganisms that contribute to the health and ecology of their hosts. The microbial communities of 13 taxonomically diverse Great Barrier Reef (GBR) sponge species were assessed by DGGE and 16S rRNA gene sequencing to determine intra and inter species variation in bacterial symbiont composition. Microbial profiling revealed communities that were largely conserved within different individuals of each species with intra species similarity ranging from 65-100%. 16S rRNA gene sequencing revealed that the communities were dominated by Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Nitrospira, and Cyanobacteria. Sponge-associated microbes were also highly host-specific with no operational taxonomic units (OTUs) common to all species and the most ubiquitous OTU found in only 5 of the 13 sponge species. In total, 91% of the OTUs were restricted to a single sponge species. However, GBR sponge microbes were more closely related to other sponge-derived bacteria than they were to environmental communities with sequences falling within 50 of the 173 previously defined sponge-(or sponge-coral) specific sequence clusters (SC). These SC spanned the Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Gemmatimonadetes, Nitrospira, and the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. The number of sequences assigned to these sponge-specific clusters across all species ranged from 0 to 92%. No relationship between host phylogeny and symbiont communities were observed across the different sponge orders, although the highest level of similarity was detected in two closely related Xestospongia species. This study identifies the core microbial inhabitants in a range of GBR sponges thereby providing the basis for future studies on sponge symbiotic function and research aiming to predict how sponge holobionts will respond to environmental perturbation.

  8. Microfluidic Air Sampler for Highly Efficient Bacterial Aerosol Collection and Identification.

    PubMed

    Bian, Xiaojun; Lan, Ying; Wang, Bing; Zhang, Yu Shrike; Liu, Baohong; Yang, Pengyuan; Zhang, Weijia; Qiao, Liang

    2016-12-06

    The early warning capability of the presence of biological aerosol threats is an urgent demand in ensuing civilian and military safety. Efficient and rapid air sample collection in relevant indoor or outdoor environment is a key step for subsequent analysis of airborne microorganisms. Herein, we report a portable battery-powered sampler that is capable of highly efficient bioaerosol collection. The essential module of the sampler is a polydimethylsiloxane (PDMS) microfluidic chip, which consisted of a 3-loop double-spiral microchannel featuring embedded herringbone and sawtooth wave-shaped structures. Vibrio parahemolyticus (V. parahemolyticus) as a model microorganism, was initially employed to validate the bioaerosol collection performance of the device. Results showed that the sampling efficacy reached as high as >99.9%. The microfluidic sampler showed greatly improved capturing efficiency compared with traditional plate sedimentation methods. The high performance of our device was attributed to the horizontal inertial centrifugal force and the vertical turbulence applied to airflow during sampling. The centrifugation field and turbulence were generated by the specially designed herringbone structures when air circulated in the double-spiral microchannel. The sawtooth wave-shaped microstructure created larger specific surface area for accommodating more aerosols. Furthermore, a mixture of bacterial aerosols formed by V. parahemolyticus, Listeria monocytogenes, and Escherichia coli was extracted by the microfluidic sampler. Subsequent integration with mass spectrometry conveniently identified the multiple bacterial species captured by the sampler. Our developed stand-alone and cable-free sampler shows clear advantages comparing with conventional strategies, including portability, easy-to-use, and low cost, indicating great potential in future field applications.

  9. The immunology of influenza virus-associated bacterial pneumonia.

    PubMed

    Robinson, Keven M; Kolls, Jay K; Alcorn, John F

    2015-06-01

    Infection with influenza virus has been a significant cause of morbidity and mortality for more than a hundred years. Severe disease and increased mortality often results from bacterial super-infection of patients with influenza virus infection. Preceding influenza infection alters the host's innate and adaptive immune responses, allowing increased susceptibility to secondary bacterial pneumonia. Recent advances in the field have helped to define how influenza alters the immune response to bacteria through the dysregulation of phagocytes, antimicrobial peptides, and lymphocytes. Viral-induced interferons play a key role in altering the phenotype of the immune response. Potential genetic modifiers of disease will help to define additional immunologic mechanisms that predispose to viral, bacterial super-infection with the overarching goal of developing effective therapeutic strategies to prevent and treat disease. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs.

    PubMed

    Yang, Hui; Huang, Xiaochang; Fang, Shaoming; He, Maozhang; Zhao, Yuanzhang; Wu, Zhenfang; Yang, Ming; Zhang, Zhiyan; Chen, Congying; Huang, Lusheng

    2017-01-01

    Gut microbiota plays fundamental roles in energy harvest, nutrient digestion, and intestinal health, especially in processing indigestible components of polysaccharides in diet. Unraveling the microbial taxa and functional capacity of gut microbiome associated with feed efficiency can provide important knowledge to improve pig feed efficiency in swine industry. In the current research, we studied the association of fecal microbiota with feed efficiency in 280 commercial Duroc pigs. All experimental pigs could be clustered into two enterotype-like groups. Different enterotypes showed the tendency of association with the feed efficiency (P = 0.07). We further identified 31 operational taxonomic units (OTUs) showing the potential associations with porcine feed efficiency. These OTUs were mainly annotated to the bacteria related to the metabolisms of dietary polysaccharides. Although we did not identify the RFI-associated bacterial species at FDR < 0.05 level, metagenomic sequencing analysis did find the distinct function capacities of gut microbiome between the high and low RFI pigs (FDR < 0.05). The KEGG orthologies related to nitrogen metabolism, amino acid metabolism, and transport system, and eight KEGG pathways including glycine, serine, and threonine metabolism were positively associated with porcine feed efficiency. We inferred that gut microbiota might improve porcine feed efficiency through promoting intestinal health by the SCFAs produced by fermenting dietary polysaccharides and improving the utilization of dietary protein. The present results provided important basic knowledge for improving porcine feed efficiency through modulating gut microbiome.

  11. Influence of external bacterial structures on the efficiency of photodynamic inactivation by a cationic porphyrin.

    PubMed

    Pereira, M A; Faustino, M A F; Tomé, J P C; Neves, M G P M S; Tomé, A C; Cavaleiro, J A S; Cunha, Â; Almeida, A

    2014-04-01

    The main targets of photodynamic inactivation (PDI) are the external bacterial structures, cytoplasmic membrane and cell wall. In this work it was evaluated how the external bacterial structures influence the PDI efficiency. To reach this objective 8 bacteria with distinct external structures were selected; 4 Gram-negative bacteria (Escherichia coli, with typical Gram-negative external structures; Aeromonas salmonicida, Aeromonas hydrophila both with an S-layer and Rhodopirellula sp., with a peptidoglycan-less proteinaceous cell wall and with cytoplasm compartmentalization) and 4 Gram-positive bacteria (Staphylococcus aureus, with typical Gram-positive external structures; Truepera radiovictrix, Deinococcus geothermalis and Deinococcus radiodurans, all with thick cell walls that give them Gram-positive stains, but including a second complex multi-layered membrane and structurally analogous to that of Gram-negative bacteria). The studies were performed in the presence of 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetraiodide (Tetra-Py(+)-Me) at 5.0 μM with white light (40 W m(-2)). The susceptibility of each bacteria to PDI by Tetra-Py(+)-Me was dependent on bacteria external structures. Although all Gram-positive bacteria were inactivated to the detection limit (reduction of ∼8 log) after 60-180 min of irradiation, the inactivation followed distinct patterns. Among the Gram-negative bacteria, E. coli was the only species to be inactivated to the detection limit (∼8 log after 180 min). The efficiency of inactivation of the two species of Aeromonas was similar (reduction of ∼5-6 log after 270 min). Rhodopirellula was less susceptible (reduction of ∼4 log after 270 min). As previously observed, the Gram-positive bacteria are more easily inactivated than Gram-negative strains, and this is even true for T. radiovictrix, D. geothermalis and D. radiodurans, which have a complex multi-layered cell wall. The results support the theory that the outer cell

  12. Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species.

    PubMed

    Su, Ming-Ming; Guo, Lei; Tao, Yun-Li; Zhang, You-Jun; Wan, Fang-Hao; Chu, Dong

    2016-01-01

    Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria. To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community. The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation.

  13. Functional plasticity and catalytic efficiency in plant and bacterial ferredoxin-NADP(H) reductases.

    PubMed

    Ceccarelli, Eduardo A; Arakaki, Adrián K; Cortez, Néstor; Carrillo, Néstor

    2004-05-06

    Ferredoxin (flavodoxin)-NADP(H) reductases (FNRs) are ubiquitous flavoenzymes that deliver NADPH or low potential one-electron donors (ferredoxin, flavodoxin, adrenodoxin) to redox-based metabolisms in plastids, mitochondria and bacteria. Two great families of FAD-containing proteins displaying FNR activity have evolved from different and independent origins. The enzymes present in mitochondria and some bacterial genera are members of the structural superfamily of disulfide oxidoreductases whose prototype is glutathione reductase. A second group, comprising the FNRs from plastids and most eubacteria, constitutes a unique family, the plant-type FNRs, totally unrelated in sequence with the former. The two-domain structure of the plant family of FNR also provides the basic scaffold for an extended superfamily of electron transfer flavoproteins. In this article we compare FNR flavoenzymes from very different origins and describe how the natural history of these reductases shaped structure, flavin conformation and catalytic activity to face the very different metabolic demands they have to deal with in their hosts. We show that plant-type FNRs can be classified into a plastidic class, characterised by extended FAD conformation and high catalytic efficiency, and a bacterial class displaying a folded FAD molecule and low turnover rates. Sequence alignments supported this classification, providing a criterion to predict the structural and biochemical properties of newly identified members of the family.

  14. Improving nitrogen utilization efficiency of aquaponics by introducing algal-bacterial consortia.

    PubMed

    Fang, Yingke; Hu, Zhen; Zou, Yina; Zhang, Jian; Zhu, Zhuoran; Zhang, Jianda; Nie, Lichao

    2017-08-22

    Aquaponics is a promising technology combining aquaculture with hydroponics. In this study, algal-bacterial consortia were introduced into aquaponics, i.e., algal-bacterial based aquaponics (AA), to improve the nitrogen utilization efficiency (NUE) of aquaponics. The results showed that the NUE of AA was 13.79% higher than that of media-based aquaponics (MA). In addition, higher NO3(-) removal by microalgae assimilation led to better water quality in AA, which made up for the deficiencies of poor aquaponic management of nitrate. As a result of lower NO3(-) concentrations and dramatically higher dissolved oxygen (DO) concentrations caused by microalgae photosynthesis in the photobioreactor, the N2O emission of AA was 89.89% lower than that of MA, although nosZ gene abundance in MA's hydroponic bed was approximately 30 times over that in AA. Considering the factors mentioned above, AA would improve the sustainability of aquaponics and have a good application foreground. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Methanol removal efficiency and bacterial diversity of an activated carbon biofilter.

    PubMed

    Babbitt, Callie W; Pacheco, Adriana; Lindner, Angela S

    2009-12-01

    Motivated by the need to establish an economical and environmentally friendly methanol control technology for the pulp and paper industry, a bench-scale activated carbon biofiltration system was developed. This system was evaluated for its performance in removing methanol from an artificially contaminated air stream and characterized for its bacterial diversity over time, under varied methanol loading rates, and in different spatial regions of the filter. The biofilter system, composed of a novel packing mixture, provided an excellent support for growth and activity of methanol-degrading bacteria, resulting in approximately 100% methanol removal efficiency for loading rates of 1-17 g/m(3) packing/h, when operated both with and without inoculum containing enriched methanol-degrading bacteria. Although bacterial diversity and abundance varied over the length of the biofilter, the populations present rapidly formed a stable community that was maintained over the entire 138-day operation of the system and through variable operating conditions, as observed by PCR-DGGE methods that targeted all bacteria as well as specific methanol-oxidizing microorganisms. Phylogenetic analysis of bands excised and sequenced from DGGE gels indicated that the biofilter system supported a diverse community of methanol-degrading bacteria, with high similarity to species in the genera Methylophilus (beta-proteobacteria), Hyphomicrobium and Methylocella (both alpha-proteobacteria).

  16. Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae

    PubMed Central

    Robertson, Veronica; Haltli, Brad; McCauley, Erin P.; Overy, David P.; Kerr, Russell G.

    2016-01-01

    Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome. PMID:27681917

  17. Filter Efficiency and Pressure Testing of Returned ISS Bacterial Filter Elements (BFEs)

    NASA Technical Reports Server (NTRS)

    Green, Robert D.; Agui, Juan H.; Berger, Gordon M.; Vijayakumar, R.; Perry, Jay L.

    2017-01-01

    The air quality control equipment aboard the International Space Station (ISS) and future deep space exploration vehicles provide the vital function of maintaining a clean cabin environment for the crew and the hardware. This becomes a serious challenge in pressurized space compartments since no outside air ventilation is possible, and a larger particulate load is imposed on the filtration system due to lack of sedimentation. The ISS Environmental Control and Life Support (ECLS) system architecture in the U.S. Segment uses a distributed particulate filtration approach consisting of traditional High-Efficiency Particulate Air (HEPA) filters deployed at multiple locations in each U.S. Seg-ment module; these filters are referred to as Bacterial Filter Elements, or BFEs. In our previous work, we presented results of efficiency and pressure drop measurements for a sample set of two returned BFEs with a service life of 2.5 years. In this follow-on work, we present similar efficiency, pressure drop, and leak tests results for a larger sample set of six returned BFEs. The results of this work can aid the ISS Program in managing BFE logistics inventory through the stations planned lifetime as well as provide insight for managing filter element logistics for future exploration missions. These results also can provide meaningful guidance for particulate filter designs under consideration for future deep space exploration missions.

  18. Development of efficient expression system for protein display on bacterial magnetic particles.

    PubMed

    Yoshino, Tomoko; Matsunaga, Tadashi

    2005-12-30

    Bacterial magnetic particles (BMPs) are utilized for various biomedical applications because they are easily manipulated by magnets, and functional proteins are easily displayed on BMPs. To establish highly expressed protein display on BMPs, strong promoters were identified using Magnetospirillum magneticum AMB-1 genome and proteome databases. Initially, several proteins highly expressed in AMB-1 were identified, and the upstream DNA sequences of the open-reading frames were evaluated using a luciferase-reporter gene assay to compare promoter activities. Consequently, luminescence intensity was 400 times higher due to the novel promoter identified in this study than the magA promoter previously used. Subsequently, efficient protein display on BMPs was performed using the newly identified promoter sequences. This developed display system will facilitate the assembly of various functional proteins onto BMPs to create novel magnetic nanoparticles.

  19. Presence of a highly efficient binding to bacterial contamination can distort data from binding studies

    SciTech Connect

    Balcar, V.J. )

    1990-12-01

    {sup 3}HGABA at low concentrations (5-10 nM) was bound by what appeared to be a GABA receptor binding site in bacterial contamination originating from a batch of distilled water. Under experimental conditions similar to those usually employed in {sup 3}HGABA binding studies, the apparent binding displayed a very high specific component and a high efficiency in terms of {sup 3}HGABA bound per mg of protein. The binding was blocked by muscimol but not by isoguvacine, SR95531 and nipecotic acid. These characteristics suggest that the presence of such spurious binding in the experiments using 3H-labeled ligands in brain homogenates may not always be very obvious and, moreover, it can result in subtle, but serious, distortions of data from such studies, which may not be immediately recognized.

  20. Fungal innate immunity induced by bacterial microbe-associated molecular patterns (MAMPs)

    USDA-ARS?s Scientific Manuscript database

    Plants and animals detect bacterial presence through Microbe-Associated Molecular Patterns (MAMPs) which induce an innate immune response. The field of fungal-bacterial interaction at the molecular level is still in its infancy and very little is known about fungal molecular responses to bacteria, a...

  1. Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows.

    PubMed

    Weimer, Paul J; Cox, Madison S; Vieira de Paula, Tania; Lin, Miao; Hall, Mary Beth; Suen, Garret

    2017-09-01

    The objectives of this study were to determine if milk production efficiency (MPE) is altered by near-total exchange of ruminal contents between high- (HE) and low-MPE (LE) cows and to characterize ruminal bacterial community composition (BCC) before exchange and over time postexchange. Three pairs of ruminally cannulated, third-lactation cows were selected whose MPE (energy-corrected milk per unit of dry matter intake) differed over their first 2 lactations. Approximately 95% of ruminal contents were exchanged between cows within each pair. Ruminal pH and volatile fatty acid (VFA) profiles, along with BCC (characterized by sequencing of the variable 4 region of 16S rRNA genes), were assessed just before feeding on d -8, -7, -5, -4, -1, 1, 2, 3, 7, 10, 14, 21, 28, 35, 42, and 56, relative to the exchange date. High-MPE cows had higher total ruminal VFA concentrations, higher molar percentages of propionate and valerate, and lower molar percentages of acetate and butyrate than did LE cows, and re-established these differences 1 d after contents exchange. Across all LE cows, MPE increased during 7 d postexchange but declined thereafter. Two of the 3 HE cows displayed decreases in MPE following introduction of the ruminal contents from the corresponding LE cow, but MPE increased in the third HE cow, which was determined to be an outlier. For all 6 cows, both liquid- and solids-associated BCC differed between individuals within a pair before contents exchange. Upon exchange, BCC of both phases in all 3 pairs was more similar to that of the donor inoculum than to preexchange host BCC. For 5 of 6 cows, the solids-associated community returned within 10 d to more resemble the preexchange community of that host than that of the donor community. Individual variability before the exchange was greater in liquids than in solids, as was the variability in response of bacterial communities to the exchange. Individual cows varied in their response, but generally moved toward re

  2. Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome.

    PubMed

    Monaco, Cynthia L; Gootenberg, David B; Zhao, Guoyan; Handley, Scott A; Ghebremichael, Musie S; Lim, Efrem S; Lankowski, Alex; Baldridge, Megan T; Wilen, Craig B; Flagg, Meaghan; Norman, Jason M; Keller, Brian C; Luévano, Jesús Mario; Wang, David; Boum, Yap; Martin, Jeffrey N; Hunt, Peter W; Bangsberg, David R; Siedner, Mark J; Kwon, Douglas S; Virgin, Herbert W

    2016-03-09

    Human immunodeficiency virus (HIV) infection is associated with increased intestinal translocation of microbial products and enteropathy as well as alterations in gut bacterial communities. However, whether the enteric virome contributes to this infection and resulting immunodeficiency remains unknown. We characterized the enteric virome and bacterial microbiome in a cohort of Ugandan patients, including HIV-uninfected or HIV-infected subjects and those either treated with anti-retroviral therapy (ART) or untreated. Low peripheral CD4 T cell counts were associated with an expansion of enteric adenovirus sequences and this increase was independent of ART treatment. Additionally, the enteric bacterial microbiome of patients with lower CD4 T counts exhibited reduced phylogenetic diversity and richness with specific bacteria showing differential abundance, including increases in Enterobacteriaceae, which have been associated with inflammation. Thus, immunodeficiency in progressive HIV infection is associated with alterations in the enteric virome and bacterial microbiome, which may contribute to AIDS-associated enteropathy and disease progression.

  3. Higher-risk behavioral practices associated with bacterial vaginosis compared with vaginal candidiasis.

    PubMed

    Bradshaw, Catriona Susan; Morton, Anna N; Garland, Suzanne M; Morris, Margaret B; Moss, Lorna M; Fairley, Christopher K

    2005-07-01

    Bacterial vaginosis has been associated with hormonal factors and sexual practices; however, the cause is unclear, and the notion that bacterial vaginosis is a sexually transmitted infection is still debated. To investigate whether bacterial vaginosis is associated with specific sexual practices or instead has features in common with a sexually transmitted infection, we compared behavioral associations in women with bacterial vaginosis to women with vaginal candidiasis. Women with symptoms of abnormal vaginal discharge or odor who attended Melbourne Sexual Health Centre between July 2003 and August 2004 were eligible for enrollment in the study. Information on demographics and behavioral and contraceptive practices were collected by self-completed questionnaire. Participants were tested for bacterial vaginosis, Candida spp (microscopy and culture), and sexually transmitted infections. Statistical comparisons were made between women with and without bacterial vaginosis and women with and without candidiasis, using univariate and multivariate analysis. A total of 342 women were enrolled in the study; 157 were diagnosed with bacterial vaginosis, 51 had candidiasis by microscopy, and 95 had candidiasis by culture. Bacterial vaginosis was associated with indicators of high-risk sexual behavior such as a new sexual partner and greater number of male partners in the last year, increased number of lifetime sexual partners, less than 13 years of education, a past history of pregnancy, and smoking (P < .05). Candidiasis was not associated with these risk behaviors and was instead related to practices such as receptive anal and oral sex and douching. The association between bacterial vaginosis and practices that are associated with sexually transmitted infections, in contrast to those observed with candidiasis, suggests a possible sexually transmitted cause. II-2.

  4. Bacterial communities associated with four ctenophore genera from the German Bight (North Sea).

    PubMed

    Hao, Wenjin; Gerdts, Gunnar; Peplies, Jörg; Wichels, Antje

    2015-01-01

    Intense research has been conducted on jellyfish and ctenophores in recent years. They are increasingly recognized as key elements in the marine ecosystem that serve as critical indicators and drivers of ecosystem performance and change. However, the bacterial community associated with ctenophores is still poorly investigated. Based on automated ribosomal intergenic spacer analysis (ARISA) and 16S ribosomal RNA gene amplicon pyrosequencing, we investigated bacterial communities associated with the frequently occurring ctenophore species Mnemiopsis leidyi, Beroe sp., Bolinopsis infundibulum and Pleurobrachia pileus at Helgoland Roads in the German Bight (North Sea). We observed significant differences between the associated bacterial communities of the different ctenophore species based on ARISA patterns. With respect to bacterial taxa, all ctenophore species were dominated by Proteobacteria as revealed by pyrosequencing. Mnemiopsis leidyi and P. pileus mainly harboured Gammaproteobacteria, with Marinomonas as the dominant phylotype of M. leidyi. By contrast, Pseudoalteromonas and Psychrobacter were the most abundant Gammaproteobacteria in P. pileus. Beroe sp. was mainly dominated by Alphaproteobacteria, particularly by the genus Thalassospira. For B. infundibulum, the bacterial community was composed of Alphaproteobacteria and Gammaproteobacteria in equal parts, which consisted of the genera Thalassospira and Marinomonas. In addition, the bacterial communities associated with M. leidyi display a clear variation over time that needs further investigation. Our results indicate that the bacterial communities associated with ctenophores are highly species- specific.

  5. Relationship between lactobacilli and opportunistic bacterial pathogens associated with vaginitis

    PubMed Central

    Razzak, Mohammad Sabri A.; Al-Charrakh, Alaa H.; AL-Greitty, Bara Hamid

    2011-01-01

    Background: Vaginitis, is an infectious inflammation of the vaginal mucosa, which sometimes involves the vulva. The balance of the vaginal flora is maintained by the Lactobacilli and its protective and probiotic role in treating and preventing vaginal infection by producing antagonizing compounds which are regarded as safe for humans. Aim: The aim of this study was to evaluate the protective role of Lactobacilli against common bacterial opportunistic pathogens in vaginitis and study the effects of some antibiotics on Lactobacilli isolates. Materials and Methods: In this study (110) vaginal swabs were obtained from women suffering from vaginitis who admitted to Babylon Hospital of Maternity and Paediatrics in Babylon province, Iraq. The study involved the role of intrauterine device among married women with vaginitis and also involved isolation of opportunistic bacterial isolates among pregnant and non pregnant women. This study also involved studying probiotic role of Lactobacilli by production of some defense factors like hydrogen peroxide, bacteriocin, and lactic acid. Results: Results revealed that a total of 130 bacterial isolates were obtained. Intrauterine device was a predisposing factor for vaginitis. The most common opportunistic bacterial isolates were Staphylococcus aureus, Escherichia coli, Streptococcus agalactiae, and Klebsiella pneumoniae. All Lactobacilli were hydrogen peroxide producers while some isolates were bacteriocin producers that inhibited some of opportunistic pathogens (S. aureus, E. coli). Lactobacilli were sensitive to erythromycin while 93.3% of them were resistant to ciprofloxacin and (40%, 53.3%) of them were resistant to amoxicillin and gentamycin respectively. Results revealed that there was an inverse relationship between Lactobacilli presence and organisms causing vaginitis. This may be attributed to the production of defense factors by Lactobacilli. Conclusion: The types of antibiotics used to treat vaginitis must be very

  6. Relationship between lactobacilli and opportunistic bacterial pathogens associated with vaginitis.

    PubMed

    Razzak, Mohammad Sabri A; Al-Charrakh, Alaa H; Al-Greitty, Bara Hamid

    2011-04-01

    Vaginitis, is an infectious inflammation of the vaginal mucosa, which sometimes involves the vulva. The balance of the vaginal flora is maintained by the Lactobacilli and its protective and probiotic role in treating and preventing vaginal infection by producing antagonizing compounds which are regarded as safe for humans. The aim of this study was to evaluate the protective role of Lactobacilli against common bacterial opportunistic pathogens in vaginitis and study the effects of some antibiotics on Lactobacilli isolates. In this study (110) vaginal swabs were obtained from women suffering from vaginitis who admitted to Babylon Hospital of Maternity and Paediatrics in Babylon province, Iraq. The study involved the role of intrauterine device among married women with vaginitis and also involved isolation of opportunistic bacterial isolates among pregnant and non pregnant women. This study also involved studying probiotic role of Lactobacilli by production of some defense factors like hydrogen peroxide, bacteriocin, and lactic acid. Results revealed that a total of 130 bacterial isolates were obtained. Intrauterine device was a predisposing factor for vaginitis. The most common opportunistic bacterial isolates were Staphylococcus aureus, Escherichia coli, Streptococcus agalactiae, and Klebsiella pneumoniae. All Lactobacilli were hydrogen peroxide producers while some isolates were bacteriocin producers that inhibited some of opportunistic pathogens (S. aureus, E. coli). Lactobacilli were sensitive to erythromycin while 93.3% of them were resistant to ciprofloxacin and (40%, 53.3%) of them were resistant to amoxicillin and gentamycin respectively. Results revealed that there was an inverse relationship between Lactobacilli presence and organisms causing vaginitis. This may be attributed to the production of defense factors by Lactobacilli. The types of antibiotics used to treat vaginitis must be very selective in order not to kill the beneficial bacteria

  7. A Cross-Taxon Analysis of Insect-Associated Bacterial Diversity

    PubMed Central

    Jones, Ryan Thomas; Sanchez, Leticia Gonzales; Fierer, Noah

    2013-01-01

    Although it is well known that plants and animals harbor microbial symbionts that can influence host traits, the factors regulating the structure of these microbial communities often remain largely undetermined. This is particularly true for insect-associated microbial communities, as few cross-taxon comparisons have been conducted to date. To address this knowledge gap and determine how host phylogeny and ecology affect insect-associated microbial communities, we collected 137 insect specimens representing 39 species, 28 families, and 8 orders, and characterized the bacterial communities associated with each specimen via 16S rRNA gene sequencing. Bacterial taxa within the phylum Proteobacteria were dominant in nearly all insects sampled. On average, the insect-associated bacterial communities were not very diverse, with individuals typically harboring fewer than 8 bacterial phylotypes. Bacterial communities also tended to be dominated by a single phylotype; on average, the most abundant phylotype represented 54.7% of community membership. Bacterial communities were significantly more similar among closely related insects than among less-related insects, a pattern driven by within-species community similarity but detected at every level of insect taxonomy tested. Diet was a poor predictor of bacterial community composition. Individual insect species harbored remarkably unique communities: the distribution of 69.0% of bacterial phylotypes was limited to unique insect species, whereas only 5.7% of phylotypes were detected in more than five insect species. Together these results suggest that host characteristics strongly regulate the colonization and assembly of bacterial communities across insect lineages, patterns that are driven either by co-evolution between insects and their symbionts or by closely related insects sharing conserved traits that directly select for similar bacterial communities. PMID:23613815

  8. A cross-taxon analysis of insect-associated bacterial diversity.

    PubMed

    Jones, Ryan Thomas; Sanchez, Leticia Gonzales; Fierer, Noah

    2013-01-01

    Although it is well known that plants and animals harbor microbial symbionts that can influence host traits, the factors regulating the structure of these microbial communities often remain largely undetermined. This is particularly true for insect-associated microbial communities, as few cross-taxon comparisons have been conducted to date. To address this knowledge gap and determine how host phylogeny and ecology affect insect-associated microbial communities, we collected 137 insect specimens representing 39 species, 28 families, and 8 orders, and characterized the bacterial communities associated with each specimen via 16S rRNA gene sequencing. Bacterial taxa within the phylum Proteobacteria were dominant in nearly all insects sampled. On average, the insect-associated bacterial communities were not very diverse, with individuals typically harboring fewer than 8 bacterial phylotypes. Bacterial communities also tended to be dominated by a single phylotype; on average, the most abundant phylotype represented 54.7% of community membership. Bacterial communities were significantly more similar among closely related insects than among less-related insects, a pattern driven by within-species community similarity but detected at every level of insect taxonomy tested. Diet was a poor predictor of bacterial community composition. Individual insect species harbored remarkably unique communities: the distribution of 69.0% of bacterial phylotypes was limited to unique insect species, whereas only 5.7% of phylotypes were detected in more than five insect species. Together these results suggest that host characteristics strongly regulate the colonization and assembly of bacterial communities across insect lineages, patterns that are driven either by co-evolution between insects and their symbionts or by closely related insects sharing conserved traits that directly select for similar bacterial communities.

  9. Efficient secretion of a folded protein domain by a monomeric bacterial autotransporter.

    PubMed

    Skillman, Kristen M; Barnard, Travis J; Peterson, Janine H; Ghirlando, Rodolfo; Bernstein, Harris D

    2005-11-01

    Bacterial autotransporters are proteins that contain a small C-terminal 'beta domain' that facilitates translocation of a large N-terminal 'passenger domain' across the outer membrane (OM) by an unknown mechanism. Here we used EspP, an autotransporter produced by Escherichia coli 0157:H7, as a model protein to gain insight into the transport reaction. Initially we found that the passenger domain of a truncated version of EspP (EspPDelta1-851) was translocated efficiently across the OM. Blue Native polyacrylamide gel electrophoresis, analytical ultracentrifugation and other biochemical methods showed that EspPDelta1-851 behaves as a compact monomer and strongly suggest that the channel formed by the beta domain is too narrow to accommodate folded polypeptides. Surprisingly, we found that a folded protein domain fused to the N-terminus of EspPDelta1-851 was efficiently translocated across the OM. Further analysis revealed that the passenger domain of wild-type EspP also folds at least partially in the periplasm. To reconcile these data, we propose that the EspP beta domain functions primarily to target and anchor the protein and that an external factor transports the passenger domain across the OM.

  10. Bacterial magnetic particles as a novel and efficient gene vaccine delivery system.

    PubMed

    Tang, Y-S; Wang, D; Zhou, C; Ma, W; Zhang, Y-Q; Liu, B; Zhang, S

    2012-12-01

    DNA vaccination is an attractive approach for eliciting antigen-specific immunity. In this study, we used magnetosomes (bacterial magnetic particles, BMPs) as carriers of a recombinant DNA composed of a secondary lymphoid tissue chemokine, human papillomavirus type E7 (HPV-E7) and Ig-Fc fragment (pSLC-E7-Fc) to generate a gene vaccine (BMP-V) for tumour immunotherapy. The results indicate that BMPs linked to DNA more efficiently in phosphate-buffered saline (pH=4-5) than in physiological saline. Efficient transfection of BMP-V in vitro and in vivo was achieved when a 600-mT static magnetic field was applied for 10 min. In a mouse tumour model, subcutaneous injection of BMP-V (5 μg, × 3 at 4-day intervals) plus magnetic exposure elicited systemic HPV-E7-specific immunity leading to significant tumour inhibition. The treated mice tolerated BMP-V immunisation well with no toxic side effects, as shown by histopathological examinations of major internal organs. Taken together, these results suggest that BMP can be used as a gene carrier to elicit a systemic immune response.

  11. International Space Station (ISS) Bacterial Filter Elements (BFEs): Filter Efficiency and Pressure Testing of Returned Units

    NASA Technical Reports Server (NTRS)

    Green, Robert D.; Agui, Juan H.; Vijayakumar, R.

    2017-01-01

    The air revitalization system aboard the International Space Station (ISS) provides the vital function of maintaining a clean cabin environment for the crew and the hardware. This becomes a serious challenge in pressurized space compartments since no outside air ventilation is possible, and a larger particulate load is imposed on the filtration system due to lack of sedimentation due to the microgravity environment in Low Earth Orbit (LEO). The ISS Environmental Control and Life Support (ECLS) system architecture in the U.S. Segment uses a distributed particulate filtration approach consisting of traditional High-Efficiency Particulate Adsorption (HEPA) media filters deployed at multiple locations in each U.S. Segment module; these filters are referred to as Bacterial Filter Elements, or BFEs. These filters see a replacement interval, as part of maintenance, of 2-5 years dependent on location in the ISS. In this work, we present particulate removal efficiency, pressure drop, and leak test results for a sample set of 8 BFEs returned from the ISS after filter replacement. The results can potentially be utilized by the ISS Program to ascertain whether the present replacement interval can be maintained or extended to balance the on-ground filter inventory with extension of the lifetime of ISS beyond 2024. These results can also provide meaningful guidance for particulate filter designs under consideration for future deep space exploration missions.

  12. An efficient system for intracellular delivery of beta-lactam antibiotics to overcome bacterial resistance

    PubMed Central

    Abed, Nadia; Saïd-Hassane, Fatouma; Zouhiri, Fatima; Mougin, Julie; Nicolas, Valérie; Desmaële, Didier; Gref, Ruxandra; Couvreur, Patrick

    2015-01-01

    The “Golden era” of antibiotics is definitely an old story and this is especially true for intracellular bacterial infections. The poor intracellular bioavailability of antibiotics reduces the efficency of many treatments and thereby promotes resistances. Therefore, the development of nanodevices coupled with antibiotics that are capable of targeting and releasing the drug into the infected-cells appears to be a promising solution to circumvent these complications. Here, we took advantage of two natural terpenes (farnesyl and geranyl) to design nanodevices for an efficient intracellular delivery of penicillin G. The covalent linkage between the terpene moieties and the antibiotic leads to formation of prodrugs that self-assemble to form nanoparticles with a high drug payload between 55–63%. Futhermore, the addition of an environmentally-sensitive bond between the antibiotic and the terpene led to an efficient antibacterial activity against the intracellular pathogen Staphylococcus aureus with reduced intracellular replication of about 99.9% compared to untreated infected cells. Using HPLC analysis, we demonstrated and quantified the intracellular release of PenG when this sensitive-bond (SB) was present on the prodrug, showing the success of this technology to deliver antibiotics directly into cells. PMID:26311631

  13. Identification of QTL associated with resistance to bacterial spot race T4 in tomato.

    PubMed

    Hutton, Samuel F; Scott, Jay W; Yang, Wencai; Sim, Sung-Chur; Francis, David M; Jones, Jeffrey B

    2010-11-01

    Bacterial spot of tomato (Solanum lycopersicum L.), caused by several Xanthomonas sp., is a serious but difficult disease to control by chemical means. Development of resistance has been hindered by emergence of races virulent to tomato, by the quantitative inheritance of resistance, and by a low correlation between seedling assays and resistance in the field. Resistance to multiple races, including race T4, has been described in the S. lycopersicum var. cerasiformae accession PI 114490. We used molecular markers to identify associations with quantitative trait loci (QTL) in an elite inbred backcross (IBC) population derived from OH 9242, PI 114490 and Fla. 7600, a breeding line with tomato accession Hawaii 7998 (H7998) in its pedigree. Race T4 resistance has also been described in the advanced breeding lines Fla. 8233, Fla. 8517, and Fla. 8326, and a selective genotyping approach was used to identify introgressions associated with resistance in segregating progeny derived from crosses with these lines. In the IBC population, loci on chromosomes 11 and 3, respectively, explained as much as 29.4 and 4.8% of resistance variation. Both these loci were also confirmed by selective genotyping: PI 114490 and H7998 alleles on chromosome 11 each provided resistance. The PI 114490 allele on chromosome 3 was confirmed in the Fla. 8517 population, and an allele of undetermined descent was confirmed at this locus in the Fla. 8326 population. A chromosome 12 allele was associated with susceptibility in the Fla. 8517 population. Additional loci contributing minor effects were also implicated in the IBC population or by selective genotyping. Selection for the major QTL in a marker-directed phenotyping approach should significantly improve the efficiency of breeding for resistance to bacterial spot race T4, although as yet undetected QTL would be necessary to carry out strict marker assisted selection.

  14. Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows

    USDA-ARS?s Scientific Manuscript database

    The objectives of this study were to determine if milk production efficiency (MPE) is altered by near-total exchange of ruminal contents between high- (HE) and low-MPE (LE) cows and to characterize ruminal bacterial community composition (BCC) prior to exchange and over time post-exchange. Three pai...

  15. Distinct antimicrobial peptide expression determines host species-specific bacterial associations

    PubMed Central

    Franzenburg, Sören; Walter, Jonas; Künzel, Sven; Wang, Jun; Baines, John F.; Bosch, Thomas C. G.; Fraune, Sebastian

    2013-01-01

    Animals are colonized by coevolved bacterial communities, which contribute to the host’s health. This commensal microbiota is often highly specific to its host-species, inferring strong selective pressures on the associated microbes. Several factors, including diet, mucus composition, and the immune system have been proposed as putative determinants of host-associated bacterial communities. Here we report that species-specific antimicrobial peptides account for different bacterial communities associated with closely related species of the cnidarian Hydra. Gene family extensions for potent antimicrobial peptides, the arminins, were detected in four Hydra species, with each species possessing a unique composition and expression profile of arminins. For functional analysis, we inoculated arminin-deficient and control polyps with bacterial consortia characteristic for different Hydra species and compared their selective preferences by 454 pyrosequencing of the bacterial microbiota. In contrast to control polyps, arminin-deficient polyps displayed decreased potential to select for bacterial communities resembling their native microbiota. This finding indicates that species-specific antimicrobial peptides shape species-specific bacterial associations. PMID:24003149

  16. Influenza-associated bacterial pneumonia; managing and controlling infection on two fronts.

    PubMed

    Campigotto, Aaron; Mubareka, Samira

    2015-01-01

    Bacterial pneumonia complicating influenza is well-recognized as a severe manifestation of influenza, accounting for a substantial number of deaths from the 1918 influenza pandemic. Influenza-associated bacterial pneumonia remains a major contributor to the burden of influenza, and poses new challenges as antibiotic-resistant organisms such as methicillin-resistant Staphylococcus aureus spread. We provide an overview of the current state of knowledge of the epidemiology and co-pathogenesis of influenza-associated bacterial pneumonia, and outline management approaches and their limitations. We review preventative measures and discuss implications for pandemic planning. Knowledge gaps are underscored and future research directions are proposed.

  17. Reservoir of four organisms associated with bacterial vaginosis suggests lack of sexual transmission.

    PubMed Central

    Holst, E

    1990-01-01

    This study consisted of a search for the possible reservoir and mode of spread of the four bacterial vaginosis-associated organisms Mobiluncus mulieris, Mobiluncus curtisii, Mycoplasma hominis, and Gardnerella vaginalis. Their occurrence in rectal, oral, and pharyngeal specimens from women with and without bacterial vaginosis, their male sexual consorts, four homosexual men, and children (altogether, 374 people) was studied. Genital samples were also obtained from all adults. All four organisms were isolated from the rectums of 45 to 62% of women with bacterial vaginosis and 10 to 14% of women without bacterial vaginosis. They also occurred in the rectums of males and children. M. hominis was recovered from the oropharynxes of 12 adults whose sexual consorts had genital occurrences of the organism. Mobiluncus spp. occurred only in the vaginas of women with bacterial vaginosis (97%). The organisms were only infrequently recovered from genital samples from 135 males. Organisms were recovered from the urethras and/or coronal sulci of 10 of 44 male consorts of women with bacterial vaginosis. However, after 2 weeks of condom use during sexual intercourse, only M. hominis remained in the urethra of one man. These findings suggest that the organisms associated with bacterial vaginosis are not spread sexually but colonize the vagina from an endogenous intestinal tract site. The pathophysiological mechanisms leading to bacterial vaginosis in a subpopulation of all women are still unknown. PMID:2229386

  18. Association between Lactobacillus species and bacterial vaginosis-related bacteria, and bacterial vaginosis scores in pregnant Japanese women

    PubMed Central

    Tamrakar, Renuka; Yamada, Takashi; Furuta, Itsuko; Cho, Kazutoshi; Morikawa, Mamoru; Yamada, Hideto; Sakuragi, Noriaki; Minakami, Hisanori

    2007-01-01

    Background Bacterial vaginosis (BV), the etiology of which is still uncertain, increases the risk of preterm birth. Recent PCR-based studies suggested that BV is associated with complex vaginal bacterial communities, including many newly recognized bacterial species in non-pregnant women. Methods To examine whether these bacteria are also involved in BV in pregnant Japanese women, vaginal fluid samples were taken from 132 women, classified as normal (n = 98), intermediate (n = 21), or BV (n = 13) using the Nugent gram stain criteria, and studied. DNA extracted from these samples was analyzed for bacterial sequences of any Lactobacillus, four Lactobacillus species, and four BV-related bacteria by PCR with primers for 16S ribosomal DNA including a universal Lactobacillus primer, Lactobacillus species-specific primers for L. crispatus, L. jensenii, L. gasseri, and L. iners, and BV-related bacterium-specific primers for BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium. Results The prevalences of L. crispatus, L. jensenii, and L. gasseri were significantly higher, while those of BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium were significantly lower in the normal group than in the BV group. Unlike other Lactobacillus species, the prevalence of L. iners did not differ between the three groups and women with L. iners were significantly more likely to have BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium. Linear regression analysis revealed associations of BVAB2 and Megasphaera with Nugent score, and multivariate regression analyses suggested a close relationship between Eggerthella-like bacterium and BV. Conclusion The BV-related bacteria, including BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium, are common in the vagina of pregnant Japanese women with BV. The presence of L. iners may be correlated with vaginal colonization by these BV-related bacteria. PMID:17986357

  19. Cannonballs in Pap Smears: Double Whammy of Bacterial Vaginosis and Associated Infections.

    PubMed

    Krishnamurthy, Vani; Satish, Suchitha; Vimalambike, Manjunath Gubbanna

    2016-01-01

    Cannonballs are structures consisting of neutrophils adherent to epithelial cells, often seen in vaginal Pap smears of patients with trichomoniasis and chlamydiasis. We frequently observed these cannonballs in inflammatory Pap smears showing evidence of bacterial vaginosis. To study the association between cannonballs and bacterial vaginosis with associated infections in inflammatory Pap smears. This was a retrospective study performed over a period of 6 months between April 2014 and September 2014. Three hundred consecutive Pap smears assessed during the study period were retrieved from the archives and studied. A total of 280 smears were studied. Neutrophilic infiltrates were seen in 83.6%, cannonballs in 82.3%, and bacterial vaginosis in 70.7% of the smears. Cannonballs were found in 84.4% of the smears showing evidence of bacterial vaginosis with associated inflammatory infiltrates. There was a significant association between cannonballs and bacterial vaginosis (p = 0.0001). The odds ratio was 13.8 (95% CI: 7.2-26.2). The present study shows a significant association between cannonballs and bacterial vaginosis and associated vaginal infections. © 2016 S. Karger AG, Basel.

  20. ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

    PubMed Central

    Didelot, Xavier; Wilson, Daniel J.

    2015-01-01

    Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/. PMID:25675341

  1. Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis.

    PubMed

    Rebollar, Eria A; Hughey, Myra C; Medina, Daniel; Harris, Reid N; Ibáñez, Roberto; Belden, Lisa K

    2016-07-01

    Symbiotic bacteria on amphibian skin can inhibit growth of the fungus Batrachochytrium dendrobatidis (Bd) that has caused dramatic population declines and extinctions of amphibians in the Neotropics. It remains unclear how the amphibians' skin microbiota is influenced by environmental bacterial reservoirs, host-associated factors such as susceptibility to pathogens, and pathogen presence in tropical amphibians. We sampled skin bacteria from five co-occurring frog species that differ in Bd susceptibility at one Bd-naive site, and sampled one of the non-susceptible species from Bd-endemic and Bd-naive sites in Panama. We hypothesized that skin bacterial communities (1) would be distinct from the surrounding environment regardless of the host habitat, (2) would differ between Bd susceptible and non-susceptible species and (3) would differ on hosts in Bd-naive and Bd-endemic sites. We found that skin bacterial communities were enriched in bacterial taxa that had low relative abundances in the environment. Non-susceptible species had very similar skin bacterial communities that were enriched in particular taxa such as the genera Pseudomonas and Acinetobacter. Bacterial communities of Craugastor fitzingeri in Bd-endemic sites were less diverse than in the naive site, and differences in community structure across sites were explained by changes in relative abundance of specific bacterial taxa. Our results indicate that skin microbial structure was associated with host susceptibility to Bd and might be associated to the history of Bd presence at different sites.

  2. Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis

    PubMed Central

    Rebollar, Eria A; Hughey, Myra C; Medina, Daniel; Harris, Reid N; Ibáñez, Roberto; Belden, Lisa K

    2016-01-01

    Symbiotic bacteria on amphibian skin can inhibit growth of the fungus Batrachochytrium dendrobatidis (Bd) that has caused dramatic population declines and extinctions of amphibians in the Neotropics. It remains unclear how the amphibians' skin microbiota is influenced by environmental bacterial reservoirs, host-associated factors such as susceptibility to pathogens, and pathogen presence in tropical amphibians. We sampled skin bacteria from five co-occurring frog species that differ in Bd susceptibility at one Bd-naive site, and sampled one of the non-susceptible species from Bd-endemic and Bd-naive sites in Panama. We hypothesized that skin bacterial communities (1) would be distinct from the surrounding environment regardless of the host habitat, (2) would differ between Bd susceptible and non-susceptible species and (3) would differ on hosts in Bd-naive and Bd-endemic sites. We found that skin bacterial communities were enriched in bacterial taxa that had low relative abundances in the environment. Non-susceptible species had very similar skin bacterial communities that were enriched in particular taxa such as the genera Pseudomonas and Acinetobacter. Bacterial communities of Craugastor fitzingeri in Bd-endemic sites were less diverse than in the naive site, and differences in community structure across sites were explained by changes in relative abundance of specific bacterial taxa. Our results indicate that skin microbial structure was associated with host susceptibility to Bd and might be associated to the history of Bd presence at different sites. PMID:26744810

  3. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Comparative molecular analysis of bacterial species associated with periodontal disease.

    PubMed

    De Iuliis, V; Ursi, S; Di Tommaso, L M; Caruso, M; Marino, A; D Ercole, S; Caputi, S; Sinjari, B; Festa, F; Macri, M; Martinotti, S; Vitullo, G; Toniato, E

    2016-01-01

    Periodontal disease is an inflammatory disorder affecting the supporting teeth structures, including gingiva, periodontal ligament and alveolar bone, causing loss of connective tissue, reabsorption of alveolar bone and formation of periodontal pockets. The aim of this study is to find a correlation between bacterial growth and periodontal disease. Fifty-seven patients aged between 21 and 65 years, median age 46 years, were enrolled. According to gingival pocket depth, ranging from 3 to 7 mm, patients were divided into two groups: the first (30 patients, 53%) with deep pockets ³ 5 mm and the second (27 patients, 47%) less than 5 mm. The samples taken were processed for microbiological analysis by absolute quantitative real-time Taq-Man technique. Patients affected by periodontal disease were 32 (56%) and patients with gingival bleeding were 35 (61%). This data showed that the presence, the type and the bacterial load in gingival pockets were strongly correlated with gingival depth, periodontal disease and gingival bleeding. Quantitative microbiological analysis is a key point to improve patient compliance, allowing to choose the specific antibiotic treatment. avoiding antibiotic resistance and ensuring the successful outcome of therapy for periodontal disease.

  5. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    PubMed

    Newman, Molli M; Hoilett, Nigel; Lorenz, Nicola; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-02-01

    Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.

  6. Yersinia pestis infection and laboratory conditions alter flea-associated bacterial communities.

    PubMed

    Jones, Ryan T; Vetter, Sara M; Montenieiri, John; Holmes, Jennifer; Bernhardt, Scott A; Gage, Kenneth L

    2013-01-01

    We collected Oropsylla montana from rock squirrels, Spermophilus varigatus, and infected a subset of collected fleas with Yersinia pestis, the etiological agent of plague. We used bar-tagged DNA pyrosequencing to characterize bacterial communities of wild, uninfected controls and infected fleas. Bacterial communities within Y. pestis-infected fleas were substantially more similar to one another than communities within wild or control fleas, suggesting that infection alters the bacterial community in a directed manner such that specific bacterial lineages are severely reduced in abundance or entirely eliminated from the community. Laboratory conditions also significantly altered flea-associated bacterial communities relative to wild communities, but much less so than Y. pestis infection. The abundance of Firmicutes decreased considerably in infected fleas, and Bacteroidetes were almost completely eliminated from both the control and infected fleas. Bartonella and Wolbachia were unaffected or responded positively to Y. pestis infection.

  7. Inter- and intraspecific variations of bacterial communities associated with marine sponges from san juan island, washington.

    PubMed

    Lee, On On; Wong, Yue Him; Qian, Pei-Yuan

    2009-06-01

    This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination

  8. Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington▿

    PubMed Central

    Lee, On On; Wong, Yue Him; Qian, Pei-Yuan

    2009-01-01

    This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in Myxilla incrustans and Haliclona rufescens, while the bacterial communities in Halichondria panicea varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of M. incrustans and H. rufescens collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for H. panicea or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured Proteobacteria. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable Bacillus sp. were found exclusively in all M. incrustans sponges, while an uncultured gammaproteobacterium was unique to H. rufescens. In contrast, the cultivation approach indicated that sponges contained a large proportion of Firmicutes, especially Bacillus, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination

  9. Complete Genome Sequence of Gluconacetobacter hansenii Strain NQ5 (ATCC 53582), an Efficient Producer of Bacterial Cellulose

    PubMed Central

    Pfeffer, Sarah; Mehta, Kalpa

    2016-01-01

    This study reports the release of the complete nucleotide sequence of Gluconacetobacter hansenii strain NQ5 (ATCC 53582). This strain was isolated by R. Malcolm Brown, Jr. in a sugar mill in North Queensland, Australia, and is an efficient producer of bacterial cellulose. The elucidation of the genome will contribute to the study of the molecular mechanisms necessary for cellulose biosynthesis. PMID:27516505

  10. Pathogenic Bacterial Species Associated with Endodontic Infection Evade Innate Immune Control by Disabling Neutrophils

    PubMed Central

    Matsui, Aritsune; Jin, Jun-O; Johnston, Christopher D.; Yamazaki, Hajime; Houri-Haddad, Yael

    2014-01-01

    Endodontic infections, in which oral bacteria access the tooth pulp chamber, are common and do not resolve once established. To investigate the effects of these infections on the innate immune response, we established a mouse subcutaneous chamber model, where a mixture of four oral pathogens commonly associated with these infections (endodontic pathogens [EP]), i.e., Fusobacterium nucleatum, Streptococcus intermedius, Parvimonas micra, and Prevotella intermedia, was inoculated into subcutaneously implanted titanium chambers. Cells that infiltrated the chamber after these infections were primarily neutrophils; however, these neutrophils were unable to control the infection. Infection with a nonpathogenic oral bacterial species, Streptococcus mitis, resulted in well-controlled infection, with bacterial numbers reduced by 4 to 5 log units after 7 days. Propidium iodide (PI) staining of the chamber neutrophils identified three distinct populations: neutrophils from EP-infected chambers were intermediate in PI staining, while cells in chambers from mice infected with S. mitis were PI positive (apoptotic) or negative (live). Strikingly, neutrophils from EP-infected chambers were severely impaired in their ability to phagocytose and to generate reactive oxygen species in vitro after removal from the chamber compared to cells from S. mitis-infected chambers. The mechanism of neutrophil impairment was necrotic cell death as determined by morphological analyses. P. intermedia alone could induce a similar neutrophil phenotype. We conclude that the endodontic pathogens, particularly P. intermedia, can efficiently disable and kill infiltrating neutrophils, allowing these infections to become established. These results can help explain the persistence of endodontic infections and demonstrate a new virulence mechanism associated with P. intermedia. PMID:25024367

  11. Pathogenic bacterial species associated with endodontic infection evade innate immune control by disabling neutrophils.

    PubMed

    Matsui, Aritsune; Jin, Jun-O; Johnston, Christopher D; Yamazaki, Hajime; Houri-Haddad, Yael; Rittling, Susan R

    2014-10-01

    Endodontic infections, in which oral bacteria access the tooth pulp chamber, are common and do not resolve once established. To investigate the effects of these infections on the innate immune response, we established a mouse subcutaneous chamber model, where a mixture of four oral pathogens commonly associated with these infections (endodontic pathogens [EP]), i.e., Fusobacterium nucleatum, Streptococcus intermedius, Parvimonas micra, and Prevotella intermedia, was inoculated into subcutaneously implanted titanium chambers. Cells that infiltrated the chamber after these infections were primarily neutrophils; however, these neutrophils were unable to control the infection. Infection with a nonpathogenic oral bacterial species, Streptococcus mitis, resulted in well-controlled infection, with bacterial numbers reduced by 4 to 5 log units after 7 days. Propidium iodide (PI) staining of the chamber neutrophils identified three distinct populations: neutrophils from EP-infected chambers were intermediate in PI staining, while cells in chambers from mice infected with S. mitis were PI positive (apoptotic) or negative (live). Strikingly, neutrophils from EP-infected chambers were severely impaired in their ability to phagocytose and to generate reactive oxygen species in vitro after removal from the chamber compared to cells from S. mitis-infected chambers. The mechanism of neutrophil impairment was necrotic cell death as determined by morphological analyses. P. intermedia alone could induce a similar neutrophil phenotype. We conclude that the endodontic pathogens, particularly P. intermedia, can efficiently disable and kill infiltrating neutrophils, allowing these infections to become established. These results can help explain the persistence of endodontic infections and demonstrate a new virulence mechanism associated with P. intermedia.

  12. Bacterial Vaginosis and Cervical Intraepithelial Neoplasia: Is there an Association or is Co-Existence Incidental?

    PubMed

    Sodhani, Pushpa; Gupta, Sanjay; Gupta, Ruchika; Mehrotra, Ravi

    2017-05-01

    Objectives: To determine associations, if any, of bacterial vaginosis with cervical pre-neoplastic lesions and evaluate any effects of sub-categorization of smears with bacterial vaginosis. Methods: All cervico-vaginal smears reported as positive for bacterial vaginosis over a five-year period were reviewed and sub-categorized into ‘type I (dysbacteriosis)’ and ‘type II (pure Gardenerella infection)’ smears by two cytopathologists (PS, SG). The proportion of smears with healthy flora and pre-neoplastic lesions was compared with those having bacterial vaginosis in conjunction with such changes. In addition, a comparison was also attempted between the frequencies of pre-neoplastic lesions with the two categories of bacterial vaginosis smears. Results: Bacterial vaginosis was diagnosed in 28.6% (7017 of the 24,565) of the 24,565 smears received in the Institute during the study period. Of these 7,017 smears with bacterial vaginosis, 53% (3717) were categorized as type I and 42.7% (3000) as type II by both cytopathologists. Pre-neoplastic lesions were detected in 10.2% of smears with bacterial vaginosis compared to 5.7% of those with healthy flora (P<0.0001). Of the sub-categories of bacterial vaginosis, the risk of detecting precancerous lesion was higher for type II smears (P<0.001). Conclusion: Sub-categorization of bacterial vaginosis, as performed in the Dutch coding system, may be worthwhile due to the strikingly different risk of associated preneoplasia. Creative Commons Attribution License

  13. Effect of bacterial inoculation, plant genotype and developmental stage on root-associated and endophytic bacterial communities in potato (Solanum tuberosum).

    PubMed

    Andreote, Fernando Dini; Rocha, Ulisses Nunes da; Araújo, Welington Luiz; Azevedo, João Lúcio; van Overbeek, Leonard Simon

    2010-05-01

    Beneficial bacteria interact with plants by colonizing the rhizosphere and roots followed by further spread through the inner tissues, resulting in endophytic colonization. The major factors contributing to these interactions are not always well understood for most bacterial and plant species. It is believed that specific bacterial functions are required for plant colonization, but also from the plant side specific features are needed, such as plant genotype (cultivar) and developmental stage. Via multivariate analysis we present a quantification of the roles of these components on the composition of root-associated and endophytic bacterial communities in potato plants, by weighing the effects of bacterial inoculation, plant genotype and developmental stage. Spontaneous rifampicin resistant mutants of two bacterial endophytes, Paenibacillus sp. strain E119 and Methylobacterium mesophilicum strain SR1.6/6, were introduced into potato plants of three different cultivars (Eersteling, Robijn and Karnico). Densities of both strains in, or attached to potato plants were measured by selective plating, while the effects of bacterial inoculation, plant genotype and developmental stage on the composition of bacterial, Alphaproteobacterial and Paenibacillus species were determined by PCR-denaturing gradient gel-electrophoresis (DGGE). Multivariate analyses revealed that the composition of bacterial communities was mainly driven by cultivar type and plant developmental stage, while Alphaproteobacterial and Paenibacillus communities were mainly influenced by bacterial inoculation. These results are important for better understanding the effects of bacterial inoculations to plants and their possible effects on the indigenous bacterial communities in relation with other plant factors such as genotype and growth stage.

  14. Efficient Associative Computation with Discrete Synapses.

    PubMed

    Knoblauch, Andreas

    2016-01-01

    Neural associative networks are a promising computational paradigm for both modeling neural circuits of the brain and implementing associative memory and Hebbian cell assemblies in parallel VLSI or nanoscale hardware. Previous work has extensively investigated synaptic learning in linear models of the Hopfield type and simple nonlinear models of the Steinbuch/Willshaw type. Optimized Hopfield networks of size n can store a large number of about n(2)/k memories of size k (or associations between them) but require real-valued synapses, which are expensive to implement and can store at most C = 0.72 bits per synapse. Willshaw networks can store a much smaller number of about n(2)/k(2) memories but get along with much cheaper binary synapses. Here I present a learning model employing synapses with discrete synaptic weights. For optimal discretization parameters, this model can store, up to a factor ζ close to one, the same number of memories as for optimized Hopfield-type learning--for example, ζ = 0.64 for binary synapses, ζ = 0.88 for 2 bit (four-state) synapses, ζ = 0.96 for 3 bit (8-state) synapses, and ζ > 0.99 for 4 bit (16-state) synapses. The model also provides the theoretical framework to determine optimal discretization parameters for computer implementations or brainlike parallel hardware including structural plasticity. In particular, as recently shown for the Willshaw network, it is possible to store C(I) = 1 bit per computer bit and up to C(S) = log n bits per nonsilent synapse, whereas the absolute number of stored memories can be much larger than for the Willshaw model.

  15. Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors.

    PubMed

    Chehoud, Christel; Stieh, Daniel J; Bailey, Aubrey G; Laughlin, Alice L; Allen, Shannon A; McCotter, Kerrie L; Sherrill-Mix, Scott A; Hope, Thomas J; Bushman, Frederic D

    2017-04-24

    We sought to investigate the effects of HIV infection on the vaginal microbiota and associations with treatment and demographic factors. We thus compared vaginal microbiome samples from HIV-infected (HIV+) and HIV-uninfected (HIV-) women collected at two Chicago area hospitals. We studied vaginal microbiome samples from 178 women analyzed longitudinally (n = 324 samples) and collected extensive data on clinical status and demographic factors. We used 16S rRNA gene sequencing to characterize the bacterial lineages present, then UniFrac, Shannon diversity, and other measures to compare community structure with sample metadata. Differences in microbiota measures were modest in the comparison of HIV+ and HIV- samples, in contrast to several previous studies, consistent with effective antiretroviral therapy. Proportions of healthy Lactobacillus species were not higher in HIV- patients overall, but were significantly higher when analyzed within each hospital in isolation. Rates of bacterial vaginosis were higher among African-American women and HIV+ women. Bacterial vaginosis was associated with higher frequency of HIV+. Unexpectedly, African-American women were more likely to switch bacterial vaginosis status between sampling times; switching was not associated with HIV+ status. The influence of HIV infection on the vaginal microbiome was modest for this cohort of well suppressed urban American women, consistent with effective antiretroviral therapy. HIV+ was found to be associated with bacterial vaginosis. Although bacterial vaginosis has previously been associated with HIV transmission, most of the women studied here became HIV+ many years before our test for bacterial vaginosis, thus implicating additional mechanisms linking HIV infection and bacterial vaginosis.

  16. Seasonal changes in bacterial communities associated with healthy and diseased Porites coral in southern Taiwan.

    PubMed

    Lin, Chorng-Horng; Chuang, Chih-Hsiang; Twan, Wen-Hung; Chiou, Shu-Fen; Wong, Tit-Yee; Liu, Jong-Kang; Kao, Chyuan-Yao; Kuo, Jimmy

    2016-12-01

    We compared the bacterial communities associated with healthy scleractinian coral Porites sp. with those associated with coral infected with pink spot syndrome harvested during summer and winter from waters off the coast of southern Taiwan. Members of the bacterial community associated with the coral were characterized by means of denaturing gradient gel electrophoresis (DGGE) of a short region of the 16S rRNA gene and clone library analysis. Of 5 different areas of the 16S rRNA gene, we demonstrated that the V3 hypervariable region is most suited to represent the coral-associated bacterial community. The DNA sequences of 26 distinct bands extracted from DGGE gels and 269 sequences of the 16S rRNA gene from clone libraries were determined. We found that the communities present in diseased coral were more heterogeneous than the bacterial communities of uninfected coral. In addition, bacterial communities associated with coral harvested in the summer were more diverse than those associated with coral collected in winter, regardless of the health status of the coral. Our study suggested that the compositions of coral-associated bacteria communities are complex, and the population of bacteria varies greatly between seasons and in coral of differing health status.

  17. Bacterial communities associated with the ctenophores Mnemiopsis leidyi and Beroe ovata.

    PubMed

    Daniels, Camille; Breitbart, Mya

    2012-10-01

    Residing in a phylum of their own, ctenophores are gelatinous zooplankton that drift through the ocean's water column. Although ctenophores are known to be parasitized by a variety of eukaryotes, no studies have examined their bacterial associates. This study describes the bacterial communities associated with the lobate ctenophore Mnemiopsis leidyi and its natural predator Beroe ovata in Tampa Bay, Florida, USA. Investigations using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of 16S rRNA genes demonstrated that ctenophore bacterial communities were distinct from the surrounding water. In addition, each ctenophore genus contained a unique microbiota. Ctenophore samples contained fewer bacterial operational taxonomic units (OTUs) by T-RFLP and lower diversity communities by 16S rRNA gene sequencing than the water column. Both ctenophore genera contained sequences related to bacteria previously described in marine invertebrates, and sequences similar to a sea anemone pathogen were abundant in B. ovata. Temporal sampling revealed that the ctenophore-associated bacterial communities varied over time, with no single OTU detected at all time points. This is the first report of distinct and dynamic bacterial communities associated with ctenophores, suggesting that these microbial consortia may play important roles in ctenophore ecology. Future work needs to elucidate the functional roles and mode of acquisition of these bacteria.

  18. Efficient production of active chicken avidin using a bacterial signal peptide in Escherichia coli

    PubMed Central

    2004-01-01

    Chicken avidin is a highly popular tool with countless applications in the life sciences. In the present study, an efficient method for producing avidin protein in the periplasmic space of Escherichia coli in the active form is described. Avidin was produced by replacing the native signal sequence of the protein with a bacterial OmpA secretion signal. The yield after a single 2-iminobiotin–agarose affinity purification step was approx. 10 mg/l of virtually pure avidin. Purified avidin had 3.7 free biotin-binding sites per tetramer and showed the same biotin-binding affinity and thermal stability as egg-white avidin. Avidin crystallized under various conditions, which will enable X-ray crystallographic studies. Avidin produced in E. coli lacks the carbohydrate chains of chicken avidin and the absence of glycosylation should decrease the non-specific binding that avidin exhibits towards many materials [Rosebrough and Hartley (1996) J. Nucl. Med. 37, 1380–1384]. The present method provides a feasible and inexpensive alternative for the production of recombinant avidin, avidin mutants and avidin fusion proteins for novel avidin–biotin technology applications. PMID:15324300

  19. Efficient production of active chicken avidin using a bacterial signal peptide in Escherichia coli.

    PubMed

    Hytönen, Vesa P; Laitinen, Olli H; Airenne, Tomi T; Kidron, Heidi; Meltola, Niko J; Porkka, Eevaleena J; Hörhä, Jarno; Paldanius, Tiina; Määttä, Juha A E; Nordlund, Henri R; Johnson, Mark S; Salminen, Tiina A; Airenne, Kari J; Ylä-Herttuala, Seppo; Kulomaa, Markku S

    2004-12-01

    Chicken avidin is a highly popular tool with countless applications in the life sciences. In the present study, an efficient method for producing avidin protein in the periplasmic space of Escherichia coli in the active form is described. Avidin was produced by replacing the native signal sequence of the protein with a bacterial OmpA secretion signal. The yield after a single 2-iminobiotin-agarose affinity purification step was approx. 10 mg/l of virtually pure avidin. Purified avidin had 3.7 free biotin-binding sites per tetramer and showed the same biotin-binding affinity and thermal stability as egg-white avidin. Avidin crystallized under various conditions, which will enable X-ray crystallographic studies. Avidin produced in E. coli lacks the carbohydrate chains of chicken avidin and the absence of glycosylation should decrease the non-specific binding that avidin exhibits towards many materials [Rosebrough and Hartley (1996) J. Nucl. Med. 37, 1380-1384]. The present method provides a feasible and inexpensive alternative for the production of recombinant avidin, avidin mutants and avidin fusion proteins for novel avidin-biotin technology applications.

  20. Efficient processing of abasic sites by bacterial nonhomologous end-joining Ku proteins

    PubMed Central

    de Ory, Ana; Zafra, Olga; de Vega, Miguel

    2014-01-01

    Intracellular reactive oxygen species as well as the exposure to harsh environmental conditions can cause, in the single chromosome of Bacillus subtilis spores, the formation of apurinic/apyrimidinic (AP) sites and strand breaks whose repair during outgrowth is crucial to guarantee cell viability. Whereas double-stranded breaks are mended by the nonhomologous end joining (NHEJ) system composed of an ATP-dependent DNA Ligase D (LigD) and the DNA-end-binding protein Ku, repair of AP sites would rely on an AP endonuclease or an AP-lyase, a polymerase and a ligase. Here we show that B. subtilis Ku (BsuKu), along with its pivotal role in allowing joining of two broken ends by B. subtilis LigD (BsuLigD), is endowed with an AP/deoxyribose 5′-phosphate (5′-dRP)-lyase activity that can act on ssDNA, nicked molecules and DNA molecules without ends, suggesting a potential role in BER during spore outgrowth. Coordination with BsuLigD makes possible the efficient joining of DNA ends with near terminal abasic sites. The role of this new enzymatic activity of Ku and its potential importance in the NHEJ pathway is discussed. The presence of an AP-lyase activity also in the homolog protein from the distantly related bacterium Pseudomonas aeruginosa allows us to expand our results to other bacterial Ku proteins. PMID:25355514

  1. Efficient processing of abasic sites by bacterial nonhomologous end-joining Ku proteins.

    PubMed

    de Ory, Ana; Zafra, Olga; de Vega, Miguel

    2014-12-01

    Intracellular reactive oxygen species as well as the exposure to harsh environmental conditions can cause, in the single chromosome of Bacillus subtilis spores, the formation of apurinic/apyrimidinic (AP) sites and strand breaks whose repair during outgrowth is crucial to guarantee cell viability. Whereas double-stranded breaks are mended by the nonhomologous end joining (NHEJ) system composed of an ATP-dependent DNA Ligase D (LigD) and the DNA-end-binding protein Ku, repair of AP sites would rely on an AP endonuclease or an AP-lyase, a polymerase and a ligase. Here we show that B. subtilis Ku (BsuKu), along with its pivotal role in allowing joining of two broken ends by B. subtilis LigD (BsuLigD), is endowed with an AP/deoxyribose 5'-phosphate (5'-dRP)-lyase activity that can act on ssDNA, nicked molecules and DNA molecules without ends, suggesting a potential role in BER during spore outgrowth. Coordination with BsuLigD makes possible the efficient joining of DNA ends with near terminal abasic sites. The role of this new enzymatic activity of Ku and its potential importance in the NHEJ pathway is discussed. The presence of an AP-lyase activity also in the homolog protein from the distantly related bacterium Pseudomonas aeruginosa allows us to expand our results to other bacterial Ku proteins. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Can immunostimulants efficiently replace antibiotic in striped catfish (Pangasianodon hypophthalmus) against bacterial infection by Edwardsiella ictaluri?

    PubMed

    Bich Hang, Bui Thi; Phuong, Nguyen Thanh; Kestemont, Patrick

    2014-10-01

    The present study was performed to determine the efficacy of lipopolysaccharide (LPS) and levamisole on immune response and disease resistance in striped catfish and to compare their respective efficiency with the one of an antibiotic treatment after infection of fish by the bacteria Edwardsiella ictaluri. Fish were divided into 3 groups and each group was injected with LPS (3 mg/kg fish), levamisole (5 mg/kg fish) or phosphate buffer saline as control. At day 21st post immunostimulant injection, fish were bled for assaying immunological variables and then challenged with E. ictaluri. Three days after bacterial infection, an antibiotic treatment was applied into fish subgroups and mortality was compared daily between antibiotic treated and untreated fish until 2 weeks post-challenge. LPS and levamisole significantly enhanced non-specific immune responses such as respiratory burst, lysozyme and complement activity in fish compared with control (p < 0.05). Respiratory burst and complement activity significantly increased in levamisole groups when compared with LPS groups while lysozyme activity did not differ significantly between immunostimulant treatments. Total immunoglobulins significantly increased in levamisole treatment compared with control. After challenge test, accumulated mortality was reduced significantly in both non-antibiotic and antibiotic subgroups of LPS and levamisole compared with control. Moreover, no differences of mortality were observed between fish treated with levamisole or LPS without antibiotics and control fish treated with antibiotics. These results support the possible replacement of antibiotics in striped catfish farming by immunostimulants such as levamisole and LPS.

  3. CnaA domains in bacterial pili are efficient dissipaters of large mechanical shocks.

    PubMed

    Echelman, Daniel J; Alegre-Cebollada, Jorge; Badilla, Carmen L; Chang, Chungyu; Ton-That, Hung; Fernández, Julio M

    2016-03-01

    Pathogenic bacteria adhere despite severe mechanical perturbations induced by the host, such as coughing. In Gram-positive bacteria, extracellular protein appendages termed pili are necessary for adherence under mechanical stress. However, little is known about the behavior of Gram-positive pili under force. Here, we demonstrate a mechanism by which Gram-positive pili are able to dissipate mechanical energy through mechanical unfolding and refolding of isopeptide bond-delimited polypeptide loops present in Ig-type CnaA domains. Using single-molecule force spectroscopy, we find that these loops of the pilus subunit SpaA of the SpaA-type pilus from Corynebacterium diphtheriae and FimA of the type 2 pilus from Actinomyces oris unfold and extend at forces that are the highest yet reported for globular proteins. Loop refolding is limited by the hydrophobic collapse of the polypeptide and occurs in milliseconds. Remarkably, both SpaA and FimA initially refold to mechanically weaker intermediates that recover strength with time or ligand binding. Based on the high force extensibility, CnaA-containing pili can dissipate ∼28-fold as much energy compared with their inextensible counterparts before reaching forces sufficient to cleave covalent bonds. We propose that efficient mechanical energy dissipation is key for sustained bacterial attachment against mechanical perturbations.

  4. CnaA domains in bacterial pili are efficient dissipaters of large mechanical shocks

    PubMed Central

    Echelman, Daniel J.; Alegre-Cebollada, Jorge; Badilla, Carmen L.; Chang, Chungyu; Ton-That, Hung; Fernández, Julio M.

    2016-01-01

    Pathogenic bacteria adhere despite severe mechanical perturbations induced by the host, such as coughing. In Gram-positive bacteria, extracellular protein appendages termed pili are necessary for adherence under mechanical stress. However, little is known about the behavior of Gram-positive pili under force. Here, we demonstrate a mechanism by which Gram-positive pili are able to dissipate mechanical energy through mechanical unfolding and refolding of isopeptide bond-delimited polypeptide loops present in Ig-type CnaA domains. Using single-molecule force spectroscopy, we find that these loops of the pilus subunit SpaA of the SpaA-type pilus from Corynebacterium diphtheriae and FimA of the type 2 pilus from Actinomyces oris unfold and extend at forces that are the highest yet reported for globular proteins. Loop refolding is limited by the hydrophobic collapse of the polypeptide and occurs in milliseconds. Remarkably, both SpaA and FimA initially refold to mechanically weaker intermediates that recover strength with time or ligand binding. Based on the high force extensibility, CnaA-containing pili can dissipate ∼28-fold as much energy compared with their inextensible counterparts before reaching forces sufficient to cleave covalent bonds. We propose that efficient mechanical energy dissipation is key for sustained bacterial attachment against mechanical perturbations. PMID:26884173

  5. Bacterial diversity associated with the tunic of the model chordate Ciona intestinalis.

    PubMed

    Blasiak, Leah C; Zinder, Stephen H; Buckley, Daniel H; Hill, Russell T

    2014-02-01

    The sea squirt Ciona intestinalis is a well-studied model organism in developmental biology, yet little is known about its associated bacterial community. In this study, a combination of 454 pyrosequencing of 16S ribosomal RNA genes, catalyzed reporter deposition-fluorescence in situ hybridization and bacterial culture were used to characterize the bacteria living inside and on the exterior coating, or tunic, of C. intestinalis adults. The 454 sequencing data set demonstrated that the tunic bacterial community structure is different from that of the surrounding seawater. The observed tunic bacterial consortium contained a shared community of <10 abundant bacterial phylotypes across three individuals. Culture experiments yielded four bacterial strains that were also dominant groups in the 454 sequencing data set, including novel representatives of the classes Alphaproteobacteria and Flavobacteria. The relatively simple bacterial community and availability of dominant community members in culture make C. intestinalis a promising system in which to investigate functional interactions between host-associated microbiota and the development of host innate immunity.

  6. Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

    PubMed Central

    Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

    2016-01-01

    ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study

  7. Compositional shifts in bacterial communities associated with the coral Palythoa caribaeorum due to anthropogenic effects.

    PubMed

    Paulino, Gustavo Vasconcelos Bastos; Broetto, Leonardo; Pylro, Victor Satler; Landell, Melissa Fontes

    2017-01-30

    Corals harbor abundant and diverse prokaryotic communities that may be strongly influenced by human activities, which in turn compromise the normal functioning of coral species and predispose them to opportunistic infections. In this study, we investigated the effect of sewage dumping on the bacterial communities associated with the soft coral Palythoa caribaeorum at two sites in the Brazilian coast. We observed a dominance of bacterial species classified as human pathogens at sites exposed to untreated sewage discharge. The microbial diversity of undisturbed sites was more homogeneous and diverse and showed greater abundance. In addition, bacterial communities differed substantially between the exposed and undisturbed areas. The microbial community associated with the samples collected from the exposed sites revealed the anthropogenic effect caused by organic matter from untreated sewage dumping, with an abundance of pathogenic bacterial species.

  8. Characterization of an endophytic bacterial community associated with Eucalyptus spp.

    PubMed

    Procópio, R E L; Araújo, W L; Maccheroni, W; Azevedo, J L

    2009-11-24

    Endophytic bacteria were isolated from stems of Eucalyptus spp (Eucalyptus citriodora, E. grandis, E. urophylla, E. camaldulensis, E. torelliana, E. pellita, and a hybrid of E. grandis and E. urophylla) cultivated at two sites; they were characterized by RAPD and amplified rDNA restriction analysis (ARDRA). Endophytic bacteria were more frequently isolated from E. grandis and E. pellita. The 76 isolates were identified by 16S rDNA sequencing as Erwinia/Pantoea (45%), Agrobacterium sp (21%), Curtobacterium sp (9%), Brevibacillus sp (8%), Pseudomonas sp (8%), Acinetobacter sp (4%), Burkholderia cepacia (2.6%), and Lactococcus lactis (2.6%). Genetic characterization of these endophytic bacteria isolates showed at least eight ARDRA haplotypes. The genetic diversity of 32 Erwinia/Pantoea and 16 Agrobacterium sp isolates was assessed with the RAPD technique. There was a high level of genetic polymorphism among all the isolates and there was positive correlation between the clusters and the geographic origin of the strains. These endophytic bacteria were further analyzed for in vitro interaction with endophytic fungi from Eucalyptus spp. We found that metabolites secreted by Erwinia/Pantoea and B. cepacia isolates had an inhibitory growth effect on some endophytic fungi, suggesting that these metabolites play a role in bacterial-fungal interactions inside the host plant. Apparently, these bacteria could have an important role in plant development; in the future they may be useful for biological control of diseases and plant growth promotion, as well as for the production of new metabolites and enzymes.

  9. Bacterial populations associated with rice seed in the tropical environment.

    PubMed

    Cottyn, B; Regalado, E; Lanoot, B; De Cleene, M; Mew, T W; Swings, J

    2001-03-01

    ABSTRACT During the 1995 wet season, harvested rice seed was collected from farmers' fields at different locations in Iloilo, Philippines. Bacterial isolations from crushed seed yielded 428 isolates. The isolates were characterized by BOX-polymerase chain reaction fingerprinting of total genomic DNA and represented 151 fingerprint types (FPT). Most FPTs were found on a single occasion, although matching fingerprints for isolates from different samples also were found. Identifications were made by cellular fatty acid methyl ester analysis and additional use of Biolog GN/GP MicroPlates and API 20E/50CHE systems. The predominant bacteria were Enterobacteriaceae (25%), Bacillus spp. (22%), and Pseu-domonas spp. (14%). Other bacteria regularly present were identified as Xanthomonas spp., Cellulomonas flavigena, and Clavibacter michiganense. Of the total number of isolated bacteria, 4% exhibited in vitro antifungal activity against Rhizoctonia solani or Pyricularia grisea. Two percent of isolates were pathogens identified as Burkholderia glumae and Burkholderia gladioli. Five percent of isolates induced sheath necrosis on only 50 to 90% of inoculated plants and were related to Bacillus pumilus, Paenibacillus spp., Pseudomonas spp., and Pantoea spp.

  10. Bacterial counts associated with poultry processing at different sampling times.

    PubMed

    Geornaras, I; von Holy, A

    2000-01-01

    Aerobic plate counts, Enterobacteriaceae counts and Pseudomonas counts were performed on neck skin samples from six processing steps in a poultry abattoir at three different sampling times. Sampling time 1 was shortly after start-up of processing operations, time 2 after a tea break which was preceded by a cold water rinse-down of equipment surfaces, and time 3 before shut-down. No significant differences (P > 0.05) in microbial numbers of neck skin samples were observed between the three sampling times at the six sampling sites. At this particular processing plant, therefore, sampling at any time of the processing shift would thus not lead to significantly different bacterial counts of neck skins. The lowest aerobic plate counts, over all three sampling times, were obtained for neck skins sampled after spray washing, and the highest for neck skins sampled after packaging. This indicated the efficacy of the washing step in reducing microbial contamination but subsequent re-contamination of carcasses. Despite the Pseudomonas counts of neck skins being lower than the Enterobacteriaceae counts at the beginning of processing, packaging of carcasses resulted in Pseudomonas counts that were higher than the Enterobacteriaceae counts.

  11. Interactions between Lactobacillus crispatus and Bacterial Vaginosis (BV)-Associated Bacterial Species in Initial Attachment and Biofilm Formation

    PubMed Central

    Machado, António; Jefferson, Kimberly Kay; Cerca, Nuno

    2013-01-01

    Certain anaerobic bacterial species tend to predominate the vaginal flora during bacterial vaginosis (BV), with Gardnerella vaginalis being the most common. However, the exact role of G. vaginalis in BV has not yet been determined. The main goal of this study was to test the hypothesis that G. vaginalis is an early colonizer, paving the way for intermediate (e.g., Fusobacterium nucleatum) and late colonizers (e.g., Prevotella bivia). Theoretically, in order to function as an early colonizer, species would need to be able to adhere to vaginal epithelium, even in the presence of vaginal lactobacilli. Therefore, we quantified adherence of G. vaginalis and other BV-associated bacteria to an inert surface pre-coated with Lactobacillus crispatus using a new Peptide Nucleic Acid (PNA) Fluorescence In Situ Hybridization (FISH) methodology. We found that G. vaginalis had the greatest capacity to adhere in the presence of L. crispatus. Theoretically, an early colonizer would contribute to the adherence and/or growth of additional species, so we next quantified the effect of G. vaginalis biofilms on the adherence and growth of other BV-associated species by quantitative Polymerase Chain Reaction (qPCR) technique. Interestingly, G. vaginalis derived a growth benefit from the addition of a second species, regardless of the species. Conversely, G. vaginalis biofilms enhanced the growth of P. bivia, and to a minor extent of F. nucleatum. These results contribute to our understanding of BV biofilm formation and the progression of the disorder. PMID:23739678

  12. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood

    PubMed Central

    Hervé, Vincent; Ketter, Elodie; Pierrat, Jean-Claude; Gelhaye, Eric; Frey-Klett, Pascale

    2016-01-01

    Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities. PMID:26824755

  13. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood.

    PubMed

    Hervé, Vincent; Ketter, Elodie; Pierrat, Jean-Claude; Gelhaye, Eric; Frey-Klett, Pascale

    2016-01-01

    Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.

  14. Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data.

    PubMed

    Francisco, Juan Carlos; Cohan, Frederick M; Krizanc, Danny

    2014-01-01

    Identification of closely related, ecologically distinct populations of bacteria would benefit microbiologists working in many fields including systematics, epidemiology and biotechnology. Several laboratories have recently developed algorithms aimed at demarcating such 'ecotypes'. We examine the ability of four of these algorithms to correctly identify ecotypes from sequence data. We tested the algorithms on synthetic sequences, with known history and habitat associations, generated under the stable ecotype model and on data from Bacillus strains isolated from Death Valley where previous work has confirmed the existence of multiple ecotypes. We found that one of the algorithms (ecotype simulation) performs significantly better than the others (AdaptML, GMYC, BAPS) in both instances. Unfortunately, it was also shown to be the least efficient of the four. While ecotype simulation is the most accurate, it is by a large margin the slowest of the algorithms tested. Attempts at improving its efficiency are underway.

  15. A highly efficient molecular cloning platform that utilises a small bacterial toxin gene.

    PubMed

    Mok, Wendy W K; Li, Yingfu

    2013-04-15

    Molecular cloning technologies that have emerged in recent years are more efficient and simpler to use than traditional strategies, but many have the disadvantages of requiring multiple steps and expensive proprietary enzymes. We have engineered cloning vectors containing variants of IbsC, a 19-residue toxin from Escherichia coli K-12. These toxic peptides offer selectivity to minimise the background, labour, and cost associated with conventional molecular cloning. As demonstrated with the cloning of reporter genes, this "detox cloning" system consistently produced over 95 % positive clones. Purification steps between digestion and ligation are not necessary, and the total time between digestion and plating of transformants can be as little as three hours. Thus, these IbsC-based cloning vectors are as reliable and amenable to high-throughput cloning as commercially available systems, and have the advantage of being more time-efficient and cost-effective.

  16. Impacts of cultivation of marine diatoms on the associated bacterial community.

    PubMed

    Sapp, Melanie; Wichels, Antje; Gerdts, Gunnar

    2007-05-01

    The composition of bacterial communities associated with four diatom species was monitored during isolation and cultivation of algal cells. Strong shifts in the associated communities, linked with an increase in the numbers of phylotypes belonging to members of the Gammaproteobacteria, were observed during cultivation.

  17. Association between BVAB1 and high Nugent scores among women with bacterial vaginosis.

    PubMed

    Muzny, Christina A; Sunesara, Imran R; Griswold, Michael E; Kumar, Ranjit; Lefkowitz, Elliot J; Mena, Leandro A; Schwebke, Jane R; Martin, David H; Swiatlo, Edwin

    2014-12-01

    As part of a larger study using 454 pyrosequencing to investigate the vaginal microbiota of women with bacterial vaginosis (BV), we found an association between a novel BV-associated bacterium (BVAB1) and high Nugent scores and propose that BVAB1 is the curved Gram-negative rod traditionally identified as Mobiluncus spp. in vaginal Gram stains.

  18. Impacts of Cultivation of Marine Diatoms on the Associated Bacterial Community▿

    PubMed Central

    Sapp, Melanie; Wichels, Antje; Gerdts, Gunnar

    2007-01-01

    The composition of bacterial communities associated with four diatom species was monitored during isolation and cultivation of algal cells. Strong shifts in the associated communities, linked with an increase in the numbers of phylotypes belonging to members of the Gammaproteobacteria, were observed during cultivation. PMID:17369346

  19. Association between BVAB1 and high Nugent scores among women with bacterial vaginosis

    PubMed Central

    Muzny, Christina A.; Sunesara, Imran R.; Griswold, Michael E.; Kumar, Ranjit; Lefkowitz, Elliot J.; Mena, Leandro A.; Schwebke, Jane R.; Martin, David H.; Swiatlo, Edwin

    2015-01-01

    As part of a larger study using 454 pyrosequencing to investigate the vaginal microbiota of women with bacterial vaginosis (BV), we found an association between a novel BV-associated bacterium (BVAB1) and high Nugent scores and propose that BVAB1 is the curved Gram-negative rod traditionally identified as Mobiluncus spp. in vaginal Gram stains. PMID:25262105

  20. Coral-associated bacterial communities on Ningaloo Reef, Western Australia.

    PubMed

    Ceh, Janja; Van Keulen, Mike; Bourne, David G

    2011-01-01

    Coral-associated microbial communities from three coral species (Pocillopora damicornis, Acropora tenuis and Favites abdita) were examined every 3 months (January, March, June, October) over a period of 1 year on Ningaloo Reef, Western Australia. Tissue from corals was collected throughout the year and additional sampling of coral mucus and seawater samples was performed in January. Tissue samples were also obtained in October from P. damicornis coral colonies on Rottnest Island off Perth, 1200 km south of Ningaloo Reef, to provide comparisons between coral-microbial associates in different locations. The community structures of the coral-associated microorganisms were analysed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse microbial profiles among all the coral species sampled. Principal component analysis revealed that samples grouped according to time and not species, indicating that coral-microbial associations may be a result of environmental drivers such as oceanographic characteristics, benthic community structure and temperature. Tissue samples from P. damicornis at Rottnest Island revealed similarities in bacteria to the samples at Ningaloo Reef. This study highlights that coral-associated microbial communities are highly diverse; however, the complex interactions that determine the stability of these associations are not necessarily dependent on coral host specificity.

  1. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes.

    PubMed

    Wang, Hang; Li, Hongyi; Gilbert, Jack A; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang; Zhang, Zhijian

    2015-11-01

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  2. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes

    PubMed Central

    Wang, Hang; Li, Hongyi; Gilbert, Jack A.; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang

    2015-01-01

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems. PMID:26296728

  3. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes

    SciTech Connect

    Wang, Hang; Li, Hongyi; Gilbert, Jack A.; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang; Zhang, Zhijian

    2015-11-01

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems.

  4. A method for isolating RNA from metabolically active bacterial flora associated with octopus.

    PubMed

    de la Cruz-Leyva, M C; Zamudio-Maya, M; Corona-Cruz, A I; González-de la Cruz, J U; Rojas-Herrera, R

    2011-07-01

    Development of a method for the isolation and purification of metagenomic RNA (mgRNA) from the ectopic bacterial flora of octopus. Modifications were made to the methods of Valenzuela-Avendaño et al. (Plant Mol Biol Rep, 2005, 23, 199a) and Chomczynski and Sacchi (Anal Biochem, 1987, 162, 156) to develop a protocol based on chemical lysis with Trizol. This proposed protocol effectively isolated mgRNA. The resulting bacterial RNA transcripts were amplified with universal primers directed to the hypervariable regions of the 16S rRNA gene by complementary DNA synthesis. Protocol efficacy in the study of metabolically active bacterial flora was proven using DGGE, which produced a banding pattern that recovered sequences mainly related to the Vibrionaceae family. The analysed samples were clearly complex, and the proposed protocol was proven to effectively isolate mgRNA from the metabolically active bacterial flora associated with octopus. This is the first protocol proposed for the isolation of bacterial mgRNA that allows identification and study of metabolically active bacterial flora associated with octopus. This is an important step forward in understanding and controlling the microbial community of this economically important fishery resource, aimed at detecting its potentially pathogenic bacteria. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  5. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health

    PubMed Central

    Wei, Zhong; Yang, Tianjie; Friman, Ville-Petri; Xu, Yangchun; Shen, Qirong; Jousset, Alexandre

    2015-01-01

    Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence and theoretical predictions suggest that species-rich communities are more resistant to pathogen invasions. Yet, the underlying mechanisms are unclear. Here, we experimentally test how the underlying resource competition networks of resident bacterial communities affect invasion resistance to the plant pathogen Ralstonia solanacearum in microcosms and in tomato plant rhizosphere. We find that bipartite resource competition networks are better predictors of invasion resistance compared with resident community diversity. Specifically, communities with a combination of stabilizing configurations (low nestedness and high connectance), and a clear niche overlap with the pathogen, reduce pathogen invasion success, constrain pathogen growth within invaded communities and have lower levels of diseased plants in greenhouse experiments. Bacterial resource competition network characteristics can thus be important in explaining positive diversity–invasion resistance relationships in bacterial rhizosphere communities. PMID:26400552

  6. Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health.

    PubMed

    Wei, Zhong; Yang, Tianjie; Friman, Ville-Petri; Xu, Yangchun; Shen, Qirong; Jousset, Alexandre

    2015-09-24

    Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence and theoretical predictions suggest that species-rich communities are more resistant to pathogen invasions. Yet, the underlying mechanisms are unclear. Here, we experimentally test how the underlying resource competition networks of resident bacterial communities affect invasion resistance to the plant pathogen Ralstonia solanacearum in microcosms and in tomato plant rhizosphere. We find that bipartite resource competition networks are better predictors of invasion resistance compared with resident community diversity. Specifically, communities with a combination of stabilizing configurations (low nestedness and high connectance), and a clear niche overlap with the pathogen, reduce pathogen invasion success, constrain pathogen growth within invaded communities and have lower levels of diseased plants in greenhouse experiments. Bacterial resource competition network characteristics can thus be important in explaining positive diversity-invasion resistance relationships in bacterial rhizosphere communities.

  7. Trogocytosis-associated cell to cell spread of intracellular bacterial pathogens.

    PubMed

    Steele, Shaun; Radlinski, Lauren; Taft-Benz, Sharon; Brunton, Jason; Kawula, Thomas H

    2016-01-23

    Macrophages are myeloid-derived phagocytic cells and one of the first immune cell types to respond to microbial infections. However, a number of bacterial pathogens are resistant to the antimicrobial activities of macrophages and can grow within these cells. Macrophages have other immune surveillance roles including the acquisition of cytosolic components from multiple types of cells. We hypothesized that intracellular pathogens that can replicate within macrophages could also exploit cytosolic transfer to facilitate bacterial spread. We found that viable Francisella tularensis, as well as Salmonella enterica bacteria transferred from infected cells to uninfected macrophages along with other cytosolic material through a transient, contact dependent mechanism. Bacterial transfer occurred when the host cells exchanged plasma membrane proteins and cytosol via a trogocytosis related process leaving both donor and recipient cells intact and viable. Trogocytosis was strongly associated with infection in mice, suggesting that direct bacterial transfer occurs by this process in vivo.

  8. Profiling of root canal bacterial communities associated with chronic apical periodontitis from Brazilian and Norwegian subjects.

    PubMed

    Siqueira, José F; Rôças, Isabela N; Debelian, Gilberto J; Carmo, Flávia L; Paiva, Simone S M; Alves, Flávio R F; Rosado, Alexandre S

    2008-12-01

    The aim of this study was to compare the bacterial community profiles of the root canal microbiota associated with chronic apical periodontitis from Brazilian and Norwegian patients using the denaturing gradient gel electrophoresis (DGGE) and the ribosomal intergenic spacer analysis (RISA) approaches. DNA extracted from root canal samples was subjected to polymerase chain reaction using primers appropriate for further DGGE or RISA analysis. The resulting banding patterns representative of the bacterial community structures in samples from the two locations were compared. DGGE and RISA fingerprints showed a great interindividual variability in the bacterial community profiles, irrespective of the geographic location of the patient. However, similarities among the bacterial community DGGE profiles revealed the existence of a geography-related pattern.

  9. Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment.

    PubMed

    Durack, Juliana; Lynch, Susan V; Nariya, Snehal; Bhakta, Nirav R; Beigelman, Avraham; Castro, Mario; Dyer, Anne-Marie; Israel, Elliot; Kraft, Monica; Martin, Richard J; Mauger, David T; Rosenberg, Sharon R; Sharp-King, Tonya; White, Steven R; Woodruff, Prescott G; Avila, Pedro C; Denlinger, Loren C; Holguin, Fernando; Lazarus, Stephen C; Lugogo, Njira; Moore, Wendy C; Peters, Stephen P; Que, Loretta; Smith, Lewis J; Sorkness, Christine A; Wechsler, Michael E; Wenzel, Sally E; Boushey, Homer A; Huang, Yvonne J

    2017-07-01

    Compositional differences in the bronchial bacterial microbiota have been associated with asthma, but it remains unclear whether the findings are attributable to asthma, to aeroallergen sensitization, or to inhaled corticosteroid treatment. We sought to compare the bronchial bacterial microbiota in adults with steroid-naive atopic asthma, subjects with atopy but no asthma, and nonatopic healthy control subjects and to determine relationships of the bronchial microbiota to phenotypic features of asthma. Bacterial communities in protected bronchial brushings from 42 atopic asthmatic subjects, 21 subjects with atopy but no asthma, and 21 healthy control subjects were profiled by using 16S rRNA gene sequencing. Bacterial composition and community-level functions inferred from sequence profiles were analyzed for between-group differences. Associations with clinical and inflammatory variables were examined, including markers of type 2-related inflammation and change in airway hyperresponsiveness after 6 weeks of fluticasone treatment. The bronchial microbiome differed significantly among the 3 groups. Asthmatic subjects were uniquely enriched in members of the Haemophilus, Neisseria, Fusobacterium, and Porphyromonas species and the Sphingomonodaceae family and depleted in members of the Mogibacteriaceae family and Lactobacillales order. Asthma-associated differences in predicted bacterial functions included involvement of amino acid and short-chain fatty acid metabolism pathways. Subjects with type 2-high asthma harbored significantly lower bronchial bacterial burden. Distinct changes in specific microbiota members were seen after fluticasone treatment. Steroid responsiveness was linked to differences in baseline compositional and functional features of the bacterial microbiome. Even in subjects with mild steroid-naive asthma, differences in the bronchial microbiome are associated with immunologic and clinical features of the disease. The specific differences identified

  10. A tale of two chitons: is habitat specialisation linked to distinct associated bacterial communities?

    PubMed

    Duperron, Sébastien; Pottier, Marie-Anne; Léger, Nelly; Gaudron, Sylvie M; Puillandre, Nicolas; Le Prieur, Stéphanie; Sigwart, Julia D; Ravaux, Juliette; Zbinden, Magali

    2013-03-01

    Although most chitons (Mollusca: Polyplacophora) are shallow-water molluscs, diverse species also occur in deep-sea habitats. We investigated the feeding strategies of two species, Leptochiton boucheti and Nierstraszella lineata, recovered on sunken wood sampled in the western Pacific, close to the Vanuatu Islands. The two species display distinctly different associations with bacterial partners. Leptochiton boucheti harbours Mollicutes in regions of its gut epithelium and has no abundant bacterium associated with its gill. Nierstraszella lineata displays no dense gut-associated bacteria, but harbours bacterial filaments attached to its gill epithelium, related to the Deltaproteobacteria symbionts found in gills of the wood-eating limpet Pectinodonta sp. Stable carbon and nitrogen isotope signatures and an absence of cellulolytic activity give evidence against a direct wood-feeding diet; both species are secondary consumers within the wood food web. We suggest that the distinct associations with bacterial partners are linked to niche specialisations of the two species. Nierstraszella lineata is in a taxonomic family restricted to sunken wood and is possibly adapted to more anoxic conditions thanks to its gill-associated bacteria. Leptochiton boucheti is phylogenetically more proximate to an ancestral form not specialised on wood and may itself be more of a generalist; this observation is congruent with its association with Mollicutes, a bacterial clade comprising gut-associated bacteria occurring in several metazoan phyla.

  11. Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host

    PubMed Central

    Staudacher, Heike; Kaltenpoth, Martin; Breeuwer, Johannes A. J.; Menken, Steph B. J.; Heckel, David G.; Groot, Astrid T.

    2016-01-01

    Microbes associated with insects can confer a wide range of ecologically relevant benefits to their hosts. Since insect-associated bacteria often increase the nutritive value of their hosts' diets, the study of bacterial communities is especially interesting in species that are important agricultural pests. We investigated the composition of bacterial communities in the noctuid moth Heliothis virescens and its variability in relation to developmental stage, diet and population (field and laboratory), using bacterial tag-encoded FLX pyrosequencing of 16S rRNA amplicons. In larvae, bacterial communities differed depending on the food plant on which they had been reared, although the within-group variation between biological replicates was high as well. Moreover, larvae originating from a field or laboratory population did not share any OTUs. Interestingly, Enterococcus sp. was found to be the dominant taxon in laboratory-reared larvae, but was completely absent from field larvae, indicating dramatic shifts in microbial community profiles upon cultivation of the moths in the laboratory. Furthermore, microbiota composition varied strongly across developmental stages in individuals of the field population, and we found no evidence for vertical transmission of bacteria from mothers to offspring. Since sample sizes in our study were small due to pooling of samples for sequencing, we cautiously conclude that the high variability in bacterial communities suggests a loose and temporary association of the identified bacteria with H. virescens. PMID:27139886

  12. Qivas Therapy for Treatment of Implant Associated MDR Bacterial Infection.

    PubMed

    Chouhan, Varun

    2016-01-01

    Orthopedic implant-associated infections are difficult to treat, both physically and psychologically, for the patient and the surgeon as well. Organisms capable of forming biofilms tend to be more virulent and have ability of causing chronic infections. Chronic implant associated infections are very difficult to treat, requires a lot of time, money and other resources. Chronic infections produce a lot of morbidity and sometimes mortality to the patient. A 40-year-old male treated for bilateral acetabular fracture sustained after fall from height due to an episode of seizure. After acetabular surgery, he developed surgical site infection unresponsive to wound wash and intravenous antibiotics. After two weeks, we started treatment with Qurion solution and Vacuum assisted suction (QiVAS) to which patient responded very well and his infection was cured. We are not aware of any study or case report using QiVAS therapy for treatment of infection associated with orthopaedic implant. Orthopaedic implant related infection can be difficult to treat especially if caused by multidrug resistant organisms capable of forming biofilm. QiVAS therapy is a new method which can be used in such difficult situations to treat infection without removal of implant within short period of time thus reducing morbidity for patients.

  13. Prevalence of Bacterial Vaginosis and Associated Risk Factors among Women Complaining of Genital Tract Infection

    PubMed Central

    Abebaw, Yeshiwork; Bekele, Delayehu; Mihret, Amete

    2017-01-01

    Background Bacterial vaginosis is a global concern due to the increased risk of acquisition of sexually transmitted infections. Objectives To determine the prevalence of bacterial vaginosis and bacteria causing aerobic vaginitis. Methods A cross-sectional study was conducted among 210 patients between September 2015 and July 2016 at St. Paul's Hospital. Gram-stained vaginal swabs were examined microscopically and graded as per Nugent's procedure. Bacteria causing aerobic vaginitis were characterized, and their antimicrobial susceptibility pattern was determined. Results The overall prevalence of bacterial vaginosis was 48.6%. Bacterial vaginosis was significantly associated with number of pants used per day (p = 0.001) and frequency of vaginal bathing (p = 0.045). Of 151 bacterial isolates, 69.5% were Gram-negative and 30.5% were Gram-positive bacteria. The overall drug resistance level of Gram-positive bacteria was high against penicillin, tetracycline, and erythromycin. Cefoxitin and tobramycin were the most active drugs against Gram-positive bacteria. The overall drug resistance level of Gram-negative bacteria was high against tetracycline, ampicillin, and amoxicillin. Amikacin and tobramycin were the most active drugs against Gram-negative bacteria. Conclusions The prevalence of bacterial vaginosis was high and was affected by individual hygiene. Routine culture of vaginal samples should be performed on patients with vaginitis and the drug susceptibility pattern of each isolate should be determined. PMID:28831285

  14. Prevalence of Bacterial Vaginosis and Associated Risk Factors among Women Complaining of Genital Tract Infection.

    PubMed

    Bitew, Adane; Abebaw, Yeshiwork; Bekele, Delayehu; Mihret, Amete

    2017-01-01

    Bacterial vaginosis is a global concern due to the increased risk of acquisition of sexually transmitted infections. To determine the prevalence of bacterial vaginosis and bacteria causing aerobic vaginitis. A cross-sectional study was conducted among 210 patients between September 2015 and July 2016 at St. Paul's Hospital. Gram-stained vaginal swabs were examined microscopically and graded as per Nugent's procedure. Bacteria causing aerobic vaginitis were characterized, and their antimicrobial susceptibility pattern was determined. The overall prevalence of bacterial vaginosis was 48.6%. Bacterial vaginosis was significantly associated with number of pants used per day (p = 0.001) and frequency of vaginal bathing (p = 0.045). Of 151 bacterial isolates, 69.5% were Gram-negative and 30.5% were Gram-positive bacteria. The overall drug resistance level of Gram-positive bacteria was high against penicillin, tetracycline, and erythromycin. Cefoxitin and tobramycin were the most active drugs against Gram-positive bacteria. The overall drug resistance level of Gram-negative bacteria was high against tetracycline, ampicillin, and amoxicillin. Amikacin and tobramycin were the most active drugs against Gram-negative bacteria. The prevalence of bacterial vaginosis was high and was affected by individual hygiene. Routine culture of vaginal samples should be performed on patients with vaginitis and the drug susceptibility pattern of each isolate should be determined.

  15. Molecular assessment of the bacterial community associated with Cassava (Manihot esculenta Crantz) cultivation in Cameroon.

    PubMed

    Sarr, Papa Saliou; Sugiyama, Akifumi; Begoude, Aime Didier Boyogueno; Yazaki, Kazufumi; Araki, Shigeru; Nawata, Eiji

    2017-04-01

    Bacterial communities play an important role in nutrient cycles and plant development. Their distribution and activity may depend on location and environmental heterogeneity. This study characterized soil bacterial communities in cassava fields of Eastern (Andom) and Southern (Bityili) Cameroon using molecular tools. In both sites, two improved varieties (TMS-96/1414; TMS-92/0326) and a local variety (Local) were grown in a randomized block design. Composite bulk soils were collected at 10months after planting from cassava plots. The 16S rDNA region was amplified, MiSeq was performed and sequence data analyzed. The same 17 bacterial phyla were present in both Andom and Bityili, while Chlorobi and Deinococcus-Thermus were only specific to Andom. The phyla Proteobacteria, Planctomycetes, Actinobacteria and Acidobacteria were dominant. Although both sites shared similar phyla, the principal coordinate analysis revealed significant variations in their composition, suggesting that the functions of the bacteria in nutrients cycling are likely to differ between Andom and Bityili. Cassava yields were generally higher in Andom which also displayed a higher diversity of bacterial communities. This study provides useful information on the composition of bacterial communities in cassava fields in two agro-ecologies of Cameroon. It constitutes to our knowledge the first report describing soil bacterial communities in association with cassava growth in the country, using molecular tools.

  16. Bacterial Vaginosis–Associated Bacteria in Men: Association of Leptotrichia/Sneathia spp. With Nongonococcal Urethritis

    PubMed Central

    Manhart, Lisa E.; Khosropour, Christine M.; Liu, Congzhu; Gillespie, Catherine W.; Depner, Kevin; Fiedler, Tina; Marrazzo, Jeanne M.; Fredricks, David N.

    2014-01-01

    Background Approximately 45% of nongonococcal urethritis cases have no identified etiology. Novel bacteria recently associated with bacterial vaginosis (BV) in women may be involved. We evaluated the association of idiopathic nongonococcal urethritis and 5 newly described BV-associated bacteria (BVAB). Methods Heterosexual men 16 years or older attending a sexually transmitted disease clinic in Seattle, Washington, from May 2007 to July 2011 and negative for Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma genitalium, and Ureaplasma urealyticum–biovar2 were eligible. Cases had urethral discharge or 5 or more polymorphonuclear leukocytes per high-power field in urethral exudates. Controls had no urethral discharge and less than 5 polymorphonuclear leukocytes per high-power field. Urine was tested for Atopobium spp., BVAB-2, BVAB-3, Megasphaera spp., and Leptotrichia/Sneathia spp. using quantitative taxon-directed polymerase chain reaction. Results Cases (n = 157) and controls (n = 102) were of similar age, education, and income, and most were white. Leptotrichia/Sneathia spp. was significantly associated with urethritis (24/157 [15.3%] vs. 6/102 [5.9%], P = 0.03). BVAB-2 was more common in cases than in controls (7/157 [4.5%] vs. 1/102 [1.0%], P = 0.15), and BVAB-3 (n = 2) and Megasphaera spp. (n = 1) were only detected in men with urethritis, but these bacteria were found only in men who also had Leptotrichia/Sneathia spp. Atopobium spp. was not associated with urethritis. The quantity of bacteria did not differ between cases and controls. Among treated cases, doxycycline was more effective than azithromycin for clinical cure of men with Leptotrichia/Sneathia spp. (9/10 vs. 7/12, P = 0.16) and BVAB-2 (3/3 vs. 0/3, P = 0.10). Conclusions Leptotrichia/Sneathia spp. may be urethral pathogens or contribute to a pathogenic microbiota that can also include BVAB-2, BVAB-3, and Megasphaera spp. Doxycycline may be more effective than

  17. Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed.

    PubMed

    Song, Liyan; Li, Lei

    2016-08-01

    Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a

  18. Mechanisms of Severe Mortality-Associated Bacterial Co-infections Following Influenza Virus Infection.

    PubMed

    Jia, Leili; Xie, Jing; Zhao, Jiangyun; Cao, Dekang; Liang, Yuan; Hou, Xuexin; Wang, Ligui; Li, Zhenjun

    2017-01-01

    Influenza virus infection remains one of the largest disease burdens on humans. Influenza-associated bacterial co-infections contribute to severe disease and mortality during pandemic and seasonal influenza episodes. The mechanisms of severe morbidity following influenza-bacteria co-infections mainly include failure of an antibacterial immune response and pathogen synergy. Moreover, failure to resume function and tolerance might be one of the main reasons for excessive mortality. In this review, recent advances in the study of mechanisms of severe disease, caused by bacterial co-infections following influenza virus pathogenesis, are summarized. Therefore, understanding the synergy between viruses and bacteria will facilitate the design of novel therapeutic approaches to prevent mortality associated with bacterial co-infections.

  19. Intracerebral Hemorrhages in Adults with Community Associated Bacterial Meningitis in Adults: Should We Reconsider Anticoagulant Therapy?

    PubMed Central

    Mook-Kanamori, Barry B.; Fritz, Daan; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2012-01-01

    Objective To study the incidence, clinical presentation and outcome of intracranial hemorrhagic complications in adult patients with community associated bacterial meningitis. Methods Nationwide prospective cohort study from all hospitals in the Netherlands, from 1 March 2006, through 31 December 2010. Results Of the 860 episodes of bacterial meningitis that were included, 24 were diagnosed with intracranial hemorrhagic complications: 8 upon presentation and 16 during clinical course. Clinical presentation between patients with or without intracranial hemorrhage was similar. Causative bacteria were Streptococcus pneumoniae in 16 patients (67%), Staphylococcus aureus in 5 (21%), Pseudomonas aeruginosa and Listeria monocytogenes both in 1 patient (4%). Occurrence of intracranial hemorrhage was associated with death (63% vs. 15%, P<0.001) and unfavorable outcome (94% vs. 34%, P<0.001). The use of anticoagulants on admission was associated with a higher incidence of intracranial hemorrhages (odds ratio 5.84, 95% confidence interval 2.17–15.76). Conclusion Intracranial hemorrhage is a rare but devastating complication in patients with community-associated bacterial meningitis. Since anticoagulant therapy use is associated with increased risk for intracranial hemorrhage, physicians may consider reversing or temporarily discontinuing anticoagulation in patients with bacterial meningitis. PMID:23028898

  20. Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod

    PubMed Central

    Ngangbam, Ajit Kumar; Baten, Abdul; Waters, Daniel L. E.; Whalan, Steve; Benkendorff, Kirsten

    2015-01-01

    Dicathais orbita is a marine mollusc recognised for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the diversity and identity of bacteria associated with the Tyrian purple producing hypobranchial gland, in comparison with foot tissue, using a high-throughput sequencing approach. Taxonomic and phylogenetic analysis of variable region V1-V3 of 16S rRNA bacterial gene amplicons in QIIME and MEGAN were carried out. This analysis revealed a highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The dominant bacterial phylum in the 16S rRNA bacterial profiling data set was Proteobacteria followed by Bacteroidetes, Tenericutes and Spirochaetes. In comparison to the foot, the hypobranchial gland had significantly lower bacterial diversity and a different community composition, based on taxonomic assignment at the genus level. A higher abundance of indole producing Vibrio spp. and the presence of bacteria with brominating capabilities in the hypobranchial gland suggest bacteria have a potential role in biosynthesis of Tyrian purple in D. orbita. PMID:26488885

  1. Bacterial communities associated with the decomposition of Fucus vesiculosus in transitional waters

    NASA Astrophysics Data System (ADS)

    Martins, Patrícia; Lopes, Marta Lobão; Rodrigues, Ana Maria; Gomes, Newton C. M.; Quintino, Victor

    2012-09-01

    In this work we study the temporal and spatial patterns of the bacterial communities associated with the decomposition of Fucus vesiculosus and a control substrate in a transitional ecosystem. Leaf-bags with 5 mm mesh-size and containing the experimental substrates were placed in three areas, euhaline, mesohaline and limnetic, covering the full salinity gradient. The substrates were submerged at day 0 and three replicates were randomly collected per site, at days 3, 7, 15, 30 and 60. The complexity and structural changes of the bacterial communities inhabiting F. vesiculosus and the control substrates were assessed by denaturing gradient gel electrophoresis (DGGE). Bacterial community fingerprints showed no significant differences between areas only at day 3, for both substrates. The bacterial community associated with F. vesiculosus showed significant differences over time in the euhaline and mesohaline areas but not in the limnetic area. A different trend was observed for the artificial substrate. Comparing the bacterial communities of F. vesiculosus and the artificial substrate, the results indicated that the significant differences between the two substrates were detected from day 7 in the euhaline area and only later, at day 15, in the other areas. These results are coherent with the fastest decomposition rate of the alga in the euhaline area, where it occurs naturally, and the slowest in the limnetic area, where it does not naturally exists.

  2. Bacterial Associates of Two Caribbean Coral Species Reveal Species-Specific Distribution and Geographic Variability

    PubMed Central

    Moss, Anthony G.; Chadwick, Nanette E.; Liles, Mark R.

    2012-01-01

    Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean, Montastraea faveolata and Porites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here that M. faveolata and P. astreoides harbor distinct, host-specific bacteria but that specificity varies by species and site. P. astreoides generally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus, Endozoicomonas, within the order Oceanospirillales. The bacterial assemblages associated with M. faveolata are significantly more diverse and exhibit higher specificity at the family level than P. astreoides assemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude

  3. Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability.

    PubMed

    Morrow, Kathleen M; Moss, Anthony G; Chadwick, Nanette E; Liles, Mark R

    2012-09-01

    Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean, Montastraea faveolata and Porites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here that M. faveolata and P. astreoides harbor distinct, host-specific bacteria but that specificity varies by species and site. P. astreoides generally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus, Endozoicomonas, within the order Oceanospirillales. The bacterial assemblages associated with M. faveolata are significantly more diverse and exhibit higher specificity at the family level than P. astreoides assemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude

  4. Host response to secondary bacterial infection associated with antecedent influenza virus infection in pigs – exacerbation associated with vaccination

    USDA-ARS?s Scientific Manuscript database

    The increasing number of annual influenza (IAV) cases, coupled with the recent IAV pandemic, has amplified concerns about its impact on human and animal health. It is appreciated that Flu is complicated by bacterial pneumonia. Vaccine-associated enhanced respiratory disease (VAERD) can occur followi...

  5. Bacterial, Archaeal, and Fungal Diversity of Spacecraft-Associated Surfaces

    NASA Astrophysics Data System (ADS)

    Venkateswaran, Kasthuri; La Duc, Myron; Vaishampayan, Parag

    2012-07-01

    The introduction of contaminant microbiota to extraterrestrial settings could have profound repercussions on the scientific integrity of in-situ and sample-return based life detection experiments. Thus a key challenge lies in providing a comprehensive account of the molecular signatures of microorganisms resident on spacecraft hardware. It will be essential to know which organisms pose the greatest threat of contamination based on recurrent isolation and/or detection on spacecraft associated surfaces, so that their presence can be preferably eliminated, or at least recognized and discriminated from any authentic extraterrestrial biosignatures. The advent of high-throughput molecular biological methodologies has dramatically increased the resolution and sensitivity of detection of various microbial lineages in mixed assemblages. At present, NASA is developing such enabling technologies capable of providing a detailed, comprehensive census of the microorganisms present on spacecraft surfaces. Establishing such a genetic inventory will prove invaluable when working to meet the anticipated requirements for potential future missions to return samples from Mars.

  6. Association of Secondhand Smoke Exposure with Pediatric Invasive Bacterial Disease and Bacterial Carriage: A Systematic Review and Meta-analysis

    PubMed Central

    Lee, Chien-Chang; Middaugh, Nicole A.; Howie, Stephen R. C.; Ezzati, Majid

    2010-01-01

    Background A number of epidemiologic studies have observed an association between secondhand smoke (SHS) exposure and pediatric invasive bacterial disease (IBD) but the evidence has not been systematically reviewed. We carried out a systematic review and meta-analysis of SHS exposure and two outcomes, IBD and pharyngeal carriage of bacteria, for Neisseria meningitidis (N. meningitidis), Haemophilus influenzae type B (Hib), and Streptococcus pneumoniae (S. pneumoniae). Methods and Findings Two independent reviewers searched Medline, EMBASE, and selected other databases, and screened articles for inclusion and exclusion criteria. We identified 30 case-control studies on SHS and IBD, and 12 cross-sectional studies on SHS and bacterial carriage. Weighted summary odd ratios (ORs) were calculated for each outcome and for studies with specific design and quality characteristics. Tests for heterogeneity and publication bias were performed. Compared with those unexposed to SHS, summary OR for SHS exposure was 2.02 (95% confidence interval [CI] 1.52–2.69) for invasive meningococcal disease, 1.21 (95% CI 0.69–2.14) for invasive pneumococcal disease, and 1.22 (95% CI 0.93–1.62) for invasive Hib disease. For pharyngeal carriage, summary OR was 1.68 (95% CI, 1.19–2.36) for N. meningitidis, 1.66 (95% CI 1.33–2.07) for S. pneumoniae, and 0.96 (95% CI 0.48–1.95) for Hib. The association between SHS exposure and invasive meningococcal and Hib diseases was consistent regardless of outcome definitions, age groups, study designs, and publication year. The effect estimates were larger in studies among children younger than 6 years of age for all three IBDs, and in studies with the more rigorous laboratory-confirmed diagnosis for invasive meningococcal disease (summary OR 3.24; 95% CI 1.72–6.13). Conclusions When considered together with evidence from direct smoking and biological mechanisms, our systematic review and meta-analysis indicates that SHS exposure may be

  7. Citrus huanglongbing shapes the structure of bacterial community associated with citrus roots

    USDA-ARS?s Scientific Manuscript database

    To examine the effect of pathogen on the diversity and structure of plant associated bacterial community, we carried out a molecular based analysis using citrus and huanglongbing as host-disease model. 16S rDNA clone library analysis of the citrus roots revealed shifts in the microbial diversity in ...

  8. Quantitative analysis of initial adhesion of bacterial vaginosis-associated anaerobes to ME-180 cells.

    PubMed

    Machado, António; Salgueiro, Débora; Harwich, Michael; Jefferson, Kimberly Kay; Cerca, Nuno

    2013-10-01

    Bacterial vaginosis is the leading vaginal disorder but the transition from health to this dysbiotic condition remains poorly characterized. Our goal was to quantify the ability of BV-associated anaerobes to adhere to epithelial cells in the presence of lactobacilli. Gardnerella vaginalis outcompeted Lactobacillus crispatus and Lactobacillus iners actually enhanced its adherence. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Geographic variation in bacterial communities associated with the red turpentine beetle (Coleoptera: Curculionidae)

    Treesearch

    Aaron S. Adams; Sandye M. Adams; Cameron R. Currie; Nancy E. Gillette; Kenneth F. Raffa

    2010-01-01

    Bacterial communities are known to play important roles in insect life histories, yet their consistency or variation across populations is poorly understood. Bacteria associated with the bark beetle Dendroctonus valens LeConte from eight populations, ranging from Wisconsin to Oregon, were evaluated and compared. We used the culture-independent technique of denaturing...

  10. 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.

  11. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis)

    PubMed Central

    Aires, Tânia; Serrão, Ester A.; Engelen, Aschwin H.

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or

  12. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).

    PubMed

    Aires, Tânia; Serrão, Ester A; Engelen, Aschwin H

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or

  13. GA-Based Selection of Vaginal Microbiome Features Associated with Bacterial Vaginosis.

    PubMed

    Carter, Joi; Beck, Daniel; Williams, Henry; Foster, James; Dozier, Gerry

    2014-01-01

    In this paper, we successfully apply GEFeS (Genetic & Evolutionary Feature Selection) to identify the key features in the human vaginal microbiome and in patient meta-data that are associated with bacterial vaginosis (BV). The vaginal microbiome is the community of bacteria found in a patient, and meta-data include behavioral practices and demographic information. Bacterial vaginosis is a disease that afflicts nearly one third of all women, but the current diagnostics are crude at best. We describe two types of classifies for BV diagnosis, and show that each is associated with one of two treatments. Our results show that the classifiers associated with the 'Treat Any Symptom' version have better performances that the classifier associated with the 'Treat Based on N-Score Value'. Our long term objective is to develop a more accurate and objective diagnosis and treatment of BV.

  14. Association between Gallbladder Ultrasound Findings and Bacterial Culture of Bile in 70 Cats and 202 Dogs.

    PubMed

    Policelli Smith, R; Gookin, J L; Smolski, W; Di Cicco, M F; Correa, M; Seiler, G S

    2017-09-01

    Bacterial cholecystitis often is diagnosed by combination of gallbladder ultrasound (US) findings and positive results of bile culture. The value of gallbladder US in determining the likelihood of bile bacterial infection in cats and dogs with suspected biliary disease is unknown. To determine the value of gallbladder US in predicting bile bacterial culture results, identify most common bacterial isolates from bile, and describe complications after cholecystocentesis in cats and dogs with suspected hepatobiliary disease. Cats (70) and dogs (202) that underwent an abdominal US and submission of bile for culture were included in the study. A cross-sectional study design was used to determine the association of gallbladder US abnormalities and the results of bile cultures, and complications of cholecystocentesis. Abnormal gallbladder US had high sensitivity (96%) but low specificity (49%) in cats with positive and negative results of bile bacterial culture, respectively. Cats with normal gallbladder US findings were unlikely to have positive bile bacterial culture (negative predictive value of 96%). Gallbladder US had lower sensitivity (81%), specificity (31%), positive predictive value (20%), and negative predictive value (88%) in dogs. The most common bacterial isolates were of enteric origin, the prevalence being higher in cats. Incidence of complications after cholecystocentesis was 3.4%. Gallbladder US has a high negative predictive value for bile culture results in cats. This modality is less predictive of infection in dogs. Percutaneous US-guided cholecystocentesis has a low complication rate. Copyright © 2017 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

  15. Bacterial abundance and viability in rainwater associated with cyclones, stationary fronts and typhoons in southwestern Japan

    NASA Astrophysics Data System (ADS)

    Hu, Wei; Murata, Kotaro; Toyonaga, Satoshi; Zhang, Daizhou

    2017-10-01

    The abundance and viability of bacterial cells in rainwater at a suburban site in southwestern Japan between October 2014 and September 2015 were measured and their distinctiveness, according to synoptic weather systems, i.e., cyclones (cold fronts), stationary fronts (including Meiyu and non-Meiyu fronts) and typhoons, was examined. On average, the cell concentration of bacteria in the rainwater was 2.3 ± 1.5 × 104 cells mL-1, and bacterial viability, the ratio of viable cells to total cells, was 80 ± 10%. In the rainwater of cyclones when clouds were induced by the intrusion of continental air, the bacterial concentration was higher (3.5 ± 1.6 × 104 cells mL-1) and the viability was lower (75 ± 8%) than in the rainwater of other types. In the rainwater of Meiyu fronts and typhoons when clouds were significantly influenced by marine air, bacterial concentrations were 1.5 ± 0.5 × 104 and 1.2 ± 0.3 × 104 cells mL-1, and bacterial viabilities were 84 ± 7% and 85 ± 7%, respectively. In the rainwater of non-Meiyu stationary fronts, the bacterial concentration was 2.4 ± 1.6 × 104 cells mL-1, and the viability was 78 ± 14%. Abundant bacteria were associated with ions nss-SO42-, nss-Ca2+, and NO3- in rainwater, but bacterial concentrations did not correlate with the ratios of airborne particle concentrations to the precipitation amounts. Further investigations with correlation and principal component analysis combining bacteria and ion species revealed that bacteria in the rainwater were likely enclosed in clouds at the stage of cloud formation in addition to below-cloud removal, and bacteria involved in the rainwater did not show confirmable growth.

  16. Bacterial communities and their association with the bio-drying of sewage sludge.

    PubMed

    Cai, Lu; Chen, Tong-Bin; Gao, Ding; Yu, Jie

    2016-03-01

    Bio-drying is a technology that aims to remove water from a material using the microbial heat originating from organic matter degradation. However, the evolution of bacterial communities that are associated with the drying process has not been researched systematically. This study was performed to investigate the variations of bacterial communities and the relationships among bacterial communities, water evaporation, water generation, and organic matter degradation during the bio-drying of sewage sludge. High-throughput pyrosequencing was used to analyze the bacterial communities, while water evaporation and water generation were determined based on an in situ water vapor monitoring device. The values of water evaporation, water generation, and volatile solids degradation were 412.9 g kg(-1) sewage sludge bio-drying material (SSBM), 65.0 g kg(-1) SSBM, and 70.2 g kg(-1) SSBM, respectively. Rarefaction curves and diversity indices showed that bacterial diversity plummeted after the temperature of the bio-drying pile dramatically increased on d 2, which coincided with a remarkable increase of water evaporation on d 2. Bacterial diversity increased when the pile cooled. During the thermophilic phase, in which Acinetobacter and Bacillus were the dominant genera, the rates of water evaporation, water generation, and VS degradation peaked. These results implied that the elevated temperature reshaped the bacterial communities, which played a key role in water evaporation, and the high temperature also contributed to the effective elimination of pathogens. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Bacterial communities associated with culex mosquito larvae and two emergent aquatic plants of bioremediation importance.

    PubMed

    Duguma, Dagne; Rugman-Jones, Paul; Kaufman, Michael G; Hall, Michael W; Neufeld, Josh D; Stouthamer, Richard; Walton, William E

    2013-01-01

    Microbes are important for mosquito nutrition, growth, reproduction and control. In this study, we examined bacterial communities associated with larval mosquitoes and their habitats. Specifically, we characterized bacterial communities associated with late larval instars of the western encephalitis mosquito (Culextarsalis), the submerged portions of two emergent macrophytes (California bulrush, Schoenoplectuscalifornicus and alkali bulrush, Schoenoplectusmaritimus), and the associated water columns to investigate potential differential use of resources by mosquitoes in different wetland habitats. Using next-generation sequence data from 16S rRNA gene hypervariable regions, the alpha diversity of mosquito gut microbial communities did not differ between pond mesocosms containing distinct monotypic plants. Proteobacteria, dominated by the genus Thorsellia (Enterobacteriaceae), was the most abundant phylum recovered from C. tarsalis larvae. Approximately 49% of bacterial OTUs found in larval mosquitoes were identical to OTUs recovered from the water column and submerged portions of the two bulrushes. Plant and water samples were similar to one another, both being dominated by Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria and Verrucomicrobia phyla. Overall, the bacterial communities within C. tarsalis larvae were conserved and did not change across sampling dates and between two distinct plant habitats. Although Thorsellia spp. dominated mosquito gut communities, overlap of mosquito gut, plant and water-column OTUs likely reveal the effects of larval feeding. Future research will investigate the role of the key indicator groups of bacteria across the different developmental stages of this mosquito species.

  18. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    PubMed

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta.

  19. Bacterial Communities Associated with Culex Mosquito Larvae and Two Emergent Aquatic Plants of Bioremediation Importance

    PubMed Central

    Duguma, Dagne; Rugman-Jones, Paul; Kaufman, Michael G.; Hall, Michael W.; Neufeld, Josh D.; Stouthamer, Richard; Walton, William E.

    2013-01-01

    Microbes are important for mosquito nutrition, growth, reproduction and control. In this study, we examined bacterial communities associated with larval mosquitoes and their habitats. Specifically, we characterized bacterial communities associated with late larval instars of the western encephalitis mosquito (Culextarsalis), the submerged portions of two emergent macrophytes (California bulrush, Schoenoplectuscalifornicus and alkali bulrush, Schoenoplectusmaritimus), and the associated water columns to investigate potential differential use of resources by mosquitoes in different wetland habitats. Using next-generation sequence data from 16S rRNA gene hypervariable regions, the alpha diversity of mosquito gut microbial communities did not differ between pond mesocosms containing distinct monotypic plants. Proteobacteria, dominated by the genus Thorsellia (Enterobacteriaceae), was the most abundant phylum recovered from C. tarsalis larvae. Approximately 49% of bacterial OTUs found in larval mosquitoes were identical to OTUs recovered from the water column and submerged portions of the two bulrushes. Plant and water samples were similar to one another, both being dominated by Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria and Verrucomicrobia phyla. Overall, the bacterial communities within C. tarsalis larvae were conserved and did not change across sampling dates and between two distinct plant habitats. Although Thorsellia spp. dominated mosquito gut communities, overlap of mosquito gut, plant and water-column OTUs likely reveal the effects of larval feeding. Future research will investigate the role of the key indicator groups of bacteria across the different developmental stages of this mosquito species. PMID:23967314

  20. Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples

    PubMed Central

    Kumar, Nikhil; Lin, Mingqun; Zhao, Xuechu; Ott, Sandra; Santana-Cruz, Ivette; Daugherty, Sean; Rikihisa, Yasuko; Sadzewicz, Lisa; Tallon, Luke J.; Fraser, Claire M.; Dunning Hotopp, Julie C.

    2016-01-01

    Despite numerous advances in genomics and bioinformatics, technological hurdles remain to examine host-microbe transcriptomics. Sometimes the transcriptome of either or both can be ascertained merely by generating more sequencing reads. However, many cases exist where bacterial mRNA needs to be enriched further to enable cost-effective sequencing of the pathogen or endosymbiont. While a suitable method is commercially available for mammalian samples of this type, development of such methods has languished for invertebrate samples. Furthermore, a common method across multiple taxa would facilitate comparisons between bacteria in invertebrate vectors and their vertebrate hosts. Here, a method is described to concurrently remove polyadenylated transcripts, prokaryotic rRNA, and eukaryotic rRNA, including those with low amounts of starting material (e.g. 100 ng). In a Wolbachia-Drosophila system, this bacterial mRNA enrichment yielded a 3-fold increase in Wolbachia mRNA abundance and a concomitant 3.3-fold increase in the percentage of transcripts detected. More specifically, 70% of the genome could be recovered by transcriptome sequencing compared to 21% in the total RNA. Sequencing of similar bacterial mRNA-enriched samples generated from Ehrlichia-infected canine cells covers 93% of the Ehrlichia genome, suggesting ubiquitous transcription across the entire Ehrlichia chaffeensis genome. This technique can potentially be used to enrich bacterial mRNA in many studies of host-microbe interactions. PMID:27713560

  1. Exploring bacterial community structure and function associated with atrazine biodegradation in repeatedly treated soils.

    PubMed

    Fang, Hua; Lian, Jianjun; Wang, Huifang; Cai, Lin; Yu, Yunlong

    2015-04-09

    Substantial application of the herbicide atrazine in agriculture leads to persistent contamination, which may damage the succeeding crops and pose potential threats to soil ecology and environmental health. Here, the degradation characteristics of atrazine and dynamic change of soil bacterial community structure and function as well as their relations were studied during three repeated treatments at the recommended, double, and five-fold doses. The results showed that the degradation half-life of atrazine obviously decreased with increased treatment frequency. Soil microbial functional diversity displayed a variation trend of suppression-recovery-stimulation, which was associated with increased degradation rate of atrazine. 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genus to potential atrazine degradation. A total of seven potentially atrazine-degrading bacterial genera were found including Nocardioides, Arthrobacter, Bradyrhizobium, Burkholderia, Methylobacterium, Mycobacterium, and Clostridium. These bacterial genera showed almost complete atrazine degradation pathways including dechlorination, dealkylation, hydroxylation, and ring cleavage. Furthermore, the relative abundance of four of them (i.e., Nocardioides, Arthrobacter, Methylobacterium, and Bradyrhizobium) increased with treatment frequency and atrazine concentration, suggesting that they may participate in atrazine degradation during repeated treatments. Our findings reveal the potential relationship between atrazine degradation and soil bacterial community structure in repeatedly treated soils. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Bacterial communities associated with Chenopodium album and Stellaria media seeds from arable soils.

    PubMed

    van Overbeek, Leonard S; Franke, Angelinus C; Nijhuis, Els H M; Groeneveld, Roel M W; da Rocha, Ulisses Nunes; Lotz, Lambertus A P

    2011-08-01

    The bacterial community compositions in Chenopodium album and Stellaria media seeds recovered from soil (soil weed seedbank), from bulk soil, and from seeds harvested from plants grown in the same soils were compared. It was hypothesized that bacterial communities in soil weed seedbanks are distinct from the ones present in bulk soils. For that purpose, bacterial polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints, made from DNA extracts of different soils and seed fractions, were analyzed by principal component analysis. Bacterial fingerprints from C. album and S. media seeds differed from each other and from soil. Further, it revealed that bacterial fingerprints from soil-recovered and plant-harvested seeds from the same species clustered together. Hence, it was concluded that microbial communities associated with seeds in soil mostly originated from the mother plant and not from soil. In addition, the results indicated that the presence of a weed seedbank in arable soils can increase soil microbial diversity. Thus, a change in species composition or size of the soil weed seedbank, for instance, as a result of a change in crop management, could affect soil microbial diversity. The consequence of increased diversity is yet unknown, but by virtue of identification of dominant bands in PCR-DGGE fingerprints as Lysobacter oryzae (among four other species), it became clear that bacteria potentially antagonizing phytopathogens dominate in C. album seeds in soil. The role of these potential antagonists on weed and crop plant growth was discussed.

  3. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    PubMed

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  4. Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota.

    PubMed

    Leiva, Diego; Clavero-León, Claudia; Carú, Margarita; Orlando, Julieta

    2016-11-01

    Definition of lichens has evolved from bi(tri)partite associations to multi-species symbioses, where bacteria would play essential roles. Besides, although soil bacterial communities are known to be affected by edaphic factors, when lichens grow upon them these could become less preponderant. We hypothesized that the structure of both the lichen microbiota and the microbiota in the soil underneath lichens is shaped by lichen intrinsic and extrinsic factors. In this work, intrinsic factors corresponded to mycobiont and cyanobiont identities of Peltigera lichens, metabolite diversity and phenoloxidase activity and extrinsic factors involved the site of the forest where lichens grow. Likewise, the genetic and metabolic structure of the lichen and soil bacterial communities were analyzed by fingerprinting. Among the results, metabolite diversity was inversely related to the genetic structure of bacterial communities of lichens and soils, highlighting the far-reaching effect of these substances; while phenoloxidase activity was inversely related to the metabolic structure only of the lichen bacterial microbiota, presuming a more limited effect of the products of these enzymes. Soil bacterial microbiota was different depending on the site and, strikingly, according to the cyanobiont present in the lichen over them, which could indicate an influence of the photobiont metabolism on the availability of soil nutrients. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Characterization of bacterial diversity associated with deep sea ferromanganese nodules from the South China Sea.

    PubMed

    Zhang, De-Chao; Liu, Yan-Xia; Li, Xin-Zheng

    2015-09-01

    Deep sea ferromanganese (FeMn) nodules contain metallic mineral resources and have great economic potential. In this study, a combination of culture-dependent and culture-independent (16S rRNA genes clone library and pyrosequencing) methods was used to investigate the bacterial diversity in FeMn nodules from Jiaolong Seamount, the South China Sea. Eleven bacterial strains including some moderate thermophiles were isolated. The majority of strains belonged to the phylum Proteobacteria; one isolate belonged to the phylum Firmicutes. A total of 259 near full-length bacterial 16S rRNA gene sequences in a clone library and 67,079 valid reads obtained using pyrosequencing indicated that members of the Gammaproteobacteria dominated, with the most abundant bacterial genera being Pseudomonas and Alteromonas. Sequence analysis indicated the presence of many organisms whose closest relatives are known manganese oxidizers, iron reducers, hydrogen-oxidizing bacteria and methylotrophs. This is the first reported investigation of bacterial diversity associated with deep sea FeMn nodules from the South China Sea.

  6. Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community.

    PubMed

    Brauer, Verena S; Stomp, Maayke; Bouvier, Thierry; Fouilland, Eric; Leboulanger, Christophe; Confurius-Guns, Veronique; Weissing, Franz J; Stal, LucasJ; Huisman, Jef

    2014-01-01

    N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N2-fixing cyanobacteria.

  7. Environmental heterogeneity and microbial inheritance influence sponge-associated bacterial composition of Spongia lamella.

    PubMed

    Noyer, Charlotte; Casamayor, Emilio O; Becerro, Mikel A

    2014-10-01

    Sponges are important components of marine benthic communities. High microbial abundance sponges host a large diversity of associated microbial assemblages. However, the dynamics of such assemblages are still poorly known. In this study, we investigated whether bacterial assemblages present in Spongia lamella remained constant or changed as a function of the environment and life cycle. Sponges were collected in multiple locations and at different times of the year in the western Mediterranean Sea and in nearby Atlantic Ocean to cover heterogeneous environmental variability. Co-occurring adult sponges and offsprings were compared at two of the sites. To explore the composition and abundance of the main bacteria present in the sponge mesohyl, embryos, and larvae, we applied both 16S rRNA gene-denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands and quantitative polymerase chain reactions (qPCR). On average, the overall core bacterial assemblage showed over 60 % similarity. The associated bacterial assemblage fingerprints varied both within and between sponge populations, and the abundance of specific bacterial taxa assessed by qPCR significantly differed among sponge populations and between adult sponge and offsprings (higher proportions of Actinobacteria in the latter). Sequences showed between 92 and 100 % identity to sequences previously reported in GenBank, and all were affiliated with uncultured invertebrate bacterial symbionts (mainly sponges). Sequences were mainly related to Chloroflexi and Acidobacteria and a few to Actinobacteria and Bacteroidetes. Additional populations may have been present under detection limits. Overall, these results support that both ecological and biological sponge features may shape the composition of endobiont bacterial communities in S. lamella.

  8. The Effect of Antibiotics on Associated Bacterial Community of Stored Product Mites

    PubMed Central

    Kopecky, Jan; Nesvorna, Marta; Mareckova-Sagova, Marketa; Hubert, Jan

    2014-01-01

    Background Bacteria are associated with the gut, fat bodies and reproductive organs of stored product mites (Acari: Astigmata). The mites are pests due to the production of allergens. Addition of antibiotics to diets can help to characterize the association between mites and bacteria. Methodology and Principal Findings Ampicillin, neomycin and streptomycin were added to the diets of mites and the effects on mite population growth (Acarus siro, Lepidoglyphus destructor and Tyrophagus putrescentiae) and associated bacterial community structure were assessed. Mites were treated by antibiotic supplementation (1 mgg−1 of diet) for 21 days and numbers of mites and bacterial communities were analyzed and compared to the untreated control. Bacterial quantities, determined by real-time PCR, significantly decreased in antibiotic treated specimens from 5 to 30 times in A. siro and T. putrescentiae, while no decline was observed in L. destructor. Streptomycin treatment eliminated Bartonella-like bacteria in the both A. siro and T. putrescentiae and Cardinium in T. putrescentiae. Solitalea-like bacteria proportion increased in the communities of neomycin and streptomycin treated A. siro specimens. Kocuria proportion increased in the bacterial communities of ampicillin and streptomycin treated A. siro and neomycin and streptomycin treated L. destructor. Conclusions/Significance The work demonstrated the changes of mite associated bacterial community under antibiotic pressure in pests of medical importance. Pre-treatment of mites by 1 mgg−1 antibiotic diets improved mite fitness as indicated accelerated population growth of A. siro pretreated streptomycin and neomycin and L. destructor pretreated by neomycin. All tested antibiotics supplemented to diets caused the decrease of mite growth rate in comparison to the control diet. PMID:25387104

  9. Use of quantitative 16S ribosomal DNA detection for diagnosis of central vascular catheter-associated bacterial infection.

    PubMed

    Warwick, S; Wilks, M; Hennessy, E; Powell-Tuck, J; Small, M; Sharp, J; Millar, M R

    2004-04-01

    Many central vascular catheters (CVCs) are removed unnecessarily because current diagnostic methods for CVC-associated infection are unreliable. A quantitative PCR assay using primers and probe targeted to bacterial 16S ribosomal DNA was used to measure the levels of bacterial DNA in blood samples drawn through the CVC in a population of patients receiving intravenous nutrition. Bacterial DNA concentrations were raised in 16 of 16 blood samples taken during episodes of probable bacterial CVC-associated infection. Bacterial DNA concentrations were raised in 4 of 29 episodes in which bacterial CVC-associated infection was unlikely. The use of this technique has the potential to substantially reduce the unnecessary removal of CVCs.

  10. Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms.

    PubMed

    Landa, Marine; Blain, Stéphane; Christaki, Urania; Monchy, Sébastien; Obernosterer, Ingrid

    2016-01-01

    Marine microbes have a pivotal role in the marine biogeochemical cycle of carbon, because they regulate the turnover of dissolved organic matter (DOM), one of the largest carbon reservoirs on Earth. Microbial communities and DOM are both highly diverse components of the ocean system, yet the role of microbial diversity for carbon processing remains thus far poorly understood. We report here results from an exploration of a mosaic of phytoplankton blooms induced by large-scale natural iron fertilization in the Southern Ocean. We show that in this unique ecosystem where concentrations of DOM are lowest in the global ocean, a patchwork of blooms is associated with diverse and distinct bacterial communities. By using on-board continuous cultures, we identify preferences in the degradation of DOM of different reactivity for taxa associated with contrasting blooms. We used the spatial and temporal variability provided by this natural laboratory to demonstrate that the magnitude of bacterial production is linked to the extent of compositional changes. Our results suggest that partitioning of the DOM resource could be a mechanism that structures bacterial communities with a positive feedback on carbon cycling. Our study, focused on bacterial carbon processing, highlights the potential role of diversity as a driving force for the cycling of biogeochemical elements.

  11. Novel diversity of bacterial communities associated with bottlenose dolphin upper respiratory tracts.

    PubMed

    Johnson, Wesley R; Torralba, Manolito; Fair, Patricia A; Bossart, Gregory D; Nelson, Karen E; Morris, Pamela J

    2009-12-01

    Respiratory illness is thought to be most the common cause of death in both wild and captive populations of bottlenose dolphins (Tursiops truncatus). The suspected pathogens that have been isolated from diseased animals have also been isolated from healthy individuals, suggesting they may be part of the normal flora. Our current understanding of the bacteria associated with the upper respiratory tract (URT) of bottlenose dolphins is based exclusively upon culture-based isolation and identification. Because < 1% of naturally occurring bacteria are culturable, a substantial fraction of the bacterial community associated with the dolphin URT remains to be described. The dolphin URT microbiota revealed by sequencing of bacterial 16S rDNA exhibits almost no overlap with the taxa indicated in culture-based studies. The most abundant sequences in our libraries were similar among all of our study animals and shared the greatest homology to sequences of bacteria belonging to the genera Cardiobacterium, Suttonella, Psychrobacter, Tenacibaculum, Fluviicola and Flavobacterium; however, they were sufficiently different from database sequences from both cultured and uncultured organisms to suggest they represent novel genera and species. Our findings also demonstrate the dominance of three of the four bacterial phyla that dominate other mammalian microbiomes, including those of humans, and show tremendous diversity at the species/strain level, suggesting tight coevolution of the dolphin host and its URT bacterial community.

  12. Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico.

    PubMed

    Neria-González, Isabel; Wang, En Tao; Ramírez, Florina; Romero, Juan M; Hernández-Rodríguez, César

    2006-06-01

    Microbial communities associated to biofilms promote corrosion of oil pipelines. The community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. To assess bacterial diversity, biofilm samples were obtained from X52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. The biofilm samples were directly used to extract metagenomic DNA, which was used as template to amplify 16S ribosomal gene by PCR. The PCR products of 16S ribosomal gene were also employed as template for sulfate-reducing bacteria (SRB) specific nested-PCR and both PCR products were utilized for the construction of gene libraries. The V3 region of the 16S rRNA gene was also amplified to analyse the bacterial diversity by analysis of denaturing gradient gel electrophoresis (DGGE). Ribosomal library and DGGE profiles exhibited limited bacterial diversity, basically including Citrobacter spp., Enterobacter spp. and Halanaerobium spp. while Desulfovibrio alaskensis and a novel clade within the genus Desulfonatronovibrio were detected from the nested PCR library. The biofilm samples were also taken for the isolation of SRB. Desulfovibrio alaskensis and Desulfovibrio capillatus, as well as some strains related to Citrobacter were isolated. SRB consists in a very small proportion of the community and Desulfovibrio spp. were the relatively abundant groups among the SRB. This is the first study directly exploring bacterial diversity in corrosive biofilms associated to steel pipelines subjected to normal operation conditions.

  13. Bacterial community structures associated with a natural spring phytoplankton bloom in the Yellow Sea, China

    NASA Astrophysics Data System (ADS)

    Liu, Min; Xiao, Tian; Sun, Jun; Wei, Hao; Wu, Ying; Zhao, Yuan; Zhang, Wuchang

    2013-12-01

    Bacterial community structures associated with a spring phytoplankton bloom were investigated using denaturing gradient gel electrophoresis (DGGE) and 16S rDNA clone libraries. Statistical and phylogenetic analyses applied on both molecular methods revealed differences in bacterial community composition between the bloom station and post-bloom station, as well as between two bloom stages (bloom- and decay-) at bloom station. At the class level, the bacterial community at the bloom station was dominated by Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, whereas Alphaproteobacteria and Gammaproteobacteria were dominant at the post-bloom station. At order level, no obvious predominant subgroup was found at the post-bloom station. In contrast, predominant subgroups were observed in bloom samples and they changed over the course of bloom. Rhodobacterales (mainly Roseobacter) and Flavobacteriales (mainly Flavobacterium) were the predominant subgroups in the bloom period, whereas Roseobacter became the unique predominant subgroup in the decay-bloom period. Rhodobacterales and Flavobacteriales, which were dominant in the bloom-associated bacterial communities in the Yellow Sea, were also reported as dominant during bloom conditions in other ocean regions, suggesting that they play an important role in bloom events.

  14. [Ozonotherapy as an efficient component of the combined treatment of the patients presenting with bacterial vaginosis].

    PubMed

    Yarustovskaya, O V; Kulikov, A G; Shtro, L P

    2015-01-01

    The objective of the present study was to evaluate the effectiveness of the combined treatment of the patients suffering from bacterial vaginosis using various methods of ozone therapy. The comprehensive clinical and laboratory examination and treatment involved 102 patients of the child-bearing age divided into 3 groups, matched for the age and the main clinical manifestations of the disease. All the patients comprising group IlIl received basic therapy alone while the treatment of the patients of group I consisted of local ozone therapy and that of the patients of group 11 of the combination of local and general ozone therapy. The study has demonstrated the enhanced effectiveness of the combined local and general ozone therapy compared with the two other modalities and the feasibility of its application for the treatment of the patients presenting with bacterial vaginosis.

  15. Surface activation of graphene oxide nanosheets by ultraviolet irradiation for highly efficient anti-bacterials

    NASA Astrophysics Data System (ADS)

    Veerapandian, Murugan; Zhang, Linghe; Krishnamoorthy, Karthikeyan; Yun, Kyusik

    2013-10-01

    A comprehensive investigation of anti-bacterial properties of graphene oxide (GO) and ultraviolet (UV) irradiated GO nanosheets was carried out. Microscopic characterization revealed that the GO nanosheet-like structures had wavy features and wrinkles or thin grooves. Fundamental surface chemical states of GO nanosheets (before and after UV irradiation) were investigated using x-ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy. Minimum inhibitory concentration (MIC) results revealed that UV irradiated GO nanosheets have more pronounced anti-bacterial behavior than GO nanosheets and standard antibiotic, kanamycin. The MIC of UV irradiated GO nanosheets was 0.125 μg ml-1 for Escherichia coli and Salmonella typhimurium, 0.25 μg ml-1 for Bacillus subtilis and 0.5 μg ml-1 for Enterococcus faecalis, ensuring its potential as an anti-infective agent for controlling the growth of pathogenic bacteria. The minimum bactericidal concentration of normal GO nanosheets was determined to be two-fold higher than its corresponding MIC value, indicating promising bactericidal activity. The mechanism of anti-bacterial action was evaluated by measuring the enzymatic activity of β-d-galactosidase for the hydrolysis of o-nitrophenol-β-d-galactopyranoside.

  16. Transient Shifts in Bacterial Communities Associated with the Temperate Gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea

    PubMed Central

    La Rivière, Marie; Roumagnac, Marie; Garrabou, Joaquim; Bally, Marc

    2013-01-01

    Background Bacterial communities that are associated with tropical reef-forming corals are being increasingly recognized for their role in host physiology and health. However, little is known about the microbial diversity of the communities associated with temperate gorgonian corals, even though these communities are key structural components of the ecosystem. In the Northwestern Mediterranean Sea, gorgonians undergo recurrent mass mortalities, but the potential relationship between these events and the structure of the associated bacterial communities remains unexplored. Because microbial assemblages may contribute to the overall health and disease resistance of their host, a detailed baseline of the associated bacterial diversity is required to better understand the functioning of the gorgonian holobiont. Methodology/Principal Findings The bacterial diversity associated with the gorgonian Paramuricea clavata was determined using denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism and the construction of clone libraries of the bacterial 16S ribosomal DNA. Three study sites were monitored for 4 years to assess the variability of communities associated with healthy colonies. Bacterial assemblages were highly dominated by one Hahellaceae-related ribotype and exhibited low diversity. While this pattern was mostly conserved through space and time, in summer 2007, a deep shift in microbiota structure toward increased bacterial diversity and the transient disappearance of Hahellaceae was observed. Conclusion/Significance This is the first spatiotemporal study to investigate the bacterial diversity associated with a temperate shallow gorgonian. Our data revealed an established relationship between P. clavata and a specific bacterial group within the Oceanospirillales. These results suggest a potential symbiotic role of Hahellaceae in the host-microbe association, as recently suggested for tropical corals. However, a transient

  17. Transient shifts in bacterial communities associated with the temperate gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea.

    PubMed

    La Rivière, Marie; Roumagnac, Marie; Garrabou, Joaquim; Bally, Marc

    2013-01-01

    Bacterial communities that are associated with tropical reef-forming corals are being increasingly recognized for their role in host physiology and health. However, little is known about the microbial diversity of the communities associated with temperate gorgonian corals, even though these communities are key structural components of the ecosystem. In the Northwestern Mediterranean Sea, gorgonians undergo recurrent mass mortalities, but the potential relationship between these events and the structure of the associated bacterial communities remains unexplored. Because microbial assemblages may contribute to the overall health and disease resistance of their host, a detailed baseline of the associated bacterial diversity is required to better understand the functioning of the gorgonian holobiont. The bacterial diversity associated with the gorgonian Paramuricea clavata was determined using denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism and the construction of clone libraries of the bacterial 16S ribosomal DNA. Three study sites were monitored for 4 years to assess the variability of communities associated with healthy colonies. Bacterial assemblages were highly dominated by one Hahellaceae-related ribotype and exhibited low diversity. While this pattern was mostly conserved through space and time, in summer 2007, a deep shift in microbiota structure toward increased bacterial diversity and the transient disappearance of Hahellaceae was observed. This is the first spatiotemporal study to investigate the bacterial diversity associated with a temperate shallow gorgonian. Our data revealed an established relationship between P. clavata and a specific bacterial group within the Oceanospirillales. These results suggest a potential symbiotic role of Hahellaceae in the host-microbe association, as recently suggested for tropical corals. However, a transient imbalance in bacterial associations can be tolerated by the holobiont

  18. Efficient bacterial inactivation in aqueous solution by low-temperature atmospheric pressure plasma application with a reduction of the solution pH

    NASA Astrophysics Data System (ADS)

    Kitano, Katsuhisa; Ikawa, Satoshi; Tani, Atsushi; Ohnishi, Naofumi; Hamaguchi, Satoshi

    2009-10-01

    With some medical applications in mind, bacterial inactivation experiments in aqueous solution have been performed with the use of low-temperature atmospheric pressure plasmas. We have successfully found that efficient bactericidal activity can be achieved if the solution is sufficiently acidic. It is interesting to note that there is a critical pH value of about 4.7 for the bactericidal effects, below which the bacteria are efficiently inactivated and above which the bacteria are hardly affected by the plasma application. When the plasmas were exposed to E. coli suspensions at pH 5.2, 4.7, 4.2 and 3.7, D values were found to be 1.92, 0.96, 0.59, and 0.21 min., respectively, under our experimental conditions. It has been also found experimentally that the presence of superoxide anion radicals O2^-in the solution is essential for bacterial inactivation by the plasma application. The critical pH value may be associated with pKa of the dissociation equilibrium between O2^-and hydroperoxy radicals HOO,hich is known to be approximately 4.8. The formation of radicals in solution by such plasma has been confirmed from ESR (Electron Spin Resonance) with spin trapping agents. The ambient gas has been found to influence the radical formation in liquid significantly.

  19. The first picoseconds in bacterial photosynthesis--ultrafast electron transfer for the efficient conversion of light energy.

    PubMed

    Zinth, Wolfgang; Wachtveitl, Josef

    2005-05-01

    In this Minireview, we describe the function of the bacterial reaction centre (RC) as the central photosynthetic energy-conversion unit by ultrafast spectroscopy combined with structural analysis, site-directed mutagenesis, pigment exchange and theoretical modelling. We show that primary energy conversion is a stepwise process in which an electron is transferred via neighbouring chromophores of the RC. A well-defined chromophore arrangement in a rigid protein matrix, combined with optimised energetics of the different electron carriers, allows a highly efficient charge-separation process. The individual molecular reactions at room temperature are well described by conventional electron-transfer theory.

  20. Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study.

    PubMed

    Wu, Tao; Zhang, Zhigang; Liu, Bin; Hou, Dezhi; Liang, Yun; Zhang, Jie; Shi, Peng

    2013-10-01

    Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gallstone patients as well as the gut of 38 normal individuals, examining and analyzing some 299, 217 bacterial 16S rRNA gene sequences from 120 samples. First, as compared with normal individuals, in gallstone patients there were significant (P < 0.001) increases of gut bacterial phylum Proteobacteria and decreases of three gut bacterial genera, Faecalibacterium, Lachnospira, and Roseburia. Second, about 70% of gut bacterial operational taxonomic units (OTUs) from gallstone patients were detectable in the biliary tract and bacteria diversity of biliary tract was significantly (P < 0.001) higher than that of gut. Third, analysis of the biliary tract core microbiome (represented by 106 bacteria OTUs) among gallstone patients showed that 33.96% (36/106) of constituents can be matched to known bacterial species (15 of which have publicly available genomes). A genome-wide search of MDR, BSH, bG, and phL genes purpotedly associated with the formation of cholesterol gallstones showed that all 15 species with known genomes (e.g., Propionibacterium acnes, Bacteroides vulgates, and Pseudomonas putida) contained at least contained one of the four genes. This finding could potentially provide underlying information needed to explain the association between biliary tract microbiota and the formation of cholesterol gallstones. To the best of our knowledge, this is the first study to discover gut microbiota dysbiosis among gallstone patients, the presence of which may be a key contributor to the complex bacteria community assembly linked with the presence of cholesterol gallstones. Likewise, this study also provides the first large-scale glimpse of biliary tract microbiota

  1. Efficient Gene Editing in Pluripotent Stem Cells by Bacterial Injection of Transcription Activator-Like Effector Nuclease Proteins

    PubMed Central

    Jia, Jingyue; Bai, Fang; Jin, Yongxin; Santostefano, Katherine E.; Ha, Un-Hwan; Wu, Donghai

    2015-01-01

    The type III secretion system (T3SS) of Pseudomonas aeruginosa is a powerful tool for direct protein delivery into mammalian cells and has successfully been used to deliver various exogenous proteins into mammalian cells. In the present study, transcription activator-like effector nuclease (TALEN) proteins have been efficiently delivered using the P. aeruginosa T3SS into mouse embryonic stem cells (mESCs), human ESCs (hESCs), and human induced pluripotent stem cells (hiPSCs) for genome editing. This bacterial delivery system offers an alternative method of TALEN delivery that is highly efficient in cleavage of the chromosomal target and presumably safer by avoiding plasmid DNA introduction. We combined the method of bacterial T3SS-mediated TALEN protein injection and transfection of an oligonucleotide template to effectively generate precise genetic modifications in the stem cells. Initially, we efficiently edited a single-base in the gfp gene of a mESC line to silence green fluorescent protein (GFP) production. The resulting GFP-negative mESC was cloned from a single cell and subsequently mutated back to a GFP-positive mESC line. Using the same approach, the gfp gene was also effectively knocked out in hESCs. In addition, a defined single-base edition was effectively introduced into the X-chromosome-linked HPRT1 gene in hiPSCs, generating an in vitro model of Lesch-Nyhan syndrome. T3SS-mediated TALEN protein delivery provides a highly efficient alternative for introducing precise gene editing within pluripotent stem cells for the purpose of disease genotype-phenotype relationship studies and cellular replacement therapies. Significance The present study describes a novel and powerful tool for the delivery of the genome editing enzyme transcription activator-like effector nuclease (TALEN) directly into pluripotent stem cells (PSCs), achieving desired base changes on the genomes of PSCs with high efficiency. This novel approach uses bacteria as a protein delivery

  2. Identification of bacterial endophytes associated with traditional medicinal plant Tridax procumbens Linn.

    PubMed

    Preveena, Jagadesan; Bhore, Subhash J

    2013-01-01

    In traditional medicine, Tridax procumbens Linn. is used in the treatment of injuries and wounds. The bacterial endophytes (BEs) of medicinal plants could produce medicinally important metabolites found in their hosts; and hence, the involvement of BEs in conferring wound healing properties to T. Procumbens cannot be ruled out. But, we do not know which types of BEs are associated with T. Procumbens. The objective of this study was to investigate the fast growing and cultivable BEs associated with T. procumbens. Leaves and stems of healthy T. Procumbens plants were collected and cultivable BEs were isolated from surface-sterilized leaf and stem tissue samples using Luria-Bertani (LB) agar (medium) at standard conditions. A polymerase chain reaction was employed to amplify 16S rRNA coding gene fragments from the isolates. Cultivable endophytic bacterial isolates (EBIs) were identified using 16S rRNA gene nucleotide sequence similarity based method of bacterial identification. Altogether, 50 culturable EBIs were isolated. 16S rRNA gene nucleotide sequences analysis using the Basic Local Alignment Search Tool (BLAST) revealed identities of the EBIs. Analysis reveals that cultivable Bacillus spp., Cronobacter sakazakii, Enterobacter spp., Lysinibacillus sphaericus, Pantoea spp., Pseudomonas spp. and Terribacillus saccharophilus are associated with T. Procumbens. Based on the results, we conclude that 24 different types of culturable BEs are associated with traditionally used medicinal plant, T. Procumbens, and require further study.

  3. Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession

    PubMed Central

    Wang, Miao; Yang, Pu; Falcão Salles, Joana

    2016-01-01

    Proper quantification of the relative influence of soil and plant host on the root-associated microbiome can only be achieved by studying its distribution along an environmental gradient. Here, we used an undisturbed salt marsh chronosequence to study the bacterial communities associated with the soil, rhizosphere and the root endopshere of Limonium vulgare using 454-pyrosequencing. We hypothesize that the selective force exerted by plants rather than soil would regulate the dynamics of the root-associated bacterial assembly along the chronosequence. Our results showed that the soil and rhizosphere bacterial communities were phylogenetically more diverse than those in the endosphere. Moreover, the diversity of the rhizosphere microbiome followed the increased complexity of the abiotic and biotic factors during succession while remaining constant in the other microbiomes. Multivariate analyses showed that the rhizosphere and soil-associated communities clustered by successional stages, whereas the endosphere communities were dispersed. Interestingly, the endosphere microbiome showed higher turnover, while the bulk and rhizosphere soil microbiomes became more similar at the end of the succession. Overall, we showed that soil characteristics exerted an overriding influence on the rhizosphere microbiome, although plant effect led to a clear diversity pattern along the succession. Conversely, the endosphere microbiome was barely affected by any of the environmental measurements and very distinct from other communities. PMID:26779222

  4. Association of Healthy Eating, Juice Consumption, and Bacterial Counts with Early Childhood Caries.

    PubMed

    AbdelAziz, Wafaa E; Dowidar, Karin M L; El Tantawi, Maha M A

    2015-01-01

    To investigate the association of healthy diet, snacking, and bacterial count with early childhood caries in a group of preschool children in Alexandria, Egypt. Sixty preschoolers were divided into three groups: (1) caries-free children; (2) children with early childhood caries (ECC); and (3) children with severe early childhood caries (S-ECC). Saliva was cultured to determine bacterial counts. A questionnaire collected information about background, oral health practices, and snacking habits. A 24-hour food recall form assessed dietary intake and was analyzed using the Health Eating Index 2005. Compared to caries-free children, children with ECC and S-ECC had significantly lower odds of drinking juices (odds ratio equals 0.10 and 0.02). Caries-free children had significantly higher Healthy Eating Index values than children with ECC and S-ECC (P=0.003 and P<0.0001). Total streptococci and Streptococcus mutans counts were significantly higher in children with ECC and S-ECC (P<0.0001 for all), whereas Streptococcus sanguis counts were lower (P=0.04 and P=0.01). Drinking juices was associated with less early childhood caries and severe early childhood caries among preschoolers. Snacking on sweets was associated with more S-ECC. Healthy eating, brushing, and bacterial counts were not significantly associated with ECC or S-ECC in multivariate regression.

  5. HIV-Enhancing Factors Are Secreted by Reproductive Epithelia upon Inoculation with Bacterial Vaginosis-Associated Bacteria.

    PubMed

    Eade, Colleen R; Diaz, Camila; Chen, Sixue; Cole, Amy L; Cole, Alexander M

    2015-01-01

    Bacterial vaginosis is a common reproductive infection in which commensal vaginal lactobacilli are displaced by a mixed population of pathogenic bacteria. Bacterial vaginosis increases susceptibility to HIV, and it has been suggested that host innate immune responses to pathogenic bacteria contribute to enhanced infection, yet the cellular mechanisms mediating the increased HIV susceptibility remain uncharacterized. We evaluated the HIV-enhancing effects of bacterial vaginosis by inoculating endocervical epithelia with Atopobium vaginae, a bacterial vaginosis-associated bacteria, and assaying secreted factors for HIV-enhancing activity. When epithelia and A. vaginae were cocultured, we observed increased HIV-enhancing activity mediated by secreted low molecular weight factors. From this complex mixture we identified several upregulated host proteins, which functioned in combination to enhance HIV infection. These studies suggest that the host immune response to bacterial vaginosis-associated bacteria results in the release of HIV-enhancing factors. The combined activity of bacterial vaginosis-induced proteins likely mediates HIV enhancement.

  6. Tolerance to lipopolysaccharide promotes an enhanced neutrophil extracellular traps formation leading to a more efficient bacterial clearance in mice

    PubMed Central

    Landoni, V I; Chiarella, P; Martire-Greco, D; Schierloh, P; van-Rooijen, N; Rearte, B; Palermo, M S; Isturiz, M A; Fernández, G C

    2012-01-01

    Tolerance to lipopolysaccharide (LPS) constitutes a stress adaptation, in which a primary contact with LPS results in a minimal response when a second exposure with the same stimulus occurs. However, active important defence mechanisms are mounted during the tolerant state. Our aim was to assess the contribution of polymorphonuclear neutrophils (PMN) in the clearance of bacterial infection in a mouse model of tolerance to LPS. After tolerance was developed, we investigated in vivo different mechanisms of bacterial clearance. The elimination of a locally induced polymicrobial challenge was more efficient in tolerant mice both in the presence or absence of local macrophages. This was related to a higher number of PMN migrating to the infectious site as a result of an increased number of PMN from the marginal pool with higher chemotactic capacity, not because of differences in their phagocytic activity or reactive species production. In vivo, neutrophils extracellular trap (NET) destruction by nuclease treatment abolished the observed increased clearance in tolerant but not in control mice. In line with this finding, in vitro NETs formation was higher in PMN from tolerant animals. These results indicate that the higher chemotactic response from an increased PMN marginal pool and the NETs enhanced forming capacity are the main mechanisms mediating bacterial clearance in tolerant mice. To sum up, far from being a lack of response, tolerance to LPS causes PMN priming effects which favour distant and local anti-infectious responses. PMID:22385250

  7. Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage.

    PubMed

    Esposito-Polesi, Natalia Pimentel; de Andrade, Pedro Avelino Maia; de Almeida, Cristina Vieira; Andreote, Fernando Dini; de Almeida, Marcílio

    2015-11-01

    Micropropagation has been applied in the recovery and rejuvenation of adult trees, which is achieved by various subcultures in the multiplication phase. This strategy has brought questions about the endophytic microbiota associated with these plants along its manipulation. Therefore, the aim of this study was to evaluate the composition of the endophytic bacterial communities associated with two explants sources [the canopy branches (CB) and the trunk base of the tree (TB)] under prolonged in vitro cultivation. In addition we analyzed the bacterial community dynamic along the subcultures in different micropropagation phases. Bacterial DNA was extracted from samples of mini-stumps (in vivo) from CB and TB and in micro-stumps produced by in vitro cultivations of these explants sources--both originated from one single matrix plant of Eucalyptus benthamii. In vitro establishment occurred in two dates and the evaluation of endophytic bacterial communities was made in vivo and in vitro samples (on 10th, 13th and 16th subcultures), when elongated shoots and roots were analyzed. Analysis was performed by PCR-DGGE based on the V6 region of ribosomal gene 16S rDNA. Bands profiles showed differences in communities between in vivo and in vitro samples, and also distinctions of communities assessed in the subcultures, elongated and rooted samples. Distinctions in the composition of endophytic bacterial communities were greater in CB micro-stumps. These results indicate a differential colonization of explants by endophytic bacteria, with predominance of common (ever-present) endophytes in TB samples and casual, here named opportunistic, in CB samples.

  8. Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis.

    PubMed

    Fredricks, David N; Fiedler, Tina L; Thomas, Katherine K; Oakley, Brian B; Marrazzo, Jeanne M

    2007-10-01

    Several novel bacterial species have been detected in subjects with bacterial vaginosis (BV) by using broad-range PCR assays, but this approach is insensitive for detecting minority species. We developed a series of taxon-directed 16S rRNA gene PCR assays for more sensitive detection of key vaginal bacteria. We sought to determine the prevalence of each species in the vagina, its association with BV, and the utility of PCR for the microbiological diagnosis of BV. Targeted PCR assays were developed for 17 vaginal bacterial species and applied to 264 vaginal-fluid samples from 81 subjects with and 183 subjects without BV. The results were compared to those of two widely accepted methods for diagnosing BV, the use of clinical findings (Amsel criteria) and the interpretation of vaginal-fluid Gram stains (Nugent criteria). Leptotrichia/Sneathia, Atopobium vaginae, an Eggerthella-like bacterium, Megasphaera species, and three novel bacteria in the order Clostridiales are among the bacterial species significantly associated with BV. PCR detection of either a Megasphaera species or one of the Clostridiales bacteria yielded a sensitivity of 99% and a specificity of 89% for diagnosis of BV compared to the Amsel clinical criteria and a sensitivity of 95.9% and a specificity of 93.7% compared to the Nugent criteria (Gram stain). PCR detection of one or more fastidious bacterial species is a more reliable indicator of BV than detection of bacteria, such as Gardnerella vaginalis, previously linked to BV, highlighting the potential of PCR for the diagnosis of BV.

  9. Targeted PCR for Detection of Vaginal Bacteria Associated with Bacterial Vaginosis▿

    PubMed Central

    Fredricks, David N.; Fiedler, Tina L.; Thomas, Katherine K.; Oakley, Brian B.; Marrazzo, Jeanne M.

    2007-01-01

    Several novel bacterial species have been detected in subjects with bacterial vaginosis (BV) by using broad-range PCR assays, but this approach is insensitive for detecting minority species. We developed a series of taxon-directed 16S rRNA gene PCR assays for more sensitive detection of key vaginal bacteria. We sought to determine the prevalence of each species in the vagina, its association with BV, and the utility of PCR for the microbiological diagnosis of BV. Targeted PCR assays were developed for 17 vaginal bacterial species and applied to 264 vaginal-fluid samples from 81 subjects with and 183 subjects without BV. The results were compared to those of two widely accepted methods for diagnosing BV, the use of clinical findings (Amsel criteria) and the interpretation of vaginal-fluid Gram stains (Nugent criteria). Leptotrichia/Sneathia, Atopobium vaginae, an Eggerthella-like bacterium, Megasphaera species, and three novel bacteria in the order Clostridiales are among the bacterial species significantly associated with BV. PCR detection of either a Megasphaera species or one of the Clostridiales bacteria yielded a sensitivity of 99% and a specificity of 89% for diagnosis of BV compared to the Amsel clinical criteria and a sensitivity of 95.9% and a specificity of 93.7% compared to the Nugent criteria (Gram stain). PCR detection of one or more fastidious bacterial species is a more reliable indicator of BV than detection of bacteria, such as Gardnerella vaginalis, previously linked to BV, highlighting the potential of PCR for the diagnosis of BV. PMID:17687006

  10. Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls.

    PubMed

    Pop Ristova, Petra; Bienhold, Christina; Wenzhöfer, Frank; Rossel, Pamela E; Boetius, Antje

    2017-01-01

    Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y) on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100-1700 m), but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were found at any time on

  11. Positive and negative bacterial associations involving Dialister pneumosintes in primary endodontic infections.

    PubMed

    Siqueira, José F Júnior; Rôças, Isabela N

    2003-07-01

    Dialister pneumosintes is an anaerobic Gram-negative rod that has been recently implicated as a candidate endodontic pathogen. In this study, samples taken from abscessed teeth and infected root canals associated with asymptomatic or symptomatic periradicular lesions were examined for the occurrence of bacterial associations involving D. pneumosintes. DNA was extracted from the samples, and the presence of D. pneumosintes and 16 other bacterial species was determined by means of species-specific nested polymerase chain reaction. Positive and negative associations involving D. pneumosintes were investigated by computing the odds ratio of D. pneumosintes being found in a sample from endodontic infection in co-infection with one of the other target species. The association between the pairs containing D. pneumosintes and the occurrence of pain also was evaluated. D. pneumosintes was always detected in mixed infections with at least two of the other target species. D. pneumosintes was positively associated with Treponema denticola, Porphyromonas endodontalis, Fusobacterium nucleatum, Peptostreptococcus micros, Campylobacter rectus, Prevotella intermedia, T. pectinovorum, and T. vincentii. Negative associations were observed with Bacteroides forsythus, P. gingivalis, and Actinomyces israelii. No pair containing D. pneumosintes was found to be significantly associated with symptomatic cases (p > 0.01). The findings of this study lend considerable support to the notion of D. pneumosintes being an important endodontic pathogen, usually in a mixed infection. Positive associations of this species with other highly prevalent species, such as T. denticola and P. endodontalis, suggest that bacterial synergism can occur and thereby play an important role in the pathogenesis of different forms of periradicular lesions.

  12. Plant and soil effects on bacterial communities associated with Miscanthus  ×  giganteus rhizosphere and rhizomes

    DOE PAGES

    Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

    2015-02-11

    Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

  13. Efficiency of ciprofloxacin for bacterial control, post-thaw quality, and in vivo fertility of buffalo spermatozoa.

    PubMed

    Akhter, S; Ansari, M S; Rakha, B A; Andrabi, S M H; Qadeer, S; Iqbal, R; Ullah, N

    2013-09-01

    Ciprofloxacin (CP) was evaluated for bacterial control, post-thaw quality, and fertility of buffalo semen. Pseudomonas aeruginosa, Escherichia coli, Proteus sp., Corynebacterium sp., Micrococcus sp., and Staphylococcus sp. were isolated from buffalo semen. Pseudomonas aeruginosa, Corynebacterium sp., and Micrococcus sp. were resistant to streptomycin, whereas P. aeruginosa and Proteus sp. were resistant to penicillin. All bacteria were susceptible to CP. In vitro dose toxicity was assessed in sodium citrate buffer containing 0, 200 to 2000 μg/mL of CP. CP up to 1000 μg/mL was found nontoxic to motility and viability of buffalo sperm. For post-thaw quality, buffalo semen was frozen in Tris-citric acid extender containing streptomycin-penicillin (SP; 1000 μg/mL-1000 IU/mL) or CP 600 μg/mL and was assessed for total aerobic bacterial count (post-thaw), motility, plasma membrane integrity, viability at 0, 2, and 4 hours post-thaw. At 4 hours post-thaw, plasma membrane integrity (%) was higher (P < 0.05) in extender containing CP than SP. Total aerobic bacterial count was 0.00 in extender containing CP compared with 0.07 × 10(4) cfu/mL with SP. To assess the in vivo fertility rate, semen (two bulls) frozen in Tris-citric acid extender containing SP or CP was used to inseminate, and 400 inseminations (200/group) were recorded. Higher (P ≤ 0.05) fertility rate was recorded with CP (55%) compared with SP (41%). In conclusion, use of CP in extender was efficient to control the bacterial contamination without compromising the post-thaw quality and fertility of cryopreserved water buffalo bull semen. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. Selection and breeding of corn to enhance associative bacterial nitrogen fixation

    SciTech Connect

    Ela, S.W.; Anderson, M.A.; Brill, W.J.

    1980-01-01

    We have increased, through screening and breeding, the ability of corn (maize, Zea mays L.) to support bacterial nitrogen fixation in or on corn roots. Isotopic N fixed from /sup 15/N/sub 2/ was found on the roots. Even though the nitrogen-fixing association depends on germ plasm from tropical corn, the activity can be bred into corn currently used in midwestern United States agriculture.

  15. Draft Genome Sequence of Gardnerella vaginalis Strain ATCC 49145 Associated with Bacterial Vaginosis.

    PubMed

    Kidane, Destaalem T; Arivett, Brock A; Crigler, Jacob; Vick, Eric J; Farone, Anthony L; Farone, Mary B

    2017-05-04

    Gardnerella vaginalis is a Gram-variable bacterium associated with bacterial vaginosis, a common vaginal inflammation in women of reproductive age. This study reports the whole-genome sequencing for the clinical isolate strain ATCC 49145. The draft genome is composed of 21 contigs containing 1,325 protein-coding sequences, 45 tRNAs and a single tmRNA (SsrA). Copyright © 2017 Kidane et al.

  16. Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables

    PubMed Central

    2013-01-01

    Background Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Results Total culturable bacteria on salad vegetables ranged from 8.0 × 103 to 5.5 × 108 CFU g-1. The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 103 to 5.8 × 105 CFU g-1. Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by

  17. Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables.

    PubMed

    Jackson, Colin R; Randolph, Kevin C; Osborn, Shelly L; Tyler, Heather L

    2013-12-01

    Plants harbor a diverse bacterial community, both as epiphytes on the plant surface and as endophytes within plant tissue. While some plant-associated bacteria act as plant pathogens or promote plant growth, others may be human pathogens. The aim of the current study was to determine the bacterial community composition of organic and conventionally grown leafy salad vegetables at the point of consumption using both culture-dependent and culture-independent methods. Total culturable bacteria on salad vegetables ranged from 8.0 × 10(3) to 5.5 × 10(8) CFU g(-1). The number of culturable endophytic bacteria from surface sterilized plants was significantly lower, ranging from 2.2 × 10(3) to 5.8 × 10(5) CFU g(-1). Cultured isolates belonged to six major bacterial phyla, and included representatives of Pseudomonas, Pantoea, Chryseobacterium, and Flavobacterium. Eleven different phyla and subphyla were identified by culture-independent pyrosequencing, with Gammaproteobacteria, Betaproteobacteria, and Bacteroidetes being the most dominant lineages. Other bacterial lineages identified (e.g. Firmicutes, Alphaproteobacteria, Acidobacteria, and Actinobacteria) typically represented less than 1% of sequences obtained. At the genus level, sequences classified as Pseudomonas were identified in all samples and this was often the most prevalent genus. Ralstonia sequences made up a greater portion of the community in surface sterilized than non-surface sterilized samples, indicating that it was largely endophytic, while Acinetobacter sequences appeared to be primarily associated with the leaf surface. Analysis of molecular variance indicated there were no significant differences in bacterial community composition between organic versus conventionally grown, or surface-sterilized versus non-sterilized leaf vegetables. While culture-independent pyrosequencing identified significantly more bacterial taxa, the dominant taxa from pyrosequence data were also detected by traditional

  18. Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments.

    PubMed

    Olapade, Ola A; Pung, Kayleigh

    2012-06-01

    Plant-microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.

  19. Validation of a Nylon-Flocked-Swab Protocol for Efficient Recovery of Bacterial Spores from Smooth and Rough Surfaces▿

    PubMed Central

    Probst, Alexander; Facius, Rainer; Wirth, Reinhard; Moissl-Eichinger, Christine

    2010-01-01

    In order to meet planetary-protection requirements, culturable bacterial spore loads are measured representatively for the total microbial contamination of spacecraft. However, the National Aeronautics and Space Administration's (NASA's) cotton swab protocols for spore load determination have not changed for decades. To determine whether a more efficient alternative was available, a novel swab was evaluated for recovery of different Bacillus atrophaeus spore concentrations on stainless steel and other surfaces. Two protocols for the nylon-flocked swab (NFS) were validated and compared to the present NASA standard protocol. The results indicate that the novel swab protocols recover 3- to 4-fold more (45.4% and 49.0% recovery efficiency) B. atrophaeus spores than the NASA standard method (13.2%). Moreover, the nylon-flocked-swab protocols were superior in recovery efficiency for spores of seven different Bacillus species, including Bacillus anthracis Sterne (recovery efficiency, 20%). The recovery efficiencies for B. atrophaeus spores from different surfaces showed a variation from 5.9 to 62.0%, depending on the roughness of the surface analyzed. Direct inoculation of the swab resulted in a recovery rate of about 80%, consistent with the results of scanning electron micrographs that allowed detailed comparisons of the two swab types. The results of this investigation will significantly contribute to the cleanliness control of future life detection missions and will provide significant improvement in detection of B. anthracis contamination for law enforcement and security efforts. PMID:20543054

  20. Effects of pressurized aeration on organic degradation efficiency and bacterial community structure of activated sludge treating saline wastewater.

    PubMed

    Zhang, Yong; Li, Bing; Xu, Rui-Xiao; Wang, Guo-Xiang; Zhou, Ying; Xie, Biao

    2016-12-01

    This study was aimed to investigate the effect of moderate pressure on organic matter removal efficiency and microbial population of activated sludge treating saline wastewater. The activated sludge was cultivated with a gradual increase of salt concentrations under gage pressure of 0.3MPa for 71days. Microbial diversities of activated sludge sampled in different stages of domestication were investigated by Illumina sequencing technology. Results showed that pressurized aeration could improve the treatment efficiency and the dehydrogenase activity (DHA) of activated sludge, especially at high salinity (35, 50gNaClL(-1)). Bacterial richness and community diversity of activated sludge in the pressurized reactor were significantly higher than those in the control reactor. Microbial population structures were quite different between the two reactors. More species originating from fresh wastewater biological treatment process would survive and remain in pressurized activated sludge. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Highly heterogeneous bacterial communities associated with the South China Sea reef corals Porites lutea, Galaxea fascicularis and Acropora millepora.

    PubMed

    Li, Jie; Chen, Qi; Zhang, Si; Huang, Hui; Yang, Jian; Tian, Xin-Peng; Long, Li-Juan

    2013-01-01

    Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species.

  2. Highly Heterogeneous Bacterial Communities Associated with the South China Sea Reef Corals Porites lutea, Galaxea fascicularis and Acropora millepora

    PubMed Central

    Li, Jie; Chen, Qi; Zhang, Si; Huang, Hui; Yang, Jian; Tian, Xin-Peng; Long, Li-Juan

    2013-01-01

    Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species. PMID:23940737

  3. Geographical variations in bacterial communities associated with soft coral Scleronephthya gracillimum.

    PubMed

    Woo, Seonock; Yang, Shan-Hua; Chen, Hsing-Ju; Tseng, Yu-Fang; Hwang, Sung-Jin; De Palmas, Stephane; Denis, Vianney; Imahara, Yukimitsu; Iwase, Fumihito; Yum, Seungshic; Tang, Sen-Lin

    2017-01-01

    Environmental impacts can alter relationships between a coral and its symbiotic microbial community. Furthermore, changes in the microbial community associated with increased seawater temperatures can cause opportunistic infections, coral disease and death. Interactions between soft corals and their associated microbes are not well understood. The species Scleronephthya gracillimum is distributed in tropical to temperate zones in coral assemblages along the Kuroshio Current region. In this study we collected S. gracillimum from various sites at different latitudes, and compared composition of their bacterial communities using Next Generation Sequencing. Coral samples from six geographically distinct areas (two sites each in Taiwan, Japan, and Korea) had considerable variation in their associated bacterial communities and diversity. Endozoicimonaceae was the dominant group in corals from Korea and Japan, whereas Mycoplasma was dominant in corals from Taiwan corals. Interestingly, the latter corals had lower relative abundance of Endozoicimonaceae, but greater diversity. These biogeographic differences in bacterial composition may have been due to varying environmental conditions among study locations, or because of host responses to prevailing environmental conditions. This study provided a baseline for future studies of soft coral microbiomes, and assessment of functions of host metabolites and soft coral holobionts.

  4. Geographical variations in bacterial communities associated with soft coral Scleronephthya gracillimum

    PubMed Central

    Chen, Hsing-Ju; Tseng, Yu-Fang; Hwang, Sung-Jin; De Palmas, Stephane; Denis, Vianney; Imahara, Yukimitsu; Iwase, Fumihito; Yum, Seungshic; Tang, Sen-Lin

    2017-01-01

    Environmental impacts can alter relationships between a coral and its symbiotic microbial community. Furthermore, changes in the microbial community associated with increased seawater temperatures can cause opportunistic infections, coral disease and death. Interactions between soft corals and their associated microbes are not well understood. The species Scleronephthya gracillimum is distributed in tropical to temperate zones in coral assemblages along the Kuroshio Current region. In this study we collected S. gracillimum from various sites at different latitudes, and compared composition of their bacterial communities using Next Generation Sequencing. Coral samples from six geographically distinct areas (two sites each in Taiwan, Japan, and Korea) had considerable variation in their associated bacterial communities and diversity. Endozoicimonaceae was the dominant group in corals from Korea and Japan, whereas Mycoplasma was dominant in corals from Taiwan corals. Interestingly, the latter corals had lower relative abundance of Endozoicimonaceae, but greater diversity. These biogeographic differences in bacterial composition may have been due to varying environmental conditions among study locations, or because of host responses to prevailing environmental conditions. This study provided a baseline for future studies of soft coral microbiomes, and assessment of functions of host metabolites and soft coral holobionts. PMID:28859111

  5. Root-associated bacterial diversities of Oryza rufipogon and Oryza sativa and their influencing environmental factors.

    PubMed

    Tian, Lei; Zhou, Xue; Ma, Lina; Xu, Shangqi; Nasir, Fahad; Tian, Chunjie

    2016-12-18

    Oryza rufipogon is the ancestor of human-cultivated Oryza sativa. However, little is known about the difference between the root-associated microorganisms of O. rufipogon and O. sativa. In this study, the root-associated bacteria of O. rufipogon, Leersia hexandra, and O. sativa from different latitudes in China were studied by DGGE analysis. Their bacterial community structures were compared by principal component analysis. The relationship between root-associated bacteria and soil properties was explored by canonical correspondence analysis. The relationships of glomalin-related soil protein (GRSP) content, soluble sugar content, proline content of the plant, and bacterial diversity indices of their root-associated microorganisms were also investigated. We found both broad-spectrum and host-specific bacteria, and the similarity, diversity and abundance indices of O. rufipogon and L. hexandra were higher than O. sativa root-associated bacteria. However, even living in the same habitat, O. rufipogon and L. hexandra selected different root-associated bacteria. Microbial composition was primarily correlated with available N, P, and K and the annual precipitation. We also found a positive correlation between the soluble sugar content of the plant and GRSP content of the root soil. The above results indicated that the community structure of root-associated bacteria differs between wild rice and cultivated rice. Human activity and the natural selection of the host plants shaped the differences, consistent with our hypothesis.

  6. Characterization of a disease susceptibility locus for exploring an efficient way to improve rice resistance against bacterial blight.

    PubMed

    Cheng, Qi; Mao, Weihua; Xie, Wenya; Liu, Qinsong; Cao, Jianbo; Yuan, Meng; Zhang, Qinglu; Li, Xianghua; Wang, Shiping

    2017-03-01

    Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is the most harmful bacterial disease of rice worldwide. Previously, we characterized major disease resistance (MR) gene xa25, which confers race-specific resistance to Xoo strain PXO339. The xa25 is a recessive allele of the SWEET13 locus, but SWEET13's interaction with PXO339 and how efficiently using this locus for rice breeding still need to be defined. Here we show that the SWEET13 allele from rice Zhenshan 97 is a susceptibility gene to PXO339. Using this allele's promoter to regulate xa25 resulted in disease, suggesting that the promoter is a key determinant in SWEET13 caused disease in Zhanshan 97 after PXO339 infection. PXO339 transcriptionally induces SWEET13 to cause disease. Partial suppressing SWEET13 expression leads to a high level of resistance to PXO339. Thus, the transcriptionally suppressed SWEET13 functions as xa25 in resistance to PXO339. Hybrid rice is widely grown in many countries. However, recessive MR genes have not been efficiently used for disease resistance breeding in hybrid rice production for both parents of the hybrid have to carry the same recessive gene. However, the suppressed SWEET13 functions dominantly, which will have advantage to improve the resistance of hybrid rice to xa25-incomptible Xoo.

  7. Addition of allochthonous fungi to a historically contaminated soil affects both remediation efficiency and bacterial diversity.

    PubMed

    Federici, Ermanno; Leonardi, Vanessa; Giubilei, Maria A; Quaratino, Daniele; Spaccapelo, Roberta; D'Annibale, Alessandro; Petruccioli, Maurizio

    2007-11-01

    Botryosphaeria rhodina DABAC P82 and Pleurotus pulmonarius CBS 664.97 were tested for their ability to grow and to degrade aromatic hydrocarbons in an aged contaminated soil. To evaluate the impact of indigenous microflora on the overall process, incubations were performed on both fumigated and nonfumigated soils. Fungal colonization by B. rhodina was unexpectedly lower in the fumigated than in the nonfumigated soil while the growth of P. pulmonarius showed an opposite response. Degradation performances and detoxification by both fungi in the nonfumigated soil were markedly higher than those observed in the fumigated one. Heterotrophic bacterial counts in nonfumigated soil augmented with either B. rhodina or P. pulmonarius were significantly higher than those of the corresponding incubation control (6.7 +/- 0.3 x 10(8) and 8.35 +/- 0.6 x 10(8), respectively, vs 9.2 +/- 0.3 x 10(7)). Bacterial communities of both incubation controls and fungal-augmented soil were compared by numerical analysis of denaturing gradient gel electrophoresis profiles of polymerase chain reaction (PCR)-amplified 16S ribosomal RNA (rRNA) genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Besides increasing overall diversity, fungal augmentation led to considerable qualitative differences with respect to the pristine soil.

  8. Reagent strips are efficient to rule out spontaneous bacterial peritonitis in cirrhotics.

    PubMed

    Oey, R C; Kuiper, J J; van Buuren, H R; de Man, R A

    2016-07-01

    The gold standard to diagnose spontaneous bacterial peritonitis (SBP) is a polymorphonuclear neutrophil count ≥ 250 cells/µl in ascitic fluid. This test is laborious and expensive. Urine reagent strips measuring leukocyte esterase activity have been proposed as a rapid and inexpensive alternative. The aim of this study was to assess the diagnostic accuracy of the Combur reagent strip for diagnosing SBP. Furthermore the possible advantage of a photospectrometer reading over visual reading of the strip was investigated. This prospective study includes all ascitic fluid samples of cirrhotic patients undergoing diagnostic or therapeutic paracentesis over a 12-month period. The samples were collected for the standard diagnostic work-up and in addition tested with a bedside Combur reagent strip. The strip was read visually and with an automated spectrometer. A total of 157 samples were obtained from 53 patients, and spontaneous bacterial peritonitis was diagnosed in 12 patients based on the ascitic polymorphonuclear neutrophil count. The sensitivity, specificity, positive predictive value and negative predictive value of the reagent strip according to the photospectrometer were 100%, 93%, 55% and 100% respectively, and 75%, 99%, 82% and 98%, respectively, for visual interpretation. The diagnostic accuracy of the photospectrometer was found to be higher than visual interpretation (p = 0.007). The diagnostic accuracy of leucocyte esterase reagent strips read out by a photospectrometer was comparable with the gold standard test and was excellent for excluding SBP. Our results support implementation of reagent strips in the diagnostic work-up of ascitic fluid.

  9. Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment

    PubMed Central

    Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C.

    2017-01-01

    ABSTRACT Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of Py

  10. Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment.

    PubMed

    Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C; Xu, Jianming

    2017-01-01

    Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of PyOMs and

  11. Two Bacterial Genera, Sodalis and Rickettsia, Associated with the Seal Louse Proechinophthirus fluctus (Phthiraptera: Anoplura)

    PubMed Central

    Allen, Julie M.; Koga, Ryuichi; Fukatsu, Takema; Sweet, Andrew D.; Johnson, Kevin P.; Reed, David L.

    2016-01-01

    ABSTRACT Roughly 10% to 15% of insect species host heritable symbiotic bacteria known as endosymbionts. The lice parasitizing mammals rely on endosymbionts to provide essential vitamins absent in their blood meals. Here, we describe two bacterial associates from a louse, Proechinophthirus fluctus, which is an obligate ectoparasite of a marine mammal. One of these is a heritable endosymbiont that is not closely related to endosymbionts of other mammalian lice. Rather, it is more closely related to endosymbionts of the genus Sodalis associated with spittlebugs and feather-chewing bird lice. Localization and vertical transmission of this endosymbiont are also more similar to those of bird lice than to those of other mammalian lice. The endosymbiont genome appears to be degrading in symbiosis; however, it is considerably larger than the genomes of other mammalian louse endosymbionts. These patterns suggest the possibility that this Sodalis endosymbiont might be recently acquired, replacing a now-extinct, ancient endosymbiont. From the same lice, we also identified an abundant bacterium belonging to the genus Rickettsia that is closely related to Rickettsia ricketsii, a human pathogen vectored by ticks. No obvious masses of the Rickettsia bacterium were observed in louse tissues, nor did we find any evidence of vertical transmission, so the nature of its association remains unclear. IMPORTANCE Many insects are host to heritable symbiotic bacteria. These heritable bacteria have been identified from numerous species of parasitic lice. It appears that novel symbioses have formed between lice and bacteria many times, with new bacterial symbionts potentially replacing existing ones. However, little was known about the symbionts of lice parasitizing marine mammals. Here, we identified a heritable bacterial symbiont in lice parasitizing northern fur seals. This bacterial symbiont appears to have been recently acquired by the lice. The findings reported here provide insights

  12. Diverse bacterial groups are associated with corrosive lesions at a Granite Mountain Record Vault (GMRV).

    PubMed

    Kan, J; Chellamuthu, P; Obraztsova, A; Moore, J E; Nealson, K H

    2011-08-01

    This study applied culture-dependent and molecular approaches to examine the bacterial communities at corrosion sites at Granite Mountain Record Vault (GMRV) in Utah, USA, with the goal of understanding the role of microbes in these unexpected corrosion events. Samples from corroded steel chunks, rock particles and waters around the corrosion pits were collected for bacterial isolation and molecular analyses. Bacteria cultivated from these sites were identified as members of Alphaproteobacteria, Gammaproteobacteria, Firmicutes and Actinobacteria. In addition, molecular genetic characterization of the communities via nested-polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) indicated the presence of a broad spectrum of bacterial groups, including Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. However, neither cultivation nor molecular approaches identified sulfate-reducing bacteria (SRB), the bacteria commonly implicated as causative organisms were found associated with corrosive lesions in a process referred to as microbially influenced corrosion (MIC). The high diversity of bacterial groups at the corrosion sites in comparison with that seen in the source waters suggested to us a role for the microbes in corrosion, perhaps being an expression of a redox-active group of microbes transferring electrons, harvesting energy and producing biomass. The corrosion sites contained highly diverse microbial communities, consistent with the involvement of microbial activities along the redox gradient at corrosion interface. We hypothesize an electron transport model for MIC, involving diverse bacterial groups such as acid-producing bacteria (APB), SRB, sulfur-oxidizing bacteria (SOB), metal-reducing bacteria (MRB) and metal-oxidizing bacteria (MOB). The characterization of micro-organisms that influence metal-concrete corrosion at GMRV has significant implications for corrosion control in high

  13. Efficient data association for move-stop-move target tracking

    NASA Astrophysics Data System (ADS)

    Sathyan, T.; McDonald, Mike; Kirubarajan, T.

    2008-04-01

    In this paper, we present an efficient data association algorithm for tracking ground targets that perform move-stop-move maneuvers using ground moving target indicator (GMTI) radar. A GMTI radar does not detect the targets whose radial velocity falls below a certain minimum detectable velocity. Hence, to avoid detection enemy targets deliberately stop for some time before moving again. When targets perform move-stop-move maneuvers, a missed detection of a target by the radar leads to an ambiguity as to whether it is because the target has stopped or due to the probability of detection being less than one. A solution to track move-stop-move target tracking is based on the variable structure interacting multiple model (VS-IMM) estimator in an ideal scenario (single target tracking with no false measurements) has been proposed. This solution did not consider the data association problem. Another solution, called two-dummy solution, considered the data association explicitly and proposed a solution based on the multiframe assignment algorithm. This solution is computationally expensive, especially when the scenario is complex (e.g., high target density) or when one wants to perform high dimensional assignment. In this paper, we propose an efficient multiframe assignment-based solution that considers the second dummy measurement as a real measurement than a dummy. The proposed algorithm builds a less complex assignment hypothesis tree, and, as a result, is more efficient in terms of computational resource requirement.

  14. Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community

    PubMed Central

    Brauer, Verena S.; Stomp, Maayke; Bouvier, Thierry; Fouilland, Eric; Leboulanger, Christophe; Confurius-Guns, Veronique; Weissing, Franz J.; Stal, LucasJ.; Huisman, Jef

    2014-01-01

    N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N2-fixing cyanobacteria. PMID:25642224

  15. Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm.

    PubMed

    Dilla-Ermita, Christine Jade; Tandayu, Erwin; Juanillas, Venice Margarette; Detras, Jeffrey; Lozada, Dennis Nicuh; Dwiyanti, Maria Stefanie; Vera Cruz, Casiana; Mbanjo, Edwige Gaby Nkouaya; Ardales, Edna; Diaz, Maria Genaleen; Mendioro, Merlyn; Thomson, Michael J; Kretzschmar, Tobias

    2017-12-01

    A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines. Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance, new genetic donors and useful molecular markers for marker-assisted breeding. A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions. Strong associations were found for novel SNPs linked with known bacterial blight resistance Xa genes, from which high utility markers for tracking and selection of resistance genes in breeding programs were designed. Furthermore, significant associations of SNPs in chromosomes 6, 9, 11, and 12 did not overlap with known resistance loci and hence might prove to be novel sources of resistance. Detailed analysis revealed haplotypes that correlated with resistance and analysis of putative resistance alleles identified resistant genotypes as potential donors of new resistance genes. The results of the GWAS validated known genes underlying resistance and identified novel loci that provide useful targets for further investigation. SNP markers and genetic donors identified in this study will help plant breeders in

  16. Bacterial properties of rainwater associated with cyclones, stationary fronts and typhoons in southwestern Japan

    NASA Astrophysics Data System (ADS)

    Zhang, D.; Hu, W.; Niu, H.

    2016-12-01

    The activities and role of bioaerosols in aerosol-cloud-precipitation links are important but unresolved issues in atmospheric and microbiological sciences. Bacteria, a main part of bioaerosols, are ubiquitous in atmospheric water. They are considered to be involved in the processes of cloud condensation and ice nuclei formation. However, to date, little information on rainwater bacteria is available. Rainwater samples were collected at a suburban site in southwestern Japan during October 2014 to September 2015. Results show that the cell concentration of rainwater bacteria was 2.3±1.5×104 cells ml-1, with a viability of 80±10% on average. The bacterial abundance and viability systematically differed with the weather systems causing rain. In cold-front-derived rain, the average bacterial concentration was the highest (3.5±1.6×104 cells ml-1), with the lowest viability as 75%. In the stationary-front-derived rain during Meiyu period and typhoon rain, the average bacterial concentrations were lower, but with higher viability. In stationary-front-derived rain during non-Meiyu period, the average abundance was higher (2.4±1.6×104 cells ml-1), while the viability was lower (78%) than those during Meiyu period. It was suggested that clouds produced by air mass from ocean areas carried fewer bacteria but with higher viability than those originated from continental regions. Bacterial concentrations in rainwater did not show good correlations with the ratios of total and decreased airborne particle concentrations to rainfall. Combining the univariate and factorial analysis of chemical compositions and bacterial abundance, we found that bacteria in rainwater were mainly associated with nss-SO42-, nss-Ca2+, and NO3-, which can act as nuclei or be produced within clouds. The cultured heterotrophic marine bacteria were of much higher abundance in stationary-front-derived rain than those in cold-front-derived rain. Bacterial genera containing ice nucleation active

  17. Gold Nanoparticles: An Efficient Antimicrobial Agent against Enteric Bacterial Human Pathogen

    PubMed Central

    Shamaila, Shahzadi; Zafar, Noshin; Riaz, Saira; Sharif, Rehana; Nazir, Jawad; Naseem, Shahzad

    2016-01-01

    Enteric bacterial human pathogens, i.e., Escherichia coli, Staphylococcus aureus, Bacillus subtilis and Klebsiella pneumoniae, are the major cause of diarrheal infections in children and adults. Their structure badly affects the human immune system. It is important to explore new antibacterial agents instead of antibiotics for treatment. This project is an attempt to explain how gold nanoparticles affect these bacteria. We investigated the important role of the mean particle size, and the inhibition of a bacterium is dose-dependent. Ultra Violet (UV)-visible spectroscopy revealed the size of chemically synthesized gold nanoparticle as 6–40 nm. Atomic force microscopy (AFM) analysis confirmed the size and X-ray diffractometry (XRD) analysis determined the polycrystalline nature of gold nanoparticles. The present findings explained how gold nanoparticles lyse Gram-negative and Gram-positive bacteria. PMID:28335198

  18. Efficient PAHs biodegradation by a bacterial consortium at flask and bioreactor scale.

    PubMed

    Moscoso, F; Teijiz, I; Deive, F J; Sanromán, M A

    2012-09-01

    In this work, the biodegradation of three polycyclic aromatic hydrocarbons (PAHs) such as Phenanthrene (PHE), Pyrene (PYR) and Benzo[a]anthracene (BaA) has been investigated. A bacterial consortium consisting of two strains was used for the first time based on preliminary promising biodegradation data. They were tentatively identified as Staphylococcus warneri and Bacillus pumilus. Degradation values higher than 85% were obtained for each single PAH when operating at flask scale, whereas minimum levels of 90% of PAHs removal were obtained after just 3 days of cultivation at bioreactor scale. The operation in cometabolic conditions led to maximum levels about 75% and 100% at flask and bioreactor scale, respectively. All the experimental data were analyzed in the light of logistic and Luedeking and Piret type models, with the purpose to better characterize the biodegradation process by S. warneri and B. pumilus. Finally, the metabolic pathway followed to degrade each PAH was ascertained.

  19. Antibiotic-Induced Change of Bacterial Communities Associated with the Copepod Nitocra spinipes

    PubMed Central

    Edlund, Anna; Ek, Karin; Breitholtz, Magnus; Gorokhova, Elena

    2012-01-01

    Environmental pressures, such as physical factors, diet and contaminants may affect interactions between microbial symbionts and their multicellular hosts. Despite obvious relevance, effects of antimicrobial contaminants on host-symbiont relations in non-target aquatic organisms are largely unknown. We show that exposure to antibiotics had negative effects on survival and juvenile development of the copepod Nitocra spinipes and caused significant alterations in copepod-associated bacterial communities. The significant positive correlations between indices of copepod development and bacterial diversity indicate that disruption of the microflora was likely to be an important factor behind retarded juvenile development in the experimental animals. Moreover, as evidenced by ribotype distribution in the bacterial clone libraries, the exposure to antibiotics caused a shift in dominance from Betaproteobacteria to Cardinium bacteria; the latter have been shown to cause reproductive manipulations in various terrestrial arthropods. Thus, in addition to providing evidence that the antibiotic-induced perturbation of the microbial community associates with reductions in fitness-related traits of the host, this study is the first record of a copepod serving as a host for endosymbiotic Cardinium. Taken together, our results suggest that (1) antimicrobial substances and possibly other stressors can affect micobiome and symbiont-mediated interactions in copepods and other hosts, and (2) Cardinium endosymbionts may occur in other copepods and affect reproduction of their hosts. PMID:22427962

  20. Antibiotic-induced change of bacterial communities associated with the copepod Nitocra spinipes.

    PubMed

    Edlund, Anna; Ek, Karin; Breitholtz, Magnus; Gorokhova, Elena

    2012-01-01

    Environmental pressures, such as physical factors, diet and contaminants may affect interactions between microbial symbionts and their multicellular hosts. Despite obvious relevance, effects of antimicrobial contaminants on host-symbiont relations in non-target aquatic organisms are largely unknown. We show that exposure to antibiotics had negative effects on survival and juvenile development of the copepod Nitocra spinipes and caused significant alterations in copepod-associated bacterial communities. The significant positive correlations between indices of copepod development and bacterial diversity indicate that disruption of the microflora was likely to be an important factor behind retarded juvenile development in the experimental animals. Moreover, as evidenced by ribotype distribution in the bacterial clone libraries, the exposure to antibiotics caused a shift in dominance from Betaproteobacteria to Cardinium bacteria; the latter have been shown to cause reproductive manipulations in various terrestrial arthropods. Thus, in addition to providing evidence that the antibiotic-induced perturbation of the microbial community associates with reductions in fitness-related traits of the host, this study is the first record of a copepod serving as a host for endosymbiotic Cardinium. Taken together, our results suggest that (1) antimicrobial substances and possibly other stressors can affect micobiome and symbiont-mediated interactions in copepods and other hosts, and (2) Cardinium endosymbionts may occur in other copepods and affect reproduction of their hosts.

  1. Antimicrobial Resistance and Virulence: a Successful or Deleterious Association in the Bacterial World?

    PubMed Central

    Beceiro, Alejandro; Tomás, María

    2013-01-01

    SUMMARY Hosts and bacteria have coevolved over millions of years, during which pathogenic bacteria have modified their virulence mechanisms to adapt to host defense systems. Although the spread of pathogens has been hindered by the discovery and widespread use of antimicrobial agents, antimicrobial resistance has increased globally. The emergence of resistant bacteria has accelerated in recent years, mainly as a result of increased selective pressure. However, although antimicrobial resistance and bacterial virulence have developed on different timescales, they share some common characteristics. This review considers how bacterial virulence and fitness are affected by antibiotic resistance and also how the relationship between virulence and resistance is affected by different genetic mechanisms (e.g., coselection and compensatory mutations) and by the most prevalent global responses. The interplay between these factors and the associated biological costs depend on four main factors: the bacterial species involved, virulence and resistance mechanisms, the ecological niche, and the host. The development of new strategies involving new antimicrobials or nonantimicrobial compounds and of novel diagnostic methods that focus on high-risk clones and rapid tests to detect virulence markers may help to resolve the increasing problem of the association between virulence and resistance, which is becoming more beneficial for pathogenic bacteria. PMID:23554414

  2. Diversity of Ixodes ricinus tick-associated bacterial communities from different forests.

    PubMed

    van Overbeek, Leo; Gassner, Fedor; van der Plas, Carin Lombaers; Kastelein, Pieter; Nunes-da Rocha, Ulisses; Takken, Willem

    2008-10-01

    Nymphal Ixodes ricinus ticks (n=180) were collected from three different areas in the Netherlands to investigate the effect of forest composition on tick-associated microbial communities. Sampled habitats differed in thickness of leaf litter and humus layers and vegetation associations and were located near Amsterdam (Beech-Oak), Ede (Birch-Oak) and Veldhoven (Birch-Oak). Analysis of nine 16S rRNA gene clone libraries made from individual ticks showed nearest matches with presumed pathogens Candidatus Neoehrlichia mikurensis and Rickettsia australis and arthropod endosymbionts Wolbachia pipientis and Candidatus Midichloria mitochondrii. Total bacterial species diversity (Shannon index) and Borrelia species infections were determined in I. ricinus by, respectively, PCR-denaturing gradient gel-electrophoresis and PCR-reverse line blot with probes specific for Borrelia burgdorferi sensu stricto, Borrelia afzelii, Borrelia garinii, Borrelia valaisiana, Borrelia lusitaniae and Borrelia ruski. Bacterial diversity differed significantly per area and was lowest in Ede. In contrast, Borrelia species-infected ticks were more abundant in Ede, Candidatus Neoehrlichia mikurensis-infected ticks in Ede and Veldhoven, and R. australis-infected ticks in Amsterdam. Borrelia afzelii was the most common Borrelia species found in all three areas. Bacterial tick diversity was influenced by local differences in forest structure, which is proposed to modulate animal populations that are commonly parasitized by I. ricinus.

  3. Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus.

    PubMed

    Alves, Marta; Pereira, Anabela; Matos, Patrícia; Henriques, Joana; Vicente, Cláudia; Aikawa, Takuya; Hasegawa, Koichi; Nascimento, Francisco; Mota, Manuel; Correia, António; Henriques, Isabel

    2016-04-05

    Monochamus beetles are the dispersing vectors of the nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease (PWD). PWD inflicts significant damages in Eurasian pine forests. Symbiotic microorganisms have a large influence in insect survival. The aim of this study was to characterize the bacterial community associated to PWD vectors in Europe and East Asia using a culture-independent approach. Twenty-three Monochamus galloprovincialis were collected in Portugal (two different locations); twelve Monochamus alternatus were collected in Japan. DNA was extracted from the insects' tracheas for 16S rDNA analysis through denaturing gradient gel electrophoresis and barcoded pyrosequencing. Enterobacteriales, Pseudomonadales, Vibrionales and Oceanospirilales were present in all samples. Enterobacteriaceae was represented by 52.2% of the total number of reads. Twenty-three OTUs were present in all locations. Significant differences existed between the microbiomes of the two insect species while for M. galloprovincialis there were no significant differences between samples from different Portuguese locations. This study presents a detailed description of the bacterial community colonizing the Monochamus insects' tracheas. Several of the identified bacterial groups were described previously in association with pine trees and B. xylophilus, and their previously described functions suggest that they may play a relevant role in PWD.

  4. Bacterial Associations Across House Fly Life History: Evidence for Transstadial Carriage From Managed Manure

    PubMed Central

    Zurek, Klara; Nayduch, Dana

    2016-01-01

    House flies (Diptera: Muscidae; Musca domestica L.) associate with microbe-rich substrates throughout life history. Because larvae utilize bacteria as a food source, most taxa present in the larval substrate, e.g., manure, are digested or degraded. However, some species survive and are present as third-instar larvae begin pupation. During metamorphosis, many bacteria are again lost during histolysis of the larval gut and subsequent remodeling to produce the gut of the imago. It has been previously demonstrated that some bacterial species survive metamorphosis, being left behind in the puparium, present on the body surface, or in the gut of the emerged adult. We used a combined culture-molecular approach to identify viable microbes from managed manure residue and a wild population of house fly larvae, pupae, puparia, and adults to assess transstadial carriage. All larval (10/10), pupal (10/10), and puparial (10/10) cultures were positive for bacteria. Several bacterial species that were present in larvae also were present either in pupae or puparia. Four viable bacterial species were detectable in 6 of 10 imagoes reared from manure. Of note is the apparent transstadial carriage of Bacillus sonorensis, which has been associated with milk spoilage at dairies, and Alcaligenes faecalis, which can harbor numerous antibiotic resistance genes on farms. The potential of newly emerged flies to harbor and disseminate bacteria from managed manure on farms is an understudied risk that deserves further evaluation. PMID:26798138

  5. Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus

    PubMed Central

    Alves, Marta; Pereira, Anabela; Matos, Patrícia; Henriques, Joana; Vicente, Cláudia; Aikawa, Takuya; Hasegawa, Koichi; Nascimento, Francisco; Mota, Manuel; Correia, António; Henriques, Isabel

    2016-01-01

    Monochamus beetles are the dispersing vectors of the nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease (PWD). PWD inflicts significant damages in Eurasian pine forests. Symbiotic microorganisms have a large influence in insect survival. The aim of this study was to characterize the bacterial community associated to PWD vectors in Europe and East Asia using a culture-independent approach. Twenty-three Monochamus galloprovincialis were collected in Portugal (two different locations); twelve Monochamus alternatus were collected in Japan. DNA was extracted from the insects’ tracheas for 16S rDNA analysis through denaturing gradient gel electrophoresis and barcoded pyrosequencing. Enterobacteriales, Pseudomonadales, Vibrionales and Oceanospirilales were present in all samples. Enterobacteriaceae was represented by 52.2% of the total number of reads. Twenty-three OTUs were present in all locations. Significant differences existed between the microbiomes of the two insect species while for M. galloprovincialis there were no significant differences between samples from different Portuguese locations. This study presents a detailed description of the bacterial community colonizing the Monochamus insects’ tracheas. Several of the identified bacterial groups were described previously in association with pine trees and B. xylophilus, and their previously described functions suggest that they may play a relevant role in PWD. PMID:27045340

  6. Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters.

    PubMed

    Galand, Pierre E; Salter, Ian; Kalenitchenko, Dimitri

    2015-12-01

    Understanding the link between community diversity and ecosystem function is a fundamental aspect of ecology. Systematic losses in biodiversity are widely acknowledged but the impact this may exert on ecosystem functioning remains ambiguous. There is growing evidence of a positive relationship between species richness and ecosystem productivity for terrestrial macro-organisms, but similar links for marine micro-organisms, which help drive global climate, are unclear. Community manipulation experiments show both positive and negative relationships for microbes. These previous studies rely, however, on artificial communities and any links between the full diversity of active bacterial communities in the environment, their phylogenetic relatedness and ecosystem function remain hitherto unexplored. Here, we test the hypothesis that productivity is associated with diversity in the metabolically active fraction of microbial communities. We show in natural assemblages of active bacteria that communities containing more distantly related members were associated with higher bacterial production. The positive phylogenetic diversity-productivity relationship was independent of community diversity calculated as the Shannon index. From our long-term (7-year) survey of surface marine bacterial communities, we also found that similarly, productive communities had greater phylogenetic similarity to each other, further suggesting that the traits of active bacteria are an important predictor of ecosystem productivity. Our findings demonstrate that the evolutionary history of the active fraction of a microbial community is critical for understanding their role in ecosystem functioning. © 2015 John Wiley & Sons Ltd.

  7. Highly Efficient CRISPR/Cas9-Mediated Homologous Recombination Promotes the Rapid Generation of Bacterial Artificial Chromosomes of Pseudorabies Virus

    PubMed Central

    Guo, Jin-Chao; Tang, Yan-Dong; Zhao, Kuan; Wang, Tong-Yun; Liu, Ji-Ting; Gao, Jia-Cong; Chang, Xiao-Bo; Cui, Hong-Yu; Tian, Zhi-Jun; Cai, Xue-Hui; An, Tong-Qing

    2016-01-01

    Bacterial artificial chromosomes (BACs) are powerful tools for the manipulation of the large genomes of DNA viruses, such as herpesviruses. However, the methods currently used to construct the recombinant viruses, an important intermediate link in the generation of BACs, involve the laborious process of multiple plaque purifications. Moreover, some fastidious viruses may be lost or damaged during these processes, making it impossible to generate BACs from these large-genome DNA viruses. Here, we introduce the CRISPR/Cas9 as a site-specific gene knock-in instrument that promotes the homologs recombination of a linearized transfer vector and the Pseudorabies virus genome through double incisions. The efficiency of recombination is as high as 86%. To our knowledge, this is the highest efficiency ever reported for Pseudorabies virus recombination. We also demonstrate that the positions and distances of the CRISPR/Cas9 single guide RNAs from the homology arms correlate with the efficiency of homologous recombination. Our work show a simple and fast cloning method of BACs with large genome inserted by greatly enhancing the HR efficiencies through CRISPR/Cas9-mediated homology-directed repair mechanism, and this method could be of helpful for manipulating large DNA viruses, and will provide a successful model for insertion of large DNA fragments into other viruses. PMID:28066407

  8. The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities.

    PubMed

    Uroz, Stephane; Kelly, Laura Catherine; Turpault, Marie-Pierre; Lepleux, Cendrella; Frey-Klett, Pascale

    2015-12-01

    Soil is composed of a mosaic of different rocks and minerals, usually considered as an inert substrata for microbial colonization. However, recent findings suggest that minerals, in soils and elsewhere, favour the development of specific microbial communities according to their mineralogy, nutritive content, and weatherability. Based upon recent studies, we highlight how bacterial communities are distributed on the surface of, and in close proximity to, minerals. We also consider the potential role of the mineral-associated bacterial communities in mineral weathering and nutrient cycling in soils, with a specific focus on nutrient-poor and acidic forest ecosystems. We propose to define this microbial habitat as the mineralosphere, where key drivers of the microbial communities are the physicochemical properties of the minerals.

  9. Exploring the plant-associated bacterial communities in Medicago sativa L.

    PubMed

    Pini, Francesco; Frascella, Arcangela; Santopolo, Luisa; Bazzicalupo, Marco; Biondi, Emanuele G; Scotti, Carla; Mengoni, Alessio

    2012-05-20

    Plant-associated bacterial communities caught the attention of several investigators which study the relationships between plants and soil and the potential application of selected bacterial species in crop improvement and protection. Medicago sativa L. is a legume crop of high economic importance as forage in temperate areas and one of the most popular model plants for investigations on the symbiosis with nitrogen fixing rhizobia (mainly belonging to the alphaproteobacterial species Sinorhizobium meliloti). However, despite its importance, no studies have been carried out looking at the total bacterial community associated with the plant. In this work we explored for the first time the total bacterial community associated with M. sativa plants grown in mesocosms conditions, looking at a wide taxonomic spectrum, from the class to the single species (S. meliloti) level. Results, obtained by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis, quantitative PCR and sequencing of 16 S rRNA gene libraries, showed a high taxonomic diversity as well as a dominance by members of the class Alphaproteobacteria in plant tissues. Within Alphaproteobacteria the families Sphingomonadaceae and Methylobacteriaceae were abundant inside plant tissues, while soil Alphaproteobacteria were represented by the families of Hyphomicrobiaceae, Methylocystaceae, Bradyirhizobiaceae and Caulobacteraceae. At the single species level, we were able to detect the presence of S. meliloti populations in aerial tissues, nodules and soil. An analysis of population diversity on nodules and soil showed a relatively low sharing of haplotypes (30-40%) between the two environments and between replicate mesocosms, suggesting drift as main force shaping S. meliloti population at least in this system. In this work we shed some light on the bacterial communities associated with M. sativa plants, showing that Alphaproteobacteria may constitute an important part of biodiversity in this

  10. Exploring the plant-associated bacterial communities in Medicago sativa L

    PubMed Central

    2012-01-01

    Background Plant-associated bacterial communities caught the attention of several investigators which study the relationships between plants and soil and the potential application of selected bacterial species in crop improvement and protection. Medicago sativa L. is a legume crop of high economic importance as forage in temperate areas and one of the most popular model plants for investigations on the symbiosis with nitrogen fixing rhizobia (mainly belonging to the alphaproteobacterial species Sinorhizobium meliloti). However, despite its importance, no studies have been carried out looking at the total bacterial community associated with the plant. In this work we explored for the first time the total bacterial community associated with M. sativa plants grown in mesocosms conditions, looking at a wide taxonomic spectrum, from the class to the single species (S. meliloti) level. Results Results, obtained by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis, quantitative PCR and sequencing of 16 S rRNA gene libraries, showed a high taxonomic diversity as well as a dominance by members of the class Alphaproteobacteria in plant tissues. Within Alphaproteobacteria the families Sphingomonadaceae and Methylobacteriaceae were abundant inside plant tissues, while soil Alphaproteobacteria were represented by the families of Hyphomicrobiaceae, Methylocystaceae, Bradyirhizobiaceae and Caulobacteraceae. At the single species level, we were able to detect the presence of S. meliloti populations in aerial tissues, nodules and soil. An analysis of population diversity on nodules and soil showed a relatively low sharing of haplotypes (30-40%) between the two environments and between replicate mesocosms, suggesting drift as main force shaping S. meliloti population at least in this system. Conclusions In this work we shed some light on the bacterial communities associated with M. sativa plants, showing that Alphaproteobacteria may constitute an important

  11. Association between milking practices and psychrotrophic bacterial counts in bulk tank milk.

    PubMed

    Molineri, Ana I; Signorini, Marcelo L; Cuatrín, Alejandra L; Canavesio, Vilma R; Neder, Verónica E; Russi, Norma B; Bonazza, Julio C; Calvinho, Luis F

    2012-01-01

    The objective of this work was to determine on-farm risk factors for psychrotrophic bacterial counts in bulk tank milk from dairy farms in Argentina. Raw milk samples from bulk tanks of 27 dairy farms were examined for total psychrotrophic counts (TPC), proteolytic psychrotrophic counts (PPC) and lipolytic psychrotrophic counts (LPC) (dependent or outcome variables). A survey recording infrastructure conditions, milking equipment and milking management (independent variables) was performed. Bivariate association proofs and logistic regression analyses were used to determine association between independent variables and psychrotrophic bacterial counts. Milk cooled in plate heat exchangers or barrel tanks were 16.39 and 10.52 times more likely to yield TPC and PPC above the standard established for high quality milk compared with milk cooled in bulk tanks, respectively. Periodic cleaning of cooling tanks (3 times a week or daily) was associated with lower TPC (approximately 1.5 log CFU/ml) than weekly cleaning frequency and farms where milkers did not wash their hands during milking time were 7.81 times more likely to have higher PPC. No association was found between LPC and any of the independent variables. The only variable associated with TPC and PPC in a logistic regression model was the refrigeration system used on the farm. Dairy farms that possessed bulk milk cooling tanks yielded the lowest bacterial counts. Results of this study highlight the importance of both the type of cooling system used on the farm and its adequate hygienic maintenance for obtaining low pshychrotrophic counts at dairy farm.

  12. Bacterial biofilm-based catheter-associated urinary tract infections: Causative pathogens and antibiotic resistance.

    PubMed

    Sabir, Nargis; Ikram, Aamer; Zaman, Gohar; Satti, Luqman; Gardezi, Adeel; Ahmed, Abeera; Ahmed, Parvez

    2017-10-01

    We sought to determine the incidence of bacterial biofilm-based catheter-associated urinary tract infections, identify variables affecting biofilm formation, and identify etiologic bacterial pathogens and antibiotic-resistance patterns associated with biofilm-based catheter-associated urinary tract infections (CAUTIs) in our setup. Patients who developed at least 2 symptoms of urinary tract infection after at least 2 days of indwelling urinary catheters were included. Urine was collected aseptically from catheter tubing and processed per standard microbiologic practices. Bacterial pathogens were identified on the basis of gram staining, colony morphology, and biochemical reactions. The detection of the biofilm was done using the tube adherence method. Drug susceptibility testing was done using the Kirby-Bauer disc diffusion method. Biofilm was detected in 73.4% isolates, whereas 26.6% of isolates were nonbiofilm producers. Mean duration of catheterization after which biofilm was detected was 5.01 ± 1.31 days. A latex catheter was used in 69.5% of patients, whereas a silicone catheter was used in 30.4% of patients. Escherichia coli was found to be the most common pathogen isolated (52.3%), whereas Enterobacter cloacae exhibited the highest biofilm production (87.5%) among isolated pathogens. Among biofilm producers, the highest resistance was observed with ampicillin (100%). Fosfomycin exhibited the lowest resistance (17.2%). Significant association with biofilm was detected for gender, duration of catheterization, and type of catheter. Biofilm-based CAUTI is an emerging problem. E coli was the most frequent isolate. High antibiotic resistance was observed in biofilm-producing strains. Using the variables affecting biofilm formation, tailored intervention strategies can be implemented to reduce biofilm-based CAUTIs. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

  13. Efficient semiparametric mean-association estimation for longitudinal binary responses.

    PubMed

    Chen, Ziqi; Shi, Ning-Zhong; Gao, Wei; Tang, Man-Lai

    2012-06-15

    Semiparametric methods for longitudinal data with association within subjects have recently received considerable attention. However, existing methods for semiparametric longitudinal binary regression modeling (i) mainly concern mean structures with association parameters treated as nuisance; (ii) generally require a correct specification of the covariance structure for misspecified covariance structure may lead to inefficient mean parameter estimates; and (iii) usually run into computation and estimation problems when the time points are irregularly and possibly subject specific. In this article, we propose a semiparametric logistic regression model, which simultaneously takes into account both the mean and response-association structures (via conditional log-odds ratio) for multivariate longitudinal binary outcomes. Our main interest lies in efficient estimation of both the marginal and association parameters. The estimators of the parameters are obtained via the profile kernel approach. We evaluate the proposed methodology through simulation studies and apply it to a real dataset. Both theoretical and empirical results demonstrate that the proposed method yields highly efficient estimators and performs satisfactorily.

  14. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

    PubMed Central

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C.; Clostio, Rachel W.; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

  15. Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

    DOE PAGES

    Staley, Christopher; Ferrieri, Abigail P.; Tfaily, Malak M.; ...

    2017-06-24

    The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated.Significantly different bacterial community structures (P = 0.031) were observed in themore » rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles.The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without

  16. Temperature and Nutrient Effects on Periphyton Associated Bacterial Communities in Continuous Flow-Through Estuarine Mesocosms

    NASA Astrophysics Data System (ADS)

    Houghton, K.; James, J. B.; Devereux, R.; Friedman, S. D.

    2016-02-01

    Nutrient pollution is a leading cause of water quality impairments and degraded aquatic ecosystem condition. Reliable and reproducible indicators of ecosystem condition are needed to help manage nutrient pollution. The diatom component of periphyton has been used as a water quality indicator due to identifiable cell morphology and existence of relationships between nutrient concentration and diatom community composition. However, morphological identification of diatoms requires highly specialized personnel, is very time consuming, and can produce variable results, suggesting the need for alternative methods that are less expensive and more reproducible. DNA sequencing of the bacterial 16S rRNA gene is well documented and provides genus-level resolution of the community structure. The goal of this study was to evaluate the effects of nutrient loading and temperature on periphyton-associated bacterial communities using standard periphytometer techniques and next generation sequencing technologies. Continuous flow mesocosms were established in an eight tank system consisting of two temperature conditions (10°C and 20°C) and four nutrient conditions (1x to 6x ambient concentrations). Experimental conditions were replicated in July/August 2013 and September 2013. Replicate DNA samples were extracted and the 16S rRNA gene was sequenced using universal Bacterial primers. Initial analyses revealed strong differences in community structure based on temperature (p < 0.01, R = 0.997) and sampling month (p < 0.01, R = 0.993) while no significant differences were detected between nutrient treatments. These results suggest that the method can detect changes in periphyton associated bacterial communities based on temperature but a more refined approach, as might be based on functional genes instead of structural genes, may be needed to differentiate nutrient effects.

  17. Healthcare-associated and nosocomial bacterial infections in cirrhosis: predictors and impact on outcome.

    PubMed

    Sargenti, Konstantina; Prytz, Hanne; Strand, Anna; Nilsson, Emma; Kalaitzakis, Evangelos

    2015-02-01

    Population-based data on the occurrence of healthcare-associated (HCA) and hospital-acquired (HA) bacterial infections in cirrhosis, their predictors, and their impact on outcome are limited. All patients with incident cirrhosis in 2001-2010 residing in an area of 600,000 inhabitants were retrospectively identified. All serious bacterial infections (resulting in or occurring during an inpatient hospital episode) during this period were registered. Acquisition type, site of infection, occurrence of infection-related acute-on-chronic liver failure (ACLF), acute kidney injury (AKI) and bacterial resistance were analysed. Patients were followed longitudinally until death, transplant or end of 2011. A total of 398 serious infections occurred in 241/633 (38%) patients. Forty-seven per cent were HCA and 21% HA. Proton pump inhibitor (PPI) use was more common in HA (80%) vs. HCA (64%) vs. community-acquired (44%) infections (P < 0.001). In regression analysis, decompensated status, use of antibiotics and PPIs at infection diagnosis were independent predictors of HCA/HA infections (P < 0.05). After adjustment for confounders, HCA/HA infections were significantly related to infection-related ACLF (P < 0.05), but not severe sepsis, AKI or infection-related mortality (P > 0.05). Antibiotic-resistant infections were more frequent among HA (17%) than HCA (6%) or community-acquired (8%) infections (P < 0.05). Antibiotic-resistant HCA/HA infections were independently related to severe sepsis (P < 0.05). In a population-based cirrhotic cohort, two-thirds of serious bacterial infections were HCA or HA. Decompensated liver disease, antibiotics and PPIs were predictors of serious HCA/HA infections, which were associated with the development of ACLF. Antibiotic resistance was frequent, especially in HA infections, and contributed to risk of severe sepsis. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  18. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    PubMed

    Lawler, Stephanie N; Kellogg, Christina A; France, Scott C; Clostio, Rachel W; Brooke, Sandra D; Ross, Steve W

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  19. Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

    USGS Publications Warehouse

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

  20. Flea-Associated Bacterial Communities across an Environmental Transect in a Plague-Endemic Region of Uganda

    PubMed Central

    Jones, Ryan Thomas; Borchert, Jeff; Eisen, Rebecca; MacMillan, Katherine; Boegler, Karen; Gage, Kenneth L.

    2015-01-01

    The vast majority of human plague cases currently occur in sub-Saharan Africa. The primary route of transmission of Yersinia pestis, the causative agent of plague, is via flea bites. Non-pathogenic flea-associated bacteria may interact with Y. pestis within fleas and it is important to understand what factors govern flea-associated bacterial assemblages. Six species of fleas were collected from nine rodent species from ten Ugandan villages between October 2010 and March 2011. A total of 660,345 16S rRNA gene DNA sequences were used to characterize bacterial communities of 332 individual fleas. The DNA sequences were binned into 421 Operational Taxonomic Units (OTUs) based on 97% sequence similarity. We used beta diversity metrics to assess the effects of flea species, flea sex, rodent host species, site (i.e. village), collection date, elevation, mean annual precipitation, average monthly precipitation, and average monthly temperature on bacterial community structure. Flea species had the greatest effect on bacterial community structure with each flea species harboring unique bacterial lineages. The site (i.e. village), rodent host, flea sex, elevation, precipitation, and temperature also significantly affected bacterial community composition. Some bacterial lineages were widespread among flea species (e.g. Bartonella spp. and Wolbachia spp.), but each flea species also harbored unique bacterial lineages. Some of these lineages are not closely related to known bacterial diversity and likely represent newly discovered lineages of insect symbionts. Our finding that flea species has the greatest effect on bacterial community composition may help future investigations between Yersinia pestis and non-pathogenic flea-associated bacteria. Characterizing bacterial communities of fleas during a plague epizootic event in the future would be helpful. PMID:26485147

  1. Flea-Associated Bacterial Communities across an Environmental Transect in a Plague-Endemic Region of Uganda.

    PubMed

    Jones, Ryan Thomas; Borchert, Jeff; Eisen, Rebecca; MacMillan, Katherine; Boegler, Karen; Gage, Kenneth L

    2015-01-01

    The vast majority of human plague cases currently occur in sub-Saharan Africa. The primary route of transmission of Yersinia pestis, the causative agent of plague, is via flea bites. Non-pathogenic flea-associated bacteria may interact with Y. pestis within fleas and it is important to understand what factors govern flea-associated bacterial assemblages. Six species of fleas were collected from nine rodent species from ten Ugandan villages between October 2010 and March 2011. A total of 660,345 16S rRNA gene DNA sequences were used to characterize bacterial communities of 332 individual fleas. The DNA sequences were binned into 421 Operational Taxonomic Units (OTUs) based on 97% sequence similarity. We used beta diversity metrics to assess the effects of flea species, flea sex, rodent host species, site (i.e. village), collection date, elevation, mean annual precipitation, average monthly precipitation, and average monthly temperature on bacterial community structure. Flea species had the greatest effect on bacterial community structure with each flea species harboring unique bacterial lineages. The site (i.e. village), rodent host, flea sex, elevation, precipitation, and temperature also significantly affected bacterial community composition. Some bacterial lineages were widespread among flea species (e.g. Bartonella spp. and Wolbachia spp.), but each flea species also harbored unique bacterial lineages. Some of these lineages are not closely related to known bacterial diversity and likely represent newly discovered lineages of insect symbionts. Our finding that flea species has the greatest effect on bacterial community composition may help future investigations between Yersinia pestis and non-pathogenic flea-associated bacteria. Characterizing bacterial communities of fleas during a plague epizootic event in the future would be helpful.

  2. Integrating Clonal Selection and Deterministic Sampling for Efficient Associative Classification

    PubMed Central

    Elsayed, Samir A. Mohamed; Rajasekaran, Sanguthevar; Ammar, Reda A.

    2013-01-01

    Traditional Associative Classification (AC) algorithms typically search for all possible association rules to find a representative subset of those rules. Since the search space of such rules may grow exponentially as the support threshold decreases, the rules discovery process can be computationally expensive. One effective way to tackle this problem is to directly find a set of high-stakes association rules that potentially builds a highly accurate classifier. This paper introduces AC-CS, an AC algorithm that integrates the clonal selection of the immune system along with deterministic data sampling. Upon picking a representative sample of the original data, it proceeds in an evolutionary fashion to populate only rules that are likely to yield good classification accuracy. Empirical results on several real datasets show that the approach generates dramatically less rules than traditional AC algorithms. In addition, the proposed approach is significantly more efficient than traditional AC algorithms while achieving a competitive accuracy. PMID:24500504

  3. A mixture of bacterial mechanical lysates is more efficient than single strain lysate and of bacterial-derived soluble products for the induction of an activating phenotype in human dendritic cells.

    PubMed

    Morandi, Barbara; Agazzi, Alessia; D'Agostino, Antonella; Antonini, Francesca; Costa, Gregorio; Sabatini, Federica; Ferlazzo, Guido; Melioli, Giovanni

    2011-07-01

    Dendritic cells (DCs), following an optimal maturation, are able to drive an efficient immune-response. For this, both co-stimulatory molecules (CD80 and CD86), activation molecules (CD83) and peptide presenting molecules (HLA) are over-expressed. The in vitro treatment of immature DC with fragments of bacterial strains, obtained by using a mechanical lysis as well as with bacterial-derived molecules (such as lipopolysaccharide and protido-glycan), induced the maturation of DCs and the secretion of a panel of cytokines and chemokines. Of note, ex vivo treated circulating DCs and plasmacytoid DCs were also activated by these bacterial bodies. However, while the particulate fraction of single bacterial strains or soluble bacterial-derived molecules induced a sub-optimal maturation (as evaluated by the expression of an activating phenotype on DCs and the amount of cytokine secretion), the addition of the mixture of the particulate fractions of the different bacterial strains was able to mediate an optimal maturation. These results were also confirmed by using the secretion of both cytokines and chemokines as markers of DC activation. All these findings suggest that the particulate fraction of bacterial lysate mixtures, because of their ability to interact with different surface structures, might be exploited not only as an immunogen, but also as an adjuvant treatment to boost an immune-response to poorly "antigenic" proteins, such as cancer antigens or allergens.

  4. Plankton metabolism and bacterial growth efficiency in offshore waters along a latitudinal transect between the UK and Svalbard

    NASA Astrophysics Data System (ADS)

    García-Martín, E. E.; McNeill, S.; Serret, P.; Leakey, R. J. G.

    2014-10-01

    Euphotic zone gross primary production, community respiration and net community production were determined from in vitro changes of dissolved oxygen, and from in vivo INT reduction capacity fractionated into two size classes, in offshore waters along a latitudinal transect crossing the North, Norwegian and Greenland Seas between the UK and Svalbard. Rates of gross primary production were higher and more variable than community respiration, so net autotrophy prevailed in the euphotic zone with an average net community production of 164±64 mmol O2 m-2 d-1. Respiration seemed to be mainly attributed to large eukaryotic cells (>0.8 μm) with smaller cells, mainly bacteria, accounting for a mean of 25% (range 5-48%) of community respiration. Estimates of bacterial growth efficiency were very variable (range 7-69%) due to uncoupling between bacterial respiration and production. Larger cells tended to contribute more towards total respiration in communities with high gross primary production and low community respiration, while bacteria contributed more towards total respiration in communities with lower gross primary production, typical of microbial-dominated systems. This suggests that community respiration is related to the size structure of the plankton community.

  5. Viral effects on bacterial respiration, production and growth efficiency: Consistent trends in the Southern Ocean and the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Bonilla-Findji, Osana; Malits, Andrea; Lefèvre, Dominique; Rochelle-Newall, Emma; Lemée, Rodolphe; Weinbauer, Markus G.; Gattuso, Jean-Pierre

    2008-03-01

    To investigate the potential effects of viruses on bacterial respiration (BR), production (BP) and growth efficiency (BGE), experiments were performed using natural microbial communities from the coastal Mediterranean Sea, from a typical high-nutrient low-chlorophyll (HNLC) region in the Southern Ocean and from a naturally iron (Fe)-fertilized algal bloom above the Kerguelen Plateau (Southern Ocean). Seawater was sequentially filtered and concentrated to produce a bacterial concentrate, a viral concentrate and a virus-free ultrafiltrate. The combination of all three fractions served as treatments with active viruses. Heating or microwaving was used to inactivate viruses for the control treatments. Despite the differences in the initial trophic state and community composition of the study sites, consistent trends were found. In the presence of active viruses, BR was stimulated (up to 113%), whereas BP and BGE were reduced (up to 51%). Our results suggest that viruses enhance the role of bacteria as oxidizers of organic matter, hence as producers of CO 2, and remineralizers of CO 2, N, P and Fe. In the context of Fe-fertilization, this has important implications for the final fate of organic carbon in marine systems.

  6. Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

    NASA Astrophysics Data System (ADS)

    Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.

    2016-12-01

    Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.

  7. Use of a DNA microarray for detection and identification of bacterial pathogens associated with fishery products.

    PubMed

    Cao, Boyang; Li, Rongrong; Xiong, Songjin; Yao, Fangfang; Liu, Xiangqian; Wang, Min; Feng, Lu; Wang, Lei

    2011-12-01

    We established a microarray for the simultaneous detection and identification of diverse putative pathogens often associated with fishery products by targeting specific genes of Listeria monocytogenes, Salmonella, Shigella, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, and Yersinia enterocolitica and the 16S-23S rRNA gene internal transcribed spacer (ITS) region of Proteus mirabilis and Proteus vulgaris. The microarray contained 26 specific probes and was tested against a total of 123 target bacterial strains that included 55 representative strains, 68 clinical isolates, and 45 strains of other bacterial species that belonged to 8 genera and 34 species, and it was shown to be specific and reproducible. A detection sensitivity of 10 ng DNA or 10 CFU/ml for pure cultures of each target organism demonstrated that the assay was highly sensitive and reproducible. Mock and real fishery product samples were tested by the microarray, and the accuracy was 100%. The DNA microarray method described in this communication is specific, sensitive, and reliable and has several advantages over traditional methods of bacterial culture and antiserum agglutination assays.

  8. Bacterial species associated with sound and Botrytis-infected grapes from a Greek vineyard.

    PubMed

    Nisiotou, Aspasia A; Rantsiou, Kalliopi; Iliopoulos, Vassilios; Cocolin, Luca; Nychas, George-John E

    2011-02-28

    Grape bacterial microbiota plays central roles in the quality of grapes and wine, yet its diversity remains poorly described. In the present study, bacterial species associated with sound and Botrytis-infected grapes of two cultivars originating from the same vineyard were assessed. Isolates were identified by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and sequence analysis of partial 16S rRNA gene. Comparable counts were recorded between Botrytis-infected and sound grape samples. In all cases, the majority of isolates belonged to different species of Enterobacteriaceae. The dominant species in the vineyard was Klebsiella oxytoca that was found in different combinations with Citrobacter freundii, Enterobacter spp., Erwinia sp., Pantoea dispersa, Tatumella ptyseos or other species. In fermenting musts, those populations declined while other species evolved, like Lactobacillus plantarum and Enterobacter ludwigii. Populations in botrytised samples persisted longer during spontaneous fermentations. Present study suggests that bacterial diversity on grapes may be wider than previously described. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes.

    PubMed

    Robinson, Georgina; Caldwell, Gary S; Wade, Matthew J; Free, Andrew; Jones, Clifford L W; Stead, Selina M

    2016-12-12

    Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.

  10. Characterization of the bacterial community associated with the surface and mucus layer of whiting (Merlangius merlangus).

    PubMed

    Smith, Cindy J; Danilowicz, Bret S; Meijer, Wim G

    2007-10-01

    The bacterial community inhabiting the mucus layer and surface of whiting was examined to determine whether the bacteria present are a reflection of the surrounding water or an indigenous bacterial flora is present. The outer mucus, mouth mucus and gut of four whiting harvested from a site in the Irish Sea and the surrounding water were examined by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA gene and clone library construction. The water community was the most diverse, with only a small number of shared water-mucus phylotypes present. The bacterial flora associated with the outer mucus layer were more diverse than that of the mouth mucus and gut. All three mucus layers were characterized by the presence of a dominant phylotype, identified as clone wom-1, highly similar to Photobacterium iliopiscarium. In addition to other Photobacterium phylotypes, members of the CFB and Clostridia groups were also detected. Subsequently, whiting from 11 different sites along the east and south coast of Ireland were compared by tRFLP analysis. Strikingly, the mucus layer of whiting at all sites was characterized by the presence and dominance of a TRF corresponding to the clone wom-1 which was virtually absent from the water column.

  11. Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

    PubMed Central

    Robinson, Georgina; Caldwell, Gary S.; Wade, Matthew J.; Free, Andrew; Jones, Clifford L. W.; Stead, Selina M.

    2016-01-01

    Deposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated. PMID:27941918

  12. Marine heterotrophic bacteria in continuous culture, the bacterial carbon growth efficiency, and mineralization at excess substrate and different temperatures.

    PubMed

    Jiménez-Mercado, Alejandrina; Cajal-Medrano, Ramón; Maske, Helmut

    2007-07-01

    To model the physiological potential of marine heterotrophic bacteria, their role in the food web, and in the biogeochemical carbon cycle, we need to know their growth efficiency response within a matrix of different temperatures and degrees of organic substrate limitation. In this work, we present one part of this matrix, the carbon growth efficiencies of marine bacteria under different temperatures and nonlimiting organic and inorganic substrate supply. We ran aerobic turbidostats with glucose enriched seawater, inoculated with natural populations of heterotrophic marine bacteria at 10, 14, 18, 22, and 26 degrees C. The average cell-specific growth rates increased with temperature from 1.17 to 2.6 h-1. At steady-state total CO2 production, biomass production [particulate organic carbon (POC) and nitrogen (PON)], and viruslike particle abundance was measured. CO2 production and specific growth rate increased with increasing temperature. Bacterial carbon growth efficiency (BCGE), the particulate carbon produced per dissolved carbon utilized, varied between 0.12 and 0.70. Maximum BCGE values and decreased specific respiration rates occurred at higher temperatures (22 and 26 degrees C) and growth rates. This trend was largely attributable to an increase in POC per cell abundance; when the BCGE was recalculated, parameterizing the biomass as the product of cell concentration and a constant cellular carbon content, the opposite trend was observed.

  13. Self-Assembled Functional Nanostructure of Plasmid DNA with Ionic Liquid [Bmim][PF₆]: Enhanced Efficiency in Bacterial Gene Transformation.

    PubMed

    Soni, Sarvesh K; Sarkar, Sampa; Mirzadeh, Nedaossadat; Selvakannan, P R; Bhargava, Suresh K

    2015-04-28

    The electrostatic interaction between the negatively charged phosphate groups of plasmid DNA and the cationic part of hydrophobic ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([Bmim][PF6]), initiates spontaneous self-assembly to form the functional nanostructures made up of DNA and ionic liquid (IL). These functional nanostructures were demonstrated as promising synthetic nonviral vectors for the efficient bacterial pGFP gene transformation in cells. In particular, the functional nanostructures that were made up of 1 μL of IL ([Bmim][PF6]) and 1 μg of plasmid DNA can increase the transformation efficiency by 300-400% in microbial systems, without showing any toxicity for E. coli DH5α cells. (31)P nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) spectroscopy, and X-ray photoelectron (XPS) spectroscopic analysis revealed that the electrostatic interaction between negatively charged phosphate oxygen and cationic Bmim(+) tends to initiate the self-assembly process. Thermogravimetric analysis of the DNA-IL functional nanostructures showed that these nanostructures consist of ∼16 wt % ionic liquid, which is considered to provide the stability to the plasmid DNA that eventually enhanced the transformation efficiency.

  14. International Space Station (ISS) Bacterial Filter Elements (BFEs): Filter Efficiency and Pressure Drop Testing of Returned Units

    NASA Technical Reports Server (NTRS)

    Green, Robert D.; Agui, Juan H.; Vijayakumar, R.; Berger, Gordon M.; Perry, Jay L.

    2017-01-01

    The air quality control equipment aboard the International Space Station (ISS) and future deep space exploration vehicles provide the vital function of maintaining a clean cabin environment for the crew and the hardware. This becomes a serious challenge in pressurized space compartments since no outside air ventilation is possible, and a larger particulate load is imposed on the filtration system due to lack of sedimentation. The ISS Environmental Control and Life Support (ECLS) system architecture in the U.S. Segment uses a distributed particulate filtration approach consisting of traditional High-Efficiency Particulate Air (HEPA) filters deployed at multiple locations in each U.S. Seg-ment module; these filters are referred to as Bacterial Filter Elements, or BFEs. In our previous work, we presented results of efficiency and pressure drop measurements for a sample set of two returned BFEs with a service life of 2.5 years. In this follow-on work, we present similar efficiency, pressure drop, and leak tests results for a larger sample set of six returned BFEs. The results of this work can aid the ISS Program in managing BFE logistics inventory through the stations planned lifetime as well as provide insight for managing filter element logistics for future exploration missions. These results also can provide meaningful guidance for particulate filter designs under consideration for future deep space exploration missions.

  15. Construction of a high efficiency copper adsorption bacterial system via peptide display and its application on copper dye polluted wastewater.

    PubMed

    Maruthamuthu, Murali Kannan; Nadarajan, Saravanan Prabhu; Ganesh, Irisappan; Ravikumar, Sambandam; Yun, Hyungdon; Yoo, Ik-Keun; Hong, Soon Ho

    2015-11-01

    For the construction of an efficient copper waste treatment system, a cell surface display strategy was employed. The copper adsorption ability of recombinant bacterial strains displaying three different copper binding peptides were evaluated in LB Luria-Bertani medium (LB), artificial wastewater, and copper phthalocyanine containing textile dye industry wastewater samples. Structural characteristics of the three peptides were also analyzed by similarity-based structure modeling. The best binding peptide was chosen for the construction of a dimeric peptide display and the adsorption ability of the monomeric and dimeric peptide displayed strains were compared. The dimeric peptide displayed strain showed superior copper adsorption in all three tested conditions (LB, artificial wastewater, and textile dye industry wastewater). When the strains were exposed to copper phthalocyanine dye polluted wastewater, the dimeric peptide display [543.27 µmol/g DCW dry cell weight (DCW)] showed higher adsorption of copper when compared with the monomeric strains (243.53 µmol/g DCW).

  16. Resistance and resilience of removal efficiency and bacterial community structure of gas biofilters exposed to repeated shock loads.

    PubMed

    Cabrol, Léa; Malhautier, Luc; Poly, Franck; Roux, Xavier Le; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

    2012-11-01

    Since full-scale biofilters are often operated under fluctuating conditions, it is critical to understand their response to transient states. Four pilot-scale biofilters treating a composting gas mixture and undergoing repeated substrate pulses of increasing intensity were studied. A systematic approach was proposed to quantify the resistance and resilience capacity of their removal efficiency, which enabled to distinguish between recalcitrant (ammonia, DMDS, ketones) and easily degradable (esters and aldehyde) compounds. The threshold of disturbing shock intensity and the influence of disturbance history depended on the contaminant considered. The spatial and temporal distribution of the bacterial community structure in response to the perturbation regime was analysed by Denaturing Gradient Gel Electrophoresis (DGGE). Even if the substrate-pulses acted as a driving force for some community characteristics (community stratification), the structure-function relationships were trickier to evidence: the distributions of resistance and composition were only partially coupled, with contradictory results depending on the contaminant considered.

  17. Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

    PubMed Central

    Leff, Jonathan W.; Fierer, Noah

    2013-01-01

    Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries) tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms) which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties

  18. Bacterial communities associated with the surfaces of fresh fruits and vegetables.

    PubMed

    Leff, Jonathan W; Fierer, Noah

    2013-01-01

    Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries) tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms) which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties

  19. Is bacterial luminescence response to low-dose radiation associated with mutagenicity?

    PubMed

    Rozhko, T V; Guseynov, O A; Guseynova, V E; Bondar, A A; Devyatlovskaya, A N; Kudryasheva, N S

    2017-10-01

    Luminous marine bacteria are widely used in bioassays with luminescence intensity being a physiological parameter tested. The purpose of the study was to determine whether bacterial genetic alteration is responsible for bioluminescence kinetics change under low-dose radiation exposure. The alpha-emitting radionuclide (241)Am and beta-emitting radionuclide (3)H were used as the sources of low-dose ionizing radiation. Changes of bioluminescence kinetics of Photobacterium phosphoreum in solutions of (241)Am(NO3)3, 7 kBq/L, and tritiated water, 100 MBq/L, were studied; bioluminescence kinetics stages (absence of effect, activation, and inhibition) were determined. Bacterial suspension was sampled at different stages of the bioluminescent kinetics; the doses accumulated by the samples were close or a little higher than a tentative limit of a low-dose interval: 0.10 and 0.85 Gy for (241)Am, or 0.11 and 0.18 Gy for (3)H. Sequence analysis of the 16S ribosomal RNA gene did not reveal a mutagenic effect of low-dose alpha and beta radiation in the bacterial samples. Previous results on bacterial DNA exposed to low-dose gamma radiation (0.25 Gy) were analyzed and compared to those for alpha and beta irradiation. It is concluded that bioluminescence activation and/or inhibition under the applied conditions of low-dose alpha, beta and gamma radioactive exposure is not associated with DNA mutations in the gene sequences tested. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Bacterial Community Associated with Healthy and Diseased Pacific White Shrimp (Litopenaeus vannamei) Larvae and Rearing Water across Different Growth Stages

    PubMed Central

    Zheng, Yanfen; Yu, Min; Liu, Jiwen; Qiao, Yanlu; Wang, Long; Li, Zhitao; Zhang, Xiao-Hua; Yu, Mingchao

    2017-01-01

    Bacterial communities are called another “organ” for aquatic animals and their important influence on the health of host has drawn increasing attention. Thus, it is important to study the relationships between aquatic animals and bacterial communities. Here, bacterial communities associated with Litopenaeus vannamei larvae at different healthy statuses (diseased and healthy) and growth stages (i.e., zoea, mysis, and early postlarvae periods) were examined using 454-pyrosequencing of the 16S rRNA gene. Bacterial communities with significant difference were observed between healthy and diseased rearing water, and several bacterial groups, such as genera Nautella and Kordiimonas could also distinguish healthy and diseased shrimp. Rhodobacteraceae was widely distributed in rearing water at all growth stages but there were several stage-specific groups, indicating that bacterial members in rearing water assembled into distinct communities throughout the larval development. However, Gammaproteobacteria, mainly family Enterobacteriaceae, was the most abundant group (accounting for more than 85%) in shrimp larvae at all growth stages. This study compared bacterial communities associated with healthy and diseased L. vannamei larvae and rearing water, and identified several health- and growth stage-specific bacterial groups, which might be provided as indicators for monitoring the healthy status of shrimp larvae in hatchery. PMID:28769916

  1. Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls

    PubMed Central

    Bienhold, Christina; Wenzhöfer, Frank; Rossel, Pamela E.; Boetius, Antje

    2017-01-01

    Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y) on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100–1700 m), but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were found at any time

  2. Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome.

    PubMed

    Pannaraj, Pia S; Li, Fan; Cerini, Chiara; Bender, Jeffrey M; Yang, Shangxin; Rollie, Adrienne; Adisetiyo, Helty; Zabih, Sara; Lincez, Pamela J; Bittinger, Kyle; Bailey, Aubrey; Bushman, Frederic D; Sleasman, John W; Aldrovandi, Grace M

    2017-07-01

    Establishment of the infant microbiome has lifelong implications on health and immunity. Gut microbiota of breastfed compared with nonbreastfed individuals differ during infancy as well as into adulthood. Breast milk contains a diverse population of bacteria, but little is known about the vertical transfer of bacteria from mother to infant by breastfeeding. To determine the association between the maternal breast milk and areolar skin and infant gut bacterial communities. In a prospective, longitudinal study, bacterial composition was identified with sequencing of the 16S ribosomal RNA gene in breast milk, areolar skin, and infant stool samples of 107 healthy mother-infant pairs. The study was conducted in Los Angeles, California, and St Petersburg, Florida, between January 1, 2010, and February 28, 2015. Amount and duration of daily breastfeeding and timing of solid food introduction. Bacterial composition in maternal breast milk, areolar skin, and infant stool by sequencing of the 16S ribosomal RNA gene. In the 107 healthy mother and infant pairs (median age at the time of specimen collection, 40 days; range, 1-331 days), 52 (43.0%) of the infants were male. Bacterial communities were distinct in milk, areolar skin, and stool, differing in both composition and diversity. The infant gut microbial communities were more closely related to an infant's mother's milk and skin compared with a random mother (mean difference in Bray-Curtis distances, 0.012 and 0.014, respectively; P < .001 for both). Source tracking analysis was used to estimate the contribution of the breast milk and areolar skin microbiomes to the infant gut microbiome. During the first 30 days of life, infants who breastfed to obtain 75% or more of their daily milk intake received a mean (SD) of 27.7% (15.2%) of the bacteria from breast milk and 10.3% (6.0%) from areolar skin. Bacterial diversity (Faith phylogenetic diversity, P = .003) and composition changes were associated with the

  3. Vegetation-associated impacts on arctic tundra bacterial and microeukaryotic communities.

    PubMed

    Shi, Yu; Xiang, Xingjia; Shen, Congcong; Chu, Haiyan; Neufeld, Josh D; Walker, Virginia K; Grogan, Paul

    2015-01-01

    The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H') were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure.

  4. Huanglongbing, a systemic disease, restructures the bacterial community associated with citrus roots.

    PubMed

    Trivedi, Pankaj; Duan, Yongping; Wang, Nian

    2010-06-01

    To examine the effect of pathogens on the diversity and structure of plant-associated bacterial communities, we carried out a molecular analysis using citrus and huanglongbing as a host-disease model. 16S rRNA gene clone library analysis of citrus roots revealed shifts in microbial diversity in response to pathogen infection. The clone library of the uninfected root samples has a majority of phylotypes showing similarity to well-known plant growth-promoting bacteria, including Caulobacter, Burkholderia, Lysobacter, Pantoea, Pseudomonas, Stenotrophomonas, Bacillus, and Paenibacillus. Infection by "Candidatus Liberibacter asiaticus" restructured the native microbial community associated with citrus roots and led to the loss of detection of most phylotypes while promoting the growth of bacteria such as Methylobacterium and Sphingobacterium. In pairwise comparisons, the clone library from uninfected roots contained significantly higher 16S rRNA gene diversity, as reflected in the higher Chao 1 richness estimation (P bacterial community changes not only qualitatively but also quantitatively. The relative proportions of different groups of bacteria changed significantly after infection with the pathogen. These data indicate that infection of citrus by "Ca. Liberibacter asiaticus" has a profound effect on the structure and composition of the bacterial community associated with citrus roots.

  5. Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

    PubMed Central

    Shi, Yu; Xiang, Xingjia; Shen, Congcong; Neufeld, Josh D.; Walker, Virginia K.

    2014-01-01

    The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H′) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. PMID:25362064

  6. Huanglongbing, a Systemic Disease, Restructures the Bacterial Community Associated with Citrus Roots▿

    PubMed Central

    Trivedi, Pankaj; Duan, Yongping; Wang, Nian

    2010-01-01

    To examine the effect of pathogens on the diversity and structure of plant-associated bacterial communities, we carried out a molecular analysis using citrus and huanglongbing as a host-disease model. 16S rRNA gene clone library analysis of citrus roots revealed shifts in microbial diversity in response to pathogen infection. The clone library of the uninfected root samples has a majority of phylotypes showing similarity to well-known plant growth-promoting bacteria, including Caulobacter, Burkholderia, Lysobacter, Pantoea, Pseudomonas, Stenotrophomonas, Bacillus, and Paenibacillus. Infection by “Candidatus Liberibacter asiaticus” restructured the native microbial community associated with citrus roots and led to the loss of detection of most phylotypes while promoting the growth of bacteria such as Methylobacterium and Sphingobacterium. In pairwise comparisons, the clone library from uninfected roots contained significantly higher 16S rRNA gene diversity, as reflected in the higher Chao 1 richness estimation (P ≤ 0.01) of 237.13 versus 42.14 for the uninfected and infected clone libraries, respectively. Similarly, the Shannon index of the uninfected clone library (4.46) was significantly higher than that of the infected clone library (2.61). Comparison of the uninfected clone library with the infected clone library using LIBSHUFF statistics showed a significant difference (P ≤ 0.05). Quantitative PCR analysis revealed that the bacterial community changes not only qualitatively but also quantitatively. The relative proportions of different groups of bacteria changed significantly after infection with the pathogen. These data indicate that infection of citrus by “Ca. Liberibacter asiaticus” has a profound effect on the structure and composition of the bacterial community associated with citrus roots. PMID:20382817

  7. Ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (Agalychnis callidryas).

    PubMed

    Antwis, Rachael E; Haworth, Rachel L; Engelmoer, Daniel J P; Ogilvy, Victoria; Fidgett, Andrea L; Preziosi, Richard F

    2014-01-01

    Amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. The conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. In addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. This could have implications for the suitability of populations intended for reintroduction, as well as the success of probiotic bacterial inoculations intended to provide amphibians with a bacterial community that resists invasion by the chytrid fungus. We aimed to investigate the effect of a carotenoid-enriched diet on the culturable bacterial community associated with captive red-eyed tree frogs (Agalychnis callidryas) and make comparisons to bacteria isolated from a wild population from the Chiquibul Rainforest in Belize. We successfully showed carotenoid availability influences the overall community composition, species richness and abundance of the bacterial community associated with the skin of captive frogs, with A. callidryas fed a carotenoid-enriched diet supporting a greater species richness and abundance of bacteria than those fed a carotenoid-free diet. Our results suggest that availability of carotenoids in the diet of captive frogs is likely to be beneficial for the bacterial community associated with the skin. We also found wild A. callidryas hosted more than double the number of different bacterial species than captive frogs with very little commonality between species. This suggests frogs in captivity may support a reduced and diverged bacterial community in comparison to wild populations of the same species, which could have particular relevance for ex situ conservation projects.

  8. Ex situ Diet Influences the Bacterial Community Associated with the Skin of Red-Eyed Tree Frogs (Agalychnis callidryas)

    PubMed Central

    Antwis, Rachael E.; Haworth, Rachel L.; Engelmoer, Daniel J. P.; Ogilvy, Victoria; Fidgett, Andrea L.; Preziosi, Richard F.

    2014-01-01

    Amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. The conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. In addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. This could have implications for the suitability of populations intended for reintroduction, as well as the success of probiotic bacterial inoculations intended to provide amphibians with a bacterial community that resists invasion by the chytrid fungus. We aimed to investigate the effect of a carotenoid-enriched diet on the culturable bacterial community associated with captive red-eyed tree frogs (Agalychnis callidryas) and make comparisons to bacteria isolated from a wild population from the Chiquibul Rainforest in Belize. We successfully showed carotenoid availability influences the overall community composition, species richness and abundance of the bacterial community associated with the skin of captive frogs, with A. callidryas fed a carotenoid-enriched diet supporting a greater species richness and abundance of bacteria than those fed a carotenoid-free diet. Our results suggest that availability of carotenoids in the diet of captive frogs is likely to be beneficial for the bacterial community associated with the skin. We also found wild A. callidryas hosted more than double the number of different bacterial species than captive frogs with very little commonality between species. This suggests frogs in captivity may support a reduced and diverged bacterial community in comparison to wild populations of the same species, which could have particular relevance for ex situ conservation projects. PMID:24416427

  9. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.

    PubMed

    Ling, Zongxin; Kong, Jianming; Liu, Fang; Zhu, Haibin; Chen, Xiaoyi; Wang, Yuezhu; Li, Lanjuan; Nelson, Karen E; Xia, Yaxian; Xiang, Charlie

    2010-09-07

    Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure and composition of vaginal microbial communities; most of the earlier studies focused on predominant vaginal bacteria in the process of BV. In the present study, the diversity and richness of vaginal microbiota in 50 BV positive and 50 healthy women from China were investigated using culture-independent PCR-denaturing gradient gel electrophoresis (DGGE) and barcoded 454 pyrosequencing methods, and validated by quantitative PCR. Our data demonstrated that there was a profound shift in the absolute and relative abundances of bacterial species present in the vagina when comparing populations associated with healthy and diseased conditions. In spite of significant interpersonal variations, the diversity of vaginal microbiota in the two groups could be clearly divided into two clusters. A total of 246,359 high quality pyrosequencing reads was obtained for evaluating bacterial diversity and 24,298 unique sequences represented all phylotypes. The most predominant phyla of bacteria identified in the vagina belonged to Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. The higher number of phylotypes in BV positive women over healthy is consistent with the results of previous studies and a large number of low-abundance taxa which were missed in previous studies were revealed. Although no single bacterium could be identified as a specific marker for healthy over diseased conditions, three phyla - Bacteroidetes, Actinobacteria and Fusobacteria, and eight genera including Gardnerella, Atopobium, Megasphaera, Eggerthella, Aerococcus, Leptotrichia/Sneathia, Prevotella and Papillibacter were strongly associated with BV (p < 0.05). These genera are potentially excellent

  10. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis

    PubMed Central

    2010-01-01

    Background Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure and composition of vaginal microbial communities; most of the earlier studies focused on predominant vaginal bacteria in the process of BV. In the present study, the diversity and richness of vaginal microbiota in 50 BV positive and 50 healthy women from China were investigated using culture-independent PCR-denaturing gradient gel electrophoresis (DGGE) and barcoded 454 pyrosequencing methods, and validated by quantitative PCR. Results Our data demonstrated that there was a profound shift in the absolute and relative abundances of bacterial species present in the vagina when comparing populations associated with healthy and diseased conditions. In spite of significant interpersonal variations, the diversity of vaginal microbiota in the two groups could be clearly divided into two clusters. A total of 246,359 high quality pyrosequencing reads was obtained for evaluating bacterial diversity and 24,298 unique sequences represented all phylotypes. The most predominant phyla of bacteria identified in the vagina belonged to Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. The higher number of phylotypes in BV positive women over healthy is consistent with the results of previous studies and a large number of low-abundance taxa which were missed in previous studies were revealed. Although no single bacterium could be identified as a specific marker for healthy over diseased conditions, three phyla - Bacteroidetes, Actinobacteria and Fusobacteria, and eight genera including Gardnerella, Atopobium, Megasphaera, Eggerthella, Aerococcus, Leptotrichia/Sneathia, Prevotella and Papillibacter were strongly associated with BV (p < 0.05). These genera are

  11. Sensitive Detection of Thirteen Bacterial Vaginosis-Associated Agents Using Multiplex Polymerase Chain Reaction.

    PubMed

    Malaguti, Natália; Bahls, Larissa Danielle; Uchimura, Nelson Shozo; Gimenes, Fabrícia; Consolaro, Marcia Edilaine Lopes

    2015-01-01

    Bacterial vaginosis (BV) is characterized by a polymicrobial proliferation of anaerobic bacteria and depletion of lactobacilli, which are components of natural vaginal microbiota. Currently, there are limited conventional methods for BV diagnosis, and these methods are time-consuming, expensive, and rarely allow for the detection of more than one agent simultaneously. Therefore, we conceived and validated a multiplex polymerase chain reaction (M-PCR) assay for the simultaneous screening of thirteen bacterial vaginosis-associated agents (BV-AAs) related to symptomatic BV: Gardnerella vaginalis, Mobiluncus curtisii, Mobiluncus mulieris, Bacteroides fragilis, Mycoplasma hominis, Atopobium vaginae, Ureaplasma urealyticum, Megasphaera type I, Clostridia-like bacteria vaginosis-associated bacteria (BVABs) 1, 2, and 3, Sneathia sanguinegens, and Mycoplasma genitalium. The overall validation parameters of M-PCR compared to single PCR (sPCR) were extremely high, including agreement of 99.1% and sensitivity, specificity, and positive predictive values of 100.0%, negative predictive value of 97.0%, accuracy of 99.3%, and agreement with Nugent results of 100.0%. The prevalence of BV-AAs was very high (72.6%), and simultaneous agents were detected in 53.0%, which demonstrates the effectiveness of the M-PCR assay. Therefore, the M-PCR assay has great potential to impact BV diagnostic methods in vaginal samples and diminish associated complications in the near future.

  12. Census of bacterial microbiota associated with the glacier ice worm Mesenchytraeus solifugus.

    PubMed

    Murakami, Takumi; Segawa, Takahiro; Bodington, Dylan; Dial, Roman; Takeuchi, Nozomu; Kohshima, Shiro; Hongoh, Yuichi

    2015-03-01

    The glacier ice worm, Mesenchytraeus solifugus, is a unique annelid, inhabiting only snow and ice in North American glaciers. Here, we analyzed the taxonomic composition of bacteria associated with M. solifugus based on the 16S rRNA gene. We analyzed four fixed-on-site and 10 starved ice worm individuals, along with glacier surface samples. In total, 1341 clones of 16S rRNA genes were analyzed for the ice worm samples, from which 65 bacterial phylotypes (99.0% cut-off) were identified. Of these, 35 phylotypes were closely related to sequences obtained from their habitat glacier and/or other components of cryosphere; whereas three dominant phylotypes were affiliated with animal-associated lineages of the class Mollicutes. Among the three, phylotype Ms-13 shared less than 89% similarity with database sequences and was closest to a gut symbiont of a terrestrial earthworm. Using fluorescence in situ hybridization, Ms-13 was located on the gut wall surface of the ice worms. We propose a novel genus and species, 'Candidatus Vermiplasma glacialis', for this bacterium. Our results raise the possibility that the ice worm has exploited indigenous glacier bacteria, while several symbiotic bacterial lineages have maintained their association with the ice worm during the course of adaptive evolution to the permanently cold environment.

  13. Sensitive Detection of Thirteen Bacterial Vaginosis-Associated Agents Using Multiplex Polymerase Chain Reaction

    PubMed Central

    Malaguti, Natália; Bahls, Larissa Danielle; Uchimura, Nelson Shozo; Gimenes, Fabrícia; Consolaro, Marcia Edilaine Lopes

    2015-01-01

    Bacterial vaginosis (BV) is characterized by a polymicrobial proliferation of anaerobic bacteria and depletion of lactobacilli, which are components of natural vaginal microbiota. Currently, there are limited conventional methods for BV diagnosis, and these methods are time-consuming, expensive, and rarely allow for the detection of more than one agent simultaneously. Therefore, we conceived and validated a multiplex polymerase chain reaction (M-PCR) assay for the simultaneous screening of thirteen bacterial vaginosis-associated agents (BV-AAs) related to symptomatic BV: Gardnerella vaginalis, Mobiluncus curtisii, Mobiluncus mulieris, Bacteroides fragilis, Mycoplasma hominis, Atopobium vaginae, Ureaplasma urealyticum, Megasphaera type I, Clostridia-like bacteria vaginosis-associated bacteria (BVABs) 1, 2, and 3, Sneathia sanguinegens, and Mycoplasma genitalium. The overall validation parameters of M-PCR compared to single PCR (sPCR) were extremely high, including agreement of 99.1% and sensitivity, specificity, and positive predictive values of 100.0%, negative predictive value of 97.0%, accuracy of 99.3%, and agreement with Nugent results of 100.0%. The prevalence of BV-AAs was very high (72.6%), and simultaneous agents were detected in 53.0%, which demonstrates the effectiveness of the M-PCR assay. Therefore, the M-PCR assay has great potential to impact BV diagnostic methods in vaginal samples and diminish associated complications in the near future. PMID:26078959

  14. Spectrum of bacterial colonization associated with urothelial cells from patients with chronic lower urinary tract symptoms.

    PubMed

    Khasriya, Rajvinder; Sathiananthamoorthy, Sanchutha; Ismail, Salim; Kelsey, Michael; Wilson, Mike; Rohn, Jennifer L; Malone-Lee, James

    2013-07-01

    Chronic lower urinary tract symptoms (LUTS), such as urgency and incontinence, are common, especially among the elderly, but their etiology is often obscure. Recent studies of acute urinary tract infections implicated invasion by Escherichia coli into the cytoplasm of urothelial cells, with persistence of long-term bacterial reservoirs, but the role of infection in chronic LUTS is unknown. We conducted a large prospective study with eligible patients with LUTS and controls over a 3-year period, comparing routine urine cultures of planktonic bacteria with cultures of shed urothelial cells concentrated in centrifuged urinary sediments. This comparison revealed large numbers of bacteria undetected by routine cultures. Next, we typed the bacterial species cultured from patient and control sediments under both aerobic and anaerobic conditions, and we found that the two groups had complex but significantly distinct profiles of bacteria associated with their shed bladder epithelial cells. Strikingly, E. coli, the organism most responsible for acute urinary tract infections, was not the only or even the main offending pathogen in this more-chronic condition. Antibiotic protection assays with shed patient cells and in vitro infection studies using patient-derived strains in cell culture suggested that LUTS-associated bacteria are within or extremely closely associated with shed epithelial cells, which explains how routine cultures might fail to detect them. These data have strong implications for the need to rethink our common diagnoses and treatments of chronic urinary tract symptoms.

  15. Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events.

    PubMed

    Sison-Mangus, Marilou P; Jiang, Sunny; Kudela, Raphael M; Mehic, Sanjin

    2016-01-01

    Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6-65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12-86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

  16. Phytoplankton-Associated Bacterial Community Composition and Succession during Toxic Diatom Bloom and Non-Bloom Events

    PubMed Central

    Sison-Mangus, Marilou P.; Jiang, Sunny; Kudela, Raphael M.; Mehic, Sanjin

    2016-01-01

    Pseudo-nitzschia blooms often occur in coastal and open ocean environments, sometimes leading to the production of the neurotoxin domoic acid that can cause severe negative impacts to higher trophic levels. Increasing evidence suggests a close relationship between phytoplankton bloom and bacterial assemblages, however, the microbial composition and succession during a bloom process is unknown. Here, we investigate the bacterial assemblages before, during and after toxic and non-toxic Pseudo-nitzschia blooms to determine the patterns of bacterial succession in a natural bloom setting. Opportunistic sampling of bacterial community profiles were determined weekly at Santa Cruz Municipal Wharf by 454 pyrosequencing and analyzed together with domoic acid levels, phytoplankton community and biomass, nutrients and temperature. We asked if the bacterial communities are similar between bloom and non-bloom events and if domoic acid or the presence of toxic algal species acts as a driving force that can significantly structure phytoplankton-associated bacterial communities. We found that bacterial diversity generally increases when Pseudo-nitzschia numbers decline. Furthermore, bacterial diversity is higher when the low-DA producing P. fraudulenta dominates the algal bloom while bacterial diversity is lower when high-DA producing P. australis dominates the algal bloom, suggesting that the presence of algal toxin can structure bacterial community. We also found bloom-related succession patterns among associated bacterial groups; Gamma-proteobacteria, were dominant during low toxic P. fraudulenta blooms comprising mostly of Vibrio spp., which increased in relative abundance (6–65%) as the bloom progresses. On the other hand, Firmicutes bacteria comprising mostly of Planococcus spp. (12–86%) dominate during high toxic P. australis blooms, with the bacterial assemblage showing the same bloom-related successional patterns in three independent bloom events. Other environmental

  17. Nitrate removal efficiency of bacterial consortium (Pseudomonas sp. KW1 and Bacillus sp. YW4) in synthetic nitrate-rich water.

    PubMed

    Rajakumar, Sundaram; Ayyasamy, Pudukadu Munusamy; Shanthi, Kuppusamy; Thavamani, Palanisami; Velmurugan, Palanivel; Song, Young Chae; Lakshmanaperumalsamy, Perumalsamy

    2008-09-15

    The efficiency of bacterial isolates to reduce nitrate from synthetic nitrate-rich water was tested using a batch scale process. Two efficient nitrate reducing bacterial species were isolated from water samples collected from Kodaikanal and Yercaud lakes. Bacterial analysis of the samples revealed the presence of nitrate reducing bacteria belonging to the genera Pseudomonas, Bacillus, Micrococcus and Alcaligenes. Among the isolates, the consortium of Pseudomonas sp. KW1 and Bacillus sp. YW4 was found to be efficient in nitrate reduction. Influences of various carbon sources, incubation temperature and pH on nitrate reduction from synthetic wastewater were also studied. The results showed a rapid and efficient process of nitrate removal (99.4%) from synthetic wastewater supplemented with starch (1%), inoculated by bacterial consortium (Pseudomonas sp. KW1 and Bacillus sp. YW4) at incubation temperature of 30 degrees C at pH 7. This observation has led to the conclusion that the bacterial consortium was responsible for nitrate removal from synthetic nitrate-rich wastewater.

  18. Differing Daphnia magna assimilation efficiencies for terrestrial, bacterial, and algal carbon and fatty acids.

    PubMed

    Taipale, Sami J; Brett, Michael T; Hahn, Martin W; Martin-Creuzburg, Dominik; Yeung, Sean; Hiltunen, Minna; Strandberg, Ursula; Kankaala, Paula

    2014-02-01

    There is considerable interest in the pathways by which carbon and growth-limiting elemental and biochemical nutrients are supplied to upper trophic levels. Fatty acids and sterols are among the most important molecules transferred across the plant-animal interface of food webs. In lake ecosystems, in addition to phytoplankton, bacteria and terrestrial organic matter are potential trophic resources for zooplankton, especially in those receiving high terrestrial organic matter inputs. We therefore tested carbon, nitrogen, and fatty acid assimilation by the crustacean Daphnia magna when consuming these resources. We fed Daphnia with monospecific diets of high-quality (Cryptomonas marssonii) and intermediate-quality (Chlamydomonas sp. and Scenedesmus gracilis) phytoplankton species, two heterotrophic bacterial strains, and particles from the globally dispersed riparian grass, Phragmites australis, representing terrestrial particulate organic carbon (t-POC). We also fed Daphnia with various mixed diets, and compared Daphnia fatty acid, carbon, and nitrogen assimilation across treatments. Our results suggest that bacteria were nutritionally inadequate diets because they lacked sterols and polyunsaturated omega-3 and omega-6 (omega-3 and omega-6) fatty acids (PUFAs). However, Daphnia were able to effectively use carbon and nitrogen from Actinobacteria, if their basal needs for essential fatty acids and sterols were met by phytoplankton. In contrast to bacteria, t-POC contained sterols and omega-6 and omega-3 fatty acids, but only at 22%, 1.4%, and 0.2% of phytoplankton levels, respectively, which indicated that t-POC food quality was especially restricted with regard to omega-3 PUFAs. Our results also showed higher assimilation of carbon than fatty acids from t-POC and bacteria into Daphnia, based on stable-isotope and fatty acids analysis, respectively. A relatively high (>20%) assimilation of carbon and fatty acids from t-POC was observed only when the proportion of t

  19. Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

    PubMed

    Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

    2013-03-01

    We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics.

  20. The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries

    PubMed Central

    Azcarate-Peril, Maria Andrea; Cadenas, Maria Belen; Butz, Natasha; Paster, Bruce J.; Chen, Tsute; Bair, Eric

    2017-01-01

    Dental caries is the most prevalent disease in humans globally. Efforts to control it have been invigorated by an increasing knowledge of the oral microbiome composition. This study aimed to evaluate the bacterial diversity in occlusal biofilms and its relationship with clinical surface diagnosis and dietary habits. Anamneses were recorded from thirteen 12-year-old children. Biofilm samples collected from occlusal surfaces of 46 permanent second molars were analyzed by 16S rRNA amplicon sequencing combined with the BLASTN-based search algorithm for species identification. The overall mean decayed, missing and filled surfaces modified index [DMFSm Index, including active white spot lesions (AWSL)] value was 8.77±7.47. Biofilm communities were highly polymicrobial collectively, representing 10 bacterial phyla, 25 classes, 29 orders, 58 families, 107 genera, 723 species. Streptococcus sp_Oral_Taxon_065, Corynebacterium matruchotii, Actinomyces viscosus, Actinomyces sp_Oral_Taxon_175, Actinomyces sp_Oral_Taxon_178, Actinomyces sp_Oral_Taxon_877, Prevotella nigrescens, Dialister micraerophilus, Eubacterium_XI G 1 infirmum were more abundant among surfaces with AWSL, and Streptococcus gordonii, Streptococcus sp._Oral_Taxon_058, Enterobacter sp._str._638 Streptococcus australis, Yersinia mollaretii, Enterobacter cloacae, Streptococcus sp._Oral_Taxon_71, Streptococcus sp._Oral_Taxon_F11, Centipeda sp._Oral_Taxon_D18 were more abundant among sound surfaces. Streptococcus mutans was detected on all surfaces in all patients, while Streptococcus sobrinus was detected only in three patients (mean relative abundances 7.1% and 0.6%, respectively). Neither species differentiated healthy from diseased sites. Diets of nine of the subjects were scored as high in fermentable carbohydrates (≧2X/day between meals). A direct association between relative abundances of bacteria and carbohydrate consumption was observed among 18 species. High consumption of fermentable carbohydrates and

  1. Investigations of the structure and function of bacterial communities associated with Sphagnum mosses.

    PubMed

    Opelt, Katja; Chobot, Vladimir; Hadacek, Franz; Schönmann, Susan; Eberl, Leo; Berg, Gabriele

    2007-11-01

    High acidity, low temperature and extremely low concentration of nutrients form Sphagnum bogs into extreme habitats for organisms. Little is known about the bacteria associated with living Sphagnum plantlets, especially about their function for the host. Therefore, we analysed the endo- and ectophytic bacterial populations associated with two widely distributed Sphagnum species, Sphagnum magellanicum and Sphagnum fallax, by a multiphasic approach. The screening of 1222 isolates for antagonistic activity resulted in 326 active isolates. The bacterial communities harboured a high proportion of antifungal (26%) but a low proportion of antibacterial isolates (0.4%). Members of the genus Burkholderia (38%) were found to be the most dominant group of antagonistic bacteria. The finding that a large proportion (89%) of the antagonistic bacteria produced antifungal compounds may provide an explanation for the well-known antimicrobial activity of certain Sphagnum species. The secondary metabolites of the Sphagnum species themselves were analysed by HPLC-PDA. The different spectra of detected compounds may not only explain the antifungal activity but also the species specificity of the microbial communities. The latter was analysed using cultivation-independent single-stranded conformation polymorphism (SSCP) analysis. Using Burkholderia-specific primers we found a high diversity of Burkholderia isolates in the endophytic and ectophytic habitats of Sphagnum. Furthermore, a high diversity of nitrogen-fixing bacteria was detected by using nifH-specific primers, especially inside Sphagnum mosses. In conclusion, this study provides evidence that both Sphagnum species were colonized by characteristic bacterial populations, which appear to be important for pathogen defence and nitrogen fixation.

  2. Bacterial Associations with Diatoms Influence Host Health in a Xenic Model System

    NASA Astrophysics Data System (ADS)

    Baker, L.; Kemp, P. F.

    2016-02-01

    Diatoms are photosynthetic unicellular eukaryotes found ubiquitously in aquatic systems. Microorganisms such as bacteria are frequently found attached to diatoms and may influence the fitness of their host. The most commonly used model organisms in studies of diatom-bacterial associations are Alteromonas and Marinobacter. Some strains of Alteromonas are capable of parasitism, producing chitinases or having algicidal interactions; some strains of Marinobacter are capable of mutualism, providing its host with vital nutrients. In this study, multiple strains of Alteromonas and Marinobacter were isolated from the centric diatom Chaetoceros sp KBDT20. Isolates were added back in varying concentration to cultures of their original xenic diatom host, and to cultures of a smaller, xenic naïve host, Chaetoceros sp. KBDT32. The growth rate of the diatom host was monitored using flow cytometry to assess the impact of the added bacterial isolates on host health. Our results suggest that all strains of Alteromonas tested have an antagonistic relationship with both the original as well as the naïve host while all strains of Marinobacter tested have a synergistic relationship with both diatom cultures. The functional basis for these relationships is being explored by supplementing xenic diatom cultures with materials essential for diatom growth that may be contributed by bacteria, such as B-vitamins and bioavailable trace metals. The colonization rates and competitive interactions between bacteria are investigated through surface colonization studies. The goal of this study is to better inform our understanding of how bacterial associates of diatom populations may contribute to their health, success, or failure in aquatic systems.

  3. The impact of deposition site on vaccination efficiency of a bacterial-based poultry vaccine

    USDA-ARS?s Scientific Manuscript database

    Vaccines are utilized within the poultry industry to minimize disease-associated losses and spray vaccination is a commonly-utilized means for the mass application of poultry vaccines. During this process, vaccine-laden particles are deposited upon target areas (e.g. eyes, nares, oral cavity) resul...

  4. Efficient genomic DNA extraction from low target concentration bacterial cultures using SCODA DNA extraction technology.

    PubMed

    So, Austin; Pel, Joel; Rajan, Sweta; Marziali, Andre

    2010-10-01

    Methods for the extraction of nucleic acids are straightforward in instances where there is ample nucleic acid mass in the sample and contamination is minimal. However, applications in areas such as metagenomics, life science research, clinical research, and forensics, that are limited by smaller amounts of starting materials or more dilute samples, require sample preparation methods that are more efficient at extracting nucleic acids. Synchronous coefficient of drag alteration (SCODA) is a novel electrophoretic nucleic acid purification technology that has been tested successfully with both highly contaminated and dilute samples and is a promising candidate for new sample preparation challenges. In this article, as an example of SCODA's performance with limited sample material, we outline a genomic DNA (gDNA) extraction protocol from low abundance cultures of Escherichia coli DH10B. This method is equally well suited to high biomass samples.

  5. H2S gas biological removal efficiency and bacterial community diversity in biofilter treating wastewater odor.

    PubMed

    Omri, Ilhem; Bouallagui, Hassib; Aouidi, Fathia; Godon, Jean-Jacques; Hamdi, Moktar

    2011-11-01

    The objective of this study was to assess the feasibility of using a biofilter system to treat hydrogen sulfide (H2S) contaminated air and to characterize its microbial community. The biofilter system was packed with peat. During the experimental work, the peat was divided in three layers (down, middle, and up). Satisfactory removal efficiencies of H2S were proved and reached 99% for the majority of the run time at an empty bed retention time (EBRT) of 60 s. The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was used to uncover the changes in the microbial community between the different layers. Analysis of SSCP profiles demonstrated significant differences in community structure from a layer to another with a strong decrease in species diversity towards the up layer. It was found that the used support was suitable for microorganism growth, and may have a potential application in H2S biofiltration system.

  6. A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains

    PubMed Central

    Suzuki, Masato; Shibayama, Keigo; Yahara, Koji

    2016-01-01

    Carbapenems are a class of last-resort antibiotics; thus, the increase in bacterial carbapenem-resistance is a serious public health threat. Acinetobacter baumannii is one of the microorganisms that can acquire carbapenem-resistance; it causes severe nosocomial infection, and is notoriously difficult to control in hospitals. Recently, a machine-learning approach was first used to analyze the genome sequences of hundreds of susceptible and resistant A. baumannii strains, including those carrying commonly acquired resistant mechanisms, to build a classifier that can predict strain resistance. A complementary approach is to explore novel genetic elements that could be associated with the antimicrobial resistance of strains, independent of known mechanisms. Therefore, we carefully selected A. baumannii strains, spanning various genotypes, from public genome databases, and conducted the first genome-wide association study (GWAS) of carbapenem resistance. We employed a recently developed method, capable of identifying any kind of genetic variation and accounting for bacterial population structure, and evaluated its effectiveness. Our study identified a surface adhesin gene that had been horizontally transferred to an ancestral branch of A. baumannii, as well as a specific region of that gene that appeared to accumulate multiple individual variations across the different branches of carbapenem-resistant A. baumannii strains. PMID:27892531

  7. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota

    PubMed Central

    Audebert, Christophe; Even, Gaël; Cian, Amandine; Safadi, Dima El; Certad, Gabriela; Delhaes, Laurence; Pereira, Bruno; Nourrisson, Céline; Poirier, Philippe; Wawrzyniak, Ivan; Delbac, Frédéric; Morelle, Christelle; Bastien, Patrick; Lachaud, Laurence; Bellanger, Anne-Pauline; Botterel, Françoise; Candolfi, Ermanno; Desoubeaux, Guillaume; Morio, Florent; Pomares, Christelle; Rabodonirina, Meja; Loywick, Alexandre; Merlin, Sophie; Viscogliosi, Eric; Chabé, Magali

    2016-01-01

    Alterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single-celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To address the issue of Blastocystis pathogenicity, we investigated the impact of colonization by this protist on the composition of the human gut microbiota. For that purpose, we conducted a cross-sectional study including 48 Blastocystis-colonized patients and 48 Blastocystis-free subjects and performed an Ion Torrent 16S rDNA gene sequencing to decipher the Blastocystis-associated gut microbiota. Here, we report a higher bacterial diversity in faecal microbiota of Blastocystis colonized patients, a higher abundance of Clostridia as well as a lower abundance of Enterobacteriaceae. Our results contribute to suggesting that Blastocystis colonization is usually associated with a healthy gut microbiota, rather than with gut dysbiosis generally observed in metabolic or infectious inflammatory diseases of the lower gastrointestinal tract. PMID:27147260

  8. Bacterial secretion system skews the fate of Legionella-containing vacuoles towards LC3-associated phagocytosis

    PubMed Central

    Hubber, Andree; Kubori, Tomoko; Coban, Cevayir; Matsuzawa, Takeshi; Ogawa, Michinaga; Kawabata, Tsuyoshi; Yoshimori, Tamotsu; Nagai, Hiroki

    2017-01-01

    The evolutionarily conserved processes of endosome-lysosome maturation and macroautophagy are established mechanisms that limit survival of intracellular bacteria. Similarly, another emerging mechanism is LC3-associated phagocytosis (LAP). Here we report that an intracellular vacuolar pathogen, Legionella dumoffii, is specifically targeted by LAP over classical endocytic maturation and macroautophagy pathways. Upon infection, the majority of L. dumoffii resides in ER-like vacuoles and replicate within this niche, which involves inhibition of classical endosomal maturation. The establishment of the replicative niche requires the bacterial Dot/Icm type IV secretion system (T4SS). Intriguingly, the remaining subset of L. dumoffii transiently acquires LC3 to L. dumoffii-containing vacuoles in a Dot/Icm T4SS-dependent manner. The LC3-decorated vacuoles are bound by an apparently undamaged single membrane, and fail to associate with the molecules implicated in selective autophagy, such as ubiquitin or adaptors. The process requires toll-like receptor 2, Rubicon, diacylglycerol signaling and downstream NADPH oxidases, whereas ULK1 kinase is dispensable. Together, we have discovered an intracellular pathogen, the survival of which in infected cells is limited predominantly by LAP. The results suggest that L. dumoffii is a valuable model organism for examining the mechanistic details of LAP, particularly induced by bacterial infection. PMID:28317932

  9. Surface-associated fucoxanthin mediates settlement of bacterial epiphytes on the rockweed Fucus vesiculosus.

    PubMed

    Saha, M; Rempt, M; Grosser, K; Pohnert, G; Weinberger, F

    2011-04-01

    The chemical defence against microfouling in the brown seaweed Fucus vesiculosus was investigated and an inhibitor of bacterial settlement was isolated by bioassay-guided fractionation of non-polar surface extracts. UV-vis and mass spectrometry were used to identify the compound as the carotenoid fucoxanthin. The metabolite was tested at the natural concentration (in a surface volume based assay) against the settlement of four bacterial strains isolated from F. vesiculosus and 11 strains isolated from co-occurring algae and marine sediment. Surface concentrations between 1.4 and 6 μg cm(-2) resulted in 50% inhibition of four of these isolates, which were studied in more detail using a surface area-based assay, while a fifth isolate proved to be less sensitive. The presence of fucoxanthin on the surface of F. vesiculosus was demonstrated with two different surface extraction methods. Fucoxanthin was detected at concentrations between 0.7 and 9 μg cm(-2) on the algal surface. Fucoxanthin was still present at the algal surface after removal of associated diatoms through mechanical cleaning and germanium dioxide treatment and was thus mainly produced by F. vesiculosus rather than by diatoms. Thus, the photosynthetic pigment fucoxanthin appears to be ecologically relevant as a surface-associated antimicrobial agent, acting against the settlement of bacteria on the surface of the macroalga F. vesiculosus.

  10. Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes.

    PubMed

    Cleary, Daniel F R; Becking, Leontine E; Polónia, Ana R M; Freitas, Rossana M; Gomes, Newton C M

    2016-05-01

    In the present study, we compared communities of bacteria in two jellyfish species (the 'golden' jellyfish Mastigias cf.papua and the box jellyfish Tripedalia cf.cystophora) and water in three marine lakes located in the Berau region of northeastern Borneo, Indonesia. Jellyfish-associated bacterial communities were compositionally distinct and less diverse than bacterioplankton communities. Alphaproteobacteria, Gammaproteobacteria, Synechococcophycidae and Flavobacteriia were the most abundant classes in water. Jellyfish-associated bacterial communities were dominated by OTUs assigned to the Gammaproteobacteria (family Endozoicimonaceae), Mollicutes, Spirochaetes and Alphaproteobacteria (orders Kiloniellales and Rhodobacterales). Mollicutes were mainly restricted to Mastigias whereas Spirochaetes and the order Kiloniellales were most abundant in Tripedalia hosts. The most abundant OTU overall in jellyfish hosts was assigned to the family Endozoicimonaceae and was highly similar to organisms in Genbank obtained from various hosts including an octocoral, bivalve and fish species. Other abundant OTUs included an OTU assigned to the order Entomoplasmatales and mainly found in Mastigias hosts and OTUs assigned to the Spirochaetes and order Kiloniellales and mainly found in Tripedalia hosts. The low sequence similarity of the Entomoplasmatales OTU to sequences in Genbank suggests that it may be a novel lineage inhabiting Mastigias and possibly restricted to marine lakes.

  11. Carbon dioxide and hydrogen sulfide associations with regional bacterial diversity patterns in microbially induced concrete corrosion.

    PubMed

    Ling, Alison L; Robertson, Charles E; Harris, J Kirk; Frank, Daniel N; Kotter, Cassandra V; Stevens, Mark J; Pace, Norman R; Hernandez, Mark T

    2014-07-01

    The microbial communities associated with deteriorating concrete corrosion fronts were characterized in 35 samples taken from wastewater collection and treatment systems in ten utilities. Bacterial communities were described using Illumina MiSeq sequencing of the V1V2 region of the small subunit ribosomal ribonucleic acid (SSU-rRNA) gene recovered from fresh corrosion products. Headspace gas concentrations (hydrogen sulfide, carbon dioxide, and methane), pore water pH, moisture content, and select mineralogy were tested for correlation to community outcomes and corrosion extent using pairwise linear regressions and canonical correspondence analysis. Corroding concrete was most commonly characterized by moisture contents greater than 10%, pore water pH below one, and limited richness (<10 taxa). Bacterial community composition was not correlated to geographic location when considered independently from other environmental factors. Corrosion was most severe in sites with high levels of hydrogen sulfide (>100 ppm) and carbon dioxide (>1%) gases, conditions which also were associated with low diversity biofilms dominated by members of the acidophilic sulfur-oxidizer genus Acidithiobacillus.

  12. 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.

  13. Bacterial communities associated with healthy and Acropora white syndrome-affected corals from American Samoa

    USGS Publications Warehouse

    Wilson, Bryan; Aeby, Greta S.; Work, Thierry M.; Bourne, David G.

    2012-01-01

    Acropora white syndrome (AWS) is characterized by rapid tissue loss revealing the white underlying skeleton and affects corals worldwide; however, reports of causal agents are conflicting. Samples were collected from healthy and diseased corals and seawater around American Samoa and bacteria associated with AWS characterized using both culture-dependent and culture-independent methods, from coral mucus and tissue slurries, respectively. Bacterial 16S rRNA gene clone libraries derived from coral tissue were dominated by the Gammaproteobacteria, and Jaccard's distances calculated between the clone libraries showed that those from diseased corals were more similar to each other than to those from healthy corals. 16S rRNA genes from 78 culturable coral mucus isolates also revealed a distinct partitioning of bacterial genera into healthy and diseased corals. Isolates identified as Vibrionaceae were further characterized by multilocus sequence typing, revealing that whilst several Vibrio spp. were found to be associated with AWS lesions, a recently described species, Vibrio owensii, was prevalent amongst cultured Vibrio isolates. Unaffected tissues from corals with AWS had a different microbiota than normal Acropora as found by others. Determining whether a microbial shift occurs prior to disease outbreaks will be a useful avenue of pursuit and could be helpful in detecting prodromal signs of coral disease prior to manifestation of lesions.

  14. Particle-associated extracellular enzyme activity and bacterial community composition across the Canadian Arctic Ocean.

    PubMed

    Kellogg, Colleen T E; Deming, Jody W

    2014-08-01

    Microbial enzymatic hydrolysis of marine-derived particulate organic carbon (POC) can be a dominant mechanism for attenuating carbon flux in cold Arctic waters during spring and summer. Whether this mechanism depends on composition of associated microbial communities and extends into other seasons is not known. Bacterial community composition (BCC) and extracellular enzyme activity (EEA, for leucine aminopeptidases, glucosidases and chitobiases) were measured on small suspended particles and potentially sinking aggregates collected during fall from waters of the biologically productive North Water and river-impacted Beaufort Sea. Although other environmental variables appeared influential, both BCC and EEA varied along a marine productivity gradient in the two regions. Aggregates harbored the most distinctive bacterial communities, with a small number of taxa driving differences between particle-size classes (1.0-60 and > 60 μm) and free-living bacteria (0.2-1.0 μm). Significant relationships between patterns in particle-associated BCC and EEA suggest strong links between these two variables. Calculations indicated that up to 80% of POC in the euphotic zone of the North Water, and 20% in the Beaufort Sea, may be hydrolyzed enzymatically, underscoring the importance of this mechanism in attenuating carbon fluxes in Arctic waters even as winter approaches. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  15. Association of Growth Substrates and Bacterial Genera with Benzo[a]pyrene Mineralization in Contaminated Soil

    PubMed Central

    Jones, Maiysha D.; Rodgers-Vieira, Elyse A.; Hu, Jing; Aitken, Michael D.

    2014-01-01

    Abstract Benzo[a]pyrene (BaP) is a carcinogenic polycyclic aromatic hydrocarbon (PAH) that is not known to be a bacterial growth substrate. Organisms capable of cometabolizing BaP in complex field-contaminated systems have not previously been identified. We evaluated BaP mineralization by a bacterial community from a bioreactor treating PAH-contaminated soil during coincubation with or after pre-enrichment on various PAHs as growth substrates. Pyrosequence libraries of 16S rRNA genes were used to identify bacteria that were enriched on the added growth substrate as a means of associating specific organisms with BaP mineralization. Coincubating the bioreactor-treated soil with naphthalene, phenanthrene, or pyrene inhibited BaP mineralization, whereas pre-enriching the soil on the same three PAHs enhanced BaP mineralization. Combined, these results suggest that bacteria in the bioreactor community that are capable of growing on naphthalene, phenanthrene, and/or pyrene can metabolize BaP, with coincubation competitively inhibiting BaP metabolism. Anthracene, fluoranthene, and benz[a]anthracene had little effect on BaP mineralization compared to incubations without an added growth substrate under either coincubation or pre-enrichment conditions. Substantial increases in relative abundance after pre-enrichment with phenanthrene, naphthalene, or pyrene, but not the other PAHs, suggest that members of the genera Cupriavidus and Luteimonas may have been associated with BaP mineralization. PMID:25469077

  16. Robust biological nitrogen fixation in a model grass-bacterial association.

    PubMed

    Pankievicz, Vânia C S; do Amaral, Fernanda P; Santos, Karina F D N; Agtuca, Beverly; Xu, Youwen; Schueller, Michael J; Arisi, Ana Carolina M; Steffens, Maria B R; de Souza, Emanuel M; Pedrosa, Fábio O; Stacey, Gary; Ferrieri, Richard A

    2015-03-01

    Nitrogen-fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C4 grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen-13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen-limiting conditions when inoculated with an ammonium-excreting strain of Azospirillum brasilense. (11)C-labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen-starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen-sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  17. Denaturing gradient gel electrophoresis analysis of bacterial communities associated with failed endodontic treatment.

    PubMed

    Rôças, Isabela N; Siqueira, José F; Aboim, Marcela C R; Rosado, Alexandre S

    2004-12-01

    A great deal of evidence indicates that persistent infections of the root canal of human teeth play an important role in the failure of the root canal treatment. The present study was undertaken to apply the PCR-DGGE fingerprinting approach to examine the structure of the bacterial population infecting previously treated root canals of humans associated with persistent periradicular lesions. Samples were taken from 14 filled root canals, DNA was extracted, and part of the 16S rDNA of all bacteria was amplified by PCR and separated by DGGE, generating banding patterns representative of the community structure. Species-specific PCR for the detection of Enterococcus faecalis was also performed. The mean number of bands detected in the 16S rDNA community profiles was about 6, ranging from 1 to 26 bands. Each sample showed a unique structure of the microbial community. The species-specific PCR assay revealed the presence of E. faecalis in 10 of 14 samples, but DGGE analysis revealed it was not the dominant species. Results revealed that the intraradicular bacterial community associated with failed endodontic treatment significantly varied in composition from teeth to teeth. Persistent intraradicular infections were present in all root-filled teeth.

  18. Analysis of bacterial communities associated with the benthic amphipod Diporeia in the Laurentian Great Lakes Basin.

    PubMed

    Winters, Andrew D; Marsh, Terence L; Brenden, Travis O; Faisal, Mohamed

    2015-01-01

    Bacterial communities play important roles in the biological functioning of crustaceans, yet little is known about their diversity, structure, and dynamics. This study was conducted to investigate the bacterial communities associated with the benthic amphipod Diporeia, an important component in the Great Lakes foodweb that has been declining over the past 3 decades. In this study, the combination of 16S rRNA gene sequencing and terminal restriction fragment length polymorphism revealed a total of 175 and 138 terminal restriction fragments (T-RFs) in Diporeia samples following treatment with the endonucleases HhaI and MspI, respectively. Relatively abundant and prevalent T-RFs were affiliated with the genera Flavobacterium and Pseudomonas and the class Betaproteobacteria. T-RFs affiliated with the order Rickettsiales were also detected. A significant difference in T-RF presence and abundance (P = 0.035) was detected among profiles generated for Diporeia collected from 4 sites in Lake Michigan. Comparison of profiles generated for Diporeia samples collected in 2 years from lakes Superior and Michigan showed a significant change in diversity for Lake Superior Diporeia but not Lake Michigan Diporeia. Profiles from one Lake Michigan site contained multiple unique T-RFs compared with other Lake Michigan Diporeia profiles, most notably one that represents the genus Methylotenera. This study generated the most extensive list of bacteria associated with Diporeia and sheds useful insights on the microbiome of Great Lakes Diporeia that may help to reveal potential causes of the decline of Diporeia populations.

  19. Efficient bio-deodorization of aniline vapor in a biotrickling filter: metabolic mineralization and bacterial community analysis.

    PubMed

    Li, Guiying; Wan, Shungang; An, Taicheng

    2012-04-01

    A biotrickling filter inoculated with commercial mixed microorganisms B350 was employed to treat N-containing odorous vapor - aniline. Results indicated no aniline could be detected when empty bed residence time (EBRT) was larger than 110s at inlet concentration of 0.30 g m(-3). The variation of inlet concentration did not change removal efficiencies when concentration is less than 0.21 g m(-3) at fixed EBRT 110s. Biodegradation mechanism of aniline was tentatively proposed based on identified intermediates and predicted biodegradation pathway as well as final mineralized products. Aniline was firstly biodegraded to catechol, and then to levulinic acid and subsequently to succinic acid. Finally, about 62% aniline carbon was completely mineralized to CO(2), while about 91% aniline nitrogen was converted into ammonia and nitrate. Bacterial community in biotrickling filter was found that at least seven bands microbes were identified for high efficiencies of bioreactor at stable state. In all, biotrickling filter seeded with B350 would be a better choice for the purification odorous gas containing high concentration aniline.

  20. Collision efficiency distribution of a bacterial suspension flowing through porous media and implications for field-scale transport.

    PubMed

    Brown, Derick G; Abramson, Alon

    2006-05-01

    The collision efficiency (alpha) distribution of a bacterial population was determined using multiple packed-bed columns of varying lengths and analyzing the bacteria clean-bed breakthrough concentrations using a distributed colloid filtration theory. This technique allows the alpha distribution to be determined independently from other effects that can cause non-exponential deposition, including detachment and blocking. It was found that multiple probability density functions (PDF's) could accurately replicate the experimental data. Regardless of which PDF was used, a distributed alpha resulted in significantly greater predicted field-scale transport than when using a single alpha. However, there were wide variations in the predicted field-scale transport between the different distributions, suggesting that lab-scale experiments may not be readily utilized to determine the specific PDF that best represents alpha at the field scale. Finally, blocking was observed in the column effluent curves, underscoring the fact that if non-clean-bed processes occur then an approach such as that utilized in the current study may be used to separate the non-clean-bed and clean-bed processes when determining the collision efficiency distribution.

  1. Disinfection efficiency of peracetic acid (PAA): inactivation of coliphages and bacterial indicators in a municipal wastewater plant.

    PubMed

    Zanetti, F; De Luca, G; Sacchetti, R; Stampi, S

    2007-11-01

    The aim of the study was to assess the efficiency of low doses of peracetic acid against viral and bacterial indicators in wastewater and to evaluate if the treatment allows regulatory requirements to be satisfied. A total of 31 samplings were carried out, each involving the collection of secondary effluent and of effluent disinfected with 1.2 or 1.5 mg l(-1) of peracetic acid (contact time 20 minutes). In each sample were measured: somatic coliphages, F-specific RNA bacteriophages, Escherichia coli, total and faecal coliforms, enterococci. Peracetic acid disinfection showed significant differences between the reductions of the microorganisms tested: E. coli showed the highest reduction (1.78 and 2.43 Log respectively with 1.2 and 1.5 mg l(-1) of peracetic acid) and phages the lowest (ranging between 0.52 and 0.60 Log). Only a concentration of 1.5 mg l(-1) of peracetic acid would enable the effluent to be discharged into surface waters in compliance with Italian regulations. The variability of microbial resistance against the peracetic acid disinfection treatment, underlines the importance of assessing disinfection efficiency by using more than one indicator microorganism. The detection of E. coli could be usefully accompanied by tests for more resistant microorganisms such as enterococci or coliphages. In conclusion, peracetic acid can be used for the disinfection of effluents even at low doses, with the advantage of reducing costs and preventing the formation of significant amounts of genotoxic by-products.

  2. Highly efficient modification of bacterial artificial chromosomes (BACs) using novel shuttle vectors containing the R6Kgamma origin of replication.

    PubMed

    Gong, Shiaoching; Yang, Xiangdong William; Li, Chenjian; Heintz, Nathaniel

    2002-12-01

    Bacterial artificial chromosome (BAC) mediated transgenesis has proven to be a highly reliable way to obtain accurate transgene expression for in vivo studies of gene expression and function. A rate-limiting step in use of this technology to characterize large numbers of genes has been the process with which BACs can be modified by homologous recombination in Escherichia coli. We report here a highly efficient method for modifying BACs by using a novel set of shuttle vectors that contain the R6Kgamma origin for DNA replication, the E. coli RecA gene for recombination, and the SacB gene for negative selection. These new vectors greatly increased the ease with which one can clone the shuttle vectors, as well as screen for co-integrated and resolved clones. Furthermore, we simplify the shuttle vector cloning to one step by incorporation of a "built-in" resolution cassette for rapid removal of the unwanted vector sequences. This new system has been used to modify a dozen BACs. It is well suited for efficient production of modified BACs for use in a variety of in vivo studies.

  3. HASE: Framework for efficient high-dimensional association analyses

    PubMed Central

    Roshchupkin, G. V.; Adams, H. H. H.; Vernooij, M. W.; Hofman, A.; Van Duijn, C. M.; Ikram, M. A.; Niessen, W. J.

    2016-01-01

    High-throughput technology can now provide rich information on a person’s biological makeup and environmental surroundings. Important discoveries have been made by relating these data to various health outcomes in fields such as genomics, proteomics, and medical imaging. However, cross-investigations between several high-throughput technologies remain impractical due to demanding computational requirements (hundreds of years of computing resources) and unsuitability for collaborative settings (terabytes of data to share). Here we introduce the HASE framework that overcomes both of these issues. Our approach dramatically reduces computational time from years to only hours and also requires several gigabytes to be exchanged between collaborators. We implemented a novel meta-analytical method that yields identical power as pooled analyses without the need of sharing individual participant data. The efficiency of the framework is illustrated by associating 9 million genetic variants with 1.5 million brain imaging voxels in three cohorts (total N = 4,034) followed by meta-analysis, on a standard computational infrastructure. These experiments indicate that HASE facilitates high-dimensional association studies enabling large multicenter association studies for future discoveries. PMID:27782180

  4. SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination.

    PubMed

    Handley, Scott A; Desai, Chandni; Zhao, Guoyan; Droit, Lindsay; Monaco, Cynthia L; Schroeder, Andrew C; Nkolola, Joseph P; Norman, Megan E; Miller, Andrew D; Wang, David; Barouch, Dan H; Virgin, Herbert W

    2016-03-09

    AIDS caused by simian immunodeficiency virus (SIV) infection is associated with gastrointestinal disease, systemic immune activation, and, in cross-sectional studies, changes in the enteric virome. Here we performed a longitudinal study of a vaccine cohort to define the natural history of changes in the fecal metagenome in SIV-infected monkeys. Matched rhesus macaques were either uninfected or intrarectally challenged with SIV, with a subset receiving the Ad26 vaccine, an adenovirus vector expressing the viral Env/Gag/Pol antigens. Progression of SIV infection to AIDS was associated with increased detection of potentially pathogenic viruses and bacterial enteropathogens. Specifically, adenoviruses were associated with an increased incidence of gastrointestinal disease and AIDS-related mortality. Viral and bacterial enteropathogens were largely absent from animals protected by the vaccine. These data suggest that the SIV-associated gastrointestinal disease is associated with the presence of both viral and bacterial enteropathogens and that protection against SIV infection by vaccination prevents enteropathogen emergence.

  5. Plant-Associated Bacterial Degradation of Toxic Organic Compounds in Soil

    PubMed Central

    McGuinness, Martina; Dowling, David

    2009-01-01

    A number of toxic synthetic organic compounds can contaminate environmental soil through either local (e.g., industrial) or diffuse (e.g., agricultural) contamination. Increased levels of these toxic organic compounds in the environment have been associated with human health risks including cancer. Plant-associated bacteria, such as endophytic bacteria (non-pathogenic bacteria that occur naturally in plants) and rhizospheric bacteria (bacteria that live on and near the roots of plants), have been shown to contribute to biodegradation of toxic organic compounds in contaminated soil and could have potential for improving phytoremediation. Endophytic and rhizospheric bacterial degradation of toxic organic compounds (either naturally occurring or genetically enhanced) in contaminated soil in the environment could have positive implications for human health worldwide and is the subject of this review. PMID:19742157

  6. RNA structures are involved in the thermoregulation of bacterial virulence-associated traits.

    PubMed

    Grosso-Becera, María Victoria; Servín-González, Luis; Soberón-Chávez, Gloria

    2015-08-01

    Pathogenic bacteria are exposed to temperature changes during colonization of the human body and during exposure to environmental conditions. Virulence-associated traits are mainly expressed by pathogenic bacteria at 37°C. We review different cases of post-transcriptional regulation of virulence-associated proteins through RNA structures (called RNA thermometers or RNATs) that modulate the translation of mRNAs. The analysis of RNATs in pathogenic bacteria has started to produce a comprehensive picture of the structures involved, and of the genes regulated by this mechanism. However, we are still not able to predict the functionality of putative RNATs predicted by bioinformatics methods, and there is not a global approach to measure the effect of these RNA structures in gene regulation during bacterial infections. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Flotillin-1 (Reggie-2) Contributes to Chlamydia pneumoniae Growth and Is Associated with Bacterial Inclusion

    PubMed Central

    Korhonen, Juha T.; Puolakkainen, Mirja; Häivälä, Reetta; Penttilä, Tuula; Haveri, Anu; Markkula, Eveliina

    2012-01-01

    Chlamydiae are obligate intracellular pathogens replicating only inside the eukaryotic host. Here, we studied the effect of human flotillin-1 protein on Chlamydia pneumoniae growth in human line (HL) and A549 epithelial cell lines. RNA interference was applied to disrupt flotillin-1-mediated endocytosis. Host-associated bacteria were detected by quantitative PCR, and C. pneumoniae growth was evaluated by inclusion counts. C. pneumoniae attachment to host cells was unaffected, but bacterial intracellular growth was attenuated in the flotillin-1-silenced cells. By using confocal microscopy, we detected flotillin-1 colocalized with the inclusion membrane protein A (IncA) in the C. pneumoniae inclusion membranes. In addition, flotillin-1 was associated with IncA in detergent-resistant membrane microdomains (DRMs) in biochemical fractioning. These results suggest that flotillin-1 localizes to the C. pneumoniae inclusion membrane and plays an important role for intracellular growth of C. pneumoniae. PMID:22215737

  8. Changes in symbiotic and associative interrelations in a higher plant-bacterial system during space flight.

    PubMed

    Kordyum, V A; Man'ko, V G; Popova, A F; Mashinsky, A L; Shcherbak, O H; Nguen, H T

    1983-01-01

    The miniature cenosis consisting of the water fern Azolla with its associated symbiotic nitrogen-fixing cyanobacterium Anabaena and the concomitant bacteria was investigated. Ecological closure was shown to produce sharp quantitative and qualitative changes in the number and type of concomitant bacteria. Changes in the distribution of bacterial types grown on beef-extract broth after space flight were recorded. Anabaena azollae underwent the most significant changes under spaceflight conditions. Its cell number per Azolla biomass unit increased substantially. Thus closure of cenosis resulted in a weakening of control over microbial development by Azolla. This tendency was augmented by spaceflight factors. Reduction in control exerted by macro-organisms over development of associated micro-organisms must be taken into account in constructing closed ecological systems in the state of weightlessness.

  9. Bacterial communities and species-specific associations with the mucus of Brazilian coral species

    PubMed Central

    Carlos, Camila; Torres, Tatiana T.; Ottoboni, Laura M. M.

    2013-01-01

    We investigated the existence of species-specific associations between Brazilian coral species and bacteria. Pyrosequencing of the V3 region of the 16S rDNA was used to analyze the taxonomic composition of bacterial communities associated with the mucus of four coral species (Madracis decactis, Mussismilia hispida, Palythoa caribaeorum, and Tubastraea coccinea) in two seasons (winter and summer), which were compared with the surrounding water and sediment. The microbial communities found in samples of mucus, water, and sediment differed according to the composition and relative frequency of OTUs. The coral mucus community seemed to be more stable and resistant to seasonal variations, compared to the water and sediment communities. There was no influence of geographic location on the composition of the communities. The sediment community was extremely diverse and might act as a "seed bank" for the entire environment. Species-specific OTUs were found in P. caribaeorum, T. coccinea, and M. hispida. PMID:23567936

  10. Efficient degradation of chlorimuron-ethyl by a bacterial consortium and shifts in the aboriginal microorganism community during the bioremediation of contaminated-soil.

    PubMed

    Li, Chunyan; Lv, Tongyang; Liu, Wanjun; Zang, Hailian; Cheng, Yi; Li, Dapeng

    2017-05-01

    Excessive application of chlorimuron-ethyl has led to soil contamination and limited crop rotation; therefore, tactics to decrease and eliminate residual chlorimuron-ethyl in the environment have attracted increasing attention. In this study, two chlorimuron-ethyl-degrading bacterial strains (Rhodococcus sp. D310-1; Enterobacter sp. D310-5) were used to ferment and prepare a chlorimuron-ethyl-degrading bacterial consortium. To improve the degradation efficiency of the bacterial consortium, the cultivation conditions were optimized using response surface methodology (RSM). The maximum biodegradation rate (87.42%) was obtained under optimal conditions (carbon concentration, 9.21gL(-1); temperature, 26.15°C; pH, 6.95). The rate of chlorimuron-ethyl degradation by the bacterial consortium in the chlorimuron-ethyl-contaminated soil was monitored and reached 80.02% at the end of a 60-d incubation period. Illumina MiSeq sequencing results showed that microbial diversity was high, and 33 phyla were identified in the analyzed samples. Proteobacteria, Acidobacteria, Acidobacteria, Firmicutes and Bacteroidetes were present in relatively high abundances in the samples. The bacterial consortium made a positive impact on the remediation of chlorimuron-ethyl-contaminated soil and somewhat altered the composition of the bacterial community in the chlorimuron-ethyl-contaminated soil. These findings provide highly valuable information on the production of bacterial consortium for the remediation of chlorimuron-ethyl and other sulfonylurea-herbicide-contaminated soil.

  11. Altering Transplantation Time to Avoid Periods of High Temperature Can Efficiently Reduce Bacterial Wilt Disease Incidence with Tomato

    PubMed Central

    Wei, Zhong; Huang, Jian-Feng; Hu, Jie; Gu, Yi-An; Yang, Chun-Lan; Mei, Xin-Lan; Shen, Qi-Rong; Xu, Yang-Chun; Friman, Ville-Petri

    2015-01-01

    Tomato bacterial wilt caused by Ralstonia solanacearum bacterium is a severe problem in Southern China, where relatively high environmental temperatures commonly prevails during the crop seasons. Previous research has indicated that bacterial wilt disease incidence generally increases during the warm months of summer leading to reduced tomato yield. Moreover, the efficacy of bio-organic fertilizers (BOFs)–organic compost fortified with pathogen-suppressive bacteria—is often lost during the periods of high environmental temperatures. Here we studied if the disease incidence could be reduced and the BOF performance enhanced by simply preponing and postponing the traditional seedling transplantation times to avoid tomato plant development during periods of high environmental temperature. To this end, a continuous, two-year field experiment was conducted to evaluate the performance of BOF in two traditional (late-spring [LS] and early-autumn [EA]) and two alternative (early-spring [ES] and late-autumn [LA]) crop seasons. We found that changing the transplantation times reduced the mean disease incidence from 33.9% (LS) and 54.7% (EA) to 11.1% (ES) and 7.1% (LA), respectively. Reduction in disease incidence correlated with the reduction in R. Solanacearum pathogen density in the tomato plant rhizosphere and stem base. Applying BOF during alternative transplantation treatments improved biocontrol efficiency from 43.4% (LS) and 3.1% (EA) to 67.4% (ES) and 64.8% (LA). On average, the mean maximum air temperatures were positively correlated with the disease incidence, and negatively correlated with the BOF biocontrol efficacy over the crop seasons. Crucially, even though preponing the transplantation time reduced the tomato yield in general, it was still economically more profitable compared to LS season due to reduced crop losses and relatively higher market prices. Preponing and postponing traditional tomato transplantation times to cooler periods could thus offer

  12. Bacteriophages of Staphylococcus aureus efficiently package various bacterial genes and mobile genetic elements including SCCmec with different frequencies.

    PubMed

    Mašlaňová, Ivana; Doškař, Jiří; Varga, Marian; Kuntová, Lucie; Mužík, Jan; Malúšková, Denisa; Růžičková, Vladislava; Pantůček, Roman

    2013-02-01

    Staphylococcus aureus is a serious human and veterinary pathogen in which new strains with increasing virulence and antimicrobial resistance occur due to acquiring new genes by horizontal transfer. It is generally accepted that temperate bacteriophages play a major role in gene transfer. In this study, we proved the presence of various bacterial genes of the S. aureus COL strain directly within the phage particles via qPCR and quantified their packaging frequency. Non-parametric statistical analysis showed that transducing bacteriophages φ11, φ80 and φ80α of serogroup B, in contrast to serogroup A bacteriophage φ81, efficiently package selected chromosomal genes localized in 4 various loci of the chromosome and 8 genes carried on variable elements, such as staphylococcal cassette chromosome SCCmec, staphylococcal pathogenicity island SaPI1, genomic islands vSaα and vSaβ, and plasmids with various frequency. Bacterial gene copy number per ng of DNA isolated from phage particles ranged between 1.05 × 10(2) for the tetK plasmid gene and 3.86 × 10(5) for the SaPI1 integrase gene. The new and crucial finding that serogroup B bacteriophages can package concurrently ccrA1 (1.16 × 10(4)) and mecA (1.26 × 10(4)) located at SCCmec type I into their capsids indicates that generalized transduction plays an important role in the evolution and emergence of new methicillin-resistant clones.

  13. Altering Transplantation Time to Avoid Periods of High Temperature Can Efficiently Reduce Bacterial Wilt Disease Incidence with Tomato.

    PubMed

    Wei, Zhong; Huang, Jian-Feng; Hu, Jie; Gu, Yi-An; Yang, Chun-Lan; Mei, Xin-Lan; Shen, Qi-Rong; Xu, Yang-Chun; Friman, Ville-Petri

    2015-01-01

    Tomato bacterial wilt caused by Ralstonia solanacearum bacterium is a severe problem in Southern China, where relatively high environmental temperatures commonly prevails during the crop seasons. Previous research has indicated that bacterial wilt disease incidence generally increases during the warm months of summer leading to reduced tomato yield. Moreover, the efficacy of bio-organic fertilizers (BOFs)-organic compost fortified with pathogen-suppressive bacteria-is often lost during the periods of high environmental temperatures. Here we studied if the disease incidence could be reduced and the BOF performance enhanced by simply preponing and postponing the traditional seedling transplantation times to avoid tomato plant development during periods of high environmental temperature. To this end, a continuous, two-year field experiment was conducted to evaluate the performance of BOF in two traditional (late-spring [LS] and early-autumn [EA]) and two alternative (early-spring [ES] and late-autumn [LA]) crop seasons. We found that changing the transplantation times reduced the mean disease incidence from 33.9% (LS) and 54.7% (EA) to 11.1% (ES) and 7.1% (LA), respectively. Reduction in disease incidence correlated with the reduction in R. Solanacearum pathogen density in the tomato plant rhizosphere and stem base. Applying BOF during alternative transplantation treatments improved biocontrol efficiency from 43.4% (LS) and 3.1% (EA) to 67.4% (ES) and 64.8% (LA). On average, the mean maximum air temperatures were positively correlated with the disease incidence, and negatively correlated with the BOF biocontrol efficacy over the crop seasons. Crucially, even though preponing the transplantation time reduced the tomato yield in general, it was still economically more profitable compared to LS season due to reduced crop losses and relatively higher market prices. Preponing and postponing traditional tomato transplantation times to cooler periods could thus offer simple

  14. Bacterial pathogens in Hawaiian coastal streams--associations with fecal indicators, land cover, and water quality.

    PubMed

    Viau, Emily J; Goodwin, Kelly D; Yamahara, Kevan M; Layton, Blythe A; Sassoubre, Lauren M; Burns, Siobhán L; Tong, Hsin-I; Wong, Simon H C; Lu, Yuanan; Boehm, Alexandria B

    2011-05-01

    This work aimed to understand the distribution of five bacterial pathogens in O'ahu coastal streams and relate their presence to microbial indicator concentrations, land cover of the surrounding watersheds, and physical-chemical measures of stream water quality. Twenty-two streams were sampled four times (in December and March, before sunrise and at high noon) to capture seasonal and time of day variation. Salmonella, Campylobacter, Staphylococcus aureus, Vibrio vulnificus, and V. parahaemolyticus were widespread -12 of 22 O'ahu streams had all five pathogens. All stream waters also had detectable concentrations of four fecal indicators and total vibrio with log mean ± standard deviation densities of 2.2 ± 0.8 enterococci, 2.7 ± 0.7 Escherichia coli, 1.1 ± 0.7 Clostridium perfringens, 1.2 ± 0.8 F(+) coliphages, and 3.6 ± 0.7 total vibrio per 100 ml. Bivariate associations between pathogens and indicators showed enterococci positively associated with the greatest number of bacterial pathogens. Higher concentrations of enterococci and higher incidence of Campylobacter were found in stream waters collected before sunrise, suggesting these organisms are sensitive to sunlight. Multivariate regression models of microbes as a function of land cover and physical-chemical water quality showed positive associations between Salmonella and agricultural and forested land covers, and between S. aureus and urban and agricultural land covers; these results suggested that sources specific to those land covers may contribute these pathogens to streams. Further, significant associations between some microbial targets and physical-chemical stream water quality (i.e., temperature, nutrients, turbidity) suggested that organism persistence may be affected by stream characteristics. Results implicate streams as a source of pathogens to coastal waters. Future work is recommended to determine infectious risks of recreational waterborne illness related to O'ahu stream exposures and to

  15. Bacterial Endotoxin Activity in Human Serum Is Associated With Dyslipidemia, Insulin Resistance, Obesity, and Chronic Inflammation

    PubMed Central

    Lassenius, Mariann I.; Pietiläinen, Kirsi H.; Kaartinen, Kati; Pussinen, Pirkko J.; Syrjänen, Jaana; Forsblom, Carol; Pörsti, Ilkka; Rissanen, Aila; Kaprio, Jaakko; Mustonen, Jukka; Groop, Per-Henrik; Lehto, Markku

    2011-01-01

    OBJECTIVE To investigate whether bacterial lipopolysaccharide (LPS) activity in human serum is associated with the components of the metabolic syndrome (MetS) in type 1 diabetic patients with various degrees of kidney disease and patients with IgA glomerulonephritis (IgAGN). RESEARCH DESIGN AND METHODS Serum LPS activity was determined with the Limulus Amoebocyte Lysate chromogenic end point assay in type 1 diabetic patients with a normal albumin excretion rate (n = 587), microalbuminuria (n = 144), macroalbuminuria (n = 173); patients with IgAGN (n = 98); and in nondiabetic control subjects (n = 345). The relationships of the LPS/HDL ratio and MetS-associated variables were evaluated with Pearson correlation. RESULTS The MetS was more prevalent in type 1 diabetic patients (48%) than in patients with IgAGN (15%). Diabetic patients with macroalbuminuria had a significantly higher serum LPS/HDL ratio than patients with IgAGN. In the normoalbuminuric type 1 diabetic group, patients in the highest LPS/HDL quartile were diagnosed as having the MetS three times more frequently than patients in the lowest quartile (69 vs. 22%; P < 0.001). High LPS activity was associated with higher serum triglyceride concentration, earlier onset of diabetes, increased diastolic blood pressure, and elevated urinary excretion of monocyte chemoattractant protein-1. CONCLUSIONS High serum LPS activity is strongly associated with the components of the MetS. Diabetic patients with kidney disease seem to be more susceptible to metabolic endotoxemia than patients with IgAGN. Bacterial endotoxins may thus play an important role in the development of the metabolic and vascular abnormalities commonly seen in obesity and diabetes-related diseases. PMID:21636801

  16. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates.

    PubMed

    Vandeputte, Doris; Falony, Gwen; Vieira-Silva, Sara; Tito, Raul Y; Joossens, Marie; Raes, Jeroen

    2016-01-01

    The assessment of potentially confounding factors affecting colon microbiota composition is essential to the identification of robust microbiome based disease markers. Here, we investigate the link between gut microbiota variation and stool consistency using Bristol Stool Scale classification, which reflects faecal water content and activity, and is considered a proxy for intestinal colon transit time. Through 16S rDNA Illumina profiling of faecal samples of 53 healthy women, we evaluated associations between microbiome richness, Bacteroidetes:Firmicutes ratio, enterotypes, and genus abundance with self-reported, Bristol Stool Scale-based stool consistency. Each sample's microbiota growth potential was calculated to test whether transit time acts as a selective force on gut bacterial growth rates. Stool consistency strongly correlates with all known major microbiome markers. It is negatively correlated with species richness, positively associated to the Bacteroidetes:Firmicutes ratio, and linked to Akkermansia and Methanobrevibacter abundance. Enterotypes are distinctly distributed over the BSS-scores. Based on the correlations between microbiota growth potential and stool consistency scores within both enterotypes, we hypothesise that accelerated transit contributes to colon ecosystem differentiation. While shorter transit times can be linked to increased abundance of fast growing species in Ruminococcaceae-Bacteroides samples, hinting to a washout avoidance strategy of faster replication, this trend is absent in Prevotella-enterotyped individuals. Within this enterotype adherence to host tissue therefore appears to be a more likely bacterial strategy to cope with washout. The strength of the associations between stool consistency and species richness, enterotypes and community composition emphasises the crucial importance of stool consistency assessment in gut metagenome-wide association studies. Published by the BMJ Publishing Group Limited. For permission to

  17. Toll-Like Receptor Gene Variants Associated with Bacterial Vaginosis among HIV-1 Infected Adolescents

    PubMed Central

    Royse, Kathryn E; Kempf, Mirjam-Colette; McGwin, Gerald; Wilson, Craig M; Tang, Jianming; Shrestha, Sadeep

    2012-01-01

    Bacterial vaginosis (BV) is a common vaginal disorder in women of reproductive age, especially among women with HIV-1 infection. Several bacterial products including lipopolysaccharides (LPS), lipoteichoic acids (LTA), and peptidoglycans (PGN) are stimulatory ligands for Toll-like receptors (TLRs), and recent evidence indicates the important role of variation in TLR genes for permitting overgrowth of gram negative and BV-type flora. We assessed whether genetic polymorphisms in five TLR genes (TLR1, TLR2, TLR4, TLR6, and TLR9) could be determinants of differential host immune responses to BV in 159 HIV-1-positive African American adolescents enrolled in the Reaching for Excellence in Adolescent Care and Health (REACH) study. BV was assessed biannually and diagnosed either by a Nugent Score of at least 7 of 10, or using the Amsel Criteria. Cox-proportional hazards regression models, adjusted for concurrent Chlamydia and Gonorrhea infections, douching, and absolute CD4 cell count, were used to identify host genetic factors associated with BV. Two SNPs were associated with BV as diagnosed by the Nugent Score and the combined criteria: a minor allele G of rs4986790 (frequency=0.07), which encodes a His to Tyr substitution in TLR4 (HR=1.47, 95% CI 1.15–1.87) and rs187084 (frequency=0.24) on TLR9. The minor allele of rs1898830 (frequency=0.13) was associated with an increased hazard of BV defined by the Amsel criteria (HR=1.86, 95%CI 1.17–2.95). Further studies are warranted to confirm the associations of TLR gene variants and also to understand the underlying pathways and immunogenetic correlates in the context of HIV-1 infection. PMID:23021866

  18. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

    PubMed Central

    Vandeputte, Doris; Falony, Gwen; Vieira-Silva, Sara; Tito, Raul Y; Joossens, Marie; Raes, Jeroen

    2016-01-01

    Objective The assessment of potentially confounding factors affecting colon microbiota composition is essential to the identification of robust microbiome based disease markers. Here, we investigate the link between gut microbiota variation and stool consistency using Bristol Stool Scale classification, which reflects faecal water content and activity, and is considered a proxy for intestinal colon transit time. Design Through 16S rDNA Illumina profiling of faecal samples of 53 healthy women, we evaluated associations between microbiome richness, Bacteroidetes:Firmicutes ratio, enterotypes, and genus abundance with self-reported, Bristol Stool Scale-based stool consistency. Each sample’s microbiota growth potential was calculated to test whether transit time acts as a selective force on gut bacterial growth rates. Results Stool consistency strongly correlates with all known major microbiome markers. It is negatively correlated with species richness, positively associated to the Bacteroidetes:Firmicutes ratio, and linked to Akkermansia and Methanobrevibacter abundance. Enterotypes are distinctly distributed over the BSS-scores. Based on the correlations between microbiota growth potential and stool consistency scores within both enterotypes, we hypothesise that accelerated transit contributes to colon ecosystem differentiation. While shorter transit times can be linked to increased abundance of fast growing species in Ruminococcaceae-Bacteroides samples, hinting to a washout avoidance strategy of faster replication, this trend is absent in Prevotella-enterotyped individuals. Within this enterotype adherence to host tissue therefore appears to be a more likely bacterial strategy to cope with washout. Conclusions The strength of the associations between stool consistency and species richness, enterotypes and community composition emphasises the crucial importance of stool consistency assessment in gut metagenome-wide association studies. PMID:26069274

  19. Efficient surveillance for healthcare-associated infections spreading between hospitals

    PubMed Central

    Ciccolini, Mariano; Donker, Tjibbe; Grundmann, Hajo; Bonten, Marc J. M.; Woolhouse, Mark E. J.

    2014-01-01

    Early detection of new or novel variants of nosocomial pathogens is a public health priority. We show that, for healthcare-associated infections that spread between hospitals as a result of patient movements, it is possible to design an effective surveillance system based on a relatively small number of sentinel hospitals. We apply recently developed mathematical models to patient admission data from the national healthcare systems of England and The Netherlands. Relatively short detection times are achieved once 10–20% hospitals are recruited as sentinels and only modest reductions are seen as more hospitals are recruited thereafter. Using a heuristic optimization approach to sentinel selection, the same expected time to detection can be achieved by recruiting approximately half as many hospitals. Our study provides a robust evidence base to underpin the design of an efficient sentinel hospital surveillance system for novel nosocomial pathogens, delivering early detection times for reduced expenditure and effort. PMID:24469791

  20. Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency

    DOE PAGES

    Eudes, Aymerick; Sathitsuksanoh, Noppadon; Baidoo, Edward E. K.; ...

    2015-01-13

    Lignin confers recalcitrance to plant biomass used as feedstocks in agro-processing industries or as source of renewable sugars for the production of bioproducts. The metabolic steps for the synthesis of lignin building blocks belong to the shikimate and phenylpropanoid pathways. Genetic engineering efforts to reduce lignin content typically employ gene knockout or gene silencing techniques to constitutively repress one of these metabolic pathways. Recently, new strategies have emerged offering better spatiotemporal control of lignin deposition, including the expression of enzymes that interfere with the normal process for cell wall lignification. In this study, we report that expression of a 3-dehydroshikimatemore » dehydratase (QsuB from Corynebacterium glutamicum) reduces lignin deposition in Arabidopsis cell walls. QsuB was targeted to the plastids to convert 3-dehydroshikimate – an intermediate of the shikimate pathway – into protocatechuate. Compared to wild-type plants, lines expressing QsuB contain higher amounts of protocatechuate, p-coumarate, p-coumaraldehyde and p-coumaryl alcohol, and lower amounts of coniferaldehyde, coniferyl alcohol, sinapaldehyde and sinapyl alcohol. 2D-NMR spectroscopy and pyrolysis-gas chromatography/mass spectrometry (pyro-GC/MS) reveal an increase of p-hydroxyphenyl units and a reduction of guaiacyl units in the lignin of QsuB lines. Size-exclusion chromatography indicates a lower degree of lignin polymerization in the transgenic lines. Therefore, our data show that the expression of QsuB primarily affects the lignin biosynthetic pathway. Finally, biomass from these lines exhibits more than a twofold improvement in saccharification efficiency. We conclude that the expression of QsuB in plants, in combination with specific promoters, is a promising gain-of-function strategy for spatiotemporal reduction of lignin in plant biomass.« less

  1. Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency.

    PubMed

    Eudes, Aymerick; Sathitsuksanoh, Noppadon; Baidoo, Edward E K; George, Anthe; Liang, Yan; Yang, Fan; Singh, Seema; Keasling, Jay D; Simmons, Blake A; Loqué, Dominique

    2015-12-01

    Lignin confers recalcitrance to plant biomass used as feedstocks in agro-processing industries or as source of renewable sugars for the production of bioproducts. The metabolic steps for the synthesis of lignin building blocks belong to the shikimate and phenylpropanoid pathways. Genetic engineering efforts to reduce lignin content typically employ gene knockout or gene silencing techniques to constitutively repress one of these metabolic pathways. Recently, new strategies have emerged offering better spatiotemporal control of lignin deposition, including the expression of enzymes that interfere with the normal process for cell wall lignification. In this study, we report that expression of a 3-dehydroshikimate dehydratase (QsuB from Corynebacterium glutamicum) reduces lignin deposition in Arabidopsis cell walls. QsuB was targeted to the plastids to convert 3-dehydroshikimate - an intermediate of the shikimate pathway - into protocatechuate. Compared to wild-type plants, lines expressing QsuB contain higher amounts of protocatechuate, p-coumarate, p-coumaraldehyde and p-coumaryl alcohol, and lower amounts of coniferaldehyde, coniferyl alcohol, sinapaldehyde and sinapyl alcohol. 2D-NMR spectroscopy and pyrolysis-gas chromatography/mass spectrometry (pyro-GC/MS) reveal an increase of p-hydroxyphenyl units and a reduction of guaiacyl units in the lignin of QsuB lines. Size-exclusion chromatography indicates a lower degree of lignin polymerization in the transgenic lines. Therefore, our data show that the expression of QsuB primarily affects the lignin biosynthetic pathway. Finally, biomass from these lines exhibits more than a twofold improvement in saccharification efficiency. We conclude that the expression of QsuB in plants, in combination with specific promoters, is a promising gain-of-function strategy for spatiotemporal reduction of lignin in plant biomass.

  2. [Endophytic bacterial community analysis of Catharanthus roseus and its association with huanglongbing pathogen].

    PubMed

    Li, Jia; Wang, Zhongkang; Xie, Pan; Wu, Dong; Yin, Youping

    2012-04-04

    To analyze the microbial diversity in healthy and HLB-affected Catharanthus roseus under manual-grafting conditions and to find the association between the endophytic bacteria and the HLB pathogen. The endophytic bacterial communities were delineated by using the traditional culturable approach and cultivation-independent techniques based on 16S rRNA gene. The endophytic bacteria were isolated from surface-sterilized C. roseus midribs of leaves and phloem of stems and roots by plating and restriction fragment length polymorphism (RFLP). By anaerobic culture, we obtained 67 strains that were identified 29 genus by GenBank. Curtobacterium sp. , Erwinia sp., Bacillus cereus and Brevundimonas sp. , Bacillus sp. were the dominant bacterial population in diseased and healthy C. roseus. However, Staphylococcus equorum was the common dominant isolate in both C. roseus. We picked 188 and 182 positive clones in 16S rDNA libraries of diseased and healthy C. roseus that were respectively restricted by the HaeIII, MspI, RsaI restriction endonuclease. Based on the similarity of the RFLP banding profiles in diseased and healthy C. roseus, we obtained 16, 23 OTUs (Operational Taxonomic Units, OTUs) respectively. In addition to Candidatus Liberibacter asiaticus, Candidatus Liberibacter sp. was the dominant bacterial population only in diseased C. roseus. With the infection of 'Ca. L. asiaticus', the diversity in diseased C. roseus decreased. The endophytic bacteria isolated from diseased and healthy C. roseus are abundant and have remarkable differences in the composition and function, suggesting that its endophytic bacteria might be inhibited by the HLB pathogen.

  3. Long-term bacterial exposure can trigger nonsuppurative destructive cholangitis associated with multifocal epithelial inflammation.

    PubMed

    Haruta, Ikuko; Kikuchi, Ken; Hashimoto, Etsuko; Nakamura, Minoru; Miyakawa, Hiroshi; Hirota, Katsuhiko; Shibata, Noriyuki; Kato, Hidehito; Arimura, Yutaka; Kato, Yoichiro; Uchiyama, Takehiko; Nagamune, Hideaki; Kobayashi, Makio; Miyake, Yoichiro; Shiratori, Keiko; Yagi, Junji

    2010-04-01

    Bacterial infection has become a focus of attention in the pathogenesis of primary biliary cirrhosis (PBC). We earlier reported that the bacterial lipoteichoic acid was detected at the sites of inflammation around damaged bile ducts in the livers of PBC, and PBC patients' sera showed high titers against streptococcal histone-like protein. Here, we investigated whether chronic bacterial exposure could trigger PBC-like epithelial cell damage in normal mouse. BALB/c mice were repeatedly inoculated with various bacteria for 8 weeks. At 1 week (Group 1) and 3, 4, or 20 months (long term; Group 2) after the final inoculation, mice were killed to obtain samples. In the livers of the Streptococcus intermedius (S.i.)-inoculated mice in Group 1, cellular infiltration was predominantly observed around the bile ducts over the hepatic parenchyma. In the S.i.-inoculated mice in Group 2, portal but not parenchymal inflammation was observed in the livers, and periductal cellular infiltrates were detected in the salivary glands. Both S.i.-inoculated Groups 1 and 2 BALB/c mice sera had antibodies against HuCCT1 biliary epithelial cells, anti-nuclear antibodies, and anti-gp210 antibodies, but not anti-mitochondrial antibodies. Immunoreactivity to histone-like DNA-binding protein of S.i. (S.i.-HLP) was detectable around the sites of chronic nonsuppurative destructive cholangitis in the portal area in the livers of both S.i.-inoculated Groups 1 and 2 BALB/c mice. Furthermore, anti-S.i.-HLP antibody bound to synthetic gp210 peptide, as well. Bacteria triggered PBC-like cholangitis, multifocal epithelial inflammation, and autoantibody production. Bacteria are likely involved in the pathogenesis of PBC and of associated multifocal epithelial inflammation.

  4. Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

    PubMed

    Fall, S; Nazaret, S; Chotte, J L; Brauman, A

    2004-08-01

    The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

  5. Environmental context shapes the bacterial community structure associated to Peltigera cyanolichens growing in Tierra del Fuego, Chile.

    PubMed

    Ramírez-Fernández, Lía; Zúñiga, Catalina; Carú, Margarita; Orlando, Julieta

    2014-03-01

    The structure of the associated bacterial community of bipartite cyanolichens of the genus Peltigera from three different environmental contexts in the Karukinka Natural Park, Tierra del Fuego, Chile, was assessed. The sampling sites represent different habitat contexts: mature native forest, young native forest and grassland. Recently it has been determined that the bacterial community associated to lichens could be highly structured according to the mycobiont or photobiont identities, to the environmental context and/or to the geographic scale. However, there are some inconsistencies in defining which of these factors would be the most significant on determining the structure of the microbial communities associated with lichens, mainly because most studies compare the bacterial communities between different lichen species and/or with different photobiont types (algae vs. cyanobacteria). In this work bipartite lichens belonging to the same genus (Peltigera) symbiotically associated with cyanobacteria (Nostoc) were analyzed by TRFLP to determine the structure of the bacterial community intimately associated with the lichen thalli and the one present in the substrate where they grow. The results indicate that the bacterial community intimately associated differs from the one of the substrate, being the former more influenced by the environmental context where the lichen grows.

  6. Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA

    PubMed Central

    Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

    2015-01-01

    Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was

  7. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

    PubMed

    Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

    2015-01-01

    Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was

  8. Association of C-Reactive Protein With Bacterial and Respiratory Syncytial Virus-Associated Pneumonia Among Children Aged <5 Years in the PERCH Study.

    PubMed

    Higdon, Melissa M; Le, Tham; O'Brien, Katherine L; Murdoch, David R; Prosperi, Christine; Baggett, Henry C; Brooks, W Abdullah; Feikin, Daniel R; Hammitt, Laura L; Howie, Stephen R C; Kotloff, Karen L; Levine, Orin S; Scott, J Anthony G; Thea, Donald M; Awori, Juliet O; Baillie, Vicky L; Cascio, Stephanie; Chuananon, Somchai; DeLuca, Andrea N; Driscoll, Amanda J; Ebruke, Bernard E; Endtz, Hubert P; Kaewpan, Anek; Kahn, Geoff; Karani, Angela; Karron, Ruth A; Moore, David P; Park, Daniel E; Rahman, Mohammed Ziaur; Salaudeen, Rasheed; Seidenberg, Phil; Somwe, Somwe Wa; Sylla, Mamadou; Tapia, Milagritos D; Zeger, Scott L; Deloria Knoll, Maria; Madhi, Shabir A

    2017-06-15

    Lack of a gold standard for identifying bacterial and viral etiologies of pneumonia has limited evaluation of C-reactive protein (CRP) for identifying bacterial pneumonia. We evaluated the sensitivity and specificity of CRP for identifying bacterial vs respiratory syncytial virus (RSV) pneumonia in the Pneumonia Etiology Research for Child Health (PERCH) multicenter case-control study. We measured serum CRP levels in cases with World Health Organization-defined severe or very severe pneumonia and a subset of community controls. We evaluated the sensitivity and specificity of elevated CRP for "confirmed" bacterial pneumonia (positive blood culture or positive lung aspirate or pleural fluid culture or polymerase chain reaction [PCR]) compared to "RSV pneumonia" (nasopharyngeal/oropharyngeal or induced sputum PCR-positive without confirmed/suspected bacterial pneumonia). Receiver operating characteristic (ROC) curves were constructed to assess the performance of elevated CRP in distinguishing these cases. Among 601 human immunodeficiency virus (HIV)-negative tested controls, 3% had CRP ≥40 mg/L. Among 119 HIV-negative cases with confirmed bacterial pneumonia, 77% had CRP ≥40 mg/L compared with 17% of 556 RSV pneumonia cases. The ROC analysis produced an area under the curve of 0.87, indicating very good discrimination; a cut-point of 37.1 mg/L best discriminated confirmed bacterial pneumonia (sensitivity 77%) from RSV pneumonia (specificity 82%). CRP ≥100 mg/L substantially improved specificity over CRP ≥40 mg/L, though at a loss to sensitivity. Elevated CRP was positively associated with confirmed bacterial pneumonia and negatively associated with RSV pneumonia in PERCH. CRP may be useful for distinguishing bacterial from RSV-associated pneumonia, although its role in discriminating against other respiratory viral-associated pneumonia needs further study.

  9. Seasonal variations in bacterial communities and antibiotic-resistant strains associated with green bottle flies (Diptera: Calliphoridae).

    PubMed

    Wei, Ting; Ishida, Ryuichi; Miyanaga, Kazuhiko; Tanji, Yasunori

    2014-05-01

    Green bottle flies occur frequently around human environments in Japan. Many species of green bottle flies have been studied with regard to their importance in forensic examinations or clinical therapies, but the bacterial communities associated with this group of flies have not been comprehensively investigated. In this research, 454 pyrosequencing was used to reveal the bacterial communities in green bottle flies collected in different seasons. Meanwhile, the bacteria were screened with selective media and tested for antibiotic susceptibility. Samples collected in three different seasons harbored distinctive bacterial communities. The predominant genera associated with green bottles flies were Staphylococcus in spring, Ignatzschineria in summer, and Vagococcus, Dysgonomonas, and an unclassified Acetobacteraceae in autumn. An upward trend in bacterial community diversity was observed from spring to autumn. Changes in climatic conditions could be the cause of these seasonal variations in fly-associated bacterial communities. The species of isolated antibiotic-resistant bacteria also differed across seasons, but it was difficult to correlate seasonal changes in antibiotic-resistant bacteria with changes in whole communities. A number of multiple-antibiotic-resistant bacteria were isolated, and some of these strains were closely affiliated with pathogens such as Enterococcus faecalis and Enterococcus faecium, which could cause serious threats to public health. Overall, this research provided us with information about the composition and seasonality of bacterial communities in green bottle flies, and highlighted the risks of fly-mediated dissemination of antibiotic-resistant pathogens.

  10. Safety and efficacy of moxifloxacin-dexamethasone eyedrops as treatment for bacterial ocular infection associated with bacterial blepharitis.

    PubMed

    Belfort, Rubens; Gabriel, Luis; Martins Bispo, Paulo José; Muccioli, Cristina; Zacharias Serapicos, Patricia Cabral; Clark, Linda; Bell, Belinda; Bartell, John; Stroman, David W; Höfling-Lima, Ana Luisa

    2012-05-01

    Treatments that offer two medications in a fixed combination have the potential to offer efficacious and safe treatment with advantages such as a regimen that is simpler than administering two separate solutions. This study evaluated the safety and efficacy of fixed-combination versus concomitant moxifloxacin 0.5% and dexamethasone 0.1% ocular solutions for the treatment of bacterial ocular inflammation and infection. The clinical study design was a randomized, double-masked, active-controlled, parallel-group trial of 102 subjects with bacterial blepharitis in which two patients also had bacterial conjunctivitis. All subjects received two bottles of study medication: either a fixed combination of moxifloxacin 0.5%/dexamethasone 0.1% ophthalmic solution and placebo eye drops (fixed-dose group), or moxifloxacin 0.5% ophthalmic solution and dexamethasone 0.1% (concomitant group). One drop of each study medication was instilled bilaterally four times per day for 7 days. Clinical resolution, signs, symptoms, and safety were assessed. Microbiological specimens were collected from the eyelid margin and conjunctivae of each eye from each patient at the time of enrollment and at the exit visit. Clinical resolution occurred similarly in both groups (81.6% of eyes, fixed-dose group; 82.3% of eyes, concomitant group). Moreover, the microbiological efficacy of the treatment was also similar for both the fixed-dose group (84%) and the concomitant group (83%). Ocular symptoms and signs improved over time, with no significant differences between groups after 7 days of treatment, except the fixed-dose group had significantly more eyes with clinical resolution in eyelid erythema (100%, n = 98/98, fixed-dose group; 92.7%, n = 89/96, concomitant group; P = 0.0194) and eyelid scaling/crusting (98%, n = 96/98, fixed-dose group; 89.6%; n = 86/96 eyes, concomitant group; P = 0.0337). Both regimens were safe and well tolerated. The fixed-dose combination of moxifloxacin, 0.5% and

  11. Associations between inverted repeats and the structural evolution of bacterial genomes.

    PubMed Central

    Achaz, Guillaume; Coissac, Eric; Netter, Pierre; Rocha, Eduardo P C

    2003-01-01

    The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong under-representation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats. PMID:12930739

  12. Incidence of Staphylococcus aureus and Analysis of Associated Bacterial Communities on Food Industry Surfaces

    PubMed Central

    Gutiérrez, Diana; Delgado, Susana; Vázquez-Sánchez, Daniel; Martínez, Beatriz; Cabo, Marta López; Rodríguez, Ana; Herrera, Juan J.

    2012-01-01

    Biofilms are a common cause of food contamination with undesirable bacteria, such as pathogenic bacteria. Staphylococcus aureus is one of the major bacteria causing food-borne diseases in humans. A study designed to determine the presence of S. aureus on food contact surfaces in dairy, meat, and seafood environments and to identify coexisting microbiota has therefore been carried out. A total of 442 samples were collected, and the presence of S. aureus was confirmed in 6.1% of samples. Sixty-three S. aureus isolates were recovered and typed by random amplification of polymorphic DNA (RAPD). Profiles were clustered into four groups which were related to specific food environments. All isolates harbored some potential virulence factors such as enterotoxin production genes, biofilm formation-associated genes, antibiotic resistance, or lysogeny. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints of bacterial communities coexisting with S. aureus revealed the presence of bacteria either involved in food spoilage or of concern for food safety in all food environments. Food industry surfaces could thus be a reservoir for S. aureus forming complex communities with undesirable bacteria in multispecies biofilms. Uneven microbiological conditions were found in each food sector, which indicates the need to improve hygienic conditions in food processing facilities, particularly the removal of bacterial biofilms, to enhance the safety of food products. PMID:23023749

  13. Incidence of Staphylococcus aureus and analysis of associated bacterial communities on food industry surfaces.

    PubMed

    Gutiérrez, Diana; Delgado, Susana; Vázquez-Sánchez, Daniel; Martínez, Beatriz; Cabo, Marta López; Rodríguez, Ana; Herrera, Juan J; García, Pilar

    2012-12-01

    Biofilms are a common cause of food contamination with undesirable bacteria, such as pathogenic bacteria. Staphylococcus aureus is one of the major bacteria causing food-borne diseases in humans. A study designed to determine the presence of S. aureus on food contact surfaces in dairy, meat, and seafood environments and to identify coexisting microbiota has therefore been carried out. A total of 442 samples were collected, and the presence of S. aureus was confirmed in 6.1% of samples. Sixty-three S. aureus isolates were recovered and typed by random amplification of polymorphic DNA (RAPD). Profiles were clustered into four groups which were related to specific food environments. All isolates harbored some potential virulence factors such as enterotoxin production genes, biofilm formation-associated genes, antibiotic resistance, or lysogeny. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints of bacterial communities coexisting with S. aureus revealed the presence of bacteria either involved in food spoilage or of concern for food safety in all food environments. Food industry surfaces could thus be a reservoir for S. aureus forming complex communities with undesirable bacteria in multispecies biofilms. Uneven microbiological conditions were found in each food sector, which indicates the need to improve hygienic conditions in food processing facilities, particularly the removal of bacterial biofilms, to enhance the safety of food products.

  14. 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.

  15. Associations between inverted repeats and the structural evolution of bacterial genomes.

    PubMed

    Achaz, Guillaume; Coissac, Eric; Netter, Pierre; Rocha, Eduardo P C

    2003-08-01

    The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong under-representation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats.

  16. Integrative Study of Physiological Changes Associated with Bacterial Infection in Pacific Oyster Larvae

    PubMed Central

    Genard, Bertrand; Miner, Philippe; Nicolas, Jean-Louis; Moraga, Dario; Boudry, Pierre; Pernet, Fabrice; Tremblay, Réjean

    2013-01-01

    Background Bacterial infections are common in bivalve larvae and can lead to significant mortality, notably in hatcheries. Numerous studies have identified the pathogenic bacteria involved in such mortalities, but physiological changes associated with pathogen exposure at larval stage are still poorly understood. In the present study, we used an integrative approach including physiological, enzymatic, biochemical, and molecular analyses to investigate changes in energy metabolism, lipid remodelling, cellular stress, and immune status of Crassostrea gigas larvae subjected to experimental infection with the pathogenic bacteria Vibrio coralliilyticus. Findings Our results showed that V. coralliilyticus exposure induced (1) limited but significant increase of larvae mortality compared with controls, (2) declined feeding activity, which resulted in energy status changes (i.e. reserve consumption, β-oxidation, decline of metabolic rate), (3) fatty acid remodeling of polar lipids (changes in phosphatidylinositol and lysophosphatidylcholine composition`, non-methylene–interrupted fatty acids accumulation, lower content of major C20 polyunsaturated fatty acids as well as activation of desaturases, phospholipase and lipoxygenase), (4) activation of antioxidant defenses (catalase, superoxide dismutase, peroxiredoxin) and cytoprotective processes (heat shock protein 70, pernin), and (5) activation of the immune response (non-self recognition, NF-κκ signaling pathway, haematopoiesis, eiconosoids and lysophosphatidyl acid synthesis, inhibitor of metalloproteinase and antimicrobial peptides). Conclusion Overall, our results allowed us to propose an integrative view of changes induced by a bacterial infection in Pacific oyster larvae, opening new perspectives on the response of marine bivalve larvae to infections. PMID:23704993

  17. Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome.

    PubMed

    Durbán, Ana; Abellán, Juan J; Jiménez-Hernández, Nuria; Salgado, Patricia; Ponce, Marta; Ponce, Julio; Garrigues, Vicente; Latorre, Amparo; Moya, Andrés

    2012-04-01

    Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder in western countries. Previous studies on IBS, mostly based on faecal samples, suggest alterations in the intestinal microbiota. However, no consensus has been reached regarding the association between specific bacteria and IBS. We explore the alterations of intestinal bacterial communities in IBS using massive sequencing of amplified 16S rRNA genes. Mucosal biopsies of the ascending and descending colon and faeces from 16 IBS patients and 9 healthy controls were analysed. Strong inter-individual variation was observed in the composition of the bacterial communities in both patients and controls. These communities showed less diversity in IBS cases. There were larger differences in the microbiota composition between biopsies and faeces than between patients and controls. We found a few over-represented and under-represented taxa in IBS cases with respect to controls. The detected alterations varied by site, with no changes being consistent across sample types. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  18. Coral-associated bacterial assemblages: current knowledge and the potential for climate-driven impacts.

    PubMed

    Mouchka, Morgan E; Hewson, Ian; Harvell, C Drew

    2010-10-01

    The importance of associations between microorganisms and their invertebrate hosts is becoming increasingly apparent. An emerging field, driven by the necessity to understand the microbial relationships that both maximize coral health and cause coral disease, is the study of coral-bacteria interactions. In this article, we review our current understanding of the diversity, specificity, development, and functions of coral-associated bacteria. We also summarize what is known regarding the role of coral microbiota in the health and disease of coral. We conduct a meta-analysis to determine whether the presence of unique taxa correlates with the state of coral health (i.e. healthy, diseased or bleached), as well as whether coral reef habitats harbor clusters of distinct taxa. We find that healthy and bleached corals harbor similar dominant taxa, although bleached corals had higher proportions of Vibrio and Acidobacteria. Diseased corals generally had more Rhodobacter, Clostridia, and Cyanobacteria sequences, and fewer Oceanospirillum sequences. We caution, however, that while 16S rRNA is useful for microbial species identification, it is a poor predictor of habitat or lifestyle, and care should be taken in interpretation of 16S rRNA surveys to identify potential pathogens amongst complex coral-microbial assemblages. Finally, we highlight evidence that coral-bacterial assemblages could be sensitive to the effects of climatic change. We suggest that the relationship between coral and their bacterial associates represents a valuable model that can be applied to the broader discipline of invertebrate-microbial interactions. © The Author 2010. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved.

  19. Ecological Inferences from a deep screening of the Complex Bacterial Consortia associated with the coral, Porites astreoides.

    PubMed

    Rodriguez-Lanetty, Mauricio; Granados-Cifuentes, Camila; Barberan, Albert; Bellantuono, Anthony J; Bastidas, Carolina

    2013-08-01

    The functional role of the bacterial organisms in the reef ecosystem and their contribution to the coral well-being remain largely unclear. The first step in addressing this gap of knowledge relies on in-depth characterization of the coral microbial community and its changes in diversity across coral species, space and time. In this study, we focused on the exploration of microbial community assemblages associated with an ecologically important Caribbean scleractinian coral, Porites astreoides, using Illumina high-throughput sequencing of the V5 fragment of 16S rRNA gene. We collected data from a large set of biological replicates, allowing us to detect patterns of geographical structure and resolve co-occurrence patterns using network analyses. The taxonomic analysis of the resolved diversity showed consistent and dominant presence of two OTUs affiliated with the order Oceanospirillales, which corroborates a specific pattern of bacterial association emerging for this coral species and for many other corals within the genus Porites. We argue that this specific association might indicate a symbiotic association with the adult coral partner. Furthermore, we identified a highly diverse rare bacterial 'biosphere' (725 OTUs) also living along with the dominant bacterial symbionts, but the assemblage of this biosphere is significantly structured along the geographical scale. We further discuss that some of these rare bacterial members show significant association with other members of the community reflecting the complexity of the networked consortia within the coral holobiont. © 2013 John Wiley & Sons Ltd.

  20. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    PubMed Central

    Lee, On On; Yang, Jiangke; Bougouffa, Salim; Wang, Yong; Batang, Zenon; Tian, Renmao; Al-Suwailem, Abdulaziz

    2012-01-01

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals. PMID:22865078

  1. Chron's disease, rare association with selective IgA immunodeficiency, and development of life-threatening bacterial infections.

    PubMed

    Manfredi, Roberto; Coronado, Olga V; Marinacci, Ginevra; Righi, Mauro; Calza, Leonardo

    2004-01-01

    Life-threatening necrotizing fasciitis and relapsing Lemierre syndrome associated with Fusobacterium necrophorum septicaemia occurred in young adults with a moderate Chron's disease and a missed profound IgA deficiency. This unexpected association of a chronic bowel inflammatory syndrome with prominent IgA abnormalities and severe bacterial infection deserves careful attention by physicians faced with young patients with Chron's disease.

  2. Bacterial isolates associated with pelvic inflammatory disease among female patients attending some hospitals in abuja, Nigeria.

    PubMed

    Spencer, T H I; Umeh, P O; Irokanulo, E; Baba, M M; Spencer, B B; Umar, A I; Ardzard, S A; Oderinde, S; Onoja, O

    2014-01-01

    Pelvic inflammatory disease refers to any infection in the female lower reproductive tract that spreads to the upper reproductive tract. The disease comprises a spectrum of inflammatory disorders of the upper female genital tract, including any combination of endometritis, salpingitis, tubo-ovarian abscess and pelvic peritonitis. PID is not a notifiable disease in most countries, so accurate statistics are not available. This situation is not in any way different here in Nigeria and more so in the Federal Capital Territory, Abuja where this research was conducted, there had never been any published report so far on PID. It therefore became pertinent that such studies be carried out to evaluate the bacterial organisms which may be associated with the disease in this part of Nigeria so that health care providers could take a better look at this affliction in women. Endocervical swabs totalling 100 were aseptically collected from patients with confirmed Pelvic Inflammatory Disease (PID), attending some hospitals in Abuja, Nigeria for detection of bacterial pathogens based on cultural and biochemical characterisation tests. Antibiogram was also conducted on the identified bacterial isolates. Out of the 100 samples analysed, 43% yielded pure cultures of bacterial isolates, 2% yielded mixed cultures while no bacterial growths were recorded from the remaining 55% samples. Organisms encountered were Staphylococcus aureus (16%), Escherichia coli (10%), Streptococcus faecalis (8%), Pseudomonas aeruginosa (4%), Streptococcus pyogenes (3%), Klebsiella pneumoniae (3%), Proteus rettgeri (2%) and Proteus mirabilis (1%). The highest percentage occurrence of pathogenic isolates was observed in polygamous married patients (90%). The age group most affected falls within the mean age 30.5 years (68%) while the least affected group falls within the mean age 40.5 years (5%). There was a significant difference in the acquisition of PID in relation to marital status (P < 0.05). However

  3. A cluster analysis of bacterial vaginosis-associated microflora and pelvic inflammatory disease.

    PubMed

    Ness, Roberta B; Kip, Kevin E; Hillier, Sharon L; Soper, David E; Stamm, Carol A; Sweet, Richard L; Rice, Peter; Richter, Holly E

    2005-09-15

    Controversy surrounds the association between bacterial vaginosis (BV) and pelvic inflammatory disease (PID). Women (N = 1,140) were ascertained at five US centers, enrolled (1999-2001), and followed up for a median of 3 years. Serial vaginal swabs were obtained for Gram's stain and cultures. PID was defined as 1) histologic endometritis or 2) pelvic pain and tenderness plus oral temperature >38.8 degrees C, leukorrhea or mucopus, erythrocyte sedimentation rate >15 mm/hour, white blood cell count >10,000, or gonococcal/chlamydial lower genital infection. Exploratory factor analysis identified two discrete clusters of genital microorganisms. The first correlated with BV by Gram's stain and consisted of the absence of hydrogen peroxide-producing lactobacillus, Gardnerella vaginalis, Mycoplasma hominis, anaerobic gram-negative rods, and, to a lesser degree, Ureaplasma urealyticum. The second, unrelated to BV by Gram's stain, consisted of Enterococcus species and Escherichia coli. Being in the highest tertile in terms of growth of BV-associated microorganisms increased PID risk (adjusted rate ratio = 2.03, 95% confidence interval: 1.16, 3.53). Carriage of non-BV-associated microorganisms did not increase PID risk. Women with heavy growth of BV-associated microorganisms and a new sexual partner appeared to be at particularly high risk (adjusted rate ratio = 8.77, 95% confidence interval: 1.11, 69.2). When identified by microbial culture, a combination of BV-related microorganisms significantly elevated the risk of acquiring PID.

  4. Bacterial vaginosis in association with spontaneous abortion and recurrent pregnancy losses

    PubMed Central

    Işik, Gözde; Demirezen, Şayeste; Dönmez, Hanife Güler; Beksaç, Mehmet Sinan

    2016-01-01

    Context: Bacterial vaginosis (BV) is related to the increased risk of miscarriage, preterm labor, and postpartum endometritis. Aims: The aim of this study was to evaluate the association between BV and the history of spontaneous abortion and recurrent pregnancy losses. We also examined periods of gestation, including the first and second trimester miscarriages. Materials and Methods: The study population consisted of 200 fertile women. Sixty one (30.5%) of 200 women had the history of a spontaneous abortion in the last six months (N = 30) and at least three recurrent pregnancy losses (N = 31). BV was diagnosed either by using Papanicolaou staining, Gram staining, or by culturing with BV-associated bacteria, Gardnerella vaginalis. Results: The presence of BV was statistically associated with the history of a spontaneous abortion in the last 6 months (P < 0.05), whereas there was no significant relationship between BV and recurrent pregnancy losses (P > 0.05). These women were also evaluated in view of periods of gestation. Forty-seven (77%) of 61 women had first trimester miscarriage (≤12 weeks) and 14 (23%) of 61 women had second trimester miscarriage (>12 weeks). There was a statistically significant relationship between BV and second trimester miscarriage (P < 0.05). Positive BV findings were not associated with discharge, itching, and pain (P > 0.05). Conclusion: BV may contribute to spontaneous abortion and second trimester miscarriage. PMID:27756985

  5. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains

    SciTech Connect

    Jones, Christopher P.; Ferré-D'Amaré, Adrian R.

    2015-08-17

    The bacterial alarmone 5-aminoimidazole-4-carboxamide riboside 5'-triphosphate (AICAR triphosphate or ZTP), derived from the monophosphorylated purine precursor ZMP, accumulates during folate starvation. ZTP regulates genes involved in purine and folate metabolism through a cognate riboswitch. The linker connecting this riboswitch's two subdomains varies in length by over 100 nucleotides. In this paper, we report the cocrystal structure of the Fusobacterium ulcerans riboswitch bound to ZMP, which spans the two subdomains whose interface also comprises a pseudoknot and ribose zipper. The riboswitch recognizes the carboxamide oxygen of ZMP through an unprecedented inner-sphere coordination with a Mg2+ ion. We show that the affinity of the riboswitch for ZMP is modulated by the linker length. Notably, ZMP can simultaneously bind to the two subdomains even when they are synthesized as separate RNAs. Finally, the ZTP riboswitch demonstrates how specific small-molecule binding can drive association of distant noncoding-RNA domains to regulate gene expression.

  6. Parasitic, bacterial, and viral enteric pathogens associated with diarrhea in the Central African Republic.

    PubMed Central

    Georges, M C; Wachsmuth, I K; Meunier, D M; Nebout, N; Didier, F; Siopathis, M R; Georges, A J

    1984-01-01

    A total of 1,197 diarrheic children less than 15 years old were investigated for parasitic, bacterial, and viral enteropathogens from March 1981 through February 1982 in the Central African Republic. One or more pathogens were identified from 49.4% of the patients. Rotavirus was the most frequently identified pathogen among children less than 18 months old. Enteropathogenic Escherichia coli was the second most frequently isolated pathogen (12.1%) in children less than 2 years of age. Campylobacter jejuni was also isolated frequently from diarrheic children less than 5 years of age (10.9%). Entamoeba histolytica was identified in very young children and was found to be the most frequent enteropathogen associated with diarrhea in children over the age of 2 years. Enterotoxigenic Escherichia coli was rarely isolated (ca. 2%). There was a peak in the incidence of rotavirus during the dry season and in the incidence of Campylobacter jejuni during the rainy season. PMID:6330161

  7. Atrazine biodegradation efficiency, metabolite detection, and trzD gene expression by enrichment bacterial cultures from agricultural soil

    PubMed Central

    Solomon, Robinson David Jebakumar; Kumar, Amit; Satheeja Santhi, Velayudhan

    2013-01-01

    Atrazine is a selective herbicide used in agricultural fields to control the emergence of broadleaf and grassy weeds. The persistence of this herbicide is influenced by the metabolic action of habituated native microorganisms. This study provides information on the occurrence of atrazine mineralizing bacterial strains with faster metabolizing ability. The enrichment cultures were tested for the biodegradation of atrazine by high-performance liquid chromatography (HPLC) and mass spectrometry. Nine cultures JS01.Deg01 to JS09.Deg01 were identified as the degrader of atrazine in the enrichment culture. The three isolates JS04.Deg01, JS07.Deg01, and JS08.Deg01 were identified as efficient atrazine metabolizers. Isolates JS04.Deg01 and JS07.Deg01 produced hydroxyatrazine (HA) N-isopropylammelide and cyanuric acid by dealkylation reaction. The isolate JS08.Deg01 generated deethylatrazine (DEA), deisopropylatrazine (DIA), and cyanuric acid by N-dealkylation in the upper degradation pathway and later it incorporated cyanuric acid in their biomass by the lower degradation pathway. The optimum pH for degrading atrazine by JS08.Deg01 was 7.0 and 16S rDNA phylogenetic typing identified it as Enterobacter cloacae strain JS08.Deg01. The highest atrazine mineralization was observed in case of isolate JS08.Deg01, where an ample amount of trzD mRNA was quantified at 72 h of incubation with atrazine. Atrazine bioremediating isolate E. cloacae strain JS08.Deg01 could be the better environmental remediator of agricultural soils and the crop fields contaminated with atrazine could be the source of the efficient biodegrading microbial strains for the environmental cleanup process. PMID:24302716

  8. Atrazine biodegradation efficiency, metabolite detection, and trzD gene expression by enrichment bacterial cultures from agricultural soil.

    PubMed

    Solomon, Robinson David Jebakumar; Kumar, Amit; Satheeja Santhi, Velayudhan

    2013-12-01

    Atrazine is a selective herbicide used in agricultural fields to control the emergence of broadleaf and grassy weeds. The persistence of this herbicide is influenced by the metabolic action of habituated native microorganisms. This study provides information on the occurrence of atrazine mineralizing bacterial strains with faster metabolizing ability. The enrichment cultures were tested for the biodegradation of atrazine by high-performance liquid chromatography (HPLC) and mass spectrometry. Nine cultures JS01.Deg01 to JS09.Deg01 were identified as the degrader of atrazine in the enrichment culture. The three isolates JS04.Deg01, JS07.Deg01, and JS08.Deg01 were identified as efficient atrazine metabolizers. Isolates JS04.Deg01 and JS07.Deg01 produced hydroxyatrazine (HA) N-isopropylammelide and cyanuric acid by dealkylation reaction. The isolate JS08.Deg01 generated deethylatrazine (DEA), deisopropylatrazine (DIA), and cyanuric acid by N-dealkylation in the upper degradation pathway and later it incorporated cyanuric acid in their biomass by the lower degradation pathway. The optimum pH for degrading atrazine by JS08.Deg01 was 7.0 and 16S rDNA phylogenetic typing identified it as Enterobacter cloacae strain JS08.Deg01. The highest atrazine mineralization was observed in case of isolate JS08.Deg01, where an ample amount of trzD mRNA was quantified at 72 h of incubation with atrazine. Atrazine bioremediating isolate E. cloacae strain JS08.Deg01 could be the better environmental remediator of agricultural soils and the crop fields contaminated with atrazine could be the source of the efficient biodegrading microbial strains for the environmental cleanup process.

  9. Efficient bioconversion from acid hydrolysate of waste oleaginous yeast biomass after microbial oil extraction to bacterial cellulose by Komagataeibacter xylinus.

    PubMed

    Luo, Mu-Tan; Huang, Chao; Chen, Xue-Fang; Huang, Qian-Lin; Qi, Gao-Xiang; Tian, Lan-Lan; Xiong, Lian; Li, Hai-Long; Chen, Xin-De

    2017-08-31

    Biomass acid hydrolysate of oleaginous yeast Trichosporon cutaneum after microbial oil extraction was applied as substrate for bacterial cellulose (BC) production by Komagataeibacter xylinus (also named as Gluconacetobacter xylinus previously) for the first time. BC was synthesized in static culture for ten days and the maximum BC yield (2.9 g/ L) was got at the 4th day of fermentation. Most carbon sources in the substrate (glucose, mannose, formic acid, acetic acid, etc.) can be utilized by K. xylinus. The highest chemical oxygen demand (COD) removal (40.7 ± 3.0%) was obtained at the 6th day of fermentation and then the COD increased possibly due to the degradation of BC. The highest BC yield on COD consumption was 38.7 ± 4.0% (w/w), suggesting this is one efficient bioconversion for BC production. The BC structure was affected little by the substrate by comparison with that generated in classical HS medium using FE-SEM, FTIR, and XRD. Overall, this technology can both solve the issue of waste oleaginous yeast biomass and produce valuable bio-polymer (BC).

  10. Bacterial vaginosis and vaginal microorganisms in idiopathic premature labor and association with pregnancy outcome.

    PubMed Central

    Holst, E; Goffeng, A R; Andersch, B

    1994-01-01

    The vaginal microflora of 49 women in idiopathic preterm labor was compared with that of 38 term controls to determine whether the presence of bacterial vaginosis (BV) and/or specific microorganisms would influence the rate of preterm delivery. Demographic factors, pregnancy outcome, and reproductive history were also studied. BV, as defined by the presence of clue cells in a vaginal wet mount and characteristic microbial findings in a stained vaginal smear and vaginal culture, was more common in women with preterm labor and delivery than in controls (P < 0.01). The condition, diagnosed in 41% of women who had both preterm labor and delivery (n = 22) and in 11% each of women who had preterm labor but term delivery (n = 27) and controls, was associated with a 2.1-fold risk (95% confidence intervals, 1.2 to 3.7) for preterm birth prior to 37 weeks of gestation. BV was associated with low birth weight. Of 49 women with preterm labor, 67% (8 of 12) of women with BV were delivered of low-birth-weight neonates (< 2,500 g) compared with 22% (8 of 37) of women without the condition (P < 0.0005). The presence of hydrogen peroxide-producing facultative Lactobacillus spp. was strongly negatively associated with both preterm delivery and BV. BV-associated microorganisms, i.e., Mobiluncus, Prevotella, and Peptostreptococcus species, Porphyromonas asaccharolytica, Fusobacterium nucleatum, Mycoplasma hominis, and high numbers of Gardnerella vaginalis were significantly associated with preterm delivery; all species also strongly associated with BV (P = 0.0001 for each comparison). Mobiluncus curtisii and Fusobacterium nucleatum were recovered exclusively from women with preterm delivery. Our study clearly indicates that BV and its associated organisms are correlated with idiopathic premature delivery. PMID:8126176

  11. Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community.

    PubMed

    Lezcano, María Ángeles; Morón-López, Jesús; Agha, Ramsy; López-Heras, Isabel; Nozal, Leonor; Quesada, Antonio; El-Shehawy, Rehab

    2016-11-03

    The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlrA gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlrA gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr⁺ and mlr(-) bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains (Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection (Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr⁺ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr(-) strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non-mlr microcystin degradation pathways. Considering the abundance of the mlr(-) bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non-mlr degradation pathways deserves special attention.

  12. Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community

    PubMed Central

    Lezcano, María Ángeles; Morón-López, Jesús; Agha, Ramsy; López-Heras, Isabel; Nozal, Leonor; Quesada, Antonio; El-Shehawy, Rehab

    2016-01-01

    The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlrA gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlrA gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr+ and mlr− bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains (Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection (Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr+ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr− strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non-mlr microcystin degradation pathways. Considering the abundance of the mlr− bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non-mlr degradation pathways deserves special attention. PMID:27827872

  13. Dandruff Is Associated with Disequilibrium in the Proportion of the Major Bacterial and Fungal Populations Colonizing the Scalp

    PubMed Central

    Clavaud, Cécile; Jourdain, Roland; Bar-Hen, Avner; Tichit, Magali; Bouchier, Christiane; Pouradier, Florence; El Rawadi, Charles; Guillot, Jacques; Ménard-Szczebara, Florence; Breton, Lionel; Latgé, Jean-Paul; Mouyna, Isabelle

    2013-01-01

    The bacterial and fungal communities associated with dandruff were investigated using culture-independent methodologies in the French subjects. The major bacterial and fungal species inhabiting the scalp subject’s were identified by cloning and sequencing of the conserved ribosomal unit regions (16S for bacterial and 28S-ITS for fungal) and were further quantified by quantitative PCR. The two main bacterial species found on the scalp surface were Propionibacterium acnes and Staphylococcus epidermidis, while Malassezia restricta was the main fungal inhabitant. Dandruff was correlated with a higher incidence of M. restricta and S. epidermidis and a lower incidence of P. acnes compared to the control population (p<0.05). These results suggested for the first time using molecular methods, that dandruff is linked to the balance between bacteria and fungi of the host scalp surface. PMID:23483996

  14. Fecal Bacterial Community Changes Associated with Isoflavone Metabolites in Postmenopausal Women after Soy Bar Consumption

    PubMed Central

    Nakatsu, Cindy H.; Armstrong, Arthur; Clavijo, Andrea P.; Martin, Berdine R.; Barnes, Stephen; Weaver, Connie M.

    2014-01-01

    Soy isoflavones and their metabolism by intestinal microbiota have gained attention because of potential health benefits, such as the alleviation of estrogen/hormone-related conditions in postmenopausal women, associated with some of these compounds. However, overall changes in gut bacterial community structure and composition in response to addition of soy isoflavones to diets and their association with excreted isoflavone metabolites in postmenopausal women has not been studied. The aim of this study was to determine fecal bacterial community changes in 17 postmenopausal women after a week of diet supplementation with soy bars containing isoflavones, and to determine correlations between microbial community changes and excreted isoflavone metabolites. Using DGGE profiles of PCR amplified 16S rRNA genes (V3 region) to compare microbial communities in fecal samples collected one week before and one week during soy supplementation revealed significant differences (ANOSIM p<0.03) before and after soy supplementation in all subjects. However, between subjects comparisons showed high inter-individual variation that resulted in clustering of profiles by subjects. Urinary excretion of isoflavone (daidzein) metabolites indicated four subjects were equol producers and all subjects produced O-desmethylangolensin (ODMA). Comparison of relative proportions of 16S rRNA genes from 454 pyrosequencing of the last fecal samples of each treatment session revealed significant increases in average proportions of Bifidobacterium after soy consumption, and Bifidobacterium and Eubacterium were significantly greater in equol vs non-S-(-)equol producers. This is the first in vivo study using pyrosequencing to characterize significant differences in fecal community structure and composition in postmenopausal women after a week of soy diet-supplementation, and relate these changes to differences in soy isoflavones and isoflavone metabolites. Trial Registration Clinicaltrials.gov NCT00244907

  15. Metagenomic Analysis of the Bacterial Community Associated with the Taproot of Sugar Beet

    PubMed Central

    Tsurumaru, Hirohito; Okubo, Takashi; Okazaki, Kazuyuki; Hashimoto, Megumi; Kakizaki, Kaori; Hanzawa, Eiko; Takahashi, Hiroyuki; Asanome, Noriyuki; Tanaka, Fukuyo; Sekiyama, Yasuyo; Ikeda, Seishi; Minamisawa, Kiwamu

    2015-01-01

    We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 105 reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 105 reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the 15N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria. PMID:25740621

  16. Variability in carbon and nitrogen isotope fractionation associated with bacterial hydrolysis of atrazine

    NASA Astrophysics Data System (ADS)

    Meyer, A.; Penning, H.; Elsner, M.

    2009-04-01

    Even after legislative prohibition in 1991 by the European Union, the pesticide atrazine and its metabolites are still detected in surface and ground water frequently exceeding the permitted drinking water concentration limit of 0,1 g/L. Despite much recent research on atrazine, its risk assessment in the environment is still a major challenge because of the difficulty of establishing mass balances in the subsurface. To obtain a better insight into the fate of atrazine, we developed compound-specific stable isotope analysis (CSIA) for atrazine. CSIA has proven valuable for assessing organic contaminants in subsurface environments, on the one hand for source identification and on the other hand to trace (bio)chemical degradation reactions through isotope fractionation in the compounds. Such assessment is based on the Rayleigh equation and therein on the isotope enrichment factor ɛ, which must be determined experimentally beforehand. In ongoing work, we therefore measured carbon and nitrogen isotope fractionation associated with biotic hydrolsis of atrazine. C and N isotope enrichment factors were determined in resting cell experiments for Pseudomonas sp. ADP, Chelatobacter heintzii and Arthrobacter aurescens TC1, strains that hydrolyse atrazine in the initial transformation reaction. Carbon and nitrogen isotope enrichment factors were distinctly different between the bacterial strains. However, when plotting shifts in carbon isotope ratios versus shifts in nitrogen isotope ratios the slopes of the different degradation experiments coincided well. These results give evidence that all bacterial strains were carrying out the same initial biochemical degradation reaction, but that the associated isotope fractionation, as represented by the enrichment factors, was masked to a different extent owing to different rate determining steps prior to the isotopically sensitive bond cleavage (commitment to catalysis). Our study therefore illustrates the benefit of multi

  17. Exploring the bacterial microbiota associated with native South American species of Aphis (Hemiptera: Aphididae).

    PubMed

    Arneodo, J D; Ortego, J

    2014-06-01

    Aphids harbor a variety of bacterial endosymbionts, including the obligate symbiont Buchnera aphidicola and diverse facultative symbionts. The former supplies its host with essential amino acids. The latter are not indispensable for insect survival, but often improve their host's fitness. To date, the study of such associations was restricted to aphids of Holarctic origin. The bacterial microbiota of seven Aphis species from Argentina was investigated. The presence of B. aphidicola was assessed by specific PCR. Additional symbionts were identified through PCR with eubacterial universal primers, cloning, and sequencing of nearly complete 16S rRNA gene, intergenic spacer region, and partial 23S rRNA gene and subjected to phylogenetic analysis. Infection with B. aphidicola was confirmed in every species analyzed. The facultative symbiont Serratia symbiotica was detected in Aphis malalhuina Mier Durante, Nieto Nafría & Ortego, 2003, Aphis senecionicoides Blanchard, 1944, and Aphis schinifoliae Blanchard, 1939, while Hamiltonella defensa was identified in Aphis mendocina Mier Durante, Ortego & Nieto Nafría, 2006. Arsenophonus sp. was found infecting Aphis melosae Mier Durante & Ortego, 1999, and a new, undescribed Aphis sp. In Aphis danielae Remaudière, 1994, no facultative symbionts could be recorded. When analyzing the highly conserved 16S rRNA gene, the phylogenetic tree grouped the S. symbiotica, H. defensa, and Arsenophonus isolates into three well-defined clusters showing little variability among clones corresponding to the same aphid host species. This article reports for the first time the endo