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Sample records for culturable bacterial populations

  1. EFFECTS OF GLYPHOSATE AND NITRAPYRIN ON SELECTED BACTERIAL POPULATIONS IN CONTINUOUS-FLOW CULTURE

    EPA Science Inventory

    This study examines the effects of Roundup [N-(phosphonomethyl)glycine] and N-Serve [2-chloro-6-(trichloromethyl)pyridine] on the culture of soil organisms in a continuous-flow column system. n this study, nitrifying and various heterotrophic bacterial populations were enumerated...

  2. Bacterial Wound Culture

    MedlinePlus

    ... Home Visit Global Sites Search Help? Bacterial Wound Culture Share this page: Was this page helpful? Also known as: Aerobic Wound Culture; Anaerobic Wound Culture Formal name: Culture, wound Related ...

  3. Culturable bacterial populations associated with ectomycorrhizae of Norway spruce stands with different degrees of decline in the Czech Republic.

    PubMed

    Avidano, Lorena; Rinaldi, Maurizio; Gindro, Roberto; Cudlín, Pavel; Martinotti, Maria Giovanna; Fracchia, Letizia

    2010-01-01

    The aim of this study was to determine which species of culturable bacteria are associated with ectomycorrhizae (ECM) of Norway spruce (Picea abies (L.) Karst) in the Sudety Mountains, exposed for years to atmospheric pollutants, acid rain, and climatic stress, and to identify particular species that have adapted to those conditions. Biolog identification was performed on bacterial species from ECM of adult spruce trees and seedlings of stands with low, intermediate, and high forest decline. Bacterial diversity in ECM associated with adult spruce trees, seedlings, and seedlings grown on monoliths was calculated; although the expected values appeared to vary widely, no significant differences among sites were observed. Dendrograms based on the identified bacterial species showed that stands with low forest decline clustered separately from the others. Principal component analysis of the normalized data for ECM-associated species showed a clear separation between stands with high forest decline and stands with low forest decline for seedlings and a less evident separation for adult spruce trees. In conclusion, shifts in ECM-associated culturable bacterial populations seem to be associated with forest decline in Norway spruce stands. Some bacterial species were preferentially associated with mycorrhizal roots depending on the degree of forest decline; this was more evident in seedlings where the species Burkholderia cepacia and Pseudomonas fluorescens were associated with, respectively, ECM of the most damaged stands and those with low forest decline. PMID:20130694

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

    PubMed

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

    2008-04-01

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

  5. Characterization of culturable bacterial populations associating with Pinus sylvestris--Suillus bovinus mycorrhizospheres.

    PubMed

    Timonen, Sari; Hurek, Thomas

    2006-08-01

    Bacterial isolations were carried out on Pinus sylvestris--Suillus bovinus mycorrhizospheres obtained directly from boreal pine forest. When samples were taken during dry weather, the numbers of bacterial colony-forming units were significantly higher in uncolonized short roots and external mycelia than in mycorrhizal roots and soil outside the mycorrhizosphere. In contrast, the colony-forming unit counts were similar in all hypogeous samples after rainy weather. Culturable bacteria were absent from most Suillus bovinus sporocarps. The bacteria isolated from all types of mycorr hizo sphere samples, i.e. short roots, mycorrhizal roots, and external mycelia, consisted primarily of Burkholderia spp., whereas most isolates from soil outside the mycorrhizosphere were identified as Paenibacillus spp. This study shows that mycorrhizal external mycelia can expand the habitat favourable for common rhizosphere bacteria into the soil far from the immediate rhizosphere. Some of these bacteria may help the trees with nitrogen acquisition, since potentially diazotrophic bacteria harbouring nitrogenase reductase (nifH) genes were isolated from mycorrhizal root tips. PMID:16917536

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

    PubMed Central

    2014-01-01

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

  7. Diversity of culturable bacterial populations associated to Tuber borchii ectomycorrhizas and their activity on T. borchii mycelial growth.

    PubMed

    Sbrana, Cristiana; Agnolucci, Monica; Bedini, Stefano; Lepera, Annamaria; Toffanin, Annita; Giovannetti, Manuela; Nuti, Marco P

    2002-06-01

    Isolation and physiological and molecular characterisation of culturable bacterial strains belonging to actinomycetes, pseudomonads and aerobic spore-forming bacteria were carried out on mycorrhizal root tips of Quercus robur var. peduncolata infected by Tuber borchii. Cellular density of the three bacterial groups in ectomycorrhizal root tips was estimated to be 1.3+/-0.11 x 10(6) cfu g(-1) dry weight for total heterotrophic bacteria and 1.08+/-0.6 x 10(5) (mean+/-S.E.), 1.3+/-0.3 x 10(5) and 1.4+/-0.2 x 10(5) cfu g(-1) dry weight for pseudomonads, actinomycetes and spore-forming bacteria respectively. Identification of pseudomonads by the Biolog system indicated, besides the most represented species Pseudomonas fluorescens (biotypes B, F and G), the occurrence of strains belonging to Pseudomonas corrugata. Amplified ribosomal DNA restriction analysis of actinomycetes and spore formers revealed at least three and six different groups of patterns, respectively. Many bacterial isolates were able to induce variations in growth rates of T. borchii mycelium; among these, 101 strains showed antifungal activity, whereas 17 isolates, belonging to spore formers, were able to increase mycelial growth up to 78% when compared to uninoculated mycelial growth. The potential role of these populations in the development and establishment of mycorrhizas is discussed. PMID:12076812

  8. Culturable and VBNC Vibrio cholerae: interactions with chironomid egg masses and their bacterial population.

    PubMed

    Halpern, Malka; Landsberg, Ori; Raats, Dina; Rosenberg, Eugene

    2007-02-01

    Vibrio cholerae, the etiologic agent of cholera, is autochthonous to various aquatic environments. Recently, it was found that chironomid (nonbiting midges) egg masses serve as a reservoir for the cholera bacterium and that flying chironomid adults are possible windborne carriers of V. cholerae non-O1 non-O139. Chironomids are the most widely distributed insect in freshwater. Females deposit egg masses at the water's edge, and each egg mass contains eggs embedded in a gelatinous matrix. Hemagglutinin/protease, an extracellular enzyme of V. cholerae, was found to degrade chironomid egg masses and to prevent them from hatching. In a yearly survey, chironomid populations and the V. cholerae in their egg masses followed phenological succession and interaction of host-pathogen population dynamics. In this report, it is shown via FISH technique that most of the V. cholerae inhabiting the egg mass are in the viable but nonculturable (VBNC) state. The diversity of culturable bacteria from chironomid egg masses collected from two freshwater habitats was determined. In addition to V. cholerae, representatives of the following genera were isolated: Acinetobacter, Aeromonas, Klebsiella, Shewanella, Pseudomonas, Paracoccus, Exiguobacterium, and unidentified bacteria. Three important human pathogens, Aeromonas veronii, A. caviae, and A. hydrophila, were isolated from chironomid egg masses, indicating that chironomid egg masses may be a natural reservoir for pathogenic Aeromonas species in addition to V. cholerae. All isolates of V. cholerae were capable of degrading chironomid egg masses. This may help explain their host-pathogen relationship with chironomids. In contrast, almost none of the other bacteria that were isolated from the egg masses possessed this ability. Studying the interaction between chironomid egg masses, the bacteria inhabiting them, and V. cholerae could contribute to our understanding of the nature of the V. cholerae-egg mass interactions. PMID:17186156

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

    PubMed Central

    Ryall, Ben; Eydallin, Gustavo

    2012-01-01

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

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

    PubMed Central

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

    2007-01-01

    Anaerobic cultures capable of reductively dechlorinating 2,3,4,5-tetrachlorobiphenyl (CB) were enriched from three different sediments, one estuarine, one marine and one riverine. Two different electron donors were used in enrichments with the estuarine sediment (elemental iron or a mixture of fatty acids). The removal of doubly flanked meta and para chlorines to form 2,3,5-CB and 2,4,5-CB was observed in all cultures. Bacterial community analysis of PCR-amplified 16S rRNA gene fragments revealed different communities in these cultures, with the exception of one common population that showed a high phylogentic relatedness to Dehalococcoides species. No Dehalococcoides-like populations were ever detected in control cultures to which no PCBs were added. In addition, the dynamics of this Dehalococcoides-like population were strongly correlated with dechlorination. Subcultures of the estuarine sediment culture demonstrated that the Dehalococcoides-like population disappeared when dechlorination was inhibited with 2-bromoethanesulfonate or when 2,3,4,5-CB had been consumed. These results provide evidence that Dehalococcoides-like populations were involved in the removal of doubly flanked chlorines from 2,3,4,5-CB. Furthermore, the successful enrichment of these populations from geographically distant and geochemically distinct environments indicates the widespread presence of these PCB-dechlorinating, Dehalococcoides-like organisms. PMID:16420633

  11. Bacterial computing with engineered populations.

    PubMed

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

    2015-07-28

    We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell-cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research. PMID:26078340

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

    PubMed

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

    2016-04-01

    The effects of hydraulic retention times (HRTs-6, 3 and 2 h) on H2 production, operational stability and bacterial population response in a continuously stirred tank reactor (CSTR) were evaluated using galactose. A peak hydrogen production rate (HPR) of 25.9 L H2/L-d was obtained at a 3 h HRT with an organic loading rate (OLR) of 120 g/L-d, while the maximum hydrogen yield (HY) of 2.21 mol H2/mol galactose was obtained at a 6 h HRT (60 g galactose/L-d). Butyrate was dominant and the lactate concentration increased as HRT decreased, which significantly affected the HY. Biomass concentration (VSS) decreased from 16 to 3g/L at a 2 h HRT, leading to failure. A 3 h HRT supported the favorable growth of Clostridium species, as indicated by an increase in their populations from 25.4% to 27%, while significantly reducing Bacilli populations from 61.6% to 54.2%, indicating that this was the optimal condition. PMID:26859326

  13. Dynamic clustering of bacterial population

    NASA Astrophysics Data System (ADS)

    Ko, Elizabeth P.; Yomo, Tetsuya; Urabe, Itaru

    1994-08-01

    Bacterial cells having the same genotype were observed to split into a few clusters of phenotypes with various levels of enzyme activity. When the mixture of these phenotypically heterogeneous but genotypically homogeneous cells was cultivated in a liquid medium, the distribution of the population size of each cluster of phenotypes showed various kinds of dynamic oscillations. In addition, when this dynamic behavior was examined for the cells of the single colony, various patterns of shifting of homogeneous to heterogeneous lineage and vice versa were observed in the population. The results imply that differentiation of the cells with the same genotype can occur without spatial information and even under the same environment where the cells interact globally without spatial constrait. This interesting phenomenon totally contradicts the conventional biology that the genotype of a cell uniquely determines the phenotype of the cell and its progeny, but is consistent with the theoretical model of cell differentiation presented in the following paper. The sources of discrepancy between the existing theory in molecular biology and our results were discussed and it is concluded that in understanding a complex living system, a simple model consisting of the essence of the complex system can be constructed justifying the observed properties of the molecules in the system which provide free interactions.

  14. Model for Mutation in Bacterial Populations

    NASA Astrophysics Data System (ADS)

    Donangelo, R.; Fort, H.

    2002-07-01

    We describe the evolution of E. coli populations through a Bak-Sneppen-type model which incorporates random mutations. We show that, for a value of the mutation level which coincides with the one estimated from experiments, this model reproduces the measures of mean fitness relative to that of a common ancestor, performed for over 10 000 bacterial generations.

  15. Insights from Genomics into Bacterial Pathogen Populations

    PubMed Central

    Wilson, Daniel J.

    2012-01-01

    Bacterial pathogens impose a heavy burden of disease on human populations worldwide. The gravest threats are posed by highly virulent respiratory pathogens, enteric pathogens, and HIV-associated infections. Tuberculosis alone is responsible for the deaths of 1.5 million people annually. Treatment options for bacterial pathogens are being steadily eroded by the evolution and spread of drug resistance. However, population-level whole genome sequencing offers new hope in the fight against pathogenic bacteria. By providing insights into bacterial evolution and disease etiology, these approaches pave the way for novel interventions and therapeutic targets. Sequencing populations of bacteria across the whole genome provides unprecedented resolution to investigate (i) within-host evolution, (ii) transmission history, and (iii) population structure. Moreover, advances in rapid benchtop sequencing herald a new era of real-time genomics in which sequencing and analysis can be deployed within hours in response to rapidly changing public health emergencies. The purpose of this review is to highlight the transformative effect of population genomics on bacteriology, and to consider the prospects for answering abiding questions such as why bacteria cause disease. PMID:22969423

  16. Population dynamics on heterogeneous bacterial substrates

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  17. Scanning electron microscopy studies of bacterial cultures

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  18. RELATIONSHIP OF TOTAL VIABLE AND CULTURABLE CELLS TO EPIPHYTIC POPULATIONS OF PSEUDOMONAS SYRINGAE

    EPA Science Inventory

    The accuracy of the plate count method used routinely for enumeration of viable bacterial populations in natural environments is limited by the culturability of the target population. he method was modified to examine epiphytic populations of Pseudomonas syringae. iable populatio...

  19. Bacterial Population Genetics in a Forensic Context

    SciTech Connect

    Velsko, S P

    2009-11-02

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

  20. Determination of Plasmid Segregational Stability in a Growing Bacterial Population.

    PubMed

    Kramer, M Gabriela

    2016-01-01

    Bacterial plasmids are extensively used as cloning vectors for a number of genes for academic and commercial purposes. Moreover, attenuated bacteria carrying recombinant plasmids expressing genes with anti-tumor activity have shown promising therapeutic results in animal models of cancer. Equitable plasmid distribution between daughter cells during cell division, i.e., plasmid segregational stability, depends on many factors, including the plasmid copy number, its replication mechanism, the levels of recombinant gene expression, the type of bacterial host, and the metabolic burden associated with all these factors. Plasmid vectors usually code for antibiotic-resistant functions, and, in order to enrich the culture with bacteria containing plasmids, antibiotic selective pressure is commonly used to eliminate plasmid-free segregants from the growing population. However, administration of antibiotics can be inconvenient for many industrial and therapeutic applications. Extensive ongoing research is being carried out to develop stably-inherited plasmid vectors. Here, I present an easy and precise method for determining the kinetics of plasmid loss or maintenance for every ten generations of bacterial growth in culture. PMID:26846807

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

    PubMed

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

    2010-05-01

    The diversity and dynamics of the dominant bacterial population during the manufacture and the ripening of two artisanal Pecorino Crotonese cheeses, provided by different farms, were investigated by the combination of culture-dependent and -independent approaches. Three hundred and thirty-three strains were isolated from selective culture media, clustered using Restriction Fragment Length Polymorphism and were identified by 16S rRNA gene sequencing. The results indicate a decrease in biodiversity during ripening, revealing the presence of Lactococcus lactis and Streptococcus thermophilus species in the curd and in aged cheese samples and the occurrence of several lactobacilli throughout cheese ripening, with the dominance of Lactobacillus rhamnosus species. Bacterial dynamics determined by Denaturant Gradient Gel Electrophoresis provided a more precise description of the distribution of bacteria, highlighting differences in the bacterial community among cheese samples, and allowed to detect Lactobacillus plantarum, Lactobacillus buchneri and Leuconostoc mesenteroides species, which were not isolated. Moreover, the concentration of flavour compounds produced throughout cheese ripening was investigated and related to lactic acid bacteria presence. Fifty-seven compounds were identified in the volatile fraction of Pecorino Crotonese cheeses by Gas Chromatography-Mass Spectrometry. Esters, alcohols and free fatty acids were the most abundant compounds, while aldehydes and hydrocarbons were present at low levels. PMID:20227601

  2. Chronic osteomyelitislike disease with negative bacterial cultures.

    PubMed

    Pelkonen, P; Ryöppy, S; Jääskeläinen, J; Rapola, J; Repo, H; Kaitila, I

    1988-11-01

    During a seven-year period we observed 14 children who had chronic osteomyelitislike disease. The bacterial cultures from the bone lesions were negative. In eight patients the findings were compatible with chronic recurrent multifocal osteomyelitis (CRMO), in four the findings were compatible with chronic sclerosing osteomyelitis of Garré, and two had osteomyelitis of the clavicle. In patients with CRMO, lymphocyte subpopulations, the responses to mitogens, and the chemotactic and chemokinetic responses showed no consistent abnormalities. After a mean follow-up of 4.5 years (range, one to ten years), all four patients with osteomyelitis of Garré were symptomatic, and two had complications. Only two of the eight patients with CRMO had active disease. The course had been complicated by growth disturbances in one patient and by thoracic outlet syndrome in another. Wegener's granulomatosis later developed in a patient with CRMO. PMID:3177323

  3. Antarctic ice core samples: culturable bacterial diversity.

    PubMed

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

    2013-01-01

    Culturable bacterial abundance at 11 different depths of a 50.26 m ice core from the Tallaksenvarden Nunatak, Antarctica, varied from 0.02 to 5.8 × 10(3) CFU ml(-1) of the melt water. A total of 138 bacterial strains were recovered from the 11 different depths of the ice core. Based on 16S rRNA gene sequence analyses, the 138 isolates could be categorized into 25 phylotypes belonging to phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. All isolates had 16S rRNA sequences similar to previously determined sequences (97.2-100%). No correlation was observed in the distribution of the isolates at the various depths either at the phylum, genus or species level. The 25 phylotypes varied in growth temperature range, tolerance to NaCl, growth pH range and ability to produce eight different extracellular enzymes at either 4 or 18 °C. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a significant proportion of the total fatty acid composition. PMID:23041141

  4. Dynamics of Genome Rearrangement in Bacterial Populations

    PubMed Central

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

    2008-01-01

    first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes. PMID:18650965

  5. Which games are growing bacterial populations playing?

    PubMed Central

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

    2015-01-01

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

  6. β-Lactam Effects on Mixed Cultures of Common Respiratory Isolates as an Approach to Treatment Effects on Nasopharyngeal Bacterial Population Dynamics

    PubMed Central

    Sevillano, David; Aguilar, Lorenzo; Alou, Luis; Giménez, María-José; González, Natalia; Torrico, Martha; Cafini, Fabio; Coronel, Pilar; Prieto, José

    2008-01-01

    Background Streptococcus pneumoniae, Streptococcus pyogenes and Haemophilus influenzae are bacteria present in the nasopharynx as part of normal flora. The ecological equilibrium in the nasopharynx can be disrupted by the presence of antibiotics. Methodology/Principal Findings A computerized two-compartment pharmacodynamic model was used to explore β-lactam effects on the evolution over time of a bacterial load containing common pharyngeal isolates by simulating free serum concentrations obtained with amoxicillin (AMX) 875 mg tid, amoxicillin/clavulanic acid (AMC) 875/125 mg tid and cefditoren (CDN) 400 mg bid regimens over 24 h. Strains and MICs (µg/ml) of AMX, AMC and CDN were: S. pyogenes (0.03, 0.03 and 0.015), S. pneumoniae (2, 2 and 0.25), a β-lactamase positive H. influenzae (BL+; >16, 2 and 0.06) and a β-lactamase positive AMC-resistant H. influenzae (BLPACR, >16, 8 and 0.06). Mixture of identical 1∶1∶1∶1 volumes of each bacterial suspension were prepared yielding an inocula of ≈4×106 cfu/ml. Antibiotic concentrations were measured both in bacterial and in bacteria-free antibiotic simulations. β-lactamase production decreased AMX concentrations and fT>MIC against S. pneumoniae (from 43.2% to 17.7%) or S. pyogenes (from 99.9% to 24.9%), and eradication was precluded. The presence of clavulanic acid countered this effect of co-pathogenicity, and S. pyogenes (but not BL+ and S. pneumoniae) was eradicated. Resistance of CDN to TEM β-lactamase avoided this co-pathogenicity effect, and CDN eradicated S. pyogenes and H. influenzae strains (fT>MIC >58%), and reduced in 94% S. pneumoniae counts (fT>MIC ≈25%). Conclusions/Significance Co-pathogenicity seems to be gradual since clavulanic acid countered this effect for strains very susceptible to AMX as S. pyogenes but not for strains with AMX MIC values in the limit of susceptibility as S. pneumoniae. There is a potential therapeutic advantage for β-lactamase resistant cephalosporins with high

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

    NASA Astrophysics Data System (ADS)

    Cogan, N. G.

    2016-06-01

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

  8. Bacterial culture preservation in frozen and dry-film methylcellulose.

    PubMed

    Suslow, T V; Schroth, M N

    1981-11-01

    Forty-seven of 61 bacterial cultures, including strains of Pseudomonas, Xanthomonas, Erwinia, Agrobacterium, Corynebacterium, Serratia, Klebsiella, and Escherichia, remained viable after storage in frozen methylcellulose or in dried methylcellulose for up to 38 months. Pathogenicity remained intact for those strains tested. Bacteria were grown on a solid medium and then removed and placed in 1.0% methylcellulose (cellulose methyl ether) to make a final suspension of 10 colony-forming units (CFU) per ml. For storage in dried form, the bacteria-methylcellulose suspension was placed in a petri dish and dried in a forced-air incubator. After 24 h of storage at 25 degrees C, viable populations of 10 CFU/mg (equivalent to 10 CFU/ml) were recovered. Populations of 10 to 10 CFU/mg were recovered after storage of up to 38 months. Similar results were obtained in frozen methylcellulose. Survival was greatly enhanced when the growth medium for the bacteria was potato dextrose peptone rather than nutrient agar, yeast dextrose calcium carbonate peptone, or King's medium B. Addition of 0.1 M MgSO(4) to the methylcellulose suspension and to the resuspending liquid also increased survival and recovery from storage for some strains. Methylcellulose storage should be a simple, inexpensive, and reliable method of maintaining cultures for short or long periods of time. PMID:16345889

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

    PubMed Central

    Musser, J. M.

    1996-01-01

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

  10. Effects of nitroethane and monensin on ruminal fluid fermentation characteristics and nitrocompound-metabolizing bacterial populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this study were to examine the effects of nitroethane (NE) and monensin (M) on ruminal fermentation, NE-degradation and nitro-degrading bacterial populations during in vitro consecutive batch culture (CBC). Treatments tested included control (C), 4.5 mM NE (1NE), 9 mM NE (2NE), 5 ...

  11. Punctuated equilibrium in an evolving bacterial population

    NASA Astrophysics Data System (ADS)

    Chaudhuri, Indranath; Bose, Indrani

    1999-08-01

    Recently, Lenski et al. have carried out an experiment on bacterial evolution. Their findings support the theory of punctuated equilibrium in biological evolution. We show that the M=2 Bak-Sneppen model can explain some of the experimental results in a qualitative manner.

  12. Defining heterogeneity within bacterial populations via single cell approaches.

    PubMed

    Davis, Kimberly M; Isberg, Ralph R

    2016-08-01

    Bacterial populations are heterogeneous, which in many cases can provide a selective advantage during changes in environmental conditions. In some instances, heterogeneity exists at the genetic level, in which significant allelic variation occurs within a population seeded by a single cell. In other cases, heterogeneity exists due to phenotypic differences within a clonal, genetically identical population. A variety of mechanisms can drive this latter strategy. Stochastic fluctuations can drive differential gene expression, but heterogeneity in gene expression can also be driven by environmental changes sensed by individual cells residing in distinct locales. Utilizing multiple single cell approaches, workers have started to uncover the extent of heterogeneity within bacterial populations. This review will first describe several examples of phenotypic and genetic heterogeneity, and then discuss many single cell approaches that have recently been applied to define heterogeneity within bacterial populations. PMID:27273675

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

    PubMed

    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 21(st) 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

  14. 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

  15. Raw Cow Milk Bacterial Population Shifts Attributable to Refrigeration

    PubMed Central

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

    2004-01-01

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

  16. Metabolic regulation in bacterial continuous cultures: I.

    PubMed

    Baloo, S; Ramkrishna, D

    1991-12-20

    Dilution rate steps in continuous culture experiments with Klebsiella pneumoniae growing on single substrate feeds have brought out interesting features of metabolic regulation not observed in batch cultures. In a step-up experiment, the adjustment of the culture to a new steady state is preceded by an undershoot in cell density. Results of a step-down experiment indicate a corresponding overshoot phenomenon. These observations of the transient behavior of the culture growing on glucose and xylose as well as the steady-state results are interpreted with cybernetic models. The development of the model explicitly accounts for the lumped internal resource, which is optimally allocated toward the synthesis of key enzymes catalyzing different cellular processes. The model also includes a description of the increased maintenance demand observed at low growth rates. It reduces to previous cybernetic models in situations where the cell does not experience a sudden change in its environment and, hence, retains their predictive capability. PMID:18600736

  17. Bacterial Cellulose as a Substrate for Microbial Cell Culture

    PubMed Central

    Yin, Na; Santos, Thiago M. A.; Auer, George K.; Crooks, John A.; Oliver, Piercen M.

    2014-01-01

    Bacterial cellulose (BC) has a range of structural and physicochemical properties that make it a particularly useful material for the culture of bacteria. We studied the growth of 14 genera of bacteria on BC substrates produced by Acetobacter xylinum and compared the results to growth on the commercially available biopolymers agar, gellan, and xanthan. We demonstrate that BC produces rates of bacterial cell growth that typically exceed those on the commercial biopolymers and yields cultures with higher titers of cells at stationary phase. The morphology of the cells did not change during growth on BC. The rates of nutrient diffusion in BC being higher than those in other biopolymers is likely a primary factor that leads to higher growth rates. Collectively, our results suggest that the use of BC may open new avenues in microbiology by facilitating bacterial cell culture and isolation. PMID:24441155

  18. Measurement of Behavioral Evolution in Bacterial Populations

    NASA Astrophysics Data System (ADS)

    Austin, Robert

    2013-03-01

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

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

    SciTech Connect

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

    2014-03-14

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

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

    PubMed Central

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

    2015-01-01

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

  1. Determining the culturability of the rumen bacterial microbiome.

    PubMed

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

    2014-09-01

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

  2. Determining the culturability of the rumen bacterial microbiome

    PubMed Central

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

    2014-01-01

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

  3. Evolution of morphology of bacterial cellulose scaffolds during early culture.

    PubMed

    Luo, Honglin; Zhang, Jing; Xiong, Guangyao; Wan, Yizao

    2014-10-13

    Morphological characteristics of a fibrous tissue engineering (TE) scaffold are key parameters affecting cell behavior. However, no study regarding the evolution of morphology of bacterial cellulose (BC) scaffolds during the culture process has been reported to date. In this work, BC scaffolds cultured for different times starting from 0.5h were characterized. The results demonstrated that the formation of an integrated scaffold and its 3D network structure, porosity, fiber diameter, light transmittance, and the morphology of hydroxyapatite (HAp)-deposited BC scaffolds changed with culture time. However, the surface and crystal structure of BC fibers did not change with culture time and no difference was found in the crystal structure of HAp deposited on BC templates regardless of BC culture time. The findings presented herein suggest that proper selection of culture time can potentially enhance the biological function of BC TE scaffold by optimizing its morphological characteristics. PMID:25037408

  4. Urban aerosols harbor diverse and dynamic bacterial populations

    PubMed Central

    Brodie, Eoin L.; DeSantis, Todd Z.; Parker, Jordan P. Moberg; Zubietta, Ingrid X.; Piceno, Yvette M.; Andersen, Gary L.

    2007-01-01

    Considering the importance of its potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known regarding the composition or dynamics of the atmosphere's microbial inhabitants. Using a custom high-density DNA microarray, we detected and monitored bacterial populations in two U.S. cities over 17 weeks. These urban aerosols contained at least 1,800 diverse bacterial types, a richness approaching that of some soil bacterial communities. We also reveal the consistent presence of bacterial families with pathogenic members including environmental relatives of select agents of bioterrorism significance. Finally, using multivariate regression techniques, we demonstrate that temporal and meteorological influences can be stronger factors than location in shaping the biological composition of the air we breathe. PMID:17182744

  5. Exploring the interactions between bacterial populations and antimicrobials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacteria are ubiquitous, covering every ecological niche known to man. Within these ecological niches bacterial populations adapt to ensure their survival. The development of antimicrobial resistance is an example of a bacterium's ability to adapt and survive. Antimicrobial resistance developed s...

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

    PubMed

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

    2013-01-01

    Nine aerobic cellulolytic bacterial cultures were obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Culture (DSMZ) and the American Type Culture Collection (ATCC). The objectives of this study were to characterize the cellulolytic bacteria and to determine the optimum moisture ratio required for solid state fermentation (SSF) of palm kernel cake (PKC). The bacteria cultures were grown on reconstituted nutrient broth, incubated at 30°C and agitated at 200 rpm. Carboxymethyl cellulase, xylanase, and mannanase activities were determined using different substrates and after SSF of PKC. The SSF was conducted for 4 and 7 days with inoculum size of 10% (v/w) on different PKC concentration-to-moisture ratios: 1 : 0.2, 1 : 0.3, 1 : 0.4, and 1 : 0.5. Results showed that Bacillus amyloliquefaciens 1067 DSMZ, Bacillus megaterium 9885 ATCC, Paenibacillus curdlanolyticus 10248 DSMZ, and Paenibacillus polymyxa 842 ATCC produced higher enzyme activities as compared to other bacterial cultures grown on different substrates. The cultures mentioned above also produced higher enzyme activities when they were incubated under SSF using PKC as a substrate in different PKC-to-moisture ratios after 4 days of incubation, indicating that these cellulolytic bacteria can be used to degrade and improve the nutrient quality of PKC. PMID:24319380

  7. Effect of emulsan on biodegradation of crude oil by pure and mixed bacterial cultures

    SciTech Connect

    Foght, J.M.; Westlake, D.W.S. ); Gutnick, D.L. )

    1989-01-01

    Crude oil was treated with purified emulsan, the heteropolysaccharide bioemulsifier produced by Acinetobacter calcoaceticus RAG-1. A mixed bacterial population as well as nine different pure cultures isolated from various sources was tested for biodegradation of emulsan-treated and untreated crude oil. Biodegradation was measured both quantitatively and qualitatively. Recovery of {sup 14}CO{sub 2} from mineralized {sup 14}C-labeled substrates yielded quantitative data on degradation of specific compounds, and capillary gas chromatography of residual unlabeled oil yielded qualitative data on a broad spectrum of crude oil components. Biodegradation of linear alkanes and other saturated hydrocarbons, both by pure cultures and by the mixed population, was reduced some 50 to 90% after emulsan pretreatment. In addition, degradation of aromatic compounds by the mixed population was reduced some 90% in emulsan-treated oil. In sharp contrast, aromatic biodegradation by pure cultures was either unaffected or slightly stimulated by emulsification of the oil.

  8. Pelagic fish hydrolysates as peptones for bacterial culture media.

    PubMed

    Beaulieu, Lucie; Desbiens, Michel; Thibodeau, Jacinthe; Thibault, Sharon

    2009-11-01

    For several years in the Quebec fisheries' industry, landings of pelagic fish have been calculated at over 4000 tons. These under-exploited species, rich in lipids and proteins, could be used in valuable new products. In the present study, hydrolysates of mackerel and herring were produced and utilized as sources of peptones in the formulation of new bacterial culture media. The molecular weight distribution analysis showed that molecules present in the hydrolysates were lower than 1300 Da for herring, and lower than 930 Da for mackerel. The formulated media were compared with reference media using 6 bacterial strains (3 lactic acid (LAB) and 3 non-lactic). The absorbance (OD) and carbohydrate measurements revealed that the formulated media possessed similar yields in comparison with the reference media. Finally, the inhibition of Listeria innocua by LAB bacteriocins was evaluated. Results obtained for Pediococcus acidilactici demonstrated high activities for each medium studied. Thus, the medium containing herring peptones generated the highest bacteriocin titre (32768 AU/mL), followed by both the medium containing mackerel peptones and the MRS7 medium (16384 AU/mL). Each medium containing the fish hydrolysates efficiently supported the growth of the bacterial strains. Pelagic fish peptones are promising as a novel bacterial culture media. PMID:19940932

  9. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    SciTech Connect

    Cherrier, J.

    2005-05-16

    Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblages collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO{sub 2} could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO{sub 2} was used as the indicator of hydrocarbon degradation and {delta}{sup 13}C analysis of the resultant CO{sub 2} was used to evaluate the source of the respired CO{sub 2} (i.e. petroleum hydrocarbons or the pinfish cometabolite

  10. Patterned progression of bacterial populations in the premature infant gut.

    PubMed

    La Rosa, Patricio S; Warner, Barbara B; Zhou, Yanjiao; Weinstock, George M; Sodergren, Erica; Hall-Moore, Carla M; Stevens, Harold J; Bennett, William E; Shaikh, Nurmohammad; Linneman, Laura A; Hoffmann, Julie A; Hamvas, Aaron; Deych, Elena; Shands, Berkley A; Shannon, William D; Tarr, Phillip I

    2014-08-26

    In the weeks after birth, the gut acquires a nascent microbiome, and starts its transition to bacterial population equilibrium. This early-in-life microbial population quite likely influences later-in-life host biology. However, we know little about the governance of community development: does the gut serve as a passive incubator where the first organisms randomly encountered gain entry and predominate, or is there an orderly progression of members joining the community of bacteria? We used fine interval enumeration of microbes in stools from multiple subjects to answer this question. We demonstrate via 16S rRNA gene pyrosequencing of 922 specimens from 58 subjects that the gut microbiota of premature infants residing in a tightly controlled microbial environment progresses through a choreographed succession of bacterial classes from Bacilli to Gammaproteobacteria to Clostridia, interrupted by abrupt population changes. As infants approach 33-36 wk postconceptional age (corresponding to the third to the twelfth weeks of life depending on gestational age at birth), the gut is well colonized by anaerobes. Antibiotics, vaginal vs. Caesarian birth, diet, and age of the infants when sampled influence the pace, but not the sequence, of progression. Our results suggest that in infants in a microbiologically constrained ecosphere of a neonatal intensive care unit, gut bacterial communities have an overall nonrandom assembly that is punctuated by microbial population abruptions. The possibility that the pace of this assembly depends more on host biology (chiefly gestational age at birth) than identifiable exogenous factors warrants further consideration. PMID:25114261

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

    PubMed

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

    2014-12-01

    Waste-based polyhydroxyalkanoate (PHA) production by bacterial enrichments generally follows a three step strategy in which first the wastewater is converted into a volatile fatty acid rich stream that is subsequently used as substrate in a selector and biopolymer production units. In this work, a bacterial community with high biopolymer production capacity was enriched using glycerol, a non-fermented substrate. The substrate versatility and PHA production capacity of this community was studied using glucose, lactate, acetate and xylitol as substrate. Except for xylitol, very high PHA producing capacities were obtained. The PHA accumulation was comparable or even higher than with glycerol as substrate. This is the first study that established a high PHA content (≈70 wt%) with glucose as substrate in a microbial enrichment culture. The results presented in this study support the development of replacing pure culture based PHA production by bacterial enrichment cultures. A process where mixtures of substrates can be easily handled and the acidification step can potentially be avoided is described. PMID:25213684

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

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

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

  13. Isolation of a Bacterial Culture That Degrades Methyl t-Butyl Ether

    PubMed Central

    Salanitro, J. P.; Diaz, L. A.; Williams, M. P.; Wisniewski, H. L.

    1994-01-01

    We have isolated a mixed bacterial culture (BC-1) which is capable of degrading the gasoline oxygenate methyl t-butyl ether (MTBE). BC-1 was developed from seed microorganisms present in a chemical plant biotreater sludge. This enrichment culture has been maintained in continuous culture treating high concentrations of MTBE (120 to 200 mg/liter) as the sole carbon source in a simple feed containing NH4+, PO43-, Mg2+, and Ca2+ nutrients. The unit had a stable MTBE removal rate when maintained with a long cell retention time (ca. 80 to 90 days); however, when operated at a ≤50-day cell waste rate, loss of MTBE-degrading activity was observed. The following three noteworthy experimental data show that MTBE is biodegraded extensively by BC-1: (i) the continuous (oxygen-sparged) culture was able to sustain a population of autotrophic ammonia-oxidizing bacteria which could nitrify influent NH4+ concentrations at high rates and obtain CO2 (sole carbon source for growth) from the metabolism of the alkyl ether, (ii) BC-1 metabolized radiolabeled either (14CH3O-MTBE) to 14CO2 (40%) and 14C-labeled cells (40%), and (iii) cell suspensions of the culture were capable of degrading (substrate depletion experiments) MTBE to t-butyl alcohol, a primary metabolite of MTBE. BC-1 is a mixed culture containing several bacterial species and is the first culture of its kind which can completely degrade an alkyl ether. PMID:16349335

  14. Culturally Competent MMPI Assessment of Hispanic Populations.

    ERIC Educational Resources Information Center

    Dana, Richard H.

    1995-01-01

    Describes culturally competent assessment practice as a context for discussing advantages and disadvantages of various "corrections" currently available for the Minnesota Multiphasic Personality Inventory with Hispanic populations. Corrections include moderator variables, special scales, special norms, translations, and aids to interpretation.…

  15. Detecting rare gene transfer events in bacterial populations.

    PubMed

    Nielsen, Kaare M; Bøhn, Thomas; Townsend, Jeffrey P

    2014-01-01

    Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research. PMID:24432015

  16. Detecting rare gene transfer events in bacterial populations

    PubMed Central

    Nielsen, Kaare M.; Bøhn, Thomas; Townsend, Jeffrey P.

    2014-01-01

    Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research. PMID:24432015

  17. Bacterial nanoscale cultures for phenotypic multiplexed antibiotic susceptibility testing.

    PubMed

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

    2014-09-01

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

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

    PubMed

    Munshi, Tulika K; Chattoo, Bharat B

    2008-08-01

    Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria ( approximately 37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes ( approximately 11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; approximately 9, 7%), Verrucomicrobia ( approximately 6, 5%), Acidobacteria ( approximately 4, 5%), Chlorobiales ( approximately 5, 5%), and Actinobacteria ( approximately 4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the beta-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria ( approximately 47%), Firmicutes ( approximately 22%), CFB group ( approximately 19%), and Actinobacteria ( approximately 13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality. PMID:18097714

  19. Diversity of culturable bacterial endophytes of saffron in Kashmir, India.

    PubMed

    Sharma, Tanwi; Kaul, Sanjana; Dhar, Manoj K

    2015-01-01

    Saffron (Crocus sativus) is a medicinally important plant. The Kashmir valley (J&K, India) emblematizes one of the major and quality saffron producing areas in the world. Nonetheless, the area has been experiencing a declining trend in the production of saffron during the last decade. Poor disease management is one of the major reasons for declining saffron production in the area. Endophytes are known to offer control against many diseases of host plant. During the present study, culturable bacterial endophytes were isolated from saffron plant, identified and assessed for plant growth promoting activities. Molecular and phylogenetic analysis grouped the fifty-four bacterial isolates into eleven different taxa, viz. Bacillus licheniformis, B. subtilis, B. cereus, B. humi, B. pumilus, Paenibacillus elgii, B. safensis, Brevibacillus sp., Pseudomonas putida, Staphylococcus hominis and Enterobacter cloacae. The results were also supported with the identification based on BIOLOG system. B. licheniformis was the dominant endophyte in both leaves and corms of saffron. 81 % isolates showed lipase activity, 57 % cellulase, 48 % protease, 38 % amylase, 33 % chitinase and 29 % showed pectinase activity. 24 % of the isolates were phosphate solublizers, 86 % showed siderophore production and 80 % phytohormone production potential. The present repository of well characterized bacterial endophytes of saffron, have plant growth promoting potential which can be explored further for their respective roles in the biology of the saffron plant. PMID:26558164

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

    PubMed

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

    2011-03-01

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

  1. Dynamics of adaptive immunity against phage in bacterial populations

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-12-01

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

  4. Attached Bacterial Populations Shared by Four Species of Aquatic Angiosperms▿

    PubMed Central

    Crump, Byron C.; Koch, Evamaria W.

    2008-01-01

    Symbiotic relationships between microbes and plants are common and well studied in terrestrial ecosystems, but little is known about such relationships in aquatic environments. We compared the phylogenetic diversities of leaf- and root-attached bacteria from four species of aquatic angiosperms using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of PCR-amplified 16S rRNA genes. Plants were collected from three beds in Chesapeake Bay at sites characterized as freshwater (Vallisneria americana), brackish (Potomogeton perfoliatus and Stuckenia pectinata), and marine (Zostera marina). DGGE analyses showed that bacterial communities were very similar for replicate samples of leaves from canopy-forming plants S. pectinata and P. perfoliatus and less similar for replicate samples of leaves from meadow-forming plants Z. marina and V. americana and of roots of all species. In contrast, bacterial communities differed greatly among plant species and between leaves and roots. DNA sequencing identified 154 bacterial phylotypes, most of which were restricted to single plant species. However, 12 phylotypes were found on more than one plant species, and several of these phylotypes were abundant in clone libraries and represented the darkest bands in DGGE banding patterns. Root-attached phylotypes included relatives of sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Deltaproteobacteria. Leaf-attached phylotypes included relatives of polymer-degrading Bacteroidetes and phototrophic Alphaproteobacteria. Also, leaves and roots of three plant species hosted relatives of methylotrophic Betaproteobacteria belonging to the family Methylophilaceae. These results suggest that aquatic angiosperms host specialized communities of bacteria on their surfaces, including several broadly distributed and potentially mutualistic bacterial populations. PMID:18676705

  5. In Vitro Culture of Previously Uncultured Oral Bacterial Phylotypes

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-04-01

    Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452,686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses. PMID:26394009

  7. Coexisting bacterial populations responsible for multiphasic mineralization kinetics in soil. [Janthinobacterium sp. Rhodococcus sp

    SciTech Connect

    Schmidt, S.K.; Gier, M.J. )

    1990-09-01

    Experiments were conducted to study populations of indigenous microorganisms capable of mineralizing 2,4-dinitrophenol (DNP) in two soils. Previous kinetic analyses indicated the presence of two coexisting populations of DNP-mineralizing microorganisms in a forest soil (soil 1). Studies in which eucaryotic and procaryotic inhibitors were added to this soil indicated that both populations were bacterial. Most-probable-number counts with media containing different concentrations of DNP indicated that more bacteria could mineralize low concentrations of DNP than could metabolize high concentrations of it. Enrichments with varying concentrations of DNP and various combinations of inhibitors consistently resulted in the isolation of the same two species of bacteria from soil 1. This soil contained a large number and variety of fungi, but no fungi capable of mineralizing DNP were isolated. The two bacterial isolates were identified as a Janthinobacterium sp. and a Rhodococcus sp. The Janthinobacterium sp. had a low {mu}{sub max} and a low K{sub m} for DNP mineralization, whereas the Rhodococcus sp. had much higher values for both parameters. These differences between the two species of bacteria were similar to differences seen when soil was incubated with different concentrations of DNP. Values for {mu}{sub max} from soil incubations were similar to {mu}{sub max} values obtained in pure culture studies. In contrast, K{sub s} and K{sub m} values showed greater variation between soil and pure culture studies.

  8. Population growth, demographic change, and cultural landscapes.

    PubMed

    Woodgate, G; Sage, C

    1994-01-01

    The inclusion of both ecological and socioeconomic components within landscapes makes possible the perception of the hierarchical character of landscape organization. A research approach is needed to conceptualize cultural landscapes as the product of interaction between society and nature. Richard Norgaard's 1984 paper on coevolutionary agricultural development attempts to meet this challenge. Coevolution is the interactive synthesis of natural and social mechanisms of change that characterize the relationship between social systems and ecosystems. The relationship between population, consumption, and environmental changes is complex. Currently industrialized countries present the biggest threat to global environmental resources. The issue of carrying capacity is the corollary of population and the environment. It is primarily the technological factor rather than population that needs to be controlled. The relationship between rich and poor countries is determined by superior economic power. An analysis of landscape change is made, tracing the coevolution of society and environment from the end of the feudal era and making comparisons with continental Europe. Over the years since 1945 the need to realize potential economies of scale has resulted in a wholesale loss of woodlands, hedgerows, and small ponds in the UK. In a global context the likely impacts of population growth and demographic change on landscapes will be influenced by such socioeconomic factors as technology and affluence; policies that ignore cause and effect; and the traditional tendency to treat the environment as a waste repository and a supply depot. PMID:12290867

  9. Enhanced bacterial metabolism of a Pseudomonas strain in response to the addition of culture filtrate of a bacteriophagous amoeba.

    PubMed

    Levrat, P; Pussard, M; Alabouvette, C

    1992-02-21

    In a previous work, Levrat et al. [21] showed an enhancement of the production of pyoverdin (siderophore) by Pseudomonas putida in the presence of amoeba. To explain the mechanism of stimulation, the hypothesis of production of stimulatory factors by amoeba was proposed. Filtrates of both mixed culture of bacteria and amoeba (Pseudomonas putida + Acanthamoeba castellanii) and of axenic culture of amoeba were added to the culture medium of Pseudomonas. The production of pyoverdin was increased in the presence of the filtrates. The maximum stimulation was observed with a 6 to 8 day old mixed culture filtrate at 2% final concentration. A higher amount of filtrate did not enhance the stimulation. General metabolisms like ammonium production or respiration were also enhanced in the presence of filtrate of mixed cultures. Filtrates of axenic culture of amoeba were also able to stimulate the production of pyoverdin by Pseudomonas. This stimulation of the bacterial metabolism was not correlated with a higher growth of the bacterial population. Then, the enhancement of the bacterial metabolic activity was not due to a rapid recycling of the bacterial biomass but rather to a production of stimulatory factors by amoeba. PMID:23194985

  10. Lysozyme as a recognition element for monitoring of bacterial population.

    PubMed

    Zheng, Laibao; Wan, Yi; Yu, Liangmin; Zhang, Dun

    2016-01-01

    Bacterial infections remain a significant challenge in biomedicine and environment safety. Increasing worldwide demand for point-of-care techniques and increasing concern on their safe development and use, require a simple and sensitive bioanalysis for pathogen detection. However, this goal is not yet achieved. A design for fluorescein isothiocyanate-labeled lysozyme (FITC-LYZ), which provides quantitative binding information for gram-positive bacteria, Micrococcus luteus, and detects pathogen concentration, is presented. The functional lysozyme is used not only as the pathogenic detection platform, but also as a tracking reagent for microbial population in antibacterial tests. A nonlinear relationship between the system response and the logarithm of the bacterial concentration was observed in the range of 1.2×10(2)-1.2×10(5) cfu mL(-1). The system has a potential for further applications and provides a facile and simple method for detection of pathogenic bacteria. Meanwhile, the fluorescein isothiocyanate -labeled lysozyme is also employed as the tracking agent for antibacterial dynamic assay, which show a similar dynamic curve compared with UV-vis test. PMID:26695267

  11. Cultural competency and recovery within diverse populations.

    PubMed

    Ida, D J

    2007-01-01

    Recovery for diverse populations with mental health problems includes communities of color, those with limited English proficiency and individuals who are lesbian, gay, bisexual or transgender (LGBT). The process of healing and recovery must take into consideration the critical role of culture and language and look at the individual within the context of an environment that is influenced by racism, sexism, colonization, homophobia, and poverty as well as the stigma and shame associated with having a mental illness. Recovery must assess the impact of isolation brought about by cultural and language barriers and work towards reducing the negative influence it has on the emotional and physical well-being of the person. It is imperative that recovery occur at multiple levels and involves the person in recovery, the service provider, the larger community and the system that establishes policies that often work against those who do not fit the mold of what mainstream society considers being "the norm." Recovery must respect the cultural and language backgrounds of the individual. PMID:17694715

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  14. Composition of bacterial communities associated with natural and laboratory populations of Asobara tabida infected with Wolbachia.

    PubMed

    Zouache, Karima; Voronin, Denis; Tran-Van, Van; Mavingui, Patrick

    2009-06-01

    Asobara tabida wasps are fly endoparasitoids that naturally harbor three Wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild A. tabida populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods. Proteobacteria and Firmicutes were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera Acetobacter, Acidomonas, Bacillus, Brevibacillus, Duganella, Herbaspirillum, Pseudomonas, Staphylococcus, and Streptococcus. In addition to Wolbachia, wild individuals harbored Rickettsia, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with Wolbachia also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family Enterobacteriaceae. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only Wolbachia being consistently found in wasp ovaries. PMID:19376923

  15. Polycyclic aromatic hydrocarbon biodegradation by a mixed bacterial culture

    SciTech Connect

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

    1995-12-31

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

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

    PubMed Central

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

    2014-01-01

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

  17. Culturable and nonculturable bacterial symbionts in the toxic benthic dinoflagellate Ostreopsis lenticularis.

    PubMed

    Ashton, Mayra; Rosado, William; Govind, Nadathur S; Tosteson, Thomas R

    2003-09-15

    The toxic benthic dinoflagellate Ostreopsis lenticularis hosts a variety of symbiont bacterial flora. Laboratory cultured Ostreopsis clones require the presence of symbiotic Pseudomonas/Alteromonas bacterial strains for growth and toxicity development. Three culturable bacterial strains associated with Ostreopsis were identified as Pseudomonas/Alteromonas strain 1, Pseudomonas/Alteromonas strain 2 and Acinetobacter. Denaturing gradient gel electrophoresis (DGGE) analyses of extracted Ostreopsis associated bacterial DNAs indicated that there were three culturable and four non-culturable associated bacterial strains. The results presented here are the first report of the presence of unculturable bacterial symbionts in a toxic benthic dinoflagellate. Ostreopsis lost toxicity when exposed to elevated temperatures in the field and laboratory culture and subsequently recovered toxicity at reduced temperatures. Ostreopsis associated culturable Pseudomonas/Alteromonas bacterial strains were significantly reduced in dinoflagellate cultures exposed to elevated temperatures. The decreased toxicity of O. lenticularis exposed to elevated temperatures and their subsequent recovery of toxicity in periods of reduced thermal stress may have resulted from the effects of elevated temperature on the spectrum of culturable and unculturable bacterial species interacting with their Ostreopsis host. PMID:14505943

  18. 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

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-09-01

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

  1. Bacterial population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: To describe, at high resolution, the bacterial population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. Methods and Results: Samples of alfalfa, ensiled alfalfa, and silage exposed to air were collected and their bacterial population stru...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age

    PubMed Central

    Stearns, Jennifer C; Davidson, Carla J; McKeon, Suzanne; Whelan, Fiona J; Fontes, Michelle E; Schryvers, Anthony B; Bowdish, Dawn M E; Kellner, James D; Surette, Michael G

    2015-01-01

    The upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1–4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease. PMID:25575312

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  6. Compositional Stability of a Salivary Bacterial Population against Supragingival Microbiota Shift following Periodontal Therapy

    PubMed Central

    Yamanaka, Wataru; Takeshita, Toru; Shibata, Yukie; Matsuo, Kazuki; Eshima, Nobuoki; Yokoyama, Takeshi; Yamashita, Yoshihisa

    2012-01-01

    Supragingival plaque is permanently in contact with saliva. However, the extent to which the microbiota contributes to the salivary bacterial population remains unclear. We compared the compositional shift in the salivary bacterial population with that in supragingival plaque following periodontal therapy. Samples were collected from 19 patients with periodontitis before and after periodontal therapy (mean sample collection interval, 25.8±2.6 months), and their bacterial composition was investigated using barcoded pyrosequencing analysis of the 16S rRNA gene. Phylogenetic community analysis using the UniFrac distance metric revealed that the overall bacterial community composition of saliva is distinct from that of supragingival plaque, both pre- and post-therapy. Temporal variation following therapy in the salivary bacterial population was significantly smaller than in the plaque microbiota, and the post-therapy saliva sample was significantly more similar to that pre-therapy from the same individual than to those from other subjects. Following periodontal therapy, microbial richness and biodiversity were significantly decreased in the plaque microbiota, but not in the salivary bacterial population. The operational taxonomic units whose relative abundances changed significantly after therapy were not common to the two microbiotae. These results reveal the compositional stability of salivary bacterial populations against shifts in the supragingival microbiota, suggesting that the effect of the supragingival plaque microbiota on salivary bacterial population composition is limited. PMID:22916162

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

    PubMed

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

    2007-02-15

    Forty-six bacterial strains were isolated from nine different sources in four treatment plants namely Indah Water Konsortium (IWK) sewage treatment plant (STP), International Islamic University Malaysia (IIUM) wastewater treatment plant-1,-2 and -3 to evaluate the bioconversion process in terms of efficient biodegradation and bioseparation. The bacterial strains isolated were found to be 52.2% (24 isolates) and 47.8% (22 isolates) in the IWK and IIUM treatment plants, respectively. The results showed that higher microbial population (9-10 x 10(4) cfu/mL) was observed in the secondary clarifier of IWK treatment plant. Among the isolates, 23 isolates were gram-positive bacillus (GPB) and gram-positive cocci (GPC), 19 isolates were gram-negative bacillus (GNB) and gram-negative cocci (GNC), and the rest were undetermined. Gram-negative cocci (GNC) were not found in the isolates from IWK. A total of 15 bacterial strains were selected for effective and efficient sludge bioconversion. All the strains were tested against sludge (1% total suspended solids, TSS) to evaluate the biosolids production (TSS% content), chemical oxygen demand (COD) removal and filtration rate (filterability test). The strain S-1 (IWK1001) showed lower TSS content (0.8% TSS), maximum COD removal (84%) and increased filterability (1.1 min/10 mL of filtrate) of treated sludge followed by the strains S-11, S-14, S-2, S-15, S-13, S-7, S-8, S-4, S-3, S-6, S-12, S-16, S-17 and S-9. The pH values in the fermentation broth were affected by the bacterial cultures and recorded as well. Effective bioconversion was observed during the first three days of sludge treatment. PMID:17365300

  8. Biogeochemical controls on the bacterial population in the eastern Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Neogi, S. B.; Koch, B. P.; Schmitt-Kopplin, P.; Pohl, C.; Kattner, G.; Yamasaki, S.; Lara, R. J.

    2011-08-01

    Little is known about bacterial dynamics in the oligotrophic ocean, particularly about its cultivable population. We examined the abundance of total and cultivable bacteria in relation to changes in biogeochemical conditions in the eastern Atlantic Ocean with special regard to Vibrio spp., a group of bacteria that can cause diseases in human and aquatic organisms. Surface, deep water and plankton samples (<20 μm, 20-55 μm and >55 μm) were collected between 50° N and 24° S. Chlorophyll-a was very low (<0.3 μg l-1) in most areas of the nutrient-poor Atlantic, except at a few locations near upwelling regions. In surface water, dissolved organic carbon (DOC) and nitrogen (DON) concentrations were 64-95 μM C and 2-10 μM N accounting for ≥90 % and ≥76 % of total organic C and N, respectively. DOC and DON gradually decreased to ~45 μM C and <5 μM N in the bottom water while dissolved inorganic nutrients (Si, P, N) increased with depth. In the surface layer, culture independent total bacteria, represented by 4´-6-diamidino-2-phenylindole (DAPI) counts, ranged mostly between 107 and 108 cells l-1, while cultivable bacterial counts (CBC) and Vibrio spp. were found at concentrations of 104-107 and 102-105 colony forming units (CFU) l-1, respectively. Most bacteria (>99 %) were found in the nanoplankton fraction (<20 μm), however, bacterial abundance did not correlate with suspended particulates (chlorophyll-a, particulate organic C and N). Instead, we found a highly significant correlation between bacterial abundance and temperature (p < 0.001) and a significant correlation with DOC and DON. Among the cultivable bacteria, the abundance of Vibrio was also highly significantly correlated with DOC and DON (p < 0.0005 and p < 0.005, respectively). In cold waters of the mid-pelagic and abyssal zones, CBC was 50 to 100-times lower than in the surface layer; however, cultivable Vibrio spp. could be isolated from the bathypelagic zone and even near the seafloor

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

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

    PubMed

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

    2014-12-01

    Bacterial genomes show substantial variations in size. The smallest bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum. PMID:25220308

  12. Total Degradation of EDTA by Mixed Cultures and a Bacterial Isolate

    PubMed Central

    Nörtemann, Bernd

    1992-01-01

    A bacterial mixed culture, which was obtained from sewage by a special enrichment procedure, utilized EDTA as the sole source of carbon and nitrogen for growth. High concentrations of mineral salts, particularly CaCl2, or the use of a mineral base without nitrogen protected the cells from inactivation after transfer into fresh medium containing 200-mg/liter (0.67 mM) EDTA. The chemical speciation did not influence the biodegradability of EDTA. However, when resting cells of the mixed culture were incubated with EDTA in the presence of an equivalent molar amount of FeCl3, the reaction came to a halt before the complete consumption of the substrate. A gram-negative isolate from the mixed population, BNC1, also metabolized EDTA in monoculture. Growth of the pure culture was promoted by biotin or folic acid but was always accompanied by the accumulation of unidentified metabolites and was slow (μmax, 0.024 h-1) compared with that of the original community (μmax, 0.036 h-1). Images PMID:16348653

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

    PubMed

    Kools, Susan; Chimwaza, Angela; Macha, Swebby

    2015-03-01

    Population health needs in developing countries are great and countries are scaling up health professional education to meet these needs. Marginalized populations, in particular, are vulnerable to poor health and health care. This paper presents a culturally appropriate diversity training program delivered to Global Health Fellows who are educators and leaders in health professions in Malawi and Zambia. The purpose of this interprofessional education experience was to promote culturally competent and humble care for marginalized populations. PMID:24842988

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Astrophysics Data System (ADS)

    Boulanouar, Mohamed

    2013-04-01

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

  16. Culturable Bacterial Microbiota of the Stomach of Helicobacter pylori Positive and Negative Gastric Disease Patients

    PubMed Central

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

    2014-01-01

    Human stomach is the only known natural habitat of Helicobacter pylori (Hp), a major bacterial pathogen that causes different gastroduodenal diseases. Despite this, the impact of Hp on the diversity and the composition of the gastric microbiota has been poorly studied. In this study, we have analyzed the culturable gastric microbiota of 215 Malaysian patients, including 131 Hp positive and 84 Hp negative individuals that were affected by different gastric diseases. Non-Hp bacteria isolated from biopsy samples were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry based biotyping and 16SrRNA sequencing. The presence of Hp did not significantly modify the diversity of the gastric microbiota. However, correlation was observed between the isolation of Streptococci and peptic ulcer disease. In addition, as a first report, Burkholderia pseudomallei was also isolated from the gastric samples of the local population. This study suggested that there may be geographical variations in the diversity of the human gastric microbiome. Geographically linked diversity in the gastric microbiome and possible interactions between Hp and other bacterial species from stomach microbiota in pathogenesis are proposed for further investigations. PMID:25105162

  17. A Bacterial Continuous Culture System Based on a Microfluidic Droplet Open Reactor.

    PubMed

    Ito, Manami; Sugiura, Haruka; Ayukawa, Shotaro; Kiga, Daisuke; Takinoue, Masahiro

    2016-01-01

    Recently, micrometer-sized bacterial culture systems have attracted attention as useful tools for synthetic biology studies. Here, we present the development of a bacterial continuous culture system based on a microdroplet open reactor consisting of two types of water-in-oil microdroplets with diameters of several hundred micrometers. A continuous culture was realized the through supply of nutrient substrates and the removal of waste and excess bacterial cells based on repeated fusion and fission of droplets. The growth dynamics was controlled by the interval of fusion. We constructed a microfluidic system and quantitatively assessed the dynamics of the bacterial growth using a mathematical model. This system will facilitate the study of synthetic biology and metabolic engineering in the future. PMID:26753707

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

    PubMed

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

    2016-01-01

    High-throughput cultivation (HTC) based on a dilution-to-extinction method has been applied broadly to the cultivation of marine bacterial groups, which has often led to the repeated isolation of abundant lineages such as SAR11 and oligotrophic marine gammaproteobacteria (OMG). In this study, to expand the phylogenetic diversity of HTC isolates, we performed a large-scale HTC with a single surface seawater sample collected from the East Sea, the Western Pacific Ocean. Phylogenetic analyses of the 16S rRNA genes from 847 putative pure cultures demonstrated that some isolates were affiliated with not-yet-cultured clades, including the OPB35 and Puniceicoccaceae marine group of Verrucomicrobia and PS1 of Alphaproteobacteria. In addition, numerous strains were obtained from abundant clades, such as SAR11, marine Roseobacter clade, OMG (e.g., SAR92 and OM60), OM43, and SAR116, thereby increasing the size of available culture resources for representative marine bacterial groups. Comparison between the composition of HTC isolates and the bacterial community structure of the seawater sample used for HTC showed that diverse marine bacterial groups exhibited various growth capabilities under our HTC conditions. The growth response of many bacterial groups, however, was clearly different from that observed with conventional plating methods, as exemplified by numerous isolates of the SAR11 clade and Verrucomicrobia. This study showed that a large number of novel bacterial strains could be obtained by an extensive HTC from even a small number of samples. PMID:26573832

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

    PubMed Central

    Nanda, Arun M.; Thormann, Kai

    2014-01-01

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

  20. Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions.

    PubMed

    Nanda, Arun M; Thormann, Kai; Frunzke, Julia

    2015-02-01

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

  1. Worldwide populations of APHIS CRACCIVORA have diverse facultative bacterial symbionts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Facultative bacterial endosymbionts can play an important role in the evolutionary trajectory of their hosts. Aphids are infected with a wide variety of facultative endosymbionts that can confer ecologically relevant traits, which in turn may drive microevolution in a dynamic selective environment....

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-10-01

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

  5. Protozoal ciliate promotes bacterial autoinducer-2 accumulation in mixed culture with Escherichia coli.

    PubMed

    Oguri, Satoshi; Hanawa, Tomoko; Matsuo, Junji; Ishida, Kasumi; Yamazaki, Tomohiro; Nakamura, Shinji; Okubo, Torahiko; Fukumoto, Tatsuya; Akizawa, Kouzi; Shimizu, Chikara; Kamiya, Shigeru; Yamaguchi, Hiroyuki

    2015-01-01

    We have previously demonstrated conjugation of Escherichia coli into vacuoles of the protozoal ciliate (Tetrahymena thermophila). This indicated a possible role of ciliates in evoking bacterial quorum sensing, directly connecting bacterial survival via accumulation in the ciliate vacuoles. We therefore assessed if ciliates promoted bacterial autoinducer (AI)-2 accumulation with vacuole formation, which controls quorum sensing. E. coli AI-2 accumulation was significantly enhanced in the supernatants of a mixed culture of ciliates and bacteria, likely depending on ciliate density rather than bacterial concentration. As expected, AI-2 production was significantly correlated with vacuole formation. The experiment with E. coli luxS mutants showed that ciliates failed to enhance bacterial AI-2 accumulation, denying a nonspecific phenomenon. Fluorescence microscopy revealed accumulation of fragmented bacteria in ciliate vacuoles, and, more importantly, expulsion of the vacuoles containing disrupted bacteria into the culture supernatant. There was no increase in the expression of luxS (encoding AI-2) or ydgG (a transporter for controlling bacterial export of AI-2). We conclude that ciliates promote bacterial AI-2 accumulation in a mixed culture, via accumulation of disrupted bacteria in ciliate vacuoles followed by expulsion of the vacuoles, independently of luxS or ydgG gene induction. This is believed to be the first demonstration of a relationship between E. coli AI-2 dynamics and ciliates. In the natural environment, ciliate biotopes may provide a survival advantage to bacteria inhabiting such biotopes, via evoking quorum sensing. PMID:26582290

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  8. Instability in bacterial populations and the curvature tensor

    NASA Astrophysics Data System (ADS)

    Melgarejo, Augusto; Langoni, Laura; Ruscitti, Claudia

    2016-09-01

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

  9. Maintenance of Bacterial Cultures on Anhydrous Silica Gel

    ERIC Educational Resources Information Center

    Lennox, John E.

    1977-01-01

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

  10. Ecological Application of Antibiotics as Respiratory Inhibitors of Bacterial Populations1

    PubMed Central

    Yetka, J. E.; Wiebe, W. J.

    1974-01-01

    Two terregenous and four marine bacterial isolates were treated with six antibiotics and antibiotic combinations. Comparisons made between responses of cells in early and late logarithmic and stationary growth phases indicated variable sensitivity to the agents. Bacteria in stationary and late log-phase cultures exhibited the greatest resistance, whereas the early log-phase cells exhibited greatest antibiotic susceptibility. We conclude that the tested antibiotics cannot be used for ecological purposes to delineate bacterial respiration in mixed microbial communities. PMID:4217588

  11. Biodegradation potential of oily sludge by pure and mixed bacterial cultures.

    PubMed

    Cerqueira, Vanessa S; Hollenbach, Emanuel B; Maboni, Franciele; Vainstein, Marilene H; Camargo, Flávio A O; do Carmo R Peralba, Maria; Bento, Fátima M

    2011-12-01

    The biodegradation capacity of aliphatic and aromatic hydrocarbons of petrochemical oily sludge in liquid medium by a bacterial consortium and five pure bacterial cultures was analyzed. Three bacteria isolated from petrochemical oily sludge, identified as Stenotrophomonas acidaminiphila, Bacillus megaterium and Bacillus cibi, and two bacteria isolated from a soil contaminated by petrochemical waste, identified as Pseudomonas aeruginosa and Bacillus cereus demonstrated efficiency in oily sludge degradation when cultivated during 40 days. The bacterial consortium demonstrated an excellent oily sludge degradation capacity, reducing 90.7% of the aliphatic fraction and 51.8% of the aromatic fraction, as well as biosurfactant production capacity, achieving 39.4% reduction of surface tension of the culture medium and an emulsifying activity of 55.1%. The results indicated that the bacterial consortium has potential to be applied in bioremediation of petrochemical oily sludge contaminated environments, favoring the reduction of environmental passives and increasing industrial productivity. PMID:21993328

  12. Relationship between oral malodor and the global composition of indigenous bacterial populations in saliva.

    PubMed

    Takeshita, Toru; Suzuki, Nao; Nakano, Yoshio; Shimazaki, Yoshihiro; Yoneda, Masahiro; Hirofuji, Takao; Yamashita, Yoshihisa

    2010-05-01

    Oral malodor develops mostly from the metabolic activities of indigenous bacterial populations within the oral cavity, but whether healthy or oral malodor-related patterns of the global bacterial composition exist remains unclear. In this study, the bacterial compositions in the saliva of 240 subjects complaining of oral malodor were divided into groups based on terminal-restriction fragment length polymorphism (T-RFLP) profiles using hierarchical cluster analysis, and the patterns of the microbial community composition of those exhibiting higher and lower malodor were explored. Four types of bacterial community compositions were detected (clusters I, II, III, and IV). Two parameters for measuring oral malodor intensity (the concentration of volatile sulfur compounds in mouth air and the organoleptic score) were noticeably lower in cluster I than in the other clusters. Using multivariate analysis, the differences in the levels of oral malodor were significant after adjustment for potential confounding factors such as total bacterial count, mean periodontal pocket depth, and tongue coating score (P < 0.001). Among the four clusters with different proportions of indigenous members, the T-RFLP profiles of cluster I were implicated as the bacterial populations with higher proportions of Streptococcus, Granulicatella, Rothia, and Treponema species than those of the other clusters. These results clearly correlate the global composition of indigenous bacterial populations with the severity of oral malodor. PMID:20228112

  13. Cultured bacterial diversity and human impact on alpine glacier cryoconite.

    PubMed

    Lee, Yung Mi; Kim, So-Yeon; Jung, Jia; Kim, Eun Hye; Cho, Kyeung Hee; Schinner, Franz; Margesin, Rosa; Hong, Soon Gyu; Lee, Hong Kum

    2011-06-01

    The anthropogenic effect on the microbial communities in alpine glacier cryoconites was investigated by cultivation and physiological characterization of bacteria from six cryoconite samples taken at sites with different amounts of human impact. Two hundred and forty seven bacterial isolates were included in Actinobacteria (9%, particularly Arthrobacter), Bacteroidetes (14%, particularly Olleya), Firmicutes (0.8%), Alphaproteobacteria (2%), Betaproteobacteria (16%, particularly Janthinobacterium), and Gammaproteobacteria (59%, particularly Pseudomonas). Among them, isolates of Arthrobacter were detected only in samples from sites with no human impact, while isolates affiliated with Enterobacteriaceae were detected only in samples from sites with strong human impact. Bacterial isolates included in Actinobacteria and Bacteroidetes were frequently isolated from pristine sites and showed low maximum growth temperature and enzyme secretion. Bacterial isolates included in Gammaproteobacteria were more frequently isolated from sites with stronger human impact and showed high maximum growth temperature and enzyme secretion. Ecotypic differences were not evident among isolates of Janthinobacterium lividum, Pseudomonas fluorescens, and Pseudomonas veronii, which were frequently isolated from sites with different degrees of anthropogenic effect. PMID:21717318

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2012-01-01

    This pilot study describes the effect of intraoperative peritoneal lavage (IOPL) on bacterial counts and outcome in clinical cases of septic peritonitis. Intraoperative samples were cultured before and after IOPL. Thirty-three dogs with presumed septic peritonitis on the basis of cytology were managed surgically during the study period. Positive pre-lavage bacterial cultures were found in 14 cases, 13 of which were a result of intestinal leakage. The post-lavage cultures showed fewer isolates in 9 cases and in 1 case became negative. The number of dogs with a decrease in the concentration of bacteria cultured from pre-lavage to post-lavage samples was not statistically significant. There was no significant effect of the change in pre- to post-lavage culture, single versus multiple types of bacteria, selection of an appropriate empiric antimicrobial on survival or the need for subsequent surgery. PMID:23450861

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

    USGS Publications Warehouse

    Goodwin, K.D.; Schaefer, J.K.; Oremland, R.S.

    1998-01-01

    Bacterial oxidation of 14CH2Br2 and 14CH3Br was measured in freshwater, estuarine, seawater, and hypersaline-alkaline samples. In general, bacteria from the various sites oxidized similar amounts of 14CH2Br2 and comparatively less 14CH3Br. Bacterial oxidation of 14CH3Br was rapid in freshwater samples compared to bacterial oxidation of 14CH3Br in more saline waters. Freshwater was also the only site in which methyl fluoride-sensitive bacteria (e.g., methanotrophs or nitrifiers) governed brominated methane oxidation. Half-life calculations indicated that bacterial oxidation of CH2Br2 was potentially significant in all of the waters tested. In contrast, only in freshwater was bacterial oxidation of CH3Br as fast as chemical removal. The values calculated for more saline sites suggested that bacterial oxidation of CH3Br was relatively slow compared to chemical and physical loss mechanisms. However, enrichment cultures demonstrated that bacteria in seawater can rapidly oxidize brominated methanes. Two distinct cultures of nonmethanotrophic methylotrophs were recovered; one of these cultures was able to utilize CH2Br2 as a sole carbon source, and the other was able to utilize CH3Br as a sole carbon source.

  17. Population Disparities in Mental Health: Insights From Cultural Neuroscience

    PubMed Central

    Blizinsky, Katherine D.

    2013-01-01

    By 2050, nearly 1 in 5 Americans (19%) will be an immigrant, including Hispanics, Blacks, and Asians, compared to the 1 in 8 (12%) in 2005. They will vary in the extent to which they are at risk for mental health disorders. Given this increase in cultural diversity within the United States and costly population health disparities across cultural groups, it is essential to develop a more comprehensive understanding of how culture affects basic psychological and biological mechanisms. We examine these basic mechanisms that underlie population disparities in mental health through cultural neuroscience. We discuss the challenges to and opportunities for cultural neuroscience research to determine sociocultural and biological factors that confer risk for and resilience to mental health disorders across the globe. PMID:23927543

  18. Population change and socio-cultural values.

    PubMed

    1982-06-01

    The developing countries of the world in general, and those of Asia and the Pacific in particular, recognize that unplanned population growth is a stumbling block to socioeconomic development. Discussion here focuses on population growth and social, economic, and institutional forces, which are referred to as sociocultural values. Generally, sociocultural values change sluggishly over time. The rate at which a country's sociocultural values change depends on several factors such as the stage of economic development and modernization and whether a country has an open or closed door policy. "The Value of Children Study: A Crossnational Study" by Fred Arnold et al. shows that there are positive and negative values attributed to children in the Asian countries. These are: positive general values--emotional benefits, economic benefits and security, self enrichment and development, identification with children, and family cohesiveness and continuity; negative general values--emotional costs, economic costs, restrictions on opportunity costs, physical demands, and family costs; large family values--sibling relationships, sex preferences, child survival; and small family values--maternal health and societal costs. Possibly the most formidable obstacle to the success of antinatalist population policies is that of religious values. It appears that the Muslim world is divided on the issue of fertility control. Conflicting views regarding fertility control is perhaps aggravated by the fact that there is no central international religious official hierarchy that issues out edicts. Despite the presence of a centralized religious hierarchy and a network of churches from the Vatican to the village levels among the Catholics, and a clearer elucidation of the Humanae Vitae, a liberal attitude to population regulation and family planning has emerged, largely because of the declining quality of life of the people resulting from unplanned births. Economic benefits of children include

  19. [Effect of Inherent Immunity Factors of Development of Antibiotic Tolerance and Survival of Bacterial Populations under Antibiotic Attack].

    PubMed

    Demkina, E V; Loiko, N G; Mulyukin, A L; Smirnova, T A; Gaponov, A M; Pisarev, V M; Tutel'yan, A V; Nikolaev, Yu A; El'-Registan, G I

    2015-01-01

    Effect of human inherent immunity factors of, a gene-encoded antibacterial peptide indolicidin (Ind) and a cytokine interleukin 1 (IL1) on formation of antibiotic-tolerant persister cells surviving in the presence of ciprofloxacin (Cpf, 100 μg/mL) and ampicillin (Amp, 100 μg/mL) in submerged bacterial cultures (Staphylococcus aureus FGA 209P, Escherichia coli K12, and Pseudomonas aeruginosa PAO1) was studied. While Ind in physiological concentrations (0.3 and 3.0 μg/mL) introduced to the lag- or exponential-phase cultures of test organisms exhibited no reliable effect on population growth, the number of persisters increased at 3.0 μg/mL. Bactericidal Ind concentrations (9 μg/mL) suppressed S. aureus growth (-0.1% of surviving cells) with subsequent recovery due to development of the more antibiotic-tolerant white variant. Treatment with Cpf after Ind addition resulted in mutual potentiation of their antimicrobial activity, with the number of S. aureus persisters 2 to 3 orders of magnitude lower than in the case of the antibiotic alone. IL1, another immunity factor, when introduced (0.1-1 ng/mL) to the exponentially growing S. aureus culture (but not to the lag phase culture) had a temporary growth-static effect, with the number of persisters surviving Cpf treatment (100 μg/mL) increasing by 1 to 2 orders of magnitude. Electron microscopy revealed significant alterations in the outer cell envelope layer of surviving S. aureus cells, which should be associated with their changed antigenic properties. Thus, the factors of human inherent immunity have a dose-dependent effect on the growth of bacterial populations. In combination with antibiotics, they exhibit synergism of antimicrobial action (indolicidin) and minimize (indolicidin) or increase (interleukin 1) the frequency of formation of persister cells responsible for survival of a population subjected to an antibiotic attack. PMID:26964355

  20. Distributed Classifier Based on Genetically Engineered Bacterial Cell Cultures

    PubMed Central

    2015-01-01

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

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

    ERIC Educational Resources Information Center

    Weese, J. Scott

    2009-01-01

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

  2. Bacterial communities in fish sauce mash using culture-dependent and -independent methods.

    PubMed

    Fukui, Youhei; Yoshida, Mitsuhiro; Shozen, Kei-ichi; Funatsu, Yasuhiro; Takano, Takashi; Oikawa, Hiroshi; Yano, Yutaka; Satomi, Masataka

    2012-01-01

    In fish sauce production, microorganisms are associated with the fermentation process; however, the sequential changes in the bacterial communities have never been examined throughout the period of fermentation. In this study, we determined the bacterial floras in a fish sauce mash over 8 months, using three different culture media and 16S rRNA gene clone library analysis. During the first 4 weeks, viable counts of non-halophilic and halophilic bacteria decreased and were dominated by Staphylococcus species. Between 4 and 6 weeks, halophilic and highly halophilic bacterial counts markedly increased from 10(7) to 10(8) cfu/g, and the predominant species changed to Tetragenococcus halophilus. The occurrence of T. halophilus was associated with an increase of lactic acid and a reduction of pH values. In contrast, non-halophilic bacterial counts decreased to 10(6) cfu/g by 6 weeks with Bacillus subtilis as the dominant isolate. Clone library analysis revealed that the dominant bacterial group also changed from Staphylococcus spp. to T. halophilus, and the changes were consistent with those of the floras of halophilic and highly halophilic isolates. This is the first report describing a combination approach of culture and clone library methods for the analysis of bacterial communities in fish sauce mash. PMID:22990487

  3. Integrated kinetic and probabilistic modeling of the growth potential of bacterial populations.

    PubMed

    George, S M; Métris, A; Baranyi, J

    2015-05-01

    When bacteria are exposed to osmotic stress, some cells recover and grow, while others die or are unculturable. This leads to a viable count growth curve where the cell number decreases before the onset of the exponential growth phase. From such curves, it is impossible to estimate what proportion of the initial cells generates the growth because it leads to an ill-conditioned numerical problem. Here, we applied a combination of experimental and statistical methods, based on optical density measurements, to infer both the probability of growth and the maximum specific growth rate of the culture. We quantified the growth potential of a bacterial population as a quantity composed from the probability of growth and the "suitability" of the growing subpopulation to the new environment. We found that, for all three laboratory media studied, the probability of growth decreased while the "work to be done" by the growing subpopulation (defined as the negative logarithm of their suitability parameter) increased with NaCl concentration. The results suggest that the effect of medium on the probability of growth could be described by a simple shift parameter, a differential NaCl concentration that can be accounted for by the change in the medium composition. Finally, we highlighted the need for further understanding of the effect of the osmoprotectant glycine betaine on metabolism. PMID:25747002

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-04-19

    Demography is increasingly being invoked to account for features of the archaeological record, such as the technological conservatism of the Lower and Middle Pleistocene, the Middle to Upper Paleolithic transition, and cultural loss in Holocene Tasmania. Such explanations are commonly justified in relation to population dynamic models developed by Henrich [Henrich J (2004)Am Antiq69:197-214] and Powell et al. [Powell A, et al. (2009)Science324(5932):1298-1301], which appear to demonstrate that population size is the crucial determinant of cultural complexity. Here, we show that these models fail in two important respects. First, they only support a relationship between demography and culture in implausible conditions. Second, their predictions conflict with the available archaeological and ethnographic evidence. We conclude that new theoretical and empirical research is required to identify the factors that drove the changes in cultural complexity that are documented by the archaeological record. PMID:27044082

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

    PubMed Central

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

    2004-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed Central

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

    1982-01-01

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

  9. Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations

    NASA Astrophysics Data System (ADS)

    Freese, Peter D.; Korolev, Kirill S.; Jiménez, José I.; Chen, Irene A.

    2014-02-01

    Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.

  10. Comparison of different culture methods on bacterial recovery in hemodialysis fluids.

    PubMed

    Punakabutra, Napawan; Nunthapisud, Pongpun; Pisitkun, Trairak; Tiranathanagul, Khajohn; Tungsanga, Kriang; Eiam-Ong, Somchai

    2004-11-01

    To examine the culture method that could provide the highest bacterial recovery, 143 reverse osmosis water samples used in hemodialysis were collected for comparison of the media (Tryptic Soy Agar, TSA vs Reasoner's 2A Agar, R2A), the temperature (20 degrees C vs 37 degrees C), the duration of incubation (48-hour vs 7-day), and the culture technique (membrane filtration vs spread plate methods). The European Best Practice Guideline method, R2A at 20 degrees Cfor 7-day incubation provided higher bacterial recovery than the Association for the Advancement of Medical Instrumentation (AAMI) method, TSA at 37 degrees C for 48-hour incubation. The membrane filtration method gave better yield than the spread plate method. As such, the European Best Practice Guideline method in combination with the membrane filtration technique would be the culture method of choice for hemodialysis fluids. PMID:15825714

  11. Comparison of bacterial growth in sonication fluid cultures with periprosthetic membranes and with cultures of biopsies for diagnosing periprosthetic joint infection.

    PubMed

    Hischebeth, Gunnar T R; Randau, Thomas M; Molitor, Ernst; Wimmer, Matthias D; Hoerauf, Achim; Bekeredjian-Ding, Isabelle; Gravius, Sascha

    2016-02-01

    Total joint arthroplasty is a common operation worldwide with infection rates between 1% and 3%. In cases of suspected periprosthetic joint infection, it is very challenging to rule out the causative microorganisms. In this study, we compared the appearance of periprosthetic membranes with the microbiological results obtained from cultures of sonication fluid and the correlation between classical microbiological cultures and cultures of sonication fluid. The results confirmed a strong correlation of bacterial growth in sonication fluid cultures with bacterial growth in classical microbiological cultures. Most importantly, however, our study documented a highly significant correlation of periprosthetic membranes typical for periprosthetic joint infection (PJI) with bacterial growth in sonication fluid. Sonication fluid cultures yielded a better sensitivity than tissue cultures (72.34-60.87%). These 3 methods are useful tools in diagnosing PJIs, and even more, sonication fluid cultures should be included in the diagnostic path of PJI. PMID:26584961

  12. DNA repair in bacterial cultures and plasmid DNA exposed to infrared laser for treatment of pain

    NASA Astrophysics Data System (ADS)

    Canuto, K. S.; Sergio, L. P. S.; Marciano, R. S.; Guimarães, O. R.; Polignano, G. A. C.; Geller, M.; Paoli, F.; Fonseca, A. S.

    2013-06-01

    Biostimulation of tissues by low intensity lasers has been described on a photobiological basis and clinical protocols are recommended for treatment of various diseases, but their effects on DNA are controversial. The objective of this work was to evaluate effects of low intensity infrared laser exposure on survival and bacterial filamentation in Escherichia coli cultures, and induction of DNA lesions in bacterial plasmids. In E. coli cultures and plasmids exposed to an infrared laser at fluences used to treat pain, bacterial survival and filamentation and DNA lesions in plasmids were evaluated by electrophoretic profile. Data indicate that the infrared laser (i) increases survival of E. coli wild type in 24 h of stationary growth phase, (ii) induces bacterial filamentation, (iii) does not alter topological forms of plasmids and (iv) does not alter the electrophoretic profile of plasmids incubated with exonuclease III or formamidopyrimidine DNA glycosylase. A low intensity infrared laser at the therapeutic fluences used to treat pain can alter survival of E. coli wild type, induce filamentation in bacterial cells, depending on physiologic conditions and DNA repair, and induce DNA lesions other than single or double DNA strand breaks or alkali-labile sites, which are not targeted by exonuclease III or formamidopyrimidine DNA glycosylase.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  15. An Observation of Bacterial Population Changes in Fields Treated with Anaerobic Soil Disinfestation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Anaerobic soil disinfestation (ASD) has proven to be effective for pathogen and nematode control as an alternative to fumigation. It has been hypothesized that various bacterial populations could play key roles in the disinfestation process through the production of secondary metabolites. In this st...

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

    PubMed

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

    2012-01-01

    Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher. PMID:22936991

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  18. Bacterial population dynamics in diary waste during aerobic and anaerobic treatment and subsequent storage.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to model a typical dairy waste stream and monitor the chemical and bacterial population dynamics that occur during aerobic or anaerobic treatment and subsequent storage in a simulated lagoon, and compare them to waste held without treatment in a simulated lagoon. Both...

  19. The Effects of Sodium Bisulfate on the Bacterial Population Structure of Dairy Cow Waste

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sodium bisulfate (SBS) is commonly used in the poultry industry, and is beginning to be used on dairies, to acidify animal waste for the reduction of ammonia emissions. However, little is know about the effects of SBS on the bacterial populations in waste. Methods: SBS was applied at 0, 50, 100, 150...

  20. Evaluation of in vitro gas production and rumen bacterial populations fermenting corn milling (co)products

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate the degradation dynamics of two commonly-fed corn (co)products fermented in vitro and investigate the shifts of the rumen bacterial populations. Previous studies have indicated that processing methods of ruminant feeds directly affect the substrate availab...

  1. Integration of Culture-Based and Molecular Analysis of a Complex Sponge-Associated Bacterial Community

    PubMed Central

    Vicente, Jan; Pittiglio, Raquel; Ravel, Jacques; Hill, Russell T.

    2014-01-01

    The bacterial communities of sponges have been studied using molecular techniques as well as culture-based techniques, but the communities described by these two methods are remarkably distinct. Culture-based methods describe communities dominated by Proteobacteria, and Actinomycetes while molecular methods describe communities dominated by predominantly uncultivated groups such as the Chloroflexi, Acidobacteria, and Acidimicrobidae. In this study, we used a wide range of culture media to increase the diversity of cultivable bacteria from the closely related giant barrel sponges, Xestospongia muta collected from the Florida Keys, Atlantic Ocean and Xestospongia testudinaria, collected from Indonesia, Pacific Ocean. Over 400 pure cultures were isolated and identified from X. muta and X. testudinaria and over 90 bacterial species were represented. Over 16,000 pyrosequences were analyzed and assigned to 976 OTUs. We employed both cultured-based methods and pyrosequencing to look for patterns of overlap between the culturable and molecular communities. Only one OTU was found in both the molecular and culturable communities, revealing limitations inherent in both approaches. PMID:24618773

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

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

  3. A portable immunomagnetic cell capture system to accelerate culture diagnosis of bacterial infections.

    PubMed

    Singh, Saurabh; Upadhyay, Mohita; Sharma, Jyoti; Gupta, Shalini; Vivekanandan, Perumal; Elangovan, Ravikrishnan

    2016-05-23

    Bacterial infections continue to be a major cause of deaths globally, particularly in resource-poor settings. In the absence of rapid and affordable diagnostic solutions, patients are mostly administered broad spectrum antibiotics leading to antibiotics resistance and poor recovery. Culture diagnosis continues to be a gold standard for diagnosis of bacterial infection, despite its long turnaround time of 24 to 48 h. We have developed a portable immunomagnetic cell capture (iMC(2)) system that allows rapid culture diagnosis of bacterial pathogens. Our approach involves the culture growth of the blood samples in broth media for 6 to 8 h, followed by immunomagnetic enrichment of the target cells using the iMC(2) device. The device comprises a disposable capture chip that has two chambers of 5 ml and 50 μl volume connected through a channel with a manual valve. Bacterial cells bound to antibody coated magnetic nanoparticles are swept from the 5 ml sample chamber into the 50 μl recovery chamber by moving an external magnetic field with respect to the capture chip using a linear positioner. This enables specific isolation and up to 100× enrichment of the target cells. The presence of bacteria in the recovered sample is confirmed visually using a lateral flow immunoassay. The system is demonstrated in buffer and blood samples spiked with S. typhi. The method has high sensitivity (10 CFU ml(-1)), specificity and a rapid turnaround time of less than 7 h, a significant improvement over conventional methods. PMID:27118505

  4. A network-based approach for resistance transmission in bacterial populations.

    PubMed

    Gehring, Ronette; Schumm, Phillip; Youssef, Mina; Scoglio, Caterina

    2010-01-01

    Horizontal transfer of mobile genetic elements (conjugation) is an important mechanism whereby resistance is spread through bacterial populations. The aim of our work is to develop a mathematical model that quantitatively describes this process, and to use this model to optimize antimicrobial dosage regimens to minimize resistance development. The bacterial population is conceptualized as a compartmental mathematical model to describe changes in susceptible, resistant, and transconjugant bacteria over time. This model is combined with a compartmental pharmacokinetic model to explore the effect of different plasma drug concentration profiles. An agent-based simulation tool is used to account for resistance transfer occurring when two bacteria are adjacent or in close proximity. In addition, a non-linear programming optimal control problem is introduced to minimize bacterial populations as well as the drug dose. Simulation and optimization results suggest that the rapid death of susceptible individuals in the population is pivotal in minimizing the number of transconjugants in a population. This supports the use of potent antimicrobials that rapidly kill susceptible individuals and development of dosage regimens that maintain effective antimicrobial drug concentrations for as long as needed to kill off the susceptible population. Suggestions are made for experiments to test the hypotheses generated by these simulations. PMID:19747924

  5. Bacterial quorum sensing and metabolic slowing in a cooperative population

    PubMed Central

    An, Jae Hyung; Goo, Eunhye; Kim, Hongsup; Seo, Young-Su; Hwang, Ingyu

    2014-01-01

    Acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) controls the production of numerous intra- and extracellular products across many species of Proteobacteria. Although these cooperative activities are often costly at an individual level, they provide significant benefits to the group. Other potential roles for QS include the restriction of nutrient acquisition and maintenance of metabolic homeostasis of individual cells in a crowded but cooperative population. Under crowded conditions, QS may function to modulate and coordinate nutrient utilization and the homeostatic primary metabolism of individual cells. Here, we show that QS down-regulates glucose uptake, substrate level and oxidative phosphorylation, and de novo nucleotide biosynthesis via the activity of the QS-dependent transcriptional regulator QsmR (quorum sensing master regulator R) in the rice pathogen Burkholderia glumae. Systematic analysis of glucose uptake and core primary metabolite levels showed that QS deficiency perturbed nutrient acquisition, and energy and nucleotide metabolism, of individuals within the group. The QS mutants grew more rapidly than the wild type at the early exponential stage and outcompeted wild-type cells in coculture. Metabolic slowing of individuals in a QS-dependent manner indicates that QS acts as a metabolic brake on individuals when cells begin to mass, implying a mechanism by which AHL-mediated QS might have evolved to ensure homeostasis of the primary metabolism of individuals under crowded conditions. PMID:25267613

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    Caton, Ingrid R.; Schneegurt, Mark A.

    2013-01-01

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

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

    PubMed

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

    2006-06-01

    Our medical institution does not have a bacterial culture facility, requiring outsourcing of bacterial culture tests. Due to the time elapsed from the time of specimen collection to culturing, the identification of causative bacteria in respiratory tract infections tends to be difficult. We therefore used transport medium for sputum bacteria examinations. Expectorated purulent or purulent-mucous sputum specimens were collected from 32 patients with lower respiratory tract infection. We divided each of the sputum specimens into the two treatment groups: transport medium (Seedswab gamma2) ndar and stad disinfection container. Paired samples prepared from each patient were sent out for bacterial culture together. The time elapsed from collection to delivery to the lab were as follows: day 0 (same day, n = 14 patients), day 1 (n = 15), day 2 (n = 2), and day 3 (n = 1). The identified causative bacteria were Streptococcus pneumoniae (n = 6 patients), Haemophilus influenzae (n =5), Pseudomonas aeruginosa (n = 4), Staphylococcus aureus (n = 2), Moraxella catarrhalis (n = 2), Klebsiella pneumoniae (n = 1), and Streptococcus agalactiae (n = 1). Samples prepared by each of the two methods gave similar results. The utility of transport medium for examination of general bacteria for lower airway infection from sputum samples was not demonstrated. The rate of detection of bacteria decreased, when the transport of samples was delayed. Therefore, we need to send the sputum specimens as quickly as possible. PMID:16841712

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  10. Associated bacterial flora, growth, and toxicity of cultured benthic dinoflagellates Ostreopsis lenticularis and Gambierdiscus toxicus.

    PubMed

    Tosteson, T R; Ballantine, D L; Tosteson, C G; Hensley, V; Bardales, A T

    1989-01-01

    The growth, toxicity, and associated bacterial flora of 10 clonal cultures of the toxic benthic dinoflagellates Ostreopsis lenticularis and Gambierdiscus toxicus isolated from the coastal waters of southwest Puerto Rico have been examined. Clonal cultures of O. lenticularis grew more rapidly and at broader temperature ranges than those of G. toxicus. All five Ostreopsis clones were toxic, while only one of the five Gambierdiscus clones was poisonous. The degree of toxicity among poisonous clones was highly variable. The number of associated bacterial genera and their frequency of occurrence were quite variable among clones of both dinoflagellate genera. Bacterial isolates represented six genera (Nocardia, Pseudomonas, Vibrio, Aeromonas, Flavobacterium, and Moraxella) in addition to coryneform bacteria. Extracts of dinoflagellate-associated bacteria grown in pure culture were not toxic. Gambierdiscus clones were characterized by the frequent presence of Pseudomonas spp. (four of five clones) and the absence of coryneforms. In O. lenticularis, only one of five clones showed the presence of Pseudomonas spp., and Moraxella sp. was absent altogether. Detailed analyses of toxicity and associated microflora in a selected Ostreopsis clone, repeatedly cultivated (four times) over a period of 160 days, showed that peak cell toxicities developed in the late static and early negative culture growth phases. Peak Ostreopsis cell toxicities in the stationary phase of culture growth were correlated with significant increases in the percent total bacteria directly associated with these cells. Changes in the quantity of bacteria directly associated with microalgal cell surfaces and extracellular matrices during culture growth may be related to variability and degree of toxicity in these laboratory-cultured benthic dinoflagellates. PMID:2705766

  11. Bacterial Community Dynamics During the Application of a Myxococcus xanthus-Inoculated Culture Medium Used for Consolidation of Ornamental Limestone

    PubMed Central

    Jimenez-Lopez, Concepcion; Sterflinger, Katja; Ettenauer, Jörg; Jroundi, Fadwa; Fernandez-Vivas, Antonia; Gonzalez-Muñoz, Maria Teresa

    2010-01-01

    In this study, we investigated under laboratory conditions the bacterial communities inhabiting quarry and decayed ornamental carbonate stones before and after the application of a Myxococcus xanthus-inoculated culture medium used for consolidation of the stones. The dynamics of the community structure and the prevalence of the inoculated bacterium, M. xanthus, were monitored during the time course of the consolidation treatment (30 days). For this purpose, we selected a molecular strategy combining fingerprinting by denaturing gradient gel electrophoresis (DGGE) with the screening of eubacterial 16S rDNA clone libraries by DGGE and sequencing. Quantification of the inoculated strain was performed by quantitative real-time PCR (qPCR) using M. xanthus-specific primers designed in this work. Results derived from DGGE and sequencing analysis showed that, irrespective of the origin of the stone, the same carbonatogenic microorganisms were activated by the application of a M. xanthus culture. Those microorganisms were Pseudomonas sp., Bacillus sp., and Brevibacillus sp. The monitoring of M. xanthus in the culture media of treated stones during the time course experiment showed disparate results depending on the applied technique. By culture-dependent methods, the detection of this bacterium was only possible in the first day of the treatment, showing the limitation of these conventional techniques. By PCR-DGGE analysis, M. xanthus was detected during the first 3–6 days of the experiment. At this time, the population of this bacterium in the culture media varied between 108–106 cells ml−1, as showed by qPCR analyses. Thereafter, DGGE analyses showed to be not suitable for the detection of M. xanthus in a mixed culture. Nevertheless, qPCR analysis using specific primers for M. xanthus showed to be a more sensitive technique for the detection of this bacterium, revealing a population of 104 cells ml−1 in the culture media of both treated stones at the end of

  12. Culture of intestinal biopsy specimens and stool culture for detection of bacterial enteropathogens in patients infected with human immunodeficiency virus. The Berlin Diarrhea/Wasting Syndrome Study Group.

    PubMed Central

    Liesenfeld, O; Schneider, T; Schmidt, W; Sandforth, J; Weinke, T; Zeitz, M; Riecken, E O; Ullrich, R

    1995-01-01

    The diagnostic yields of stool cultures and biopsy specimens for the detection of enteric bacterial pathogens in 213 human immunodeficiency virus-infected patients were compared. Forty-five percent (19 of 42) of the pathogens were detected exclusively by stool culture, 2% (1 of 42) of the isolates were detected exclusively by culture of biopsy specimens, and 53% (22 of 42) were detected by both methods. Repeated stool cultures remain the most important means of diagnosing enteric bacterial pathogens, which were encountered in 20% (40 of 213) of all patients. The additional culture of biopsy specimens should be reserved for patients with suspected mycobacteriosis. PMID:7751389

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  16. Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations

    PubMed Central

    Perron, Gabriel G.; Lee, Alexander E. G.; Wang, Yun; Huang, Wei E.; Barraclough, Timothy G.

    2012-01-01

    Bacterial recombination is believed to be a major factor explaining the prevalence of multi-drug-resistance (MDR) among pathogenic bacteria. Despite extensive evidence for exchange of resistance genes from retrospective sequence analyses, experimental evidence for the evolutionary benefits of bacterial recombination is scarce. We compared the evolution of MDR between populations of Acinetobacter baylyi in which we manipulated both the recombination rate and the initial diversity of strains with resistance to single drugs. In populations lacking recombination, the initial presence of multiple strains resistant to different antibiotics inhibits the evolution of MDR. However, in populations with recombination, the inhibitory effect of standing diversity is alleviated and MDR evolves rapidly. Moreover, only the presence of DNA harbouring resistance genes promotes the evolution of resistance, ruling out other proposed benefits for recombination. Together, these results provide direct evidence for the fitness benefits of bacterial recombination and show that this occurs by mitigation of functional interference between genotypes resistant to single antibiotics. Although analogous to previously described mechanisms of clonal interference among alternative beneficial mutations, our results actually highlight a different mechanism by which interactions among co-occurring strains determine the benefits of recombination for bacterial evolution. PMID:22048956

  17. Census of the Bacterial Community of the Gypsy Moth Larval Midgut by Using Culturing and Culture-Independent Methods

    PubMed Central

    Broderick, Nichole A.; Raffa, Kenneth F.; Goodman, Robert M.; Handelsman, Jo

    2004-01-01

    Little is known about bacteria associated with Lepidoptera, the large group of mostly phytophagous insects comprising the moths and butterflies. We inventoried the larval midgut bacteria of a polyphagous foliivore, the gypsy moth (Lymantria dispar L.), whose gut is highly alkaline, by using traditional culturing and culture-independent methods. We also examined the effects of diet on microbial composition. Analysis of individual third-instar larvae revealed a high degree of similarity of microbial composition among insects fed on the same diet. DNA sequence analysis indicated that most of the PCR-amplified 16S rRNA genes belong to the γ-Proteobacteria and low G+C gram-positive divisions and that the cultured members represented more than half of the phylotypes identified. Less frequently detected taxa included members of the α-Proteobacterium, Actinobacterium, and Cytophaga/Flexibacter/Bacteroides divisions. The 16S rRNA gene sequences from 7 of the 15 cultured organisms and 8 of the 9 sequences identified by PCR amplification diverged from previously reported bacterial sequences. The microbial composition of midguts differed substantially among larvae feeding on a sterilized artificial diet, aspen, larch, white oak, or willow. 16S rRNA analysis of cultured isolates indicated that an Enterococcus species and culture-independent analysis indicated that an Entbacter sp. were both present in all larvae, regardless of the feeding substrate; the sequences of these two phylotypes varied less than 1% among individual insects. These results provide the first comprehensive description of the microbial diversity of a lepidopteran midgut and demonstrate that the plant species in the diet influences the composition of the gut bacterial community. PMID:14711655

  18. Acquisition and Elimination of Bacterial Vaginosis During Pregnancy: A Danish Population-Based Study

    PubMed Central

    Vogel, Ida; Thorsen, Poul; Jeune, Bernard; Jacobsson, Bo; Ebbesen, Niels; Arpi, Magnus; Bremmelgaard, Annie; Møller, Birger R.

    2006-01-01

    Objectives: the aim was to examine factors associated with acquisition and elimination of bacterial vaginosis in pregnancy. Methods: a group of 229 pregnant women were randomly selected from a population-based prospective cohort study of 2927. They were examined at enrollment (mean gestational weeks 16w + 0d) and again in mid-third trimester (mean gestational age 32w + 3d). Measures: BV (Amsel's clinical criteria), microbiological cultures of the genital tract and questionnaire data. Results: BV prevalence decreased from 17% in early second trimester to 14% in mid-third trimester due to a tenfold higher elimination rate (39%) than incidence rate (4%). Heavy smokers (> 10/d) in early pregnancy were at increased risk (5.3 [1.1–25]) for the acquisition of BV during pregnancy, as were women receiving public benefits (4.8 [1.0–22]), having a vaginal pH above 4.5 (6.3 [1.4–29]) or vaginal anaerobe bacteria (18 [2.7–122]) at enrollment. A previous use of combined oral contraceptives was preventive for the acquisition of BV (0.2 [0.03–0.96]). Elimination of BV in pregnancy tended to be associated with a heavy growth of Lactobacillus (3.2 [0.8–13]) at enrollment. Conclusions: acquisition of BV during pregnancy is rare and is associated with smoking, while the presence of anaerobe bacteria and a vaginal pH > 4.5 are interpreted as steps on a gradual change towards BV. In the same way heavy growth of Lactobacillus spp in early pregnancy may be an indicator of women on the way to eliminate BV. PMID:17485815

  19. Changes to the rumen bacterial population of sheep with the addition of 2,4,6-trinitrotoluene to their diet.

    PubMed

    Perumbakkam, Sudeep; Mitchell, Edward A; Craig, A Morrie

    2011-02-01

    Previous work has shown that bacterial isolates from the sheep rumen are capable of detoxifying 2,4,6-trinitrotoluene (TNT) into polar constituents. In this study, the dietary effects of TNT on the sheep rumen microbial community were evaluated using molecular microbiology ecology tools. Rumen samples were collected from sheep fed with and without TNT added to their diet, genomic DNA was extracted, and the 16S rRNA-V3 gene marker was used to quantify changes in the microbial population in the rumen. Control and treatment samples yielded 533 sequences. Phylogenetic analyses were performed to determine the microbial changes between the two conditions. Results indicated the predominant bacterial populations present in the rumen were comprised of the phyla Firmicutes and Bacteroidetes, irrespective of presence/absence of TNT in the diet. Significant differences (P < 0.001) were found between the community structure of the bacteria under TNT (-) and TNT (+) diets. Examination of the TNT (+) diet showed an increase in the clones belonging to family Ruminococcaceae, which have previously been shown to degrade TNT in pure culture experiments. PMID:20607404

  20. A method for eliminating bacterial contamination from in vitro moss cultures1

    PubMed Central

    Carey, Sarah B.; Payton, Adam C.; McDaniel, Stuart F.

    2015-01-01

    • Premise of the study: Bacterial contamination is a major problem in plant tissue culture, resulting in loss of experimental strains or preventing use of field-collected isolates. Here we evaluated an agar embedding method for eliminating bacteria from experimental cultures of the mosses Ceratodon purpureus and Physcomitrella patens. • Methods and Results: We blended moss protonema that had been inoculated with bacteria and embedded the cell fragments in antibiotic-containing, low-concentration agar. The plants were placed in a growth chamber and allowed to grow until the moss grew out of the media. The plants were then transferred to new plates and observed for contamination. The embedding method consistently outperformed standard procedures. • Conclusions: The embedding method places moss in direct contact with antibiotics, arresting bacterial replication and allowing moss to outgrow contamination. We anticipate this method will prove valuable for other plants capable of clonal propagation by blending. PMID:25606353

  1. Cytotoxicity in bacterial cultures: interaction and cell-specificity, possible factors in periodontal disease.

    PubMed

    Johansson, A; Bergenholtz, A; Holm, S E

    1994-09-01

    Cytotoxicity in culture media of various growing bacterial strains was estimated by Cr-51 release of labelled target-cells. Interaction studies were made by adding each of the different UV-killed bacteria to the medium with viable bacteria. The reference oral bacterial strains were: Actinobacillus actinomycetemcomitans Y4, Porphyromonas gingivalis, Fusobacterium nucleatum and Streptococcus mitis, which were compared with the reference bacteria Staphylococcus aureus 209 and Staphylococcus epidermidis. The target cells were: gingival fibroblasts (GF), periodontal membrane fibroblasts (PMF), pulpal fibroblasts (PF), HeLa-cells (HeLa), and lymphoid neoplasm cells (LN). Synergistic, as well as antagonistic, effects on target cells were observed. The cytotoxicity of A. actinomycetemcomitans in presence of P. gingivalis is neutralized while in presence of S. aureus it was increased. Bacterial interactions with F. nucleatum and P. gingivalis cytotoxicity were observed. The cytotoxicity of F. nucleatum was increased when cultured together with A. actinomycetemcomitans. Each cell type reacted differently to the toxicity of the supernatant of growth medium in which the same bacterial strain had been cultivated, which indicates cell specificity of the toxins. PMID:7799211

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-07-01

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

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

    PubMed

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

    2015-06-01

    Cultured pearls are the product of grafting and rearing of Pinctada margaritifera pearl oysters in their natural environment. Nucleus rejections and oyster mortality appear to result from bacterial infections or from an inappropriate grafting practice. To reduce the impact of bacterial infections, synthetic antibiotics have been applied during the grafting practice. However, the use of such antibiotics presents a number of problems associated with their incomplete biodegradability, limited efficacy in some cases, and an increased risk of selecting for antimicrobial resistant bacteria. We investigated the application of a marine antimicrobial peptide, tachyplesin, which is present in the Japanese horseshoe crab Tachypleus tridentatus, in combination with two marine bacterial exopolymers as alternative treatment agents. In field studies, the combination treatment resulted in a significant reduction in graft failures vs. untreated controls. The combination of tachyplesin (73 mg/L) with two bacterial exopolysaccharides (0.5% w/w) acting as filming agents, reduces graft-associated bacterial contamination. The survival data were similar to that reported for antibiotic treatments. These data suggest that non-antibiotic treatments of pearl oysters may provide an effective means of improving oyster survival following grafting procedures. PMID:26110895

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

    PubMed Central

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

    2015-01-01

    Cultured pearls are the product of grafting and rearing of Pinctada margaritifera pearl oysters in their natural environment. Nucleus rejections and oyster mortality appear to result from bacterial infections or from an inappropriate grafting practice. To reduce the impact of bacterial infections, synthetic antibiotics have been applied during the grafting practice. However, the use of such antibiotics presents a number of problems associated with their incomplete biodegradability, limited efficacy in some cases, and an increased risk of selecting for antimicrobial resistant bacteria. We investigated the application of a marine antimicrobial peptide, tachyplesin, which is present in the Japanese horseshoe crab Tachypleus tridentatus, in combination with two marine bacterial exopolymers as alternative treatment agents. In field studies, the combination treatment resulted in a significant reduction in graft failures vs. untreated controls. The combination of tachyplesin (73 mg/L) with two bacterial exopolysaccharides (0.5% w/w) acting as filming agents, reduces graft-associated bacterial contamination. The survival data were similar to that reported for antibiotic treatments. These data suggest that non-antibiotic treatments of pearl oysters may provide an effective means of improving oyster survival following grafting procedures. PMID:26110895

  6. Exploiting Bacterial Peptide Display Technology to Engineer Biomaterials for Neural Stem Cell Culture

    PubMed Central

    Little, Lauren; Dane, Karen; Daugherty, Patrick; Healy, Kevin; Schaffer, David

    2010-01-01

    Stem cells are often cultured on substrates that present extracellular matrix (ECM) proteins; however, the heterogeneous and poorly defined nature of ECM proteins presents challenges both for basic biological investigation of cell-matrix investigations and translational applications of stem cells. Therefore, fully synthetic, defined materials conjugated with bioactive ligands, such as adhesive peptides, are preferable for stem cell biology and engineering. However, identifying novel ligands that engage cellular receptors can be challenging, and we have thus developed a high throughput approach to identify new adhesive ligands. We selected an unbiased bacterial peptide display library for the ability to bind adult neural stem cells (NSCs), and 44 bacterial clones expressing peptides were identified and found to bind to NSCs with high avidity. Of these clones, four contained RGD motifs commonly found in integrin binding domains, and three exhibited homology to ECM proteins. Three peptide clones were chosen for further analysis, and their synthetic analogs were adsorbed on tissue culture polystyrene (TCPS) or grafted onto an interpenetrating polymer network (IPN) for cell culture. These three peptides were found to support neural stem cell self-renewal in defined medium as well as multi-lineage differentiation. Therefore, bacterial peptide display offers unique advantages to isolate bioactive peptides from large, unbiased libraries for applications in biomaterials engineering. PMID:21129772

  7. Extracellular enzyme activity in anaerobic bacterial cultures: evidence of pullulanase activity among mesophilic marine bacteria.

    PubMed

    Arnosti, C; Repeta, D J

    1994-03-01

    The extracellular enzymatic activity of a mixed culture of anaerobic marine bacteria enriched on pullulan [alpha(1,6)-linked maltotriose units] was directly assessed with a combination of gel permeation chromatography (GPC) and nuclear magnetic resonance spectroscopy (NMR). Hydrolysis products of pullulan were separated by GPC into three fractions with molecular weights of > or = 10,000, approximately 5,000, and < or = 1,200. NMR spectra of these fractions demonstrated that pullulan was rapidly and specifically hydrolyzed at alpha(1,6) linkages by pullulanase enzymes, most likely type II pullulanase. Although isolated pullulanase enzymes have been shown to hydrolyze pullulan completely to maltotriose (S. H. Brown, H. R. Costantino, and R. M. Kelly, Appl. Environ. Microbiol. 56:1985-1991, 1990; M. Klingeberg, H. Hippe, and G. Antranikian, FEMS Microbiol. Lett. 69:145-152, 1990; R. Koch, P. Zablowski, A. Spreinat, and G. Antranikian, FEMS Microbiol. Lett. 71:21-26, 1990), the smallest carbohydrate detected in the bacterial cultures consisted of two maltotriose units linked through one alpha(1,6) linkage. Either the final hydrolysis step was closely linked to substrate uptake, or specialized porins similar to maltoporin might permit direct transport of large oligosaccharides into the bacterial cell. This is the first report of pullulanase activity among mesophilic marine bacteria. The combination of GPC and NMR could easily be used to assess other types of extracellular enzyme activity in bacterial cultures. PMID:8161177

  8. Occult bacterial lower urinary tract infections in cats-urinalysis and culture findings.

    PubMed

    Litster, Annette; Moss, Susan; Platell, Joanne; Trott, Darren J

    2009-04-14

    Bacterial urinary tract infections (UTIs) can be detected in feline urine submitted for urinalysis and culture as part of the diagnostic workup for a variety of conditions. Our aim was to investigate urinalysis and culture findings in urine specimens from cats with no history of lower urinary tract signs. Study inclusion criteria required cystocentesis specimens from cats with no history of lower urinary tract signs, inappropriate urination, or previous UTI (including pyelonephritis). Of 132 specimens, 38 were culture positive and 94 were culture negative. Culture positive urine specimens were more likely to come from older female cats (p=0.03, p<0.001, respectively) and they had higher pH (p=0.001), erythrocyte (p=0.013) and leukocyte counts (p=0.003) than culture negative urine specimens. Gram-negative infected specimens (n=15) had lower urine specific gravity and higher leukocyte counts than Gram-positive infected specimens (n=21; p=0.0012, p=0.005, respectively) and culture negative specimens (p=0.003, p<0.0001, respectively). Urine protein:creatinine ratio was higher in Gram-negative infected urine than in culture negative urine (p=0.013). Enterococcus faecalis was the most commonly isolated bacteria (19 of a total of 44 isolates; 43.2%) and E. coli phylogenetic group B2 was the most common Gram-negative isolate (14 of a total of 44 isolates; 31.8%). We conclude that feline bacterial urinary tract infections can occur in cats without lower urinary tract signs, particularly older females and that they are associated with high urine erythrocyte and leukocyte counts. PMID:19056189

  9. Birth interval study in a culturally stable urban population.

    PubMed

    Ayangade, S O

    1978-01-01

    Five hundred women were interviewed within 2 days of delivery to examine indigenous birth spacing among the urban and rural population of Ife township. The crude birth interval was between 30 and 40 months due mainly to cultural attitudes towards lactation and sexual abstinence. The women studied possessed considerable knowledge of Western contraceptive methods, but they rejected them. The possible cause of this rejection is examined and solutions to the problem are suggested. PMID:29795

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

    PubMed Central

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

    2014-01-01

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

  11. Dietary format alters fecal bacterial populations in the domestic cat (Felis catus)

    PubMed Central

    Bermingham, Emma N; Young, Wayne; Kittelmann, Sandra; Kerr, Katherine R; Swanson, Kelly S; Roy, Nicole C; Thomas, David G

    2013-01-01

    The effects of short-term (5-week) exposure to wet or dry diets on fecal bacterial populations in the cat were investigated. Sixteen mixed-sex, neutered, domestic short-haired cats (mean age = 6 years; mean bodyweight = 3.4 kg) were randomly allocated to wet or dry diets in a crossover design. Fecal bacterial DNA was isolated and bacterial 16S rRNA gene amplicons generated and analyzed by 454 Titanium pyrosequencing. Cats fed dry diets had higher abundances (P < 0.05) of Actinobacteria (16.5% vs. 0.1%) and lower abundances of Fusobacteria (0.3% vs. 23.1%) and Proteobacteria (0.4% vs. 1.1%) compared with cats fed the wet diet. Of the 46 genera identified, 30 were affected (P < 0.05) by diet, with higher abundances of Lactobacillus (31.8% vs. 0.1%), Megasphaera (23.0% vs. 0.0%), and Olsenella (16.4% vs. 0.0%), and lower abundances of Bacteroides (0.6% vs. 5.7%) and Blautia (0.3% vs. 2.3%) in cats fed the dry diet compared with cats fed the wet diet. These results demonstrate that short-term dietary exposure to diet leads to large shifts in fecal bacterial populations that have the potential to affect the ability of the cat to process macronutrients in the diet. PMID:23297252

  12. In vitro bacterial growth and in vivo ruminal microbiota populations associated with bloat in steers grazing wheat forage.

    PubMed

    Min, B R; Pinchak, W E; Anderson, R C; Hume, M E

    2006-10-01

    The role of ruminal bacteria in the frothy bloat complex common to cattle grazing winter wheat has not been previously determined. Two experiments, one in vitro and another in vivo, were designed to elucidate the effects of fresh wheat forage on bacterial growth, biofilm complexes, rumen fermentation end products, rumen bacterial diversity, and bloat potential. In Exp. 1, 6 strains of ruminal bacteria (Streptococcus bovis strain 26, Prevotella ruminicola strain 23, Eubacterium ruminantium B1C23, Ruminococcus albus SY3, Fibrobacter succinogenes ssp. S85, and Ruminococcus flavefaciens C94) were used in vitro to determine the effect of soluble plant protein from winter wheat forage on specific bacterial growth rate, biofilm complexes, VFA, and ruminal H2 and CH4 in mono or coculture with Methanobrevibacter smithii. The specific growth rate in plant protein medium containing soluble plant protein (3.27% nitrogen) was measured during a 24-h incubation at 39 degrees C in Hungate tubes under a CO2 gas phase. A monoculture of M. smithii was grown similarly, except under H2:CO2 (1:1), in a basal methanogen growth medium supplemented likewise with soluble plant protein. In Exp. 2, 6 ruminally cannulated steers grazing wheat forage were used to evaluate the influence of bloat on the production of biofilm complexes, ruminal microbial biodiversity patterns, and ruminal fluid protein fractions. In Exp. 1, cultures of R. albus (P < 0.01) and R. flavefaciens (P < 0.05) produced the most H2 among strains and resulted in greater (P < 0.01) CH4 production when cocultured with M. smithii than other coculture combinations. Cultures of S. bovis and E. ruminantium + M. smithii produced the most biofilm mass among strains. In Exp. 2, when diets changed from bermudagrass hay to wheat forage, biofilm production increased (P < 0.01). Biofilm production, concentrations of whole ruminal content (P < 0.01), and cheesecloth filtrate protein fractions (P < 0.05) in the ruminal fluid were greater

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

    NASA Astrophysics Data System (ADS)

    Wan, Zhenmao; Goddard, Noel

    2012-02-01

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

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

    SciTech Connect

    Boopathy, R.; Manning, J.

    1997-08-01

    The degradation of several munitions compounds was studied. The compounds included 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine, 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrotoluene. All of the compounds studied were degraded by the sulfate reducing bacterial (SRB) enrichment culture. The SRB culture did not use the munitions compounds as their sole source of carbon. However, all the munitions compounds tested served as the sole source of nitrogen for the SRB culture. Degradation of munitions compounds was achieved by a co-metabolic process. The SRB culture used a variety of carbon sources including pyruvate, ethanol, formate, lactate, and H{sub 2}-CO{sub 2}. The SRB culture was an incomplete oxidizer, unable to carry out the terminal oxidation of organic substrates to CO{sub 2} as the sole product, and it did not use acetate or methanol as a carbon source. In addition to serving as nitrogen sources, the munitions compounds also served as electron acceptors in the absence of sulfate. A soil slurry experiment with 5% and 10% munitions compounds-contaminated soil showed that the contaminant TNT was metabolized by the SRB culture in the presence of pyruvate as electron donor. This culture may be useful in decontaminating munitions compounds-contaminated soil and water under anaerobic conditions.

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

    PubMed

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

    2015-02-01

    Bacterial cellulose (BC) is used in different fields as a biological material due to its unique properties. Despite there being many BC applications, there still remain many problems associated with bioprocess technology, such as increasing productivity and decreasing production cost. New technologies that use waste from the food industry as raw materials for culture media promote economic advantages because they reduce environmental pollution and stimulate new research for science sustainability. For this reason, BC production requires optimized conditions to increase its application. The main objective of this study was to evaluate BC production by Gluconacetobacter xylinus using industry waste, namely, rotten fruits and milk whey, as culture media. Furthermore, the structure of BC produced at different conditions was also determined. The culture media employed in this study were composed of rotten fruit collected from the disposal of free markets, milk whey from a local industrial disposal, and their combination, and Hestrin and Schramm media was used as standard culture media. Although all culture media studied produced BC, the highest BC yield-60 mg/mL-was achieved with the rotten fruit culture. Thus, the results showed that rotten fruit can be used for BC production. This culture media can be considered as a profitable alternative to generate high-value products. In addition, it combines environmental concern with sustainable processes that can promote also the reduction of production cost. PMID:25472434

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Beisker, Wolfgang; Meier, H.

    1998-04-01

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

  18. Efficacy and safety of azithromycin 1.5% eye drops in paediatric population with purulent bacterial conjunctivitis

    PubMed Central

    Bremond-Gignac, Dominique; Nezzar, Hachemi; Bianchi, Paolo Emilio; Messaoud, Riadh; Lazreg, Sihem; Voinea, Liliana; Speeg-Schatz, Claude; Hartani, Dahbia; Kaercher, Thomas; Kocyla-Karczmarewicz, Beata; Murta, Joaquim; Delval, Laurent; Renault, Didier; Chiambaretta, Frédéric

    2014-01-01

    Objective To determine the efficacy and safety of azithromycin 1.5% eye drops in a paediatric population with purulent bacterial conjunctivitis. Patients and methods This was a multicentre, international, randomised, investigator-masked study in 286 children with purulent discharge and bulbar conjunctival injection. Patients received either azithromycin 1.5% eye drops (twice daily for 3 days) or tobramycin 0.3% eye drops (every 2 h for 2 days, then four times daily for 5 days). Clinical signs were evaluated on day (D) 0, 3 and 7, and cultures on D0 and D7. The primary variable was the clinical cure (absence of bulbar conjunctival injection and discharge) on D3 in the worse eye for patients with positive cultures on D0. Results 286 patients (mean age 3.2 years; range 1 day–17 years) were included; 203 had positive cultures on D0. Azithromycin was superior to tobramycin in clinical cure rate on D3 (47.1% vs 28.7%, p=0.013) and was non-inferior to tobramycin on D7 (89.2% vs 78.2%, respectively). Azithromycin treatment eradicated causative pathogens, including resistant species, with a similar resolution rate to tobramycin (89.8% vs 87.2%, respectively). These results were confirmed in a subgroup of patients younger than 24 months old. Conclusions Azithromycin 1.5% eye drops provided a more rapid clinical cure than tobramycin 0.3% eye drops in the treatment of purulent bacterial conjunctivitis in children, with a more convenient twice-a-day dosing regimen. PMID:24526744

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Chandra, Ram; Bharagava, Ram Naresh

    2013-11-01

    Pulp paper mill effluent has high pollution load due to presence of lignin and its derivatives as major colouring and polluting constituents. In this study, two lignin degrading bacteria IITRL1 and IITRSU7 were isolated and identified as Citrobacter freundii (FJ581026) and Citrobacter sp. (FJ581023), respectively. In degradation study by axenic and mixed culture, mixed bacterial culture was found more effective compared to axenic culture as it decolourized 85 and 62% of synthetic and kraft lignin whereas in axenic conditions, bacterium IITRL1 and IITRSU7 decolourized 61 and 64% synthetic and 49 and 54% kraft lignin, respectively. Further, the mixed bacterial culture also showed the removal of 71, 58% TOC; 78, 53% AOX; 70, 58% COD and 74, 58% lignin from synthetic and kraft lignin, respectively. The ligninolytic enzyme was characterized as manganese peroxidase by SDS-PAGE yielding a single band of 43 KDa. The HPLC analysis of degraded samples showed reduction as well as shifting of peaks compared to control indicating the degradation as well as transformation of compounds. Further, in GC-MS analysis of synthetic and kraft lignin degraded samples, hexadecanoic acid was found as recalcitrant compounds while 2,4,6-trichloro-phenol, 2,3,4,5-tetrachloro-phenol and pentachloro-phenol were detected as new metabolites. PMID:24555327

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

    ERIC Educational Resources Information Center

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

    2005-01-01

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

  2. 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. PMID:23812968

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

    PubMed

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

    2015-11-13

    The root cause of the antibiotic resistance crisis is the ability of bacteria to evolve resistance to a multitude of antibiotics and other environmental toxins. The regulation of adaptation is difficult to pinpoint due to extensive phenotypic heterogeneity arising during evolution. Here, we investigate the mechanisms underlying general bacterial adaptation by evolving wild-type Escherichia coli populations to dissimilar chemical toxins. We demonstrate the presence of extensive inter- and intrapopulation phenotypic heterogeneity across adapted populations in multiple traits, including minimum inhibitory concentration, growth rate, and lag time. To search for a common response across the heterogeneous adapted populations, we measured gene expression in three stress-response networks: the mar regulon, the general stress response, and the SOS response. While few genes were differentially expressed, clustering revealed that interpopulation gene expression variability in adapted populations was distinct from that of unadapted populations. Notably, we observed both increases and decreases in gene expression variability upon adaptation. Sequencing select genes revealed that the observed gene expression trends are not necessarily attributable to genetic changes. To further explore the connection between gene expression variability and adaptation, we propagated single-gene knockout and CRISPR (clustered regularly interspaced short palindromic repeats) interference strains and quantified impact on adaptation to antibiotics. We identified significant correlations that suggest genes with low expression variability have greater impact on adaptation. This study provides evidence that gene expression variability can be used as an indicator of bacterial adaptive resistance, even in the face of the pervasive phenotypic heterogeneity underlying adaptation. PMID:27623410

  4. Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract

    PubMed Central

    Charlson, Emily S.; Bittinger, Kyle; Haas, Andrew R.; Fitzgerald, Ayannah S.; Frank, Ian; Yadav, Anjana; Bushman, Frederic D.

    2011-01-01

    Rationale: Defining the biogeography of bacterial populations in human body habitats is a high priority for understanding microbial–host relationships in health and disease. The healthy lung was traditionally considered sterile, but this notion has been challenged by emerging molecular approaches that enable comprehensive examination of microbial communities. However, studies of the lung are challenging due to difficulties in working with low biomass samples. Objectives: Our goal was to use molecular methods to define the bacterial microbiota present in the lungs of healthy individuals and assess its relationship to upper airway populations. Methods: We sampled respiratory flora intensively at multiple sites in six healthy individuals. The upper tract was sampled by oral wash and oro-/nasopharyngeal swabs. Two bronchoscopes were used to collect samples up to the glottis, followed by serial bronchoalveolar lavage and lower airway protected brush. Bacterial abundance and composition were analyzed by 16S rDNA Q-PCR and deep sequencing. Measurements and Main Results: Bacterial communities from the lung displayed composition indistinguishable from the upper airways, but were 2 to 4 logs lower in biomass. Lung-specific sequences were rare and not shared among individuals. There was no unique lung microbiome. Conclusions: In contrast to other organ systems, the respiratory tract harbors a homogenous microbiota that decreases in biomass from upper to lower tract. The healthy lung does not contain a consistent distinct microbiome, but instead contains low levels of bacterial sequences largely indistinguishable from upper respiratory flora. These findings establish baseline data for healthy subjects and sampling approaches for sequence-based analysis of diseases. PMID:21680950

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

    PubMed Central

    2014-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  7. Antimicrobial cocktails to control bacterial and fungal contamination in Chlamydomonas reinhardtii cultures.

    PubMed

    Wang, Liang; Yang, Fengyuan; Chen, Huiyi; Fan, Zhiyue; Zhou, Yongkang; Lu, Jun; Zheng, Yuanlin

    2016-01-01

    Chlamydomonas reinhardtii is a unicellular green alga widely used for research in photosynthesis, cell cycle regulation, ciliary biogenesis, and other physiological processes. Sterile cultures are needed for these studies, but contamination from bacteria and fungi occurs frequently. Although the One-shot Solution cocktail consisting of carbendazim, ampicillin, and cefotaxime has been developed for removing these contaminants from algal cultures, it is not always effective. Here we report two new antimicrobial cocktails for treating mixed bacterial and fungal contamination of Chlamydomonas cultures. A combination of the bactericide nalidixic acid with one of two fungicides, azoxystrobin or tebuconazole, was more effective than the One-shot Solution cocktail. In some of our tests, we find that alternating use of our new cocktails with One-shot Solution is needed to remove obstinate contaminants. PMID:26956093

  8. The effect of electromagnetic fields, from two commercially available water treatment devices, on bacterial culturability.

    PubMed

    Piyadasa, Chathuri; Yeager, Thomas R; Gray, Stephen R; Stewart, Matthew B; Ridgway, Harry F; Pelekani, Con; Orbell, John D

    2016-01-01

    Commercially available pulsed-electromagnetic field (PEMF) devices are currently being marketed and employed to ostensibly manage biofouling. The reliable application and industry acceptance of such technologies require thorough scientific validation - and this is currently lacking. We have initiated proof-of-principle research in an effort to investigate whether such commercially available PEMF devices can influence the viability (culturability) of planktonic bacteria in an aqueous environment. Thus two different commercial PEMF devices were investigated via a static (i.e. non-flowing) treatment system. 'Healthy' Escherichia coli cells, as well as cultures that were physiologically compromised by silver nano-particles, were exposed to the PEMFs from both devices under controlled conditions. Although relatively minor, the observed effects were nevertheless statistically significant and consistent with the hypothesis that PEMF exposure under controlled conditions may result in a decrease in cellular viability and culturability. It has also been observed that under certain conditions bacterial growth is actually stimulated. PMID:27003078

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

    SciTech Connect

    Stampfer, Martha R; Garbe, James C

    2015-02-24

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

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

    DOEpatents

    Stampfer, Martha R.; Garbe, James C.

    2016-06-28

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

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

    PubMed

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

    2016-04-22

    The endophytic fungus Aspergillus austroafricanus isolated from leaves of the aquatic plant Eichhornia crassipes was fermented axenically on solid rice medium as well as in mixed cultures with Bacillus subtilis or with Streptomyces lividans. Chromatographic analysis of EtOAc extract of axenic cultures afforded two new metabolites, namely, the xanthone dimer austradixanthone (1) and the sesquiterpene (+)-austrosene (2), along with five known compounds (3-7). Austradixanthone (1) represents the first highly oxygenated heterodimeric xanthone derivative. When A. austroafricanus was grown in mixed cultures with B. subtilis or with S. lividans, several diphenyl ethers (8-11) including the new austramide (8) were induced up to 29-fold. The structures of new compounds were unambiguously elucidated using 1D- and 2D-NMR spectroscopy, HRESIMS, and chemical derivatization. Compound 7 exhibited weak cytotoxicity against the murine lymphoma L5178Y cell line (EC50 is 12.6 μM). In addition, compounds 9 and 10, which were enhanced in mixed fungal/bacterial cultures, proved to be active against Staphylococcus aureus (ATCC 700699) with minimal inhibitory concentrations (MICs) of 25 μM each (6.6 μg/mL), whereas compound 11 revealed moderate antibacterial activity against B. subtilis 168 trpC2 with an MIC value of 34.8 μM (8 μg/mL). PMID:27070198

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

    PubMed

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

    2016-01-01

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

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

    SciTech Connect

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

    2014-06-18

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

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

    SciTech Connect

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

    2014-05-12

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

  15. Fast, high-throughput measurement of collective behaviour in a bacterial population

    PubMed Central

    Colin, R.; Zhang, R.; Wilson, L. G.

    2014-01-01

    Swimming bacteria explore their environment by performing a random walk, which is biased in response to, for example, chemical stimuli, resulting in a collective drift of bacterial populations towards ‘a better life’. This phenomenon, called chemotaxis, is one of the best known forms of collective behaviour in bacteria, crucial for bacterial survival and virulence. Both single-cell and macroscopic assays have investigated bacterial behaviours. However, theories that relate the two scales have previously been difficult to test directly. We present an image analysis method, inspired by light scattering, which measures the average collective motion of thousands of bacteria simultaneously. Using this method, a time-varying collective drift as small as 50 nm s−1 can be measured. The method, validated using simulations, was applied to chemotactic Escherichia coli bacteria in linear gradients of the attractant α-methylaspartate. This enabled us to test a coarse-grained minimal model of chemotaxis. Our results clearly map the onset of receptor methylation, and the transition from linear to logarithmic sensing in the bacterial response to an external chemoeffector. Our method is broadly applicable to problems involving the measurement of collective drift with high time resolution, such as cell migration and fluid flows measurements, and enables fast screening of tactic behaviours. PMID:25030384

  16. Bacterial populations in epilithic biofilms along two oligotrophic rivers in the Tohoku region in Japan.

    PubMed

    Honma, Hajime; Asano, Ryoki; Obara, Masahiko; Otawa, Kenichi; Suyama, Yoshihisa; Nakai, Yutaka

    2009-10-01

    Bacterial populations in epilithic biofilms collected from two distinct oligotrophic rivers of Japan were studied using denaturing gradient gel electrophoresis (DGGE). PCR-DGGE of the 16S rRNA gene and subsequent sequencing analysis suggested that in freshwater biofilms, members of the Cytophaga-Flavobacterium-Bacteroides (CFB) group were the most dominant, followed by those of alpha, beta, gamma, and delta-Proteobacteria; Leptospiraceae; and unidentified bacteria. Members of the CFB group, alpha-Proteobacteria, and cyanobacteria/plastid DNA were also detected from the biofilms collected from the estuary site, but the species in these samples differed from those detected in biofilms in the freshwater areas of the rivers. A comparison between the determined sequences revealed that similar bacterial species existed in biofilms at different sites of a river, and identical species existed in biofilms of distinct rivers. The results suggested that bacterial species in biofilms found in the estuary were different from those found in the freshwater areas of the rivers; however, the common bacterial species were distributed in biofilms collected from not only different sites along the same river but also sites in distinct oligotrophic rivers. PMID:19940382

  17. Obligate bacterial mutualists evolving from environmental bacteria in natural insect populations.

    PubMed

    Hosokawa, Takahiro; Ishii, Yoshiko; Nikoh, Naruo; Fujie, Manabu; Satoh, Nori; Fukatsu, Takema

    2016-01-01

    Diverse organisms are associated with obligate microbial mutualists. How such essential symbionts have originated from free-living ancestors is of evolutionary interest. Here we report that, in natural populations of the stinkbug Plautia stali, obligate bacterial mutualists are evolving from environmental bacteria. Of six distinct bacterial lineages associated with insect populations, two are uncultivable with reduced genomes, four are cultivable with non-reduced genomes, one uncultivable symbiont is fixed in temperate populations, and the other uncultivable symbiont coexists with four cultivable symbionts in subtropical populations. Symbiont elimination resulted in host mortality for all symbionts, while re-infection with any of the symbionts restored normal host growth, indicating that all the symbionts are indispensable and almost equivalent functionally. Some aseptic newborns incubated with environmental soils acquired the cultivable symbionts and normal growth was restored, identifying them as environmental Pantoea spp. Our finding uncovers an evolutionary transition from a free-living lifestyle to obligate mutualism that is currently ongoing in nature. PMID:27571756

  18. Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

    PubMed Central

    Pulido-Tamayo, Sergio; Sánchez-Rodríguez, Aminael; Swings, Toon; Van den Bergh, Bram; Dubey, Akanksha; Steenackers, Hans; Michiels, Jan; Fostier, Jan; Marchal, Kathleen

    2015-01-01

    Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples. PMID:25990729

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

    PubMed

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

    2006-05-01

    In the horse, carbohydrate overload is thought to play an integral role in the onset of laminitis by drastically altering the profile of bacterial populations in the hindgut. The objectives of this study were to develop and validate microbial ecology methods to monitor changes in bacterial populations throughout the course of experimentally induced laminitis and to identify the predominant oligofructose-utilizing organisms. Laminitis was induced in five horses by administration of oligofructose. Faecal specimens were collected at 8 h intervals from 72 h before to 72 h after the administration of oligofructose. Hindgut microbiota able to utilize oligofructose were enumerated throughout the course of the experiment using habitat-simulating medium. Isolates were collected and representatives identified by 16S rRNA gene sequencing. The majority of these isolates collected belonged to the genus Streptococcus, 91% of which were identified as being most closely related to Streptococcus infantarius ssp. coli. Furthermore, S. infantarius ssp. coli was the predominant oligofructose-utilizing organism isolated before the onset of lameness. Fluorescence in situ hybridization probes developed to specifically target the isolated Streptococcus spp. demonstrated marked population increases between 8 and 16 h post oligofructose administration. This was followed by a rapid population decline which corresponded with a sharp decline in faecal pH and subsequently lameness at 24-32 h post oligofructose administration. This research suggests that streptococci within the Streptococcus bovis/equinus complex may be involved in the series of events which precede the onset of laminitis in the horse. PMID:16623745

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

    PubMed Central

    Kong, H L; Sayler, G S

    1983-01-01

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

  1. A survey of the bacterial composition of kurut from Tibet using a culture-independent approach.

    PubMed

    Liu, W J; Sun, Z H; Zhang, Y B; Zhang, C L; Menghebilige; Yang, M; Sun, T S; Bao, Q H; Chen, W; Zhang, H P

    2012-03-01

    Kurut (fermented yak milk) made by natural fermentation is a very important dairy food for the local people in Tibet (China). It is important to fully understand the bacterial composition of kurut for quality improvement and industrial production. Because more than 99% of prokaryotes cannot be cultured and identified by methods currently used in taxonomy, we applied a culture-independent approach to explore the microbial biodiversity of this traditional food. In this study, a bacterial 16S rRNA gene clone library, including 460 clones, was constructed using total DNA extracted from 30 samples of kurut. After screening by restriction fragment length polymorphism (RFLP) analysis, 56 operational taxonomic units (OTU) with unique RFLP patterns were obtained. Then, 1 representative sequence of every OTU was sequenced and phylogenetically analyzed. The representative phylotypes were affiliated with 5 groups, including Lactococcus lactis ssp. lactis, Lactobacillus helveticus, Streptococcus thermophilus, Lactobacillus delbrueckii ssp. bulgaricus, and Acetobacter. In addition, nearly one-third of the representative clones (132 clones) had low similarity to species in GenBank (<97%), and these phylotypes were regarded as unknown bacteria. The characteristics of kurut are determined not only by lactic acid bacteria well known by the culture-dependent approach but also by bacteria that have not yet been identified. PMID:22365190

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

    PubMed

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

    2014-09-18

    The great therapeutic achievements of antibiotics have been dramatically undercut by the evolution of bacterial strategies that overcome antibiotic stress. These strategies fall into two classes. 'Resistance' makes it possible for a microorganism to grow in the constant presence of the antibiotic, provided that the concentration of the antibiotic is not too high. 'Tolerance' allows a microorganism to survive antibiotic treatment, even at high antibiotic concentrations, as long as the duration of the treatment is limited. Although both resistance and tolerance are important reasons for the failure of antibiotic treatments, the evolution of resistance is much better understood than that of tolerance. Here we followed the evolution of bacterial populations under intermittent exposure to the high concentrations of antibiotics used in the clinic and characterized the evolved strains in terms of both resistance and tolerance. We found that all strains adapted by specific genetic mutations, which became fixed in the evolved populations. By monitoring the phenotypic changes at the population and single-cell levels, we found that the first adaptive change to antibiotic stress was the development of tolerance through a major adjustment in the single-cell lag-time distribution, without a change in resistance. Strikingly, we found that the lag time of bacteria before regrowth was optimized to match the duration of the antibiotic-exposure interval. Whole genome sequencing of the evolved strains and restoration of the wild-type alleles allowed us to identify target genes involved in this antibiotic-driven phenotype: 'tolerance by lag' (tbl). Better understanding of lag-time evolution as a key determinant of the survival of bacterial populations under high antibiotic concentrations could lead to new approaches to impeding the evolution of antibiotic resistance. PMID:25043002

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

    PubMed

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

    2014-11-01

    Glaciers are important ecosystems, hosting bacterial communities that are adapted to cold conditions and scarcity of available nutrients. Several works focused on the composition of bacterial communities in glaciers and on the long-range atmospheric deposition of pollutants in glaciers, but it is not clear yet if ski resorts can represent a source of point pollution in near-by glaciers, and if these pollutants can influence the residing bacterial communities. To test these hypotheses, 12 samples were analyzed in Madaccio Glacier, in a 3200 ma.s.l. from two areas, one undisturbed and one close to a summer ski resort that is active since the 1930s. Chemical analyses found concentrations up to 43 ng L(-1) for PCBs and up to 168 μg L(-1) for PAHs in the contaminated area: these values are significantly higher than the ones found in undisturbed glaciers because of long-range atmospheric deposition events, and can be explained as being related to the near-by ski resort activities. Isolation of strains on rich medium plates and PCR-DGGE analyses followed by sequencing of bands allowed the identification of a bacterial community with phylogenetic patterns close to other glacier environments, with Proteobacteria and Actinobacteria the mostly abundant phyla, with Acidobacteria, Firmicutes and Cyanobacteria also represented in the culture-independent analyses. A number of isolates were identified by molecular and biochemical methods as phylogenetic related to known xenobiotic-degrading strains: glaciers subjected to chemical contamination can be important reservoirs of bacterial strains with potential applications in bioremediation. PMID:25117971

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

    PubMed

    Ghosh, Soma; Sar, Pinaki

    2013-12-01

    Diversity of culturable bacterial populations within the Arsenic (As) contaminated groundwater of North Eastern state (Assam) of India is studied. From nine As contaminated samples 89 bacterial strains are isolated. 16S rRNA gene sequence analysis reveals predominance of Brevundimonas (35%) and Acidovorax (23%) along with Acinetobacter (10%), Pseudomonas (9%) and relatively less abundant (<5%) Undibacterium, Herbaspirillum, Rhodococcus, Staphylococcus, Bosea, Bacillus, Ralstonia, Caulobacter and Rhizobiales members. High As(III) resistance (MTC 10-50 mM) is observed for the isolates obtained from As(III) enrichment, particularly for 3 isolates of genus Brevundimonas (MTC 50 mM). In contrast, high resistance to As(V) (MTC as high as 550 mM) is present as a ubiquitous property, irrespective of isolates' enrichment condition. Bacterial genera affiliated to other groups showed relatively lower degree of As resistance [MTCs of 15-20 mM As(III) and 250-350 mM As(V)]. As(V) reductase activity is detected in strains with high As(V) as well as As(III) resistance. A strong correlation could be established among isolates capable of reductase activity and siderophore production as well as As(III) tolerance. A large number of isolates (nearly 50%) is capable of anaerobic respiration using alternate inorganic electron acceptors [As(V), Se(VI), Fe(III), [NO(3)(2), SO(4)(2), S(2)O(3)(2). Ability to utilize different carbon sources ranging from C2-C6 compounds along with some complex sugars is also observed. Particularly, a number of strains is found to possess ability to grow chemolithotrophically using As(III) as the electron donor. The study reports for the first time the identity and metabolic abilities of bacteria in As contaminated ground water of North East India, useful to elucidate the microbial role in influencing mobilization of As in the region. PMID:24210546

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

    PubMed

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

    2015-07-15

    Changing climatic conditions have influenced the monsoon pattern in recent years. Variations in bacterial population in one such tropical environment were observed everyday over two years and point out intra and inter annual changes driven by the intensity of rainfall. Vibrio spp. were abundant during the monsoon and so were faecal coliforms. Vibrio alginolyticus were negatively influenced by nitrate, whereas, silicate and rainfall positively influenced Vibrio parahaemolyticus numbers. It is also known that pathogenic bacteria are associated with the plankton. Changes in the abundance of plankton, which are governed mainly by environmental changes, could be responsible for variation in pathogenic bacterial abundance during monsoon, other than the land runoff due to precipitation and influx of fresh water. PMID:25956443

  6. Effect of oenological practices on microbial populations using culture-independent techniques.

    PubMed

    Andorrà, Imma; Landi, Sara; Mas, Albert; Guillamón, José M; Esteve-Zarzoso, Braulio

    2008-10-01

    Sulphur dioxide (SO(2)) addition and yeast inoculation are well-established practices in winemaking for restricting the growth of indigenous yeasts and bacterial populations. The effect of these oenological practices on wine microbial populations has been evaluated using culture-independent methods. These are quantitative PCR (qPCR) for the enumeration of yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB), and PCR-DGGE to determine the yeast and bacteria species diversity. The PCR-DGGE method detected a low yeast and bacteria species diversity. On the contrary, the specificity of the primers designed for the qPCR allowed that minor microbial groups such as Hanseniaspora were accurately quantified regardless of a large presence of other microbial groups such as Saccharomyces. From an oenological point of view, inoculation increased the proportion of Saccharomyces vs. non-Saccharomyces in a shorter time. Hanseniaspora increased during the first phase and decreased during the latter phases of the process, especially in the sulphited fermentations. Both yeast inoculation and SO(2) kept the LAB populations at very low level, while the AAB populations were hardly affected by these two practices. PMID:18721672

  7. Bacterial Community Profiling of Milk Samples as a Means to Understand Culture-Negative Bovine Clinical Mastitis

    PubMed Central

    Kuehn, Joanna S.; Gorden, Patrick J.; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J.; Wang, Chong; Phillips, Gregory J.

    2013-01-01

    Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1–V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease. PMID:23634219

  8. Changes in sulfate-reducing bacterial populations during the onset of black band disease.

    PubMed

    Bourne, David G; Muirhead, Andrew; Sato, Yui

    2011-03-01

    Factors that facilitate the onset of black band disease (BBD) of corals remain elusive, though anoxic conditions under the complex microbial mat and production of sulfide are implicated in necrosis of underlying coral tissues. This study investigated the diversity and quantitative shifts of sulfate-reducing bacterial (SRB) populations during the onset of BBD using real-time PCR (RT-PCR) and cloning approaches targeting the dissimilatory (bi)sulfite reductase (dsrA) gene. A quantitative-PCR (qPCR) assay targeting the 16S rRNA gene also provided an estimate of total bacteria, and allowed the relative percentage of SRB within the lesions to be determined. Three Montipora sp. coral colonies identified with lesions previously termed cyanobacterial patches (CPs) (comprising microbial communities unlike those of BBD lesions), were tagged and followed through time as CP developed into BBD. The dsrA-targeted qPCR detected few copies of the gene in the CP samples (<65 per ng DNA), though copy numbers increased in BBD lesions (>2500 per ng DNA). SRB in CP samples were less than 1% of the bacterial population, though represented up to 7.5% of the BBD population. Clone libraries also demonstrated a shift in the dominant dsrA sequences as lesions shifted from CP into BBD. Results from this study confirm that SRB increase during the onset of BBD, likely increasing sulfide concentrations at the base of the microbial mat and facilitating the pathogenesis of BBD. PMID:20811471

  9. Changes in sulfate-reducing bacterial populations during the onset of black band disease

    PubMed Central

    Bourne, David G; Muirhead, Andrew; Sato, Yui

    2011-01-01

    Factors that facilitate the onset of black band disease (BBD) of corals remain elusive, though anoxic conditions under the complex microbial mat and production of sulfide are implicated in necrosis of underlying coral tissues. This study investigated the diversity and quantitative shifts of sulfate-reducing bacterial (SRB) populations during the onset of BBD using real-time PCR (RT-PCR) and cloning approaches targeting the dissimilatory (bi)sulfite reductase (dsrA) gene. A quantitativePCR (qPCR) assay targeting the 16S rRNA gene also provided an estimate of total bacteria, and allowed the relative percentage of SRB within the lesions to be determined. Three Montipora sp. coral colonies identified with lesions previously termed cyanobacterial patches (CPs) (comprising microbial communities unlike those of BBD lesions), were tagged and followed through time as CP developed into BBD. The dsrA-targeted qPCR detected few copies of the gene in the CP samples (<65 per ng DNA), though copy numbers increased in BBD lesions (>2500 per ng DNA). SRB in CP samples were less than 1% of the bacterial population, though represented up to 7.5% of the BBD population. Clone libraries also demonstrated a shift in the dominant dsrA sequences as lesions shifted from CP into BBD. Results from this study confirm that SRB increase during the onset of BBD, likely increasing sulfide concentrations at the base of the microbial mat and facilitating the pathogenesis of BBD. PMID:20811471

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

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

    PubMed

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

    2016-06-01

    Marama bean (Tylosema esculentum) is an indigenous non-nodulating legume to the arid agro-ecological parts of Southern Africa. It is a staple food for the Khoisan and Bantu people from these areas. It is intriguing how it is able to synthesize the high-protein content in the seeds since its natural habitat is nitrogen deficient. The aim of the study was to determine the presence of seed transmittable bacterial endophytes that may have growth promoting effects, which may be particularly important for the harsh conditions. Marama bean seeds were surface sterilized and gnotobiotically grown to 2 weeks old seedlings. From surface-sterilized shoots and roots, 123 distinct bacterial isolates were cultured using three media, and identified by BOX-PCR fingerprinting and sequence analyses of the 16S rRNA and nifH genes. Phylogenetic analyses of 73 putative endophytes assigned them to bacterial species from 14 genera including Proteobacteria (Rhizobium, Massilia, Kosakonia, Pseudorhodoferax, Caulobacter, Pantoea, Sphingomonas, Burkholderia, Methylobacterium), Firmicutes (Bacillus), Actinobacteria (Curtobacterium, Microbacterium) and Bacteroidetes (Mucilaginibacter, Chitinophaga). Screening for plant growth-promoting activities revealed that the isolates showed production of IAA, ACC deaminase, siderophores, endoglucanase, protease, AHLs and capacities to solubilize phosphate and fix nitrogen. This is the first report that marama bean seeds may harbor endophytes that can be cultivated from seedlings; in this community of bacteria, physiological characteristics that are potentially plant growth promoting are widespread. PMID:27118727

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2015-12-01

    Twenty-nine culturable bacterial endophytes were isolated from surface-sterilized tissues (root, stem and leaf) of Aloe vera and molecularly characterized to 13 genera: Pseudomonas, Bacillus, Enterobacter, Pantoea, Chryseobacterium, Sphingobacterium, Aeromonas, Providencia, Cedecea, Klebsiella, Cronobacter, Macrococcus and Shigella. The dominant genera include Bacillus (20.7%), Pseudomonas (20.7%) and Enterobacter (13.8%). The crude and ethyl acetate fractions of the metabolites of six isolates, species of Pseudomonas, Bacillus, Chryseobacterium and Shigella, have broad spectral antimicrobial activities against pathogenic Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus cereus, Salmonella Typhimurium, Proteus vulgaris, Klebsiella pneumoniae, Escherichia coli, Streptococcus pyogenes and Candida albicans, with inhibition zones ranging from 6.0 ± 0.57 to 16.6 ± 0.57 mm. In addition, 80% of the bacterial endophytes produced 1,1-diphenyl-2-picrylhydrazyl (DPPH) with scavenging properties of over 75% when their crude metabolites were compared with ascorbic acid (92%). In conclusion, this study revealed for the first time the endophytic bacteria communities from A. vera (Pseudomonas hibiscicola, Macrococcus caseolyticus, Enterobacter ludwigii, Bacillus anthracis) that produce bioactive compounds with high DPPH scavenging properties (75-88%) and (Bacillus tequilensis, Pseudomonas entomophila, Chryseobacterium indologenes, Bacillus aerophilus) that produce bioactive compounds with antimicrobial activities against bacterial pathogens. Hence, we suggest further investigation and characterization of their bioactive compounds. PMID:26454221

  14. Culturable bacterial microbiota of Plagiodera versicolora (L.) (Coleoptera: Chrysomelidae) and virulence of the isolated strains.

    PubMed

    Demirci, Meryem; Sevim, Elif; Demir, İsmail; Sevim, Ali

    2013-05-01

    Plagiodera versicolora (Laicharting, 1781) (Coleoptera: Chrysomelidae) is an important forest pest which damages many trees such as willow, poplar, and hazelnut. In order to find new microbes that can be utilized as a possible microbial control agent against this pest, we investigated the culturable bacterial flora of it and tested the isolated bacteria against P. versicolora larvae and adults. We were able to isolate nine bacteria from larvae and adults. The isolates were characterized using a combination of morphological, biochemical, and physiological methods. Additionally, we sequenced the partial sequence of the 16S rRNA gene to verify conventional identification results. Based on characterization studies, the isolates were identified as Staphylococcus sp. Pv1, Rahnella sp. Pv2, Rahnella sp. Pv3, Rahnella sp. Pv4, Rahnella sp. Pv5, Pantoea agglomerans Pv6, Staphylococcus sp. Pv7, Micrococcus luteus Pv8, and Rahnella sp. Pv9. The highest insecticidal activity against larvae and adults was obtained from M. luteus Pv8 with 50 and 40 % mortalities within 10 days after treatment, respectively. Extracellular enzyme activity of the bacterial isolates such as amylase, proteinase, lipase, cellulose, and chitinase was also determined. Consequently, our results show that M. luteus Pv8 might be a good candidate as a possible microbial control agent against P. versicolora and were discussed with respect to biocontrol potential of the bacterial isolates. PMID:23054688

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-01-18

    Whey is a valuable co-product from cheese making that serves as a raw material for a wide range of products. Its rich nutritional content lends itself to rapid spoilage, thus it typically needs to be pasteurised and refrigerated promptly. Despite the extensive literature on milk spoilage bacteria, little is known about the spoilage bacteria of whey. The utility of carbon dioxide (CO2) to extend the shelf-life of raw milk and cottage cheese has been well established, but its application in whey preservation has not yet been explored. This study aims to characterise the microbial populations of fresh and spoiled sweet whey by culture-independent community profiling using 454 pyrosequencing of 16S rRNA gene amplicons and to determine whether carbonation is effective in inhibiting bacterial growth in sweet whey. The microbiota of raw Cheddar and Mozzarella whey was dominated by cheese starter bacteria. After pasteurisation, two out of the three samples studied became dominated by diverse environmental bacteria from various phyla, with Proteobacteria being the most dominant. Diverse microbial profiles were maintained until spoilage occurred, when the entire population was dominated by just one or two genera. Whey spoilage bacteria were found to be similar to those of milk. Pasteurised Cheddar and Mozzarella whey was spoiled by Bacillus sp. or Pseudomonas sp., and raw Mozzarella whey was spoiled by Pseudomonas sp., Serratia sp., and other members of the Enterobacteriaceae family. CO2 was effective in inhibiting bacterial growth of pasteurised Cheddar and Mozzarella whey stored at 15°C and raw Mozzarella whey stored at 4°C. The spoilage bacteria of the carbonated samples were similar to those of the non-carbonated controls. PMID:26476573

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

    PubMed

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2015-07-01

    Cypermethrin is widely used for insect control; however, its toxicity toward aquatic life requires its complete removal from contaminated areas where the natural degradation ability of microbes can be utilized. Agricultural soil with extensive history of CM application was used to prepare enrichment cultures using cypermethrin as sole carbon source for isolation of cypermethrin degrading bacteria and bacterial community analysis using PCR-DGGE of 16 S rRNA gene. DGGE analysis revealed that dominant members of CM enrichment culture were associated with α-proteobacteria followed by γ-proteobacteria, Firmicutes, and Actinobacteria. Three potential CM-degrading isolates identified as Ochrobactrum anthropi JCm1, Bacillus megaterium JCm2, and Rhodococcus sp. JCm5 degraded 86-100% of CM (100 mg L(-1) ) within 10 days. These isolates were also able to degrade other pyrethroids, carbofuran, and cypermethrin degradation products. Enzyme activity assays revealed that enzymes involved in CM-degradation were inducible and showed activity when strains were grown on cypermethrin. Degradation kinetics of cypermethrin (200 mg kg(-1)) in soils inoculated with isolates JCm1, JCm2, and JCm5 suggested time-dependent disappearance of cypermethrin with rate constants of 0.0516, 0.0425, and 0.0807 d(-1), respectively, following first order rate kinetics. The isolated bacterial strains were among dominant genera selected under CM enriched conditions and represent valuable candidates for in situ bioremediation of contaminated soils and waters. PMID:25656248

  19. Video processing analysis for the determination and evaluation of the chemotactic response in bacterial populations.

    PubMed

    Nisenbaum, Melina; Maldonado, Emilio; Martínez Arca, Jorge; González, Jorge F; Passoni, Lucía I; Murialdo, Silvia E

    2016-08-01

    The aim of the present work was to design a methodology based on video processing to obtain indicators of bacterial population motility that allow the quantitative and qualitative analysis and comparison of the chemotactic phenomenon with different attractants in the agarose-in plug bridge method. Video image sequences were processed applying Shannon's entropy to the intensity time series of each pixel, which conducted to a final pseudo colored image resembling a map of the dynamic bacterial clusters. Processed images could discriminate perfectly between positive and negative attractant responses at different periods of time from the beginning of the assay. An index of spatial and temporal motility was proposed to quantify the bacterial response. With this index, this video processing method allowed obtaining quantitative information of the dynamic changes in space and time from a traditional qualitative assay. We conclude that this computational technique, applied to the traditional agarose-in plug assay, has demonstrated good sensitivity for identifying chemotactic regions with a broad range of motility. PMID:27291715

  20. Diversity of bacterial symbionts in populations of Sitobion miscanthi (Hemiptera: Aphididae) in China.

    PubMed

    Li, T; Xiao, J H; Wu, Y Q; Huang, D W

    2014-06-01

    Aphids are a group of insects frequently associated with bacterial symbionts. Although Chinese aphids harbor a high level of species diversity, the associations between Chinese aphids and bacterial symbionts are less known. In this study, we uncovered the diversity of bacterial symbionts in a Chinese widespread aphid, Sitobion miscanthi (Takahashi). In this study, we detected the aphid obligate symbiont Buchnera aphidicola, and two secondary symbionts, Hamiltonella defensa and Regiella insecticola, with the diagnostic polymerase chain reaction method in S. miscanthi samples. In addition, symbiotic species of Acinetobacter, Aeromonas, Enterobacter, Pantoea, and Pseudomonas, and the family Enterobacteriaceae were also found. Geographically, sporadic occurrences were detected for H. defensa and R. insecticola. Moreover, the infection rates of them vary widely among the infected populations: H. defensa (5.26-95.2%) and R. insecticola (5.26-46.7%). Phylogenetic analyses indicated that the strain of B. aphidicola mirrored the history and divergence of S. miscanthi; however, the H. defensa and R. insecticola strains were probably experienced horizontal transmission among S. miscanthi and its distantly related species. PMID:24874152

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  2. Aflatoxin B1 degradation by liquid cultures and lysates of three bacterial strains.

    PubMed

    Adebo, Oluwafemi Ayodeji; Njobeh, Patrick Berka; Sidu, Sibusiso; Tlou, Matsobane Godfrey; Mavumengwana, Vuyo

    2016-09-16

    Aflatoxin contamination remains a daunting issue to address in food safety. In spite of the efforts geared towards prevention and elimination of this toxin, it still persists in agricultural commodities. This has necessitated the search for other measures such as microbial degradation to combat this hazard. In this study, we investigated the biodegradation of aflatoxin B1 (AFB1), using lysates of three bacterial strains (Pseudomonas anguilliseptica VGF1, Pseudomonas fluorescens and Staphylococcus sp. VGF2) isolated from a gold mine aquifer. The bacterial cells were intermittently lysed in the presence and absence of protease inhibitors to obtain protease free lysates, subsequently incubated with AFB1 for 3, 6, 12, 24, and 48h to investigate whether any possible AFB1 degradation occurred using high performance liquid chromatography (HPLC) for detection. Results obtained revealed that after 6h of incubation, protease inhibited lysates of Staphylococcus sp. VGF2 demonstrated the highest degradation capacity of 100%, whereas P. anguilliseptica VGF1 and P. fluorescens lysates degraded AFB1 by 66.5 and 63%, respectively. After further incubation to 12h, no residual AFB1 was detected for all the lysates. Lower degrading ability was however observed for liquid cultures and uninhibited lysates. Data on cytotoxicity studies against human lymphocytes showed that the degraded products were less toxic than the parent AFB1. From this study, it can thus be deduced that the mechanism of degradation by these bacterial lysates is enzymatic. This study shows the efficacy of crude bacterial lysates for detoxifying AFB1 indicating potential for application in the food and feed industry. PMID:27294556

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

    NASA Astrophysics Data System (ADS)

    Lambert, Guillaume; Kussell, Edo

    2013-03-01

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

  4. Depth variation of bacterial extracellular enzyme activity and population diversity in the northeastern North Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Davey, Katherine E.; Kirby, Richard R.; Turley, Carol M.; Weightman, Andrew J.; Fry, John C.

    Distinct profiles of extracellular proteolytic enzyme activity were observed in the water column of the North Atlantic, with maximum potential proteolytic activity occurring in the top 35 m. The proteolytic enzyme Vmax values varied significantly and decreased from 1.46 nM min -1 in surface waters to 0.365 nM min -1 at 100 m. In contrast, Km values increased with depth from about 70 to 360 μM. Cell-associated enzymes accounted for the majority of the observed proteolytic activity. Dissolved enzymes comprised only 30-40% of the total extracellular enzyme activity and exhibited a low substrate affinity ( Km=˜1000 μM). These observations indicate clear stratification of bacterial associated extracellular enzyme activity, with the maximum activity in surface waters. This is consistent with some environmental changes in the water column, especially algal biomass and nitrate concentration. Bacterial mediated nitrogen remineralization in surface waters was approximately three times the total nitrogen demand of phytoplankton and bacteria. We determined bacterial population diversity using 16S rRNA sequence analysis and found evidence for stratification, with a higher representation of the Cytophaga/Flexibacter/Bacteriodes group at 5 m compared to 100 m. No similar stratification was observed among the α-proteobacterial SAR11 cluster, which were especially prevalent in the PRIME eddy. However, sequences phylogenetically related to another marine cluster, SAR122, were only observed at 100 m. We suggest that stratification of proteolytic activity within the water column may be explained at least in part, by differences in the composition of the bacterial community.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  6. Population density and taxonomic composition of bacterial nanoforms in soils of Russia

    NASA Astrophysics Data System (ADS)

    Lysak, L. V.; Lapygina, E. V.; Konova, I. A.; Zvyagintsev, D. G.

    2010-07-01

    The population density, physiological state, and taxonomic composition of bacterial nanoforms were first studied in soils of Russia. It was demonstrated with the help of fluorescent microscopy that the populations of nanoforms in the studied soils are very high and comprise tens and hundreds of millions of cells per 1 g of soil. The portion of cells with undamaged cell membranes was significantly higher in the nanoforms (95-98%) than in the cells of common size (about 50%), and this fact suggests the viability of the nanoforms. The taxonomic diversity of the nanoforms is great; the representatives of the main phylogenetic groups widespread in the soils were found among the nanoforms, namely, Archaea, Actinobacteria, Cytophaga, and Proteobacteria. The results allow assuming that the transformation of the cells into nanoforms is a relatively common event in the life of soil bacteria, allowing them to remain viable under unfavorable conditions and participate actively in soil processes.

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

    PubMed

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

    2016-01-01

    Diamondback moth (DBM), Plutella xylostella (Linnaeus), is a notorious pest of brassica crops worldwide and is resistant to all groups of insecticides. The insect system harbors diverse groups of microbiota, which in turn helps in enzymatic degradation of xenobiotic-like insecticides. The present study aimed to determine the diversity of gut microflora in DBM, quantify esterase activity and elucidate their possible role in degradation of indoxacarb. We screened 11 geographic populations of DBM in India and analyzed them for bacterial diversity. The culturable gut bacterial flora underwent molecular characterization with 16S rRNA. We obtained 25 bacterial isolates from larvae (n=13) and adults (n=12) of DBM. In larval gut isolates, gammaproteobacteria was the most abundant (76%), followed by bacilli (15.4%). Molecular characterization placed adult gut bacterial strains into three major classes based on abundance: gammaproteobacteria (66%), bacilli (16.7%) and flavobacteria (16.7%). Esterase activity from 19 gut bacterial isolates ranged from 0.072 to 2.32μmol/min/mg protein. Esterase bands were observed in 15 bacterial strains and the banding pattern differed in Bacillus cereus - KC985225 and Pantoea agglomerans - KC985229. The bands were characterized as carboxylesterase with profenofos used as an inhibitor. Minimal media study showed that B. cereus degraded indoxacarb up to 20%, so it could use indoxacarb for metabolism and growth. Furthermore, esterase activity was greater with minimal media than control media: 1.87 versus 0.26μmol/min/mg protein. Apart from the insect esterases, bacterial carboxylesterase may aid in the degradation of insecticides in DBM. PMID:26991291

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

    PubMed Central

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

    2003-01-01

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

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

    SciTech Connect

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

    1998-01-01

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

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

    PubMed

    Merritt, Jason; Kuehn, Seppe

    2016-01-01

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

  11. Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation.

    PubMed

    Mao, Junwen; Lu, Ting

    2016-01-01

    Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays an essential role in bacterial adaptation, evolution, and speciation. Although its molecular underpinnings have been increasingly revealed, natural transformation is not well characterized in terms of its quantitative ecological roles. Here, by using Neisseria gonorrhoeae as an example, we developed a population-dynamic model for natural transformation and analyzed its dynamic characteristics with nonlinear tools and simulations. Our study showed that bacteria capable of natural transformation can display distinct population behaviors ranging from extinction to coexistence and to bistability, depending on their HGT rate and selection coefficient. With the model, we also illustrated the roles of environmental DNA sources-active secretion and passive release-in impacting population dynamics. Additionally, by constructing and utilizing a stochastic version of the model, we examined how noise shapes the steady and dynamic behaviors of the system. Notably, we found that distinct waiting time statistics for HGT events, namely a power-law distribution, an exponential distribution, and a mix of the both, are associated with the dynamics in the regimes of extinction, coexistence, and bistability accordingly. This work offers a quantitative illustration of natural transformation by revealing its complex population dynamics and associated characteristics, therefore advancing our ecological understanding of natural transformation as well as HGT in general. PMID:26745428

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

    SciTech Connect

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

    2004-12-01

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

  13. Integrative approach to produce hydrogen and polyhydroxybutyrate from biowaste using defined bacterial cultures.

    PubMed

    Patel, Sanjay K S; Kumar, Prasun; Singh, Mamtesh; Lee, Jung-Kul; Kalia, Vipin C

    2015-01-01

    Biological production of hydrogen (H2) and polyhydroxybutyrate (PHB) from pea-shell slurry (PSS) was investigated using defined mixed culture (MMC4, composed of Enterobacter, Proteus, Bacillus spp.). Under batch culture, 19.0LH2/kg of PSS (total solid, TS, 2%w/v) was evolved. Using effluent from the H2 producing stage, Bacillus cereus EGU43 could produce 12.4% (w/w) PHB. Dilutions of PSS hydrolysate containing glucose (0.5%, w/v) resulted in 45-75LH2/kg TS fed and 19.1% (w/w) of PHB content. Under continuous culture, MMC4 immobilized on coconut coir (CC) lead to an H2 yield of 54L/kg TS fed and a PHB content of 64.7% (w/w). An improvement of 2- and 3.7-fold in H2 and PHB yields were achieved in comparison to control. This integrative approach using defined set of bacterial strains can prove effective in producing biomolecules from biowastes. PMID:25460994

  14. Release of Toll-Like Receptor-2-Activating Bacterial Lipoproteins in Shigella flexneri Culture Supernatants

    PubMed Central

    Aliprantis, Antonios O.; Weiss, David S.; Radolf, Justin D.; Zychlinsky, Arturo

    2001-01-01

    Shigella spp. cause dysentery, a severe form of bloody diarrhea. Apoptosis, or programmed cell death, is induced during Shigella infections and has been proposed to be a key event in the pathogenesis of dysentery. Here, we describe a novel cytotoxic activity in the sterile-culture supernatants of Shigella flexneri. An identical activity was identified in purified S. flexneri endotoxin, defined here as a mixture of lipopolysaccharide (LPS) and endotoxin-associated proteins (EP). Separation of endotoxin into EP and LPS revealed the activity to partition exclusively to the EP fraction. Biochemical characterization of S. flexneri EP and culture supernatants, including enzymatic deactivation, reverse-phase high-pressure liquid chromatography analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and a Toll-like receptor-2 (TLR2) activation assay, indicates that the cytotoxic component is a mixture of bacterial lipoproteins (BLP). We show that biologically active BLP are liberated into culture supernatants of actively growing S. flexneri. In addition, our data indicate that BLP, and not LPS, are the component of endotoxin of gram-negative organisms responsible for activating TLR2. The activation of apoptosis by BLP shed from S. flexneri is discussed as a novel aspect of the interaction of bacteria with the host. PMID:11553567

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

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kravchenko, Irina; Sukhacheva, Marina; Kizilova, Anna

    2014-05-01

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

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

    PubMed

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

    2009-01-01

    The aim of this study was to investigate the microbial community thriving at two shallow hydrothermal vents off Panarea Island (Italy). Physico-chemical characteristics of thermal waters were examined in order to establish the effect of the vents on biodiversity of both Bacteria and Archaea. Water and adjacent sediment samples were collected at different times from two vents, characterised by different depth and temperature, and analysed to evaluate total microbial abundances, sulphur-oxidising and thermophilic aerobic bacteria. Total microbial abundances were on average of the order of 10(5) cells ml(-1), expressed as picoplanktonic size fraction. Picophytoplanktonic cells accounted for 0.77-3.83% of the total picoplanktonic cells. The contribution of bacterial and archaeal taxa to prokaryotic community diversity was investigated by PCR-DGGE fingerprinting method. The number of bands derived from bacterial DNA was highest in the DGGE profiles of water sample from the warmest and deepest site (site 2). In contrast, archaeal richness was highest in the water of the coldest and shallowest site (site 1). Sulphur-oxidising bacteria were detected by both culture-dependent and -independent methods. The primary production at the shallow hydrothermal system of Panarea is supported by a complex microbial community composed by phototrophs and chemolithotrophs. PMID:19050821

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

    PubMed

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

    2016-11-01

    Improving lipid productivity and preventing overgrowth of contaminating bacteria are critical issues relevant to the commercialization of the mixotrophic microalgae cultivation process. In this paper, we report the use of magnesium aminoclay (MgAC) nanoparticles for enhanced lipid production from oleaginous Chlorella sp. KR-1 with simultaneous control of KR-1-associated bacterial growth in mixotrophic cultures with glucose as the model substrate. Addition of 0.01-0.1g/L MgAC promoted microalgal biomass production better than the MgAC-less control, via differential biocidal effects on microalgal and bacterial cells (the latter being more sensitive to MgAC's bio-toxicity than the former). The inhibition effect of MgAC on co-existing bacteria was, as based on density-gradient-gel-electrophoresis (DGGE) analysis, largely dosage-dependent and species-specific. MgAC also, by inducing an oxidative stress environment, increased both the cell size and lipid content of KR-1, resulting in a considerable, ∼25% improvement of mixotrophic algal lipid productivity (to ∼410mgFAME/L/d) compared with the untreated control. PMID:27543952

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

    NASA Astrophysics Data System (ADS)

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

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

  20. High nitrate removal from synthetic wastewater with the mixed bacterial culture.

    PubMed

    Foglar, Lucija; Briski, Felicita; Sipos, Laszlo; Vuković, Marija

    2005-05-01

    The applicability of the mixed bacterial culture, originated from two-stage anaerobic-aerobic industrial yeasts production wastewater treatment plant for high rate denitrification processes was investigated. After acclimation to nitrate, the dominant strains were Pseudomonas and Paracoccus sp. Complete denitrification with low accumulation of nitrite-N (0.1 mg/l) was found in synthetic wastewater, obeying a zero-order reaction with respect to nitrate and a first-order reaction with respect to biomass concentration. Denitrification was then monitored in the continuous-flow stirred reactor at different hydraulic retention time, HRT (62-28 h) in order to achieve the optimal HRT. Nitrate was completely removed during following 45 days, at 25 degrees C with HRT, which we reduced from 62 to 28 h. Yet still, at 28 h HRT, high average specific denitrification rate of 142 mg NO3- -N/g VSS h was obtained. PMID:15627558

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

    PubMed

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

    2016-01-01

    Acute respiratory tract infections are leading causes of morbidity in poultry farms allover the world. Six pathogens; Escherichia coli, Mycoplasma gallisepticum, Staphylococcus aureus, Pasteurella multocida, Mannheimia haemolytica and Pseudomonas aeruginosa were involved in respiratory infections in poultry. Herein, conventional identification procedures and polymerase chain reaction (PCR) were applied for detection of the most common respiratory bacterial pathogens in clinical specimens of poultry obtained from 53 Egyptian farms with various respiratory problems and the results were compared statistically. The analyzed data demonstrated a significantly higher rate of detection of the most recovered microorganisms (P<0.05) by PCR comparing to classical culture procedures. Further, multiplex PCR could detect E. coli, M. gallisepticum, S. aureus and Ps. aeruginosa in a single reaction, however, M. haemolytica was reported in a uinplex system. According to PCR results, the most commonly recorded bacterial pathogens in examined poultry farms were E. coli and Ps. aeruginosa (54.71% each), followed by M. haemolylica (35.85%) and M. gallisepticum (20.75%). In conclusion, PCR assay offered an effective alternative to traditional typing methods for the identification and simultaneous detection of the most clinically relevant respiratory pathogens in poultry. PMID:26950451

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

    PubMed Central

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

    1996-01-01

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

  3. Biogeochemical controls on the bacterial populations in the eastern Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Neogi, S. B.; Koch, B. P.; Schmitt-Kopplin, P.; Pohl, C.; Kattner, G.; Yamasaki, S.; Lara, R. J.

    2011-12-01

    Little is known about bacterial dynamics in the oligotrophic ocean, particularly about cultivable bacteria. We examined the abundance of total and cultivable bacteria in relation to changes in biogeochemical conditions in the eastern Atlantic Ocean with special regard to Vibrio spp., a group of bacteria that can cause diseases in human and aquatic organisms. Surface, deep water and plankton (<20 μm, 20-55 μm and >55 μm) samples were collected between 50° N and 24° S. Chlorophyll-a was very low (<0.3 μg l-1) in most areas of the nutrient-poor Atlantic, except at a few locations near upwelling regions. In surface water, dissolved organic carbon (DOC) and nitrogen (DON) concentrations were 64-95 μM C and 2-10 μM N accounting for ≥90 % and ≥76 % of total organic C and N, respectively. DOC and DON gradually decreased to ~45 μM C and <5 μM N in the bottom water. In the surface layer, culture independent total bacteria and other prokaryotes represented by 4´-6-diamidino-2-phenylindole (DAPI) counts, ranged mostly between 107 and 108 cells l-1, while cultivable bacterial counts (CBC) and Vibrio spp. were found at concentrations of 104-107 and 102-105 colony forming units (CFU) l-1, respectively. Most bacteria (>99 %) were found in the nanoplankton fraction (<20 μm), however, bacterial abundance did not correlate with suspended particulates (chlorophyll-a, particulate organic C [POC] and N [PON]). Instead, we found a highly significant correlation between bacterial abundance and temperature (p < 0.001) and a significant correlation with DOC and DON (p < 0.005 and <0.01, respectively). In comparison to CBC and DAPI-stained prokaryotes, cultivable Vibrio showed a stronger and highly significant correlation with DOC and DON (p < 0.0005 and p < 0.005, respectively). In cold waters of the mesopelagic and abyssal zones, CBC was 50 to 100-times lower than in the surface layer; however, cultivable Vibrio spp. could be isolated from the bathypelagic zone and even

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

    PubMed

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

    2010-09-30

    Soidon is a non-salted acidic fermented food prepared from the succulent bamboo shoot tip of Schizostachyum capitatum Munro by using a traditional liquid starter called "soidon mahi" in Manipur state of India. In this study, 163 bacterial isolates associated with this starter samples were identified and their population distribution was investigated by amplified ribosomal DNA restriction analysis (ARDRA), 16S rDNA sequencing and randomly amplified polymorphic DNA (RAPD) analysis. This acidic starter (pH 4.5+/-0.15) was dominated by a characteristic association of Bacillus and lactic acid bacteria (LAB) together. The population distribution of dominant species were Bacillus subtilis 29.3%, Bacillus cereus 35.7%, Bacillus pumilus 2.6%, Lactobacillus brevis 9.6%, Lactobacillus plantarum 5.1%, Carnobacterium sp. 11.9%, Enterococcus faecium 1.2% and Pseudomonas fluorescens 4.6%. Alarming population load (10(6)-10(7)cfu/ml) of B. cereus in 87% of starter samples studied should raise concern regarding biosafety of soidon consumption. PCR amplification of 16S-23S rDNA intergenic transcribed spacer (ITS) region and ITS-RFLP profiles revealed a high diversity with eight subgroups in B. subtilis, five subgroups in B. cereus and three subgroups in L. brevis isolates. The most abundant B. subtilis subgroup IB.1 distributed in most of the samples showed very less clonal variability during RAPD analysis. The molecular methods used in this study identified the dominant strains of Bacillus and LAB distributed in most of the starter samples. These dominant strains of B. subtilis, L. brevis and L. plantarum would allow for developing a defined starter culture for the production of quality soidon. PMID:20696489

  5. Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations.

    PubMed

    Helfrich, Stefan; Pfeifer, Eugen; Krämer, Christina; Sachs, Christian Carsten; Wiechert, Wolfgang; Kohlheyer, Dietrich; Nöh, Katharina; Frunzke, Julia

    2015-11-01

    Almost all bacterial genomes contain DNA of viral origin, including functional prophages or degenerated phage elements. A frequent but often unnoted phenomenon is the spontaneous induction of prophage elements (SPI) even in the absence of an external stimulus. In this study, we have analyzed SPI of the large, degenerated prophage CGP3 (187 kbp), which is integrated into the genome of the Gram-positive Corynebacterium glutamicum ATCC 13032. Time-lapse fluorescence microscopy of fluorescent reporter strains grown in microfluidic chips revealed the sporadic induction of the SOS response as a prominent trigger of CGP3 SPI but also displayed a considerable fraction (∼30%) of RecA-independent SPI. Whereas approx. 20% of SOS-induced cells recovered from this stress and resumed growth, the spontaneous induction of CGP3 always led to a stop of growth and likely cell death. A carbon source starvation experiment clearly emphasized that SPI only occurs in actively proliferating cells, whereas sporadic SOS induction was still observed in resting cells. These data highlight the impact of sporadic DNA damage on the activity of prophage elements and provide a time-resolved, quantitative description of SPI as general phenomenon of bacterial populations. PMID:26235130

  6. Structural and functional dynamics of sulfate-reducing populations in bacterial biofilms

    SciTech Connect

    Santegoeds, C.M.; Ferdelman, T.G.; Muyzer, G.; Beer, D. de

    1998-10-01

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

  7. Impact of water quality on the bacterial populations and off-flavours in recirculating aquaculture systems.

    PubMed

    Auffret, Marc; Yergeau, Étienne; Pilote, Alexandre; Proulx, Émilie; Proulx, Daniel; Greer, Charles W; Vandenberg, Grant; Villemur, Richard

    2013-05-01

    A variety of factors affecting water quality in recirculating aquaculture systems (RAS) are associated with the occurrence of off-flavours. In this study, we report the impact of water quality on the bacterial diversity and the occurrence of the geosmin-synthesis gene (geoA) in two RAS units operated for 252 days. Unit 2 displayed a higher level of turbidity and phosphate, which affected the fresh water quality compared with unit 1. In the biofilter, nitrification is one of the major processes by which high water quality is maintained. The bacterial population observed in the unit 1 biofilter was more stable throughout the experiment, with a higher level of nitrifying bacteria compared with the unit 2 biofilter. Geosmin appeared in fish flesh after 84 days in unit 2, whereas it appeared in unit 1 after 168 days, but at a much lower level. The geoA gene was detected in both units, 28 days prior to the detection of geosmin in fish flesh. In addition, we detected sequences associated with Sorangium and Nannocystis (Myxococcales): members of these genera are known to produce geosmin. These sequences were observed at an earlier time in unit 2 and at a higher level than in unit 1. This study confirms the advantages of new molecular methods to understand the occurrence of geosmin production in RAS. PMID:23228051

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2012-10-01

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

  10. Slow Protein Fluctuations Explain the Emergence of Growth Phenotypes and Persistence in Clonal Bacterial Populations

    PubMed Central

    Rocco, Andrea; Kierzek, Andrzej M.; McFadden, Johnjoe

    2013-01-01

    One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or drug tolerance. Its characteristic signature is the biphasic kill curve, whereby microbes exposed to a bactericidal agent are initially killed very rapidly but then much more slowly. Here we relate this problem to the more general problem of understanding the emergence of distinct growth phenotypes in clonal populations. We address the problem mathematically by adopting the framework of the phenomenon of so-called weak ergodicity breaking, well known in dynamical physical systems, which we extend to the biological context. We show analytically and by direct stochastic simulations that distinct growth phenotypes can emerge as a consequence of slow-down of stochastic fluctuations in the expression of a gene controlling growth rate. In the regime of fast gene transcription, the system is ergodic, the growth rate distribution is unimodal, and accounts for one phenotype only. In contrast, at slow transcription and fast translation, weakly non-ergodic components emerge, the population distribution of growth rates becomes bimodal, and two distinct growth phenotypes are identified. When coupled to the well-established growth rate dependence of antibiotic killing, this model describes the observed fast and slow killing phases, and reproduces much of the phenomenology of bacterial persistence. The model has major implications for efforts to develop control strategies for persistent infections. PMID:23382887

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

    PubMed

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

    2009-12-01

    Gut physiology, host phylogeny, and diet determine the composition of the intestinal microbiota. Grizzly bears (Ursus arctos horribilis) belong to the Order Carnivora, yet feed on an omnivorous diet. The role of intestinal microflora in grizzly bear digestion has not been investigated. Microbiota and microbial activity were analysed from the feces of wild and captive grizzly bears. Bacterial composition was determined using culture-dependent and culture-independent methods. The feces of wild and captive grizzly bears contained log 9.1 +/- 0.5 and log 9.2 +/- 0.3 gene copies x g(-1), respectively. Facultative anaerobes Enterobacteriaceae and enterococci were dominant in wild bear feces. Among the strict anaerobes, the Bacteroides-Prevotella-Porphyromonas group was most prominent. Enterobacteriaceae were predominant in the feces of captive grizzly bears, at log 8.9 +/- 0.5 gene copies x g(-1). Strict anaerobes of the Bacteroides-Prevotella-Porphyromonas group and the Clostridium coccoides cluster were present at log 6.7 +/- 0.9 and log 6.8 +/- 0.8 gene copies x g(-1), respectively. The presence of lactate and short-chain fatty acids (SCFAs) verified microbial activity. Total SCFA content and composition was affected by diet. SCFA composition in the feces of captive grizzly bears resembled the SCFA composition of prey-consuming wild animals. A consistent data set was obtained that associated fecal microbiota and metabolites with the distinctive gut physiology and diet of grizzly bears. PMID:20029525

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

    PubMed Central

    Minard, G.; Tran, F. H.; Van, Van Tran; Goubert, C.; Bellet, C.; Lambert, G.; Kim, Khanh Ly Huynh; Thuy, Trang Huynh Thi; Mavingui, P.; Valiente Moro, C.

    2015-01-01

    The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype) and bacterial diversity (16S rDNA metabarcoding) were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects. PMID:26441903

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

    PubMed

    Sire, Clément; Chavanis, Pierre-Henri

    2008-12-01

    We study the critical dynamics of the generalized Smoluchowski-Poisson system (for self-gravitating Langevin particles) or generalized Keller-Segel model (for the chemotaxis of bacterial populations). These models [P. H. Chavanis and C. Sire, Phys. Rev. E 69, 016116 (2004)] are based on generalized stochastic processes leading to the Tsallis statistics. The equilibrium states correspond to polytropic configurations with index n similar to polytropic stars in astrophysics. At the critical index n_{3}=d(d-2) (where d>or=2 is the dimension of space), there exists a critical temperature Theta_{c} (for a given mass) or a critical mass M_{c} (for a given temperature). For Theta>Theta_{c} or MM_{c} the system collapses and forms, in a finite time, a Dirac peak containing a finite fraction M_{c} of the total mass surrounded by a halo. We study these regimes numerically and, when possible, analytically by looking for self-similar or pseudo-self-similar solutions. This study extends the critical dynamics of the ordinary Smoluchowski-Poisson system and Keller-Segel model in d=2 corresponding to isothermal configurations with n_{3}-->+infinity . We also stress the analogy between the limiting mass of white dwarf stars (Chandrasekhar's limit) and the critical mass of bacterial populations in the generalized Keller-Segel model of chemotaxis. PMID:19256806

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

    NASA Astrophysics Data System (ADS)

    Sire, Clément; Chavanis, Pierre-Henri

    2008-12-01

    We study the critical dynamics of the generalized Smoluchowski-Poisson system (for self-gravitating Langevin particles) or generalized Keller-Segel model (for the chemotaxis of bacterial populations). These models [P. H. Chavanis and C. Sire, Phys. Rev. E 69, 016116 (2004)] are based on generalized stochastic processes leading to the Tsallis statistics. The equilibrium states correspond to polytropic configurations with index n similar to polytropic stars in astrophysics. At the critical index n3=d/(d-2) (where d⩾2 is the dimension of space), there exists a critical temperature Θc (for a given mass) or a critical mass Mc (for a given temperature). For Θ>Θc or MMc the system collapses and forms, in a finite time, a Dirac peak containing a finite fraction Mc of the total mass surrounded by a halo. We study these regimes numerically and, when possible, analytically by looking for self-similar or pseudo-self-similar solutions. This study extends the critical dynamics of the ordinary Smoluchowski-Poisson system and Keller-Segel model in d=2 corresponding to isothermal configurations with n3→+∞ . We also stress the analogy between the limiting mass of white dwarf stars (Chandrasekhar’s limit) and the critical mass of bacterial populations in the generalized Keller-Segel model of chemotaxis.

  15. Differential carbohydrate media and anaerobic replica plating techniques in delineating carbohydrate-utilizing subgroups in rumen bacterial populations.

    PubMed Central

    Leedle, J A; Hespell, R B

    1980-01-01

    A basal (BC) medium devoid of added carbohydrates, a complete (CC) medium containing nine carbohydrates were developed for enumerating rumen bacteria. The colony counts on the BC medium were 85 to 100% of those obtained on the CC medium. These colonies were pinpoint size (less than or equal to mm in diameter) but increased in size (2 to 5 mm in diameter) when carbohydrates were subsequently added. With the CC medium or other media tested, the colony counts were 20 to 50% higher on plates than on roll tubes and were about 35% of the direct cell counts. The lower colony counts on roll tubes were shown to result primarily from the loss of viability due to heat stress. The DC media were found by plating techniques to be suitable for differentiating mixed rumen bacterial populations into subgroups based upon carbohydrate utilization as shown by differences in subgroup profiles found within solid and liquid fractions of rumen contents, within rumen contents from animals fed high-forage and high-grain diets, and by correct colony formations by pure cultures of rumen bacteria on appropriate DC media. With simple modifications and use of an anaerobic glove box, replica plating methods and the CC and DC media were found to be a suitable means of rapidly determining the range of utilizable carbohydrate energy sources of rumen bacteria. PMID:6769390

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

    PubMed

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

    2011-04-01

    Host-associated differentiation (HAD) is the presence of genetically divergent, host-associated populations. It has been suggested that microbial symbionts of insect herbivores may play a role in HAD by allowing their insect hosts to use different plant species. The objective of this study was to document if host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory corresponded with differences in the composition of their associated bacteria. To test this hypothesis, we characterized the symbionts present in P. notabilis associated with these two tree species through metagenomic analyses using 454 sequencing. Differences in bacterial diversity were found between P. notabilis populations associated with pecan and water hickory. The bacteria, Pantoea agglomerans and Serratia marcescens, were absent in the P. notabilis water hickory population, whereas both species accounted for more than 69.72% of bacterial abundance in the pecan population. PMID:21261774

  17. Stable isotopic studies of n-alkane metabolism by a sulfate-reducing bacterial enrichment culture.

    PubMed

    Davidova, Irene A; Gieg, Lisa M; Nanny, Mark; Kropp, Kevin G; Suflita, Joseph M

    2005-12-01

    Gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy were used to study the metabolism of deuterated n-alkanes (C6 to C12) and 1-13C-labeled n-hexane by a highly enriched sulfate-reducing bacterial culture. All substrates were activated via fumarate addition to form the corresponding alkylsuccinic acid derivatives as transient metabolites. Formation of d14-hexylsuccinic acid in cell extracts from exogenously added, fully deuterated n-hexane confirmed that this reaction was the initial step in anaerobic alkane metabolism. Analysis of resting cell suspensions amended with 1-13C-labeled n-hexane confirmed that addition of the fumarate occurred at the C-2 carbon of the parent substrate. Subsequent metabolism of hexylsuccinic acid resulted in the formation of 4-methyloctanoic acid, and 3-hydroxy-4-methyloctanoic acid was tentatively identified. We also found that 13C nuclei from 1-13C-labeled n-hexane became incorporated into the succinyl portion of the initial metabolite in a manner that indicated that 13C-labeled fumarate was formed and recycled during alkane metabolism. Collectively, the findings obtained with a sulfate-reducing culture using isotopically labeled alkanes augment and support the previously proposed pathway (H. Wilkes, R. Rabus, T. Fischer, A. Armstroff, A. Behrends, and F. Widdel, Arch. Microbiol. 177:235-243, 2002) for metabolism of deuterated n-hexane by a denitrifying bacterium. PMID:16332800

  18. Production of bacterial cellulose using different carbon sources and culture media.

    PubMed

    Mohammadkazemi, Faranak; Azin, Mehrdad; Ashori, Alireza

    2015-03-01

    In this work, the effects of carbon sources and culture media on the production and structural properties of bacterial cellulose (BC) have been studied. BC nanofibers were synthesized using Gluconacetobacter xylinus strain PTCC 1734. Media used were Hestrin-Schramm (H), Yamanaka (Y), and Zhou (Z). Five different carbon sources, namely date syrup, glucose, mannitol, sucrose, and food-grade sucrose were used in these media. All the produced BC pellicles were characterized in terms of dry weight production, biomass yield, thermal stability, crystallinity and morphology by thermogravimetric analysis (TGA), x-ray diffraction (XRD), and field emission scanning electron microscopy (FE-SEM). The obtained results showed that mannitol lead to the highest yield, followed by sucrose. The highest production efficiency of mannitol might be due to the nitrogen source, which plays an important role. The maximum improvement on the thermal stability of the composites was achieved when mannitol was used in H medium. In addition, the crystallinity was higher in BC formed in H medium compared to other media. FE-SEM micrographs illustrated that the BC pellicles, synthesized in the culture media H and Z, were stable, unlike those in medium Y that were unstable. The micrographs of BC produced in media containing mannitol and sucrose provided evidence of the strong interfacial adhesion between the BC fibers without noticeable aggregates. PMID:25498666

  19. Rapid detection of Mannheimia haemolytica in lung tissues of sheep and from bacterial culture

    PubMed Central

    Kumar, Jyoti; Dixit, Shivendra Kumar; Kumar, Rajiv

    2015-01-01

    Aim: This study was aimed to detect Mannheimia haemolytica in lung tissues of sheep and from a bacterial culture. Introduction: M. haemolytica is one of the most important and well-established etiological agents of pneumonia in sheep and other ruminants throughout the world. Accurate diagnosis of M. haemolytica primarily relies on bacteriological examination, biochemical characteristics and, biotyping and serotyping of the isolates. In an effort to facilitate rapid M. haemolytica detection, polymerase chain reaction assay targeting Pasteurella haemolytica serotype-1 specific antigens (PHSSA), Rpt2 and 12S ribosomal RNA (rRNA) genes were used to detect M. haemolytica directly from lung tissues and from bacterial culture. Materials and Methods: A total of 12 archived lung tissues from sheep that died of pneumonia on an organized farm were used. A multiplex polymerase chain reaction (mPCR) based on two-amplicons targeted PHSSA and Rpt2 genes of M. haemolytica were used for identification of M. haemolytica isolates in culture from the lung samples. All the 12 lung tissue samples were tested for the presence M. haemolytica by PHSSA and Rpt2 genes based PCR and its confirmation by sequencing of the amplicons. Results: All the 12 lung tissue samples tested for the presence of PHSSA and Rpt2 genes of M. haemolytica by mPCR were found to be positive. Amplification of 12S rRNA gene fragment as internal amplification control was obtained with each mPCR reaction performed from DNA extracted directly from lung tissue samples. All the M. haemolytica were also positive for mPCR. No amplified DNA bands were observed for negative control reactions. All the three nucleotide sequences were deposited in NCBI GenBank (Accession No. KJ534629, KJ534630 and KJ534631). Sequencing of the amplified products revealed the identity of 99-100%, with published sequence of PHSSA and Rpt2 genes of M. haemolytica available in the NCBI database. Sheep specific mitochondrial 12S rRNA gene sequence

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

    PubMed

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

    2016-01-01

    To assess relationships of inflammatory markers and 2 related clinical factors with blood culture results, we retrospectively investigated inpatients' blood culture and blood chemistry findings that were recorded from January to December 2014 using electronic medical records and analyzed the data of 852 subjects (426 culture-positive and 426 culture-negative). Results suggested that the risk of positive blood culture statistically increased as inflammatory marker levels and the number of related factors increased. Concerning the effectiveness of inflammatory markers, when the outcome definition was also changed for C-reactive protein (CRP), the odds ratio had a similar value, whereas when the outcome definition of blood culture positivity was used for procalcitonin (PCT), the greatest effectiveness of that was detected. Therefore, the current results suggest that PCT is more useful than CRP as an auxiliary indication of bacterial infection. PMID:26525643

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

    NASA Astrophysics Data System (ADS)

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

    2011-04-01

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

  2. Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats.

    PubMed

    Ali, Nidaa; Dashti, Narjes; Salamah, Samar; Sorkhoh, Naser; Al-Awadhi, Husain; Radwan, Samir

    2016-03-01

    This study describes a bench-scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture-independent analysis of seawater from continuous cultures revealed high-bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate. PMID:26751253

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

    PubMed

    Indekeu, J O; Sznajd-Weron, K

    2003-12-01

    In order to describe biological colonies with a conspicuous hierarchical structure, a time- and space-discrete model for the growth of a rapidly saturating local biological population N(x,t) is derived from a hierarchical random deposition process previously studied in statistical physics. Two biologically relevant parameters, the probabilities of birth, B, and of death, D, determine the carrying capacity K. Due to the randomness the population depends strongly on position x and there is a distribution of carrying capacities, Pi(K). This distribution has self-similar character owing to the exponential slowing down of the growth, assumed in this hierarchical model. The most probable carrying capacity and its probability are studied as a function of B and D. The effective growth rate decreases with time, roughly as in a Verhulst process. The model is possibly applicable, for example, to bacteria forming a "towering pillar" biofilm, a structure poorly described by standard Eden or diffusion-limited-aggregation models. The bacteria divide on randomly distributed nutrient-rich regions and are exposed to a random local bactericidal agent (antibiotic spray). A gradual overall temperature or chemical change away from optimal growth conditions reduces bacterial reproduction, while biofilm development degrades antimicrobial susceptibility, causing stagnation into a stationary state. PMID:14754231

  4. Screening of wheat varieties and associated bacterial population in old alluvial soil of Burdwan, West Bengal.

    PubMed

    Datta, J K; Chakraborty, S; Gupta, S; Saha, R N; Mondal, N

    2007-01-01

    In order to screen out the best variety of wheat (Triticum aestivum) out of eight varieties (viz., HP 1633, BW 11, NW 1014, Sonalika, HUW 468, K 9107, HP 1731 and HUW 234), a field experiment was conducted (from Dec. 2002 to April 2003) in a randomized block design replicated thrice at Crop Research and Seed Multiplication Farm, Burdwan University, West Bengal, India. Various morpho physiological parameters viz., plant population, length of shoot and root, leaf area index (LAI), crop growth rate (CGR), leaf area ratio (LAR), leaf area duration (LAD), net assimilation rate (NAR), yield attributes viz., length of panicles, number of grains per panicle, grain yield, straw yield, pigment content in flag leaf (chlorophyll a, b and total chlorophyll and carotenoid content) were estimated and analyzed statistically Soil bacterial populations were also estimated in the fallow land before sowing of seeds and after harvesting of crop. The HUW 468 variety records higher grain yield, maximum panicle length and maximum chlorophyll b and total chlorophyll content. PMID:17717978

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

    ERIC Educational Resources Information Center

    Smithsonian Institution, Washington, DC.

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

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

    PubMed

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

    2012-01-01

    Present investigation was made to bring out the pattern of biofilm formation by heterotrophic bacteria on nontoxic material, polyvinyl chloride (PVC) sheet fitted wooden rack that was immersed in seawater and the study was conducted in Tuticorin coast. Samplings were made over a period of 7 days with the following time period intervals: 30 min, 1, 2, 4, 24, 48, 72, 96, 120 and 144 hr. Bacterial enumeration was made by spread plate method on nutrient agar medium and characterization of bacterial isolates up to generic level was done. Gram-negative bacteria like Pseudomonas sp., Enterobacter sp., Aeromonas sp., Cytophaga sp. and Flavobacterium sp. were found to be the pioneer in colonizing the surface within 30 min and seven genera were represented in the biofilm. Among them two genera were found belonging to Gram-positive groups which included Micrococcus and Bacillus sp. The early stage biofilm i.e. up to 24th hr was wholly constituted by Gram-negative groups. However, the population density of Pseudomonas sp. was found to be higher (315 CFU) when compared to other Gram-negative forms. Occurrence of Gram-positive group was noted only at 48th hr old biofilm (28 to 150 CFU). The period between 48 and 96th hr was the transition where both the Gram-negative and Gram-positive groups co- existed. After 96th hr, the biofilm was found constituted only by Gram-positive groups. The isolates of early stage biofilm were found to produce allelopathic substance like bacteriocin. PMID:23033644

  7. Arsenic oxidation capabilities of a chemoautotrophic bacterial population: Use for the treatment of an arsenic contaminated wastewater

    NASA Astrophysics Data System (ADS)

    Dictor, M.-C.; Battaglia-Brunet, F.; Garrido, F.; Baranger, P.

    2003-05-01

    An autotrophic bacterial population, named CAsOl, able to oxidise arsenic has been isolated from a former gold mine (Saint-Yrieix, France). This bacterial population was composed of two microorganisms: a bacterial strain close to Ralstonia picketii and the second one related to Thiomonas genus (identification by 16S rDNA sequencing). This microbial consortium was able to oxidise arsenic with CO2 as the carbon source, arsenite as electron donor and oxygen as electron accepter. A significant oxidising activity was observed in a pH range comprised between 3 to 8 (pH optimum 5 7). A laboratory experiment for the biological treatment of a synthetic effluent containing 100 mg.L^{-1} of arsenic has been carried out. A mineral support, pouzzolana, has been colonised by the population CAsOl and the column was fed continuously with a synthetic medium in order to determine the maximal arsenic oxidation rate and the optimal residence time. In our experimental conditions, the maximum arsenic oxidation rate was 3,9 g As(Ill). L^{-1}.day^{-1} with a residence time of 1 hour after 55 days of continuous running. The performance of our bacterial population for arsenite oxidation in arsenic contaminated wastewater are especially important in the case of a treatment of arsenious wastewater as it presents advantages compared to physico-chemical treatments (consumption and cost of chemicals, potential toxic by-products generation...).

  8. Microsatellite markers reveal genetic divergence among wild and cultured populations of Chinese sucker Myxocyprinus asiaticus.

    PubMed

    Cheng, W W; Wang, D Q; Wang, C Y; Du, H; Wei, Q W

    2016-01-01

    Studies of genetic diversity and genetic population structure are critical for the conservation and management of endangered species. The Chinese sucker Myxocyprinus asiaticus is a vulnerable monotypic species in China, which is at a risk of decline owing to fluctuations in effective population size and other demographic and environmental factors. We screened 11 microsatellite loci in 214 individuals to assess genetic differentiation in both wild and cultured populations. The single extant wild population had a higher number of alleles (13) than the cultured populations (average 7.3). High levels of genetic diversity, expressed as observed and expected heterozygosity (HO = 0.771, HE = 0.748, respectively), were found in both wild and cultured populations. We also report significant differentiation among wild and cultured populations (global FST = 0.023, P < 0.001). Both STRUCTURE analysis and neighbor-joining tree revealed three moderately divergent primary genetic clusters: the wild Yangtze population and the Sichuan population were each identified as an individual cluster, with the remaining populations clustered together. Twenty-two samples collected from the Yangtze River were assigned to the cultured population, demonstrating the efficacy of artificial propagation to avoid drastic reduction in the population size of M. asiaticus. These genetic data support the endangered status of the M. asiaticus and have implications for conservation management planning. PMID:27173283

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

    2011-01-01

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

  12. Sulfonamide and tetracycline resistance genes in total- and culturable-bacterial assemblages in South African aquatic environments.

    PubMed

    Suzuki, Satoru; Ogo, Mitsuko; Koike, Tatsuya; Takada, Hideshige; Newman, Brent

    2015-01-01

    Antibiotic resistant bacteria are ubiquitous in the natural environment. The introduction of effluent derived antibiotic resistance genes (ARGs) into aquatic environments is of concern in the spreading of genetic risk. This study showed the prevalence of sulfonamide and tetracycline resistance genes, sul1, sul2, sul3, and tet(M), in the total bacterial assemblage and colony forming bacterial assemblage in river and estuarine water and sewage treatment plants (STP) in South Africa. There was no correlation between antibiotic concentrations and ARGs, suggesting the targeted ARGs are spread in a wide area without connection to selection pressure. Among sul genes, sul1 and sul2 were major genes in the total (over 10(-2) copies/16S) and colony forming bacteria assemblages (∼10(-1) copies/16S). In urban waters, the sul3 gene was mostly not detectable in total and culturable assemblages, suggesting sul3 is not abundant. tet(M) was found in natural assemblages with 10(-3) copies/16S level in STP, but was not detected in colony forming bacteria, suggesting the non-culturable (yet-to-be cultured) bacterial community in urban surface waters and STP effluent possess the tet(M) gene. Sulfamethoxazole (SMX) resistant (SMX(r)) and oxytetracycline (OTC) resistant (OTC(r)) bacterial communities in urban waters possessed not only sul1 and sul2 but also sul3 and tet(M) genes. These genes are widely distributed in SMX(r) and OTC(r) bacteria. In conclusion, urban river and estuarine water and STP effluent in the Durban area were highly contaminated with ARGs, and the yet-to-be cultured bacterial community may act as a non-visible ARG reservoir in certain situations. PMID:26300864

  13. Sulfonamide and tetracycline resistance genes in total- and culturable-bacterial assemblages in South African aquatic environments

    PubMed Central

    Suzuki, Satoru; Ogo, Mitsuko; Koike, Tatsuya; Takada, Hideshige; Newman, Brent

    2015-01-01

    Antibiotic resistant bacteria are ubiquitous in the natural environment. The introduction of effluent derived antibiotic resistance genes (ARGs) into aquatic environments is of concern in the spreading of genetic risk. This study showed the prevalence of sulfonamide and tetracycline resistance genes, sul1, sul2, sul3, and tet(M), in the total bacterial assemblage and colony forming bacterial assemblage in river and estuarine water and sewage treatment plants (STP) in South Africa. There was no correlation between antibiotic concentrations and ARGs, suggesting the targeted ARGs are spread in a wide area without connection to selection pressure. Among sul genes, sul1 and sul2 were major genes in the total (over 10-2 copies/16S) and colony forming bacteria assemblages (∼10-1 copies/16S). In urban waters, the sul3 gene was mostly not detectable in total and culturable assemblages, suggesting sul3 is not abundant. tet(M) was found in natural assemblages with 10-3 copies/16S level in STP, but was not detected in colony forming bacteria, suggesting the non-culturable (yet-to-be cultured) bacterial community in urban surface waters and STP effluent possess the tet(M) gene. Sulfamethoxazole (SMX) resistant (SMXr) and oxytetracycline (OTC) resistant (OTCr) bacterial communities in urban waters possessed not only sul1 and sul2 but also sul3 and tet(M) genes. These genes are widely distributed in SMXr and OTCr bacteria. In conclusion, urban river and estuarine water and STP effluent in the Durban area were highly contaminated with ARGs, and the yet-to-be cultured bacterial community may act as a non-visible ARG reservoir in certain situations. PMID:26300864

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

    PubMed Central

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

    2015-01-01

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

  15. Optimization of Culture Parameters for Maximum Polyhydroxybutyrate Production by Selected Bacterial Strains Isolated from Rhizospheric Soils.

    PubMed

    Lathwal, Priyanka; Nehra, Kiran; Singh, Manpreet; Jamdagni, Pragati; Rana, Jogender S

    2015-01-01

    The enormous applications of conventional non-biodegradable plastics have led towards their increased usage and accumulation in the environment. This has become one of the major causes of global environmental concern in the present century. Polyhydroxybutyrate (PHB), a biodegradable plastic is known to have properties similar to conventional plastics, thus exhibiting a potential for replacing conventional non-degradable plastics. In the present study, a total of 303 different bacterial isolates were obtained from soil samples collected from the rhizospheric area of three crops, viz., wheat, mustard and sugarcane. All the isolates were screened for PHB (Poly-3-hydroxy butyric acid) production using Sudan Black staining method, and 194 isolates were found to be PHB positive. Based upon the amount of PHB produced, the isolates were divided into three categories: high, medium and low producers. Representative isolates from each category were selected for biochemical characterization; and for optimization of various culture parameters (carbon source, nitrogen source, C/N ratio, different pH, temperature and incubation time periods) for maximizing PHB accumulation. The highest PHB yield was obtained when the culture medium was supplemented with glucose as the carbon source, ammonium sulphate at a concentration of 1.0 g/l as the nitrogen source, and by maintaining the C/N ratio of the medium as 20:1. The physical growth parameters which supported maximum PHB accumulation included a pH of 7.0, and an incubation temperature of 30 degrees C for a period of 48 h. A few isolates exhibited high PHB accumulation under optimized conditions, thus showing a potential for their industrial exploitation. PMID:26638531

  16. Duodenal mucosal T cell subpopulation and bacterial cultures in acquired immune deficiency syndrome.

    PubMed

    Budhraja, M; Levendoglu, H; Kocka, F; Mangkornkanok, M; Sherer, R

    1987-05-01

    Enteric infections, chronic diarrhea frequently with no obvious etiology, and weight loss cause major morbidity and mortality in acquired immune deficiency syndrome (AIDS). Alterations in mucosal immunity may explain the increased incidence of enteric infections, and contamination of the upper small intestine with bacteria may be the cause of weight loss observed in these patients. To test this hypothesis we studied the mucosal T lymphocyte subset in duodenal mucosal biopsies in 14 AIDS and seven control patients. Duodenal fluid was also cultured for aerobic and anaerobic bacteria. There was a significant decrease among leu-3a T cells (helper/inducer) subset in AIDS. The proportion of mucosal T cells reacting with leu-2a (cytotoxic/suppressor) was significantly increased in AIDS patients. These patients also had a significant reversal of the normal mucosal helper/suppressor T cell ratio. There was no change in the number of leu-7 cells (cells mediate natural killer and antibody-dependent cellular cytotoxicity) as compared to controls. All patients with diarrhea and three of five patients without diarrhea had bacteria in their duodenal fluid. Mean number of organisms was 4.5 X 10(4)/ml. Cultures were negative in all control subjects. The results reveal that the abnormalities of T cell subpopulation in the blood of AIDS patients also occur in their duodenal mucosa. This immunological abnormality is associated with the bacterial colonization of upper gastrointestinal tract which may explain the diarrhea and weight loss observed in majority of our patients. The results also indicate that increased incidence of enteric infections in AIDS may be explained on the basis of altered mucosal immunity. PMID:2953237

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

    USGS Publications Warehouse

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

    1991-01-01

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

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

    PubMed

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

    2016-02-01

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

  19. A bioremediation approach using natural transformation in pure-culture and mixed-population biofilms.

    PubMed

    Perumbakkam, Sudeep; Hess, Thomas F; Crawford, Ronald L

    2006-12-01

    Bacterial transformation by naked DNA is thought to contribute to gene transfer and microbial evolution within natural environments. In nature many microbial communities exist as complex assemblages known as biofilms where genetic exchange is facilitated. It may be possible to take advantage of natural transformation processes to modify the phenotypes of biofilm communities giving them specific and desirable functions. Work described here shows that biofilms composed of either pure cultures or mixed populations can be transformed with specific catabolic genes such that the communities acquire the ability to degrade a particular xenobiotic compound. Biofilms were transformed by plasmids bearing genes encoding green fluorescent protein (mut2) and/or atrazine chlorohydrolase (atzA). Confocal microscopy was used to quantify the number of transformants expressing mut2 in the biofilms. Degradation of atrazine by expressed atzA was quantified by tandem mass spectrometry. PCR analysis was performed to confirm the presence of atzA in transformed biofilms. These results indicate that it should be possible to use natural transformation to enhance bioremediation processes performed by biofilms. PMID:16477353

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

    PubMed

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

    2014-06-25

    The present work reports on the production and characterization of polyhydroxyalkanoates (PHAs) with different valerate contents, which were synthesized from microbial mixed cultures, and the subsequent development of nanocomposites incorporating bacterial cellulose nanowhiskers (BCNW) via solution casting processing. The characterization of the pure biopolyesters showed that the properties of PHAs may be strongly modified by varying the valerate ratio in the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) copolymer, as expected. Increasing the valerate content was seen to greatly decrease the melting temperature and enthalpy of the material, as well as its rigidity and stiffness, resulting in a more ductile behaviour. Additionally, the higher valerate PHA displayed higher permeability to water and oxygen and higher moisture sensitivity. Subsequently, BCNW were incorporated into both PHA grades, achieving a high level of dispersion for a 1 wt.-% loading, whereas some agglomeration took place for 3 wt.-% BCNW. As evidenced by DSC analyses, BCNW presented a nucleating effect on the PHA matrices. BCNW also increased the thermal stability of the polymeric matrices when properly dispersed due to strong matrix-filler interactions. Barrier properties were seen to depend on relative humidity and improved at low nanofiller loadings and low relative humidity. PMID:23827196

  1. Breast Cancer Screening: Cultural Beliefs and Diverse Populations

    ERIC Educational Resources Information Center

    Simon, Cassandra E.

    2006-01-01

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

  2. Association between Toll-like receptor 9 gene polymorphisms and risk of bacterial meningitis in a Chinese population.

    PubMed

    Wang, X H; Shi, H P; Li, F J

    2016-01-01

    We determined whether two common single nucleotide polymorphisms (SNPs) in the Toll-like receptor 9 gene (TLR9) (TLR9+2848 rs352140 and TLR9-1237 rs5743836) influenced susceptibility to bacterial meningitis in a Chinese population. The study comprised 126 patients with bacterial meningitis and 252 control subjects, all of whom were recruited from the Tuberculosis Hospital of Shanxi Province. Genotyping of TLR9+2848 rs352140 and TLR9-1237 rs5743836 was performed by polymerase chain reaction coupled with restriction fragment length polymorphism. Using logistic regression analysis, we found that individuals with the AA genotype were associated with an increased risk of bacterial meningitis compared with those with the GG genotype (OR = 0.43, 95%CI = 0.19-0.95; P = 0.03). In a recessive model, the AA genotype was correlated with an elevated risk of bacterial meningitis compared with the GG+GA genotype (OR = 0.49, 95%CI = 0.22-0.99; P = 0.04). However, no significant differences were observed in the association between the TLR9-1237 rs5743836 polymorphism and the risk of bacterial meningitis in the codominant, dominant, or recessive models. In conclusion, the results of our study suggest an association between the TLR9+2848 polymorphism and a reduced risk of bacterial meningitis in the codominant and recessive models. PMID:27525854

  3. The soil flagellate Heteromita globosa accelerates bacterial degradation of alkylbenzenes through grazing and acetate excretion in batch culture.

    PubMed

    Mattison, R G; Taki, H; Harayama, S

    2005-01-01

    The impact of grazing by soil flagellates Heteromita globosa on aerobic biodegradation of benzene by Pseudomonas strain PS+ was examined in batch culture. Growth of H. globosa on these bacteria obeyed Monod kinetics (mu(max), 0.17 +/- 0.03 h(-1); K(s), 1.1 +/- 0.2 x 10(7) bacteria mL(-1)) and was optimal at a bacteria/ flagellate ratio of 2000. Carbon mass balance showed that 5.2% of total [ring-U-(14)C]benzene fed to bacteria was subsequently incorporated into flagellate biomass. Growth-inhibiting concentrations (IC50) of alkylbenzenes (benzene, toluene, ethylbenzene) were inversely related with their octanol/ water partitioning coefficients, and benzene was least toxic for bacteria and flagellates with IC50 values of 4392 (+/- 167) microM and 2770 (+/- 653) microM, respectively. The first-order rate constant for benzene degradation (k1, 0.48 +/- 0.12 day(-1)) was unaffected by the presence or absence of flagellates in cultures. However, the rate of benzene degradation by individual bacteria averaged three times higher in the presence of flagellates (0.73 +/- 0.13 fmol cell(-1) h(-1)) than in their absence (0.26 +/- 0.03 fmol cell(-1) h(-1)). Benzene degradation also coincided with higher levels of dissolved oxygen and a higher rate of nitrate reduction in the presence of flagellates (p < 0.02). Grazing by flagellates may have increased the availability of dissolved oxygen to a smaller surviving population of bacteria engaged in the aerobic reactions initiating benzene degradation. In addition, flagellates may also have increased the rate of nitrate reduction through the excretion of acetate as an additional electron donor for these bacteria. Indeed, acetate was shown to progressively accumulate in cultures where flagellates grazed on heat-killed bacteria. This study provided evidence that grazing flagellates stimulate bacterial degradation of alkylbenzenes and provide a link for carbon cycling to consumers at higher trophic levels. This may have important

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2016-01-01

    Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs. PMID:26599433

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

    PubMed

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

    2015-01-01

    Mosquito-microbe interactions tend to influence larval nutrition, immunity, and development, as well as fitness and vectorial capacity of adults. Understanding the role of different bacterial species not only improves our knowledge of the physiological and ecological consequences of these interactions, but also provides the basis for developing novel strategies for controlling mosquito-borne diseases. We used culture-dependent and culture-independent techniques to characterize the bacterial composition and abundance in water and midgut samples of larval and adult females of Aedes japonicus (Theobald), Aedes triseriatus (Say), and Culex restuans (Theobald) collected from waste tires at two wooded study sites in Urbana, IL. The phylum-specific real-time quantitative polymerase chain reaction assay revealed a higher proportion of Actinobacteria and a lower proportion of gamma-Proteobacteria and Bacteroidetes in water samples and larval midguts compared to adult female midguts. Only 15 of the 57 bacterial species isolated in this study occurred in both study sites. The number of bacterial species was highest in water samples (28 species from Trelease Woods; 25 species from South Farms), intermediate in larval midguts (13 species from Ae. japonicus; 12 species from Ae. triseriatus; 8 species from Cx. restuans), and lowest in adult female midguts (2 species from Ae. japonicus; 3 species from Ae. triseriatus). These findings suggest that the composition and richness of bacterial communities varies both between habitats and among mosquito species and that the reduction in bacteria diversity during metamorphosis is more evident among bacteria detected using the culture-dependent method. PMID:26336281

  7. Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica.

    PubMed

    Bottos, Eric M; Woo, Anthony C; Zawar-Reza, Peyman; Pointing, Stephen B; Cary, Stephen C

    2014-01-01

    Bacteria are assumed to disperse widely via aerosolized transport due to their small size and resilience. The question of microbial endemicity in isolated populations is directly related to the level of airborne exogenous inputs, yet this has proven hard to identify. The ice-free terrestrial ecosystem of Antarctica, a geographically and climatically isolated continent, was used to interrogate microbial bio-aerosols in relation to the surrounding ecology and climate. High-throughput sequencing of bacterial ribosomal RNA (rRNA) genes was combined with analyses of climate patterns during an austral summer. In general terms, the aerosols were dominated by Firmicutes, whereas surrounding soils supported Actinobacteria-dominated communities. The most abundant taxa were also common to aerosols from other continents, suggesting that a distinct bio-aerosol community is widely dispersed. No evidence for significant marine input to bioaerosols was found at this maritime valley site, instead local influence was largely from nearby volcanic sources. Back trajectory analysis revealed transport of incoming regional air masses across the Antarctic Plateau, and this is envisaged as a strong selective force. It is postulated that local soil microbial dispersal occurs largely via stochastic mobilization of mineral soil particulates. PMID:24121801

  8. Bacterial Population Adherent to the Epithelium on the Roo of the Dorsal Rumen of Sheep †

    PubMed Central

    Dehority, Burk A.; Grubb, Jean A.

    1981-01-01

    By anaerobic procedures, the total number of adherent bacteria was determined on tissue samples obtained from the roof of the dorsal rumen of three sheep. After four washings, 1.91 × 107, 0.34 × 107, and 1.23 × 107 bacteria per cm2 were still attached to the rumen epithelium in sheep 1, 2, and 3, respectively. A total of 95 strains of bacteria were isolated from these three samples. Based on morphology, Gram stain, anaerobiosis, motility, and fermentation end products, they were presumptively identified as follows: Butyrivibrio fibrisolvens, 30 strains; atypical Butyrivibrio, 5 strains; Bacteroides ruminicola, 22 strains; Lactobacillus, 1 strain; and unknown Bacteroides species, 37 strains. For sheep 3, washing the rumen epithelium a total of 10 times reduced the adherent bacterial population by 93% (8.4 × 105 bacteria per cm2). Of 30 strains isolated from this sample, 22 were presumptively identified as Butyrivibrio and Bacteroides types. These results suggest that the epithelium on the roof of the dorsal rumen is primarily colonized by two genera of bacteria, Butyrivibrio and Bacteroides. Most Butyrivibrio and Bacteroides ruminicola strains appeared to be similar to previously isolated rumen strains. However, the unknown Bacteroides species differed considerably from the three species of this genus which are commonly isolated from rumen contents. PMID:16345797

  9. Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens

    PubMed Central

    Qiu, Yongjin; Nakao, Ryo; Ohnuma, Aiko; Kawamori, Fumihiko; Sugimoto, Chihiro

    2014-01-01

    Ticks are one of the most important blood-sucking vectors for infectious microorganisms in humans and animals. When feeding they inject saliva, containing microbes, into the host to facilitate the uptake of blood. An understanding of the microbial populations within their salivary glands would provide a valuable insight when evaluating the vectorial capacity of ticks. Three tick species (Ixodes ovatus, I. persulcatus and Haemaphysalis flava) were collected in Shizuoka Prefecture of Japan between 2008 and 2011. Each tick was dissected and the salivary glands removed. Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. The composition of the microbial populations of each tick species were assessed by principal component analysis (PCA) using the Metagenomics RAST (MG-RAST) metagenomic analysis tool. Rickettsia-specific PCR was used for the characterization of rickettsial species. Almost full length of 16S rDNA was amplified in order to characterize unclassified bacterial sequences obtained in I. persulcatus female samples. The numbers of bacterial genera identified for the tick species were 71 (I. ovatus), 127 (I. persulcatus) and 59 (H. flava). Eighteen bacterial genera were commonly detected in all tick species. The predominant bacterial genus observed in all tick species was Coxiella. Spiroplasma was detected in Ixodes, and not in H. flava. PCA revealed that microbial populations in tick salivary glands were different between tick species, indicating that host specificities may play an important role in determining the microbial complement. Four female I. persulcatus samples contained a high abundance of several sequences belonging to Alphaproteobacteria symbionts. This study revealed the microbial populations within the salivary glands of three species of ticks, and the

  10. Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus

    PubMed Central

    Su, Xiao-Mei; Liu, Yin-Dong; Hashmi, Muhammad Zaffar; Ding, Lin-Xian; Shen, Chao-Feng

    2015-01-01

    Biphenyl (BP)-degrading bacteria were identified to degrade various polychlorinated BP (PCB) congers in long-term PCB-contaminated sites. Exploring BP-degrading capability of potentially useful bacteria was performed for enhancing PCB bioremediation. In the present study, the bacterial composition of the PCB-contaminated sediment sample was first investigated. Then extracellular organic matter (EOM) from Micrococcus luteus was used to enhance BP biodegradation. The effect of the EOM on the composition of bacterial community was investigated by combining with culture-dependent and culture-independent methods. The obtained results indicate that Proteobacteria and Actinobacteria were predominant community in the PCB-contaminated sediment. EOM from M. luteus could stimulate the activity of some potentially difficult-to-culture BP degraders, which contribute to significant enhancement of BP biodegradation. The potentially difficult-to-culture bacteria in response to EOM addition were mainly Rhodococcus and Pseudomonas belonging to Gammaproteobacteria and Actinobacteria respectively. This study provides new insights into exploration of functional difficult-to-culture bacteria with EOM addition and points out broader BP/PCB degrading, which could be employed for enhancing PCB-bioremediation processes. PMID:25675850

  11. Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus.

    PubMed

    Su, Xiao-Mei; Liu, Yin-Dong; Hashmi, Muhammad Zaffar; Ding, Lin-Xian; Shen, Chao-Feng

    2015-05-01

    Biphenyl (BP)-degrading bacteria were identified to degrade various polychlorinated BP (PCB) congers in long-term PCB-contaminated sites. Exploring BP-degrading capability of potentially useful bacteria was performed for enhancing PCB bioremediation. In the present study, the bacterial composition of the PCB-contaminated sediment sample was first investigated. Then extracellular organic matter (EOM) from Micrococcus luteus was used to enhance BP biodegradation. The effect of the EOM on the composition of bacterial community was investigated by combining with culture-dependent and culture-independent methods. The obtained results indicate that Proteobacteria and Actinobacteria were predominant community in the PCB-contaminated sediment. EOM from M. luteus could stimulate the activity of some potentially difficult-to-culture BP degraders, which contribute to significant enhancement of BP biodegradation. The potentially difficult-to-culture bacteria in response to EOM addition were mainly Rhodococcus and Pseudomonas belonging to Gammaproteobacteria and Actinobacteria respectively. This study provides new insights into exploration of functional difficult-to-culture bacteria with EOM addition and points out broader BP/PCB degrading, which could be employed for enhancing PCB-bioremediation processes. PMID:25675850

  12. Culture free DGGE and cloning based monitoring of changes in bacterial communities of salad due to processing.

    PubMed

    Handschur, M; Pinar, G; Gallist, B; Lubitz, W; Haslberger, A G

    2005-11-01

    To assess the possibilities of a culture-independent monitoring of bacterial communities in the food chain, samples of salad from farming sites as well as corresponding, processed products in stores were analysed. The bacterial DNA was extracted using a modified soil extraction protocol. Amplification of 16S rDNA was carried out using primers specific for eubacteria and enterobacteriaceae. Fingerprints of 200/370 bp respectively were obtained by denaturing gradient gel electrophoresis (DGGE) analysis following PCR and nested PCR amplification. In parallel to DGGE analysis, clone libraries containing PCR fragments of the ribosomal gene were constructed and clones were screened by DGGE. DGGE analysis indicated a high diversity of bacterial communities in salad samples. Fingerprints indicated clearly reduced diversity of bacterial communities in processed samples from markets compared to field-grown salads. Surprisingly, primers pointed out in literature as specific for enterobacteriaceae did amplify pseudomonadeceae as well. Therefore, the more specific primers fD2 and rP1 were used subsequently in this study to amplify specific members of the family enterobacteriaceae. A total of 11 different 16S rDNA sequences were obtained and subjected to sequencing and phylogenetic affiliation. Sequences derived from the eubacterial clone library from organically farmed salad were affiliated to the family microbacteriaceae and pseudomonadaceae. In addition, a potential new genus within the family of enterobacteriaceae was detected. Furthermore, a sequence showing 98.9% similarity to Pseudomonas libaniensis (fluorescence subgroup) was found in a processed salad sample but not in the corresponding field samples. This species is generally known as an opportunistic pathogen. Whereas molecular based monitoring of bacterial communities in food still may need more experience and standardisation to detect specific bacteria present, the monitoring strategy presented in this paper

  13. Environmental factors shaping cultured free-living amoebae and their associated bacterial community within drinking water network.

    PubMed

    Delafont, Vincent; Bouchon, Didier; Héchard, Yann; Moulin, Laurent

    2016-09-01

    Free-living amoebae (FLA) constitute an important part of eukaryotic populations colonising drinking water networks. However, little is known about the factors influencing their ecology in such environments. Because of their status as reservoir of potentially pathogenic bacteria, understanding environmental factors impacting FLA populations and their associated bacterial community is crucial. Through sampling of a large drinking water network, the diversity of cultivable FLA and their bacterial community were investigated by an amplicon sequencing approach, and their correlation with physicochemical parameters was studied. While FLA ubiquitously colonised the water network all year long, significant changes in population composition were observed. These changes were partially explained by several environmental parameters, namely water origin, temperature, pH and chlorine concentration. The characterisation of FLA associated bacterial community reflected a diverse but rather stable consortium composed of nearly 1400 OTUs. The definition of a core community highlighted the predominance of only few genera, majorly dominated by Pseudomonas and Stenotrophomonas. Co-occurrence analysis also showed significant patterns of FLA-bacteria association, and allowed uncovering potentially new FLA - bacteria interactions. From our knowledge, this study is the first that combines a large sampling scheme with high-throughput identification of FLA together with associated bacteria, along with their influencing environmental parameters. Our results demonstrate the importance of physicochemical parameters in the ecology of FLA and their bacterial community in water networks. PMID:27219048

  14. Effect of Lactobacillus johnsonii CRL1647 on different parameters of honeybee colonies and bacterial populations of the bee gut.

    PubMed

    Audisio, M C; Sabaté, D C; Benítez-Ahrendts, M R

    2015-01-01

    Lactobacillus johnsonii CRL1647, isolated from the intestinal tract of a worker-bee in Salta, Argentina, was delivered to Apis mellifera L. honey bee colonies according to two different administration schedules: 1×10(5) cfu/ml every 15 days (2011) or monthly (2012). The effect of each treatment on the bee-colony performance was monitored by measuring honey production, and the prevalence of varroasis and nosemosis. Worker bees from each assay were randomly captured 3 days after administration and assayed for the following intestinal culturable and defined bacterial populations: total aerobic microorganisms, Bacillus spp. spores, Lactobacillus spp., Enterococcus spp. and enterobacteria. Interestingly, both treatments generated a similar increase in honey production in treated colonies compared to controls: 36.8% (every 15 days) and 36.3% (monthly). Nosema index always exhibited a reduction when lactobacilli were administered; in turn, Varroa incidence was lower when the lactobacilli were administered once a month. Moreover, the administration of L. johnsonii CRL1647 every 15 days produced an increase in the total number of aerobic microorganisms and in bacteria belonging to the genera Lactobacillus and Enterococcus; at the same time, a decrease was observed in the number of total spores at the end of the treatment. The number of enterobacteria was constant and remained below that of control hives at the end of the assay. On the other hand, the delivery of lactobacilli once a month only showed an increase in the number of bacteria belonging to the genus Lactobacillus; meanwhile, viable counts of the remaining microorganisms assayed were reduced. Even though it seems that both treatments were similar, those bee colonies that received L. johnsonii CRL1647 every 15 days became so strong that they swarmed. PMID:25809216

  15. The Resistant-Population Cutoff (RCOFF): a New Concept for Improved Characterization of Antimicrobial Susceptibility Patterns of Non-Wild-Type Bacterial Populations

    PubMed Central

    Valsesia, Giorgia; Hombach, Michael; Maurer, Florian P.; Courvalin, Patrice; Roos, Malgorzata

    2015-01-01

    This study aimed to determine resistant-population cutoffs (RCOFFs) to allow for improved characterization of antimicrobial susceptibility patterns in bacterial populations. RCOFFs can complement epidemiological cutoff (ECOFF)-based settings of clinical breakpoints (CBPs) by systematically describing the correlation between non-wild-type and wild-type populations. We illustrate this concept by describing three paradigmatic examples of wild-type and non-wild-type Escherichia coli populations from our clinical strain database of disk diffusion diameters. The statistical determination of RCOFFs and ECOFFs and their standardized applications in antimicrobial susceptibility testing (AST) facilitates the assignment of isolates to wild-type or non-wild-type populations. This should improve the correlation of in vitro AST data and distinct antibiotic resistance mechanisms with clinical outcome facilitating the setting and validation of CBPs. PMID:25762769

  16. A culturally diverse staff population: challenges and opportunities for nurses.

    PubMed

    Mattson, Susan

    2009-01-01

    The United States is seeing an increase in ethnic and cultural diversity that is reflected (albeit to a smaller extent) in the nursing workforce. There are also more nurses who are foreign-born and educated. These nurses bring elements of their ethnic culture to the healthcare setting, including that of the "healthcare provider" culture of their home country. Often these values conflict with, or at least differ from, many American values seen in the workplace, such as autonomy of patients, an individualistic approach to relationships, peer relationships rather than hierarchical ones, democracy as an ideal norm, optimal health is ideal, and an emphasis on time/schedules and use of technology. A major cultural difference in the work setting has to do with the meaning of "work" itself, which can vary among cultural groups; in addition, some cultures are viewed as more "collective" in nature than the American ones, which are considered "individualistic." In particular, foreign-born and educated nurses from different healthcare systems bring with them values of the political system in which they work, the concept of a socialized system of medicine, language and accent differences, different concepts of nursing duties, and varying psychosocial skills. PMID:19704294

  17. Linkage disequilibrium in wild and cultured populations of Pacific oyster ( Crassostrea gigas)

    NASA Astrophysics Data System (ADS)

    Guo, Xiang; Li, Qi; Kong, Lingfeng; Yu, Hong

    2016-04-01

    Linkage disequilibrium (LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping. The feasibility and efficacy of association studies are strongly dependent on the extent of LD which determines the number and density of markers in the studied population, as well as the experimental design for an association analysis. In this study, we first characterized the extent of LD in a wild population and a cultured mass-selected line of Pacific oyster ( Crassostrea gigas). A total of 88 wild and 96 cultured individuals were selected to assess the level of genome-wide LD with 53 microsatellites, respectively. For syntenic marker pairs, no significant association was observed in the wild population; however, three significant associations occurred in the cultured population, and the significant LD extended up to 12.7 cM, indicating that strong artificial selection is a key force for substantial increase of genome-wide LD in cultured population. The difference of LD between wild and cultured populations showed that association studies in Pacific oyster can be achieved with reasonable marker densities at a relatively low cost by choosing an association mapping population. Furthermore, the frequent occurrence of LD between non-syntenic loci and rare alleles encourages the joint application of linkage analysis and LD mapping when mapping genes in oyster. The information on the linkage disequilibrium in the cultured population is useful for future association mapping in oyster.

  18. Monitoring Bacterial Communities in Raw Milk and Cheese by Culture-Dependent and -Independent 16S rRNA Gene-Based Analyses▿

    PubMed Central

    Delbès, Céline; Ali-Mandjee, Leila; Montel, Marie-Christine

    2007-01-01

    The diversity and dynamics of bacterial populations in Saint-Nectaire, a raw-milk, semihard cheese, were investigated using a dual culture-dependent and direct molecular approach combining single-strand conformation polymorphism (SSCP) fingerprinting and sequencing of 16S rRNA genes. The dominant clones, among 125 16S rRNA genes isolated from milk, belonged to members of the Firmicutes (58% of the total clones) affiliated mainly with the orders Clostridiales and the Lactobacillales, followed by the phyla Proteobacteria (21.6%), Actinobacteria (16.8%), and Bacteroidetes (4%). Sequencing the 16S rRNA genes of 126 milk isolates collected from four culture media revealed the presence of 36 different species showing a wider diversity in the Gammaproteobacteria phylum and Staphylococcus genus than that found among clones. In cheese, a total of 21 species were obtained from 170 isolates, with dominant species belonging to the Lactobacillales and subdominant species affiliated with the Actinobacteria, Bacteroidetes (Chryseobacterium sp.), or Gammaproteobacteria (Stenotrophomonas sp.). Fingerprinting DNA isolated from milk by SSCP analysis yielded complex patterns, whereas analyzing DNA isolated from cheese resulted in patterns composed of a single peak which corresponded to that of lactic acid bacteria. SSCP fingerprinting of mixtures of all colonies harvested from plate count agar supplemented with crystal violet and vancomycin showed good potential for monitoring the subdominant Proteobacteria and Bacteroidetes (Flavobacteria) organisms in milk and cheese. Likewise, analyzing culturable subcommunities from cheese-ripening bacterial medium permitted assessment of the diversity of halotolerant Actinobacteria and Staphylococcus organisms. Direct and culture-dependent approaches produced complementary information, thus generating a more accurate view of milk and cheese microbial ecology. PMID:17259356

  19. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature.

    PubMed

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N; Golyshina, Olga V; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I; Golyshin, Peter N; Yakimov, Michail M; Daffonchio, Daniele; Ferrer, Manuel

    2015-01-01

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills. PMID:26119183

  20. Looking Beyond Respiratory Cultures: Microbiome-Cytokine Signatures of Bacterial Pneumonia and Tracheobronchitis in Lung Transplant Recipients.

    PubMed

    Shankar, J; Nguyen, M H; Crespo, M M; Kwak, E J; Lucas, S K; McHugh, K J; Mounaud, S; Alcorn, J F; Pilewski, J M; Shigemura, N; Kolls, J K; Nierman, W C; Clancy, C J

    2016-06-01

    Bacterial pneumonia and tracheobronchitis are diagnosed frequently following lung transplantation. The diseases share clinical signs of inflammation and are often difficult to differentiate based on culture results. Microbiome and host immune-response signatures that distinguish between pneumonia and tracheobronchitis are undefined. Using a retrospective study design, we selected 49 bronchoalveolar lavage fluid samples from 16 lung transplant recipients associated with pneumonia (n = 8), tracheobronchitis (n = 12) or colonization without respiratory infection (n = 29). We ensured an even distribution of Pseudomonas aeruginosa or Staphylococcus aureus culture-positive samples across the groups. Bayesian regression analysis identified non-culture-based signatures comprising 16S ribosomal RNA microbiome profiles, cytokine levels and clinical variables that characterized the three diagnoses. Relative to samples associated with colonization, those from pneumonia had significantly lower microbial diversity, decreased levels of several bacterial genera and prominent multifunctional cytokine responses. In contrast, tracheobronchitis was characterized by high microbial diversity and multifunctional cytokine responses that differed from those of pneumonia-colonization comparisons. The dissimilar microbiomes and cytokine responses underlying bacterial pneumonia and tracheobronchitis following lung transplantation suggest that the diseases result from different pathogenic processes. Microbiomes and cytokine responses had complementary features, suggesting that they are closely interconnected in the pathogenesis of both diseases. PMID:26693965

  1. A screening algorithm for diagnosing bacterial gastroenteritis by real-time PCR in combination with guided culture.

    PubMed

    Van Lint, P; De Witte, E; Ursi, J P; Van Herendael, B; Van Schaeren, J

    2016-06-01

    We have introduced a real-time PCR for the simultaneous detection of Campylobacter jejuni, Salmonella spp., Shigella spp./enteroinvasive Escherichia coli and Yersinia enterocolitica in fecal samples in our routine laboratory. This new approach showed consistent results, with minimal inter-sample variation. When compared to conventional culture, the hands-on time decreased by 13 h/wk, and the median turnaround time drastically shortened from 73 to 29 h (P < .0001). Moreover, the detection rate of the targeted pathogens seemed to increase: the positivity rate registered over a twelve month period increased from 4.98% when using bacterial culture, compared to 8.56% when using real-time PCR (P < .0001). For antimicrobial susceptibility testing, samples that are found to be PCR positive are additionally cultured after the PCR result is known. Using this algorithm, we got a positive culture for 71.0% of the PCR positive samples. The samples missed by guided culture had significantly higher quantification cycle (Cq) values compared to the samples picked up by guided culture (P = .0003). Finally; we also tested the effect of extended sample storage on the performance of guided culture. Storage time prior to inoculation did have an effect on the positivity rate of culture; interestingly, these effects were clearly species-dependent. PMID:27107537

  2. Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

    PubMed Central

    McKenzie, Valerie J; Bowers, Robert M; Fierer, Noah; Knight, Rob; Lauber, Christian L

    2012-01-01

    Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens. PMID:21955991

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

    PubMed Central

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

    2015-01-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts. PMID:25750710

  4. Studies on mixed populations of human intestinal bacteria grown in single-stage and multistage continuous culture systems.

    PubMed Central

    Allison, C; McFarlan, C; MacFarlane, G T

    1989-01-01

    Mixed intestinal bacteria were grown for 336 h in two identical single-stage chemostats at low growth rates in a carbohydrate-limited medium. Complex bacterial populations were maintained and anaerobes always outnumbered aerobes. The predominant organisms belonged to the genera Bacteroides, Bifidobacterium, Lactobacillus, Clostridium, Eubacterium, Propionbacterium, Peptococcus, and Peptostreptococcus. Bacteroides species predominated in both fermentors, particularly B. ovatus and B. thetaiotaomicron. A high degree of reproducibility of bacteriological and fermentation product data was obtained in these experiments. When gut contents were inoculated into a five-stage continuous culture system (retention time of 79 or 38 h) containing soya bran, the medium flow rate had little quantitative effect on the formation of acidic fermentation products; however, more oxidized fermentation acids were produced at the higher retention time. Diverse bacterial populations were maintained in every vessel at each flow rate. Bacteroides fragilis group organisms, especially B. ovatus, were numerically the most important. The viability of bacteria decreased through the system, especially at a retention time of 79 h, when the bacteria were growing under severely nutrient-limited conditions. PMID:2930171

  5. Influence of zinc on bacterial populations and their proteolytic enzyme activities in freshwater environments: a cross-site comparison.

    PubMed

    Rasmussen, Lauren; Olapade, Ola A

    2016-04-01

    Temporal responses of indigenous bacterial populations and proteolytic enzyme (i.e., aminopeptidase) activities in the bacterioplankton assemblages from 3 separate freshwater environments were examined after exposure to various zinc (Zn) concentrations under controlled microcosm conditions. Zn concentrations (ranging from 0 to 10 μmol/L) were added to water samples collected from the Kalamazoo River, Rice Creek, and Huron River and examined for bacterial abundance and aminopeptidase activities at various time intervals over a 48 h incubation period in the dark. The results showed that the Zn concentrations did not significantly influence total bacterial counts directly; however, aminopeptidase activities varied significantly to increasing zinc treatments over time. Also, analysis of variance and linear regression analyses revealed significant positive relationships between bacterial numbers and their hydrolytic enzyme activities, suggesting that both probably co-vary with increasing Zn concentrations in aquatic systems. The results from this study serve as additional evidence of the ecological role of Zn as an extracellular peptidase cofactor on the dynamics of bacterial assemblages in aquatic environments. PMID:26877164

  6. On the number of independent cultural traits carried by individuals and populations

    PubMed Central

    Lehmann, Laurent; Aoki, Kenichi; Feldman, Marcus W.

    2011-01-01

    In species subject to individual and social learning, each individual is likely to express a certain number of different cultural traits acquired during its lifetime. If the process of trait innovation and transmission reaches a steady state in the population, the number of different cultural traits carried by an individual converges to some stationary distribution. We call this the trait-number distribution. In this paper, we derive the trait-number distributions for both individuals and populations when cultural traits are independent of each other. Our results suggest that as the number of cultural traits becomes large, the trait-number distributions approach Poisson distributions so that their means characterize cultural diversity in the population. We then analyse how the mean trait number varies at both the individual and population levels as a function of various demographic features, such as population size and subdivision, and social learning rules, such as conformism and anti-conformism. Diversity at the individual and population levels, as well as at the level of cultural homogeneity within groups, depends critically on the details of population demography and the individual and social learning rules. PMID:21199846

  7. Effects of Aeration Cycles on Nitrifying Bacterial Populations and Nitrogen Removal in Intermittently Aerated Reactors

    PubMed Central

    Mota, Cesar; Head, Melanie A.; Ridenoure, Jennifer A.; Cheng, Jay J.; de los Reyes, Francis L.

    2005-01-01

    The effects of the lengths of aeration and nonaeration periods on nitrogen removal and the nitrifying bacterial community structure were assessed in intermittently aerated (IA) reactors treating digested swine wastewater. Five IA reactors were operated in parallel with different aeration-to-nonaeration time ratios (ANA). Populations of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were monitored using 16S rRNA slot blot hybridizations. AOB species diversity was assessed using amoA gene denaturant gradient gel electrophoresis. Nitrosomonas and Nitrosococcus mobilis were the dominant AOB and Nitrospira spp. were the dominant NOB in all reactors, although Nitrosospira and Nitrobacter were also detected at lower levels. Reactors operated with the shortest aeration time (30 min) showed the highest Nitrosospira rRNA levels, and reactors operated with the longest anoxic periods (3 and 4 h) showed the lowest levels of Nitrobacter, compared to the other reactors. Nitrosomonas sp. strain Nm107 was detected in all reactors, regardless of the reactor's performance. Close relatives of Nitrosomonas europaea, Nitrosomonas sp. strain ENI-11, and Nitrosospira multiformis were occasionally detected in all reactors. Biomass fractions of AOB and effluent ammonia concentrations were not significantly different among the reactors. NOB were more sensitive than AOB to long nonaeration periods, as nitrite accumulation and lower total NOB rRNA levels were observed for an ANA of 1 h:4 h. The reactor with the longest nonaeration time of 4 h performed partial nitrification, followed by denitrification via nitrite, whereas the other reactors removed nitrogen through traditional nitrification and denitrification via nitrate. Superior ammonia removal efficiencies were not associated with levels of specific AOB species or with higher AOB species diversity. PMID:16332848

  8. Haemophilus influenzae Type b Carriage and Novel Bacterial Population Structure among Children in Urban Kathmandu, Nepal▿

    PubMed Central

    Williams, E. J.; Lewis, J.; John, T.; Hoe, J. C.; Yu, L.; Dongol, S.; Kelly, D. F.; Griffiths, D. T.; Shah, A.; Limbu, B.; Pradhan, R.; Mawas, F.; Shrestha, S.; Thorson, S.; Werno, A. M.; Murdoch, D. R.; Adhikari, N.; Pollard, A. J.

    2011-01-01

    Haemophilus influenzae type b (Hib) is a major cause of invasive bacterial infection in children that can be prevented by a vaccine, but there is still uncertainty about its relative importance in Asia. This study investigated the age-specific prevalence of Hib carriage and its molecular epidemiology in carriage and disease in Nepal. Oropharyngeal swabs were collected from children in Kathmandu, Nepal, from 3 different settings: a hospital outpatient department (OPD), schools, and children's homes. Hib was isolated using Hib antiserum agar plates, and serotyping was performed with latex agglutination. Hib isolates from children with invasive disease were obtained during active microbiological surveillance at Patan Hospital, Kathmandu, Nepal. Genotyping of disease and carriage isolates was undertaken using multilocus sequence typing (MLST). Swabs were taken from 2,195 children, including 1,311 children at an OPD, 647 children attending schools, and 237 children in homes. Overall, Hib was identified in 5.0% (110/2,195; 95% confidence interval [95% CI], 3.9% to 6.4%). MLST was performed on 108 Hib isolates from children carrying Hib isolates and 15 isolates from children with invasive disease. Thirty-one sequence types (STs) were identified, and 20 of these were novel STs. The most common ST isolates were sequence type 6 (ST6) and the novel ST722. There was marked heterogeneity among the STs from children with disease and children carrying Hib. STs identified from invasive infections were those commonly identified in carriage. This study provides evidence of Hib carriage among children in urban Nepal with genetically diverse strains prior to introduction of universal vaccination. The Hib carriage rate in Nepal was similar to the rates observed in other populations with documented high disease rates prior to vaccination, supporting implementation of Hib vaccine in Nepal in 2009. PMID:21270225

  9. Listeria monocytogenes virulence factor Listeriolysin O favors bacterial growth in co-culture with the ciliate Tetrahymena pyriformis, causes protozoan encystment and promotes bacterial survival inside cysts

    PubMed Central

    2010-01-01

    Background The gram-positive pathogenic bacterium Listeria monocytogenes is widely spread in the nature. L. monocytogenes was reported to be isolated from soil, water, sewage and sludge. Listeriolysin O (LLO) is a L. monocytogenes major virulence factor. In the course of infection in mammals, LLO is required for intracellular survival and apoptosis induction in lymphocytes. In this study, we explored the potential of LLO to promote interactions between L. monocytogenes and the ubiquitous inhabitant of natural ecosystems bacteriovorous free-living ciliate Tetrahymena pyriformis. Results Wild type L. monocytogenes reduced T. pyriformis trophozoite counts and stimulated encystment. The effects were observed starting from 48 h of co-incubation. On the day 14, trophozoites were eliminated from the co-culture while about 5 × 104 cells/ml remained in the axenic T. pyriformis culture. The deficient in the LLO-encoding hly gene L. monocytogenes strain failed to cause mortality among protozoa and to trigger protozoan encystment. Replenishment of the hly gene in the mutant strain restored toxicity towards protozoa and induction of protozoan encystment. The saprophytic non-haemolytic species L. innocua transformed with the LLO-expressing plasmid caused extensive mortality and encystment in ciliates. During the first week of co-incubation, LLO-producing L. monocytogenes demonstrated higher growth rates in association with T. pyriformis than the LLO-deficient isogenic strain. At latter stages of co-incubation bacterial counts were similar for both strains. T. pyriformis cysts infected with wild type L. monocytogenes caused listerial infection in guinea pigs upon ocular and oral inoculation. The infection was proved by bacterial plating from the internal organs. Conclusions The L. monocytogenes virulence factor LLO promotes bacterial survival and growth in the presence of bacteriovorous ciliate T. pyriformis. LLO is responsible for L. monocytogenes toxicity for protozoa and

  10. Mass culture strategy for bacterial yeast co-culture for degradation of petroleum hydrocarbons in marine environment.

    PubMed

    Priya, Anchal; Mandal, Ajoy K; Ball, Andrew S; Manefield, Mike; Lal, Banwari; Sarma, Priyangshu M

    2015-11-15

    In the present study a metabolically versatile co-culture with two Bacilli and one yeast strain was developed using enrichment culture techniques. The developed co-culture had affinity to degrade both aliphatic and aromatic fractions of petroleum crude oil. Degradation kinetics was established for designing the fermentation protocol of the co-culture. The developed mass culture strategy led to achieve the reduction in surface tension (26dynescm(-1) from 69 dynescm(-1)) and degradation of 67% in bench scale experiments. The total crude oil degradation of 96% was achieved in 4000l of natural seawater after 28days without adding any nutrients. The survival of the augmented co-culture was maintained (10(9)cellsml(-1)) in contaminated marine environment. The mass culture protocol devised for the bioaugmentation was a key breakthrough that was subsequently used for pilot scale studies with 100l and 4000l of natural seawater for potential application in marine oil spills. PMID:26384865

  11. Bacterial Population Dynamics in a Laboratory Activated Sludge Reactor Monitored by Pyrosequencing of 16S rRNA

    PubMed Central

    Satoh, Hiroyasu; Oshima, Kenshiro; Suda, Wataru; Ranasinghe, Purnika; Li, Ning; Gunawardana, Egodaha Gedara Wasana; Hattori, Masahira; Mino, Takashi

    2013-01-01

    The microbial population in a laboratory activated sludge reactor was monitored for 245 d at 75 time points by pyrosequencing of 16S rRNA. Synthetic wastewater was used as the influent, and the reactor was operated under the same conditions throughout the experiment. The behaviors of different bacterial operational taxonomic units (OTUs) were observed. Multiple OTUs showed periodic propagation and recession. One of the OTUs showed sharp recession, which suggests that cells in the OTU were selectively killed. The behaviors of different phylogenetic lineages of Candidatus ‘Accumulibacter phosphatis’ were also visualized. It was clearly demonstrated that pyrosequencing with barcoded primers is a very effective tool to clarify the dynamics of the bacterial population in activated sludge. PMID:23100021

  12. Clinical Value of Assessing Cytokine Levels for the Differential Diagnosis of Bacterial Meningitis in a Pediatric Population

    PubMed Central

    Ye, Qing; Shao, Wen-Xia; Shang, Shi-Qiang; Shen, Hong-Qiang; Chen, Xue-Jun; Tang, Yong-Min; Yu, Yong-Lin; Mao, Jian-Hua

    2016-01-01

    Abstract We performed a prospective observational study to evaluate the utility of measuring inflammatory cytokine levels to discriminate bacterial meningitis from similar common pediatric diseases. Inflammatory cytokine levels and other cerebrospinal fluid (CSF) physicochemical indicators were evaluated in 140 patients who were diagnosed with bacterial meningitis via microbiological culture or PCR assay. The CSF concentrations of interleukin (IL)-6 and IL-10, CSF/blood IL-6 and IL-10 ratios, CSF white blood cell count, and CSF micro total protein were significantly elevated in bacterial meningitis patients compared with healthy children or patients with viral encephalitis, epilepsy, or febrile convulsions (P < 0.001). The area under the curve values for CSF concentrations of IL-6 and IL-10, CSF/blood IL-6 and IL-10 ratios, CSF white blood cell count, and CSF micro total protein to identify bacterial meningitis episodes by receiver-operating characteristic analysis were 0.988, 0.949, 0.995, 0.924, 0.945, and 0.928, respectively. The area under the curve for the combination of CSF IL-6 and CSF/blood IL-6 ratio was larger than that for either parameter alone, and the combination exhibited enhanced specificity and positive predictive value. After effective meningitis treatment, CSF IL-6 levels dropped significantly. These results suggest that CSF IL-6 and CSF/blood IL-6 ratio are good biomarkers in discriminating bacterial meningitis. Evaluating CSF IL-6 and CSF/blood IL-6 ratio in combination can improve diagnostic efficiency. Additionally, CSF IL-6 levels can be used to monitor the effects of bacterial meningitis treatment. PMID:27043692

  13. Reorganization of the bacterial and archaeal populations associated with organic loading conditions in a thermophilic anaerobic digester.

    PubMed

    Hori, Tomoyuki; Haruta, Shin; Sasaki, Daisuke; Hanajima, Dai; Ueno, Yoshiyuki; Ogata, Atsushi; Ishii, Masaharu; Igarashi, Yasuo

    2015-03-01

    Organic loading conditions are an important factor influencing reactor performances in methanogenic bioreactors. Yet the underlying microbiological basis of the process stability, deterioration, and recovery remains to be understood. Here, structural responses of the bacterial and archaeal populations to the change of organic loading conditions in a thermophilic anaerobic digester were investigated by process analyses and 16S rRNA gene-based molecular approaches. The biogas was produced stably without the accumulation of volatile fatty acids (VFAs) at low organic loading rates (OLRs) in the beginning of reactor operation. Increasing OLR in stages disrupted the stable reactor performance, and high OLR conditions continued the deteriorated performance with slight biogas production and high accumulation of VFAs. Thereafter, the gradual decrease of OLR resulted in the recovery from the deterioration, giving rise to the stable performance again. The stable performances before and after the high OLR conditions conducted were associated with compositionally similar but not identical methanogenic consortia. The bacterial and archaeal populations were synchronously changed at both the transient phases toward the deteriorated performance and in recovery process, during which the dynamic shift of aceticlastic and hydrogenotrophic methanogens including the recently identified Methanomassiliicoccus might contribute to the maintenance of the methanogenic activity. The distinctive bacterial population with a high predominance of Methanobacterium formicicum as archaeal member was found for the deteriorated performance. The results in this study indicate the coordinated reorganization of the bacterial and archaeal populations in response to functional states induced by the change of organic loading conditions in the anaerobic digester. PMID:25293692

  14. Culture-independent bacterial community profiling of carbon dioxide treated raw milk.

    PubMed

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

    2016-09-16

    Due to technical simplicity and strong inhibition against the growth of psychrotrophic bacteria in milk, CO2 treatment has emerged as an attractive processing aid to increase the storage time of raw milk before downstream processing. However, it is yet to be adopted by the industry. In order to further explore the suitability of CO2 treatment for raw milk processing, the bacterial populations of carbonated raw milk collected locally from five different sources in Australia were analysed with next-generation sequencing. Growth inhibition by CO2 was confirmed, with spoilage delayed by at least 7days compared with non-carbonated controls. All non-carbonated controls were spoiled by Gammaproteobacteria, namely Pseudomonas fluorescens group bacteria, Serratia and Erwinia. Two out of the five carbonated samples shared the same spoilage bacteria as their corresponding controls. The rest of the three carbonated samples were spoiled by the lactic acid bacterium (LAB) Leuconostoc. This is consistent with higher tolerance of LAB towards CO2 and selection of LAB in meat products stored in CO2-enriched modified atmosphere packaging. No harmful bacteria were found to be selected by CO2. LAB are generally regarded as safe (GRAS), thus the selection for Leuconostoc by CO2 in some of the samples poses no safety concern. In addition, we have confirmed previous findings that 454 pyrosequencing and Illumina sequencing of 16S rRNA gene amplicons from the same sample yield highly similar results. This supports comparison of results obtained with the two different sequencing platforms, which may be necessary considering the imminent discontinuation of 454 pyrosequencing. PMID:27344229

  15. Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase.

    PubMed

    Prats, Clara; López, Daniel; Giró, Antoni; Ferrer, Jordi; Valls, Joaquim

    2006-08-21

    The lag phase has been widely studied for years in an effort to contribute to the improvement of food safety. Many analytical models have been built and tested by several authors. The use of Individual-based Modelling (IbM) allows us to probe deeper into the behaviour of individual cells; it is a bridge between theories and experiments when needed. INDividual DIScrete SIMulation (INDISIM) has been developed and coded by our group as an IbM simulator and used to study bacterial growth, including the microscopic causes of the lag phase. First of all, the evolution of cellular masses, specifically the mean mass and biomass distribution, is shown to be a determining factor in the beginning of the exponential phase. Secondly, whenever there is a need for an enzyme synthesis, its rate has a direct effect on the lag duration. The variability of the lag phase with different factors is also studied. The known decrease of the lag phase with an increase in the temperature is also observed in the simulations. An initial study of the relationship between individual and collective lag phases is presented, as a complement to the studies already published. One important result is the variability of the individual lag times and generation times. It has also been found that the mean of the individual lags is greater than the population lag. This is the first in a series of studies of the lag phase that we are carrying out. Therefore, the present work addresses a generic system by making a simple set of assumptions. PMID:16524598

  16. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques

    PubMed Central

    Ceuppens, Siele; Delbeke, Stefanie; De Coninck, Dieter; Boussemaere, Jolien; Boon, Nico; Uyttendaele, Mieke

    2015-01-01

    Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth. PMID:26308033

  17. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques.

    PubMed

    Ceuppens, Siele; Delbeke, Stefanie; De Coninck, Dieter; Boussemaere, Jolien; Boon, Nico; Uyttendaele, Mieke

    2015-08-01

    Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth. PMID:26308033

  18. Population dynamics of a Salmonella lytic phage and its host: implications of the host bacterial growth rate in modelling.

    PubMed

    Santos, Sílvio B; Carvalho, Carla; Azeredo, Joana; Ferreira, Eugénio C

    2014-01-01

    The prevalence and impact of bacteriophages in the ecology of bacterial communities coupled with their ability to control pathogens turn essential to understand and predict the dynamics between phage and bacteria populations. To achieve this knowledge it is essential to develop mathematical models able to explain and simulate the population dynamics of phage and bacteria. We have developed an unstructured mathematical model using delay-differential equations to predict the interactions between a broad-host-range Salmonella phage and its pathogenic host. The model takes into consideration the main biological parameters that rule phage-bacteria interactions likewise the adsorption rate, latent period, burst size, bacterial growth rate, and substrate uptake rate, among others. The experimental validation of the model was performed with data from phage-interaction studies in a 5 L bioreactor. The key and innovative aspect of the model was the introduction of variations in the latent period and adsorption rate values that are considered as constants in previous developed models. By modelling the latent period as a normal distribution of values and the adsorption rate as a function of the bacterial growth rate it was possible to accurately predict the behaviour of the phage-bacteria population. The model was shown to predict simulated data with a good agreement with the experimental observations and explains how a lytic phage and its host bacteria are able to coexist. PMID:25051248

  19. Population Dynamics of a Salmonella Lytic Phage and Its Host: Implications of the Host Bacterial Growth Rate in Modelling

    PubMed Central

    Santos, Sílvio B.; Carvalho, Carla; Azeredo, Joana; Ferreira, Eugénio C.

    2014-01-01

    The prevalence and impact of bacteriophages in the ecology of bacterial communities coupled with their ability to control pathogens turn essential to understand and predict the dynamics between phage and bacteria populations. To achieve this knowledge it is essential to develop mathematical models able to explain and simulate the population dynamics of phage and bacteria. We have developed an unstructured mathematical model using delay-differential equations to predict the interactions between a broad-host-range Salmonella phage and its pathogenic host. The model takes into consideration the main biological parameters that rule phage-bacteria interactions likewise the adsorption rate, latent period, burst size, bacterial growth rate, and substrate uptake rate, among others. The experimental validation of the model was performed with data from phage-interaction studies in a 5 L bioreactor. The key and innovative aspect of the model was the introduction of variations in the latent period and adsorption rate values that are considered as constants in previous developed models. By modelling the latent period as a normal distribution of values and the adsorption rate as a function of the bacterial growth rate it was possible to accurately predict the behaviour of the phage-bacteria population. The model was shown to predict simulated data with a good agreement with the experimental observations and explains how a lytic phage and its host bacteria are able to coexist. PMID:25051248

  20. Culturally tailored postsecondary nutrition and health education curricula for indigenous populations

    PubMed Central

    McConnell, Sarah

    2013-01-01

    Background In preparation for the initial offering of the University of Alaska Fairbanks (UAF), Interior–Aleutians Campus Rural Nutrition Services (RNS) program, a literature review was conducted to establish the need for the proposed program and to substantiate the methodology for delivering integrated, culturally tailored postsecondary education and extension to Alaska Natives and rural Alaskans. There was a striking absence of peer-reviewed journal articles describing culturally tailored postsecondary health curricula for indigenous populations. Objective To complete and discuss a current (November 2012) literature review for culturally tailored postsecondary health curricula designed and delivered for indigenous populations. Methods/Design The author conducted an expanded online search that employed multiple configurations of key terms using Google and Google Scholar, as well as pertinent sources. The author located archived reports in person and contacted authors by email. Results The expanded search produced a modest amount of additional literature for review. A disappointing number of publications describing or evaluating culturally tailored postsecondary health curricula in mainstream institutions are available. Related resources on culturally tailored extension and resources for the development and delivery of culturally tailored nutrition and health curricula were identified. Conclusions The present results demonstrate a significant absence of literature on the topic, which may or may not indicate the absence of sufficient culturally tailored postsecondary health curricula for indigenous populations. There are indications that culturally tailored postsecondary health curricula for indigenous populations have the potential to effectively address certain issues of health literacy and health disparities. PMID:23967420

  1. Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India

    PubMed Central

    2010-01-01

    Background Sundarban is the world's largest coastal sediment comprising of mangrove forest which covers about one million hectares in the south-eastern parts of India and southern parts of Bangladesh. The microbial diversity in this sediment is largely unknown till date. In the present study an attempt has been made to understand the microbial diversity in this sediment using a cultivation-independent molecular approach. Results Two 16 S rRNA gene libraries were constructed and partial sequencing of the selected clones was carried out to identify bacterial strains present in the sediment. Phylogenetic analysis of partially sequenced 16 S rRNA gene sequences revealed the diversity of bacterial strains in the Sundarban sediment. At least 8 different bacterial phyla were detected. The major divisions of detected bacterial phyla were Proteobacteria (alpha, beta, gamma, and delta), Flexibacteria (CFB group), Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, Planctomycetes and Gammatimonadates. Conclusion The gammaproteobacteria were found to be the most abundant bacterial group in Sundarban sediment. Many clones showed similarity with previously reported bacterial lineages recovered from various marine sediments. The present study indicates a probable hydrocarbon and oil contamination in this sediment. In the present study, a number of clones were identified that have shown similarity with bacterial clones or isolates responsible for the maintenance of the S-cycle in the saline environment. PMID:20163727

  2. DEGRADATION OF PROPANIL BY BACTERIAL ISOLATES AND MIXED POPULATIONS FROM A PRISTINE LAKE

    EPA Science Inventory

    The microbial transformation rates of propanil, a commonly used herbicide, were investigated using water from a pristine lake in northeast Georgia. Microbial degradation rates were measured using natural water microflora amended with five bacterial species (Aerobacter aerogenes, ...

  3. Bacterial populations on brewery filling hall surfaces as revealed by next-generation sequencing.

    PubMed

    Priha, Outi; Raulio, Mari; Maukonen, Johanna; Vehviläinen, Anna-Kaisa; Storgårds, Erna

    2016-01-01

    Due to the presence of moisture and nutrients, brewery filling line surfaces are susceptible to unwanted microbial attachment. Knowledge of the attaching microbes will aid in designing hygienic control of the process. In this study the bacterial diversity present on brewery filling line surfaces was revealed by next generation sequencing. The two filling lines studied maintained their characteristic bacterial community throughout three sampling times (13-163 days). On the glass bottle line, γ-proteobacteria dominated (35-82% of all OTUs), whereas on the canning line α-, β- and γ-proteobacteria and actinobacteria were most common. The most frequently detected genera were Acinetobacter, Propinobacterium and Pseudomonas. The halophilic genus Halomonas was commonly detected, which might be due to its tolerance to alkaline foam cleaners. This study has revealed a detailed overall picture of the bacterial groups present on filling line surfaces. Further effort should be given to determine the efficacy of washing procedures on different bacterial groups. PMID:27064426

  4. Effects of an enteric anaerobic bacterial culture supernatant and deoxycholate on intestinal calcium absorption and disaccharidase activity.

    PubMed Central

    Walshe, K; Healy, M J; Speekenbrink, A B; Keane, C T; Weir, D G; O'Moore, R R

    1990-01-01

    Fifty two strains of anaerobic bacteria isolated from the upper gut of patients with small intestinal bacterial overgrowth were screened for phospholipase activity. Bacteroides melaninogenicus spp intermedius had the greatest activity. The effects of culture supernatants of this organism and deoxycholate on intestinal calcium absorption and disaccharidase activity were studied using a rat closed loop model. The supernatant decreased the in vitro uptake of calcium by 15% (p less than 0.001). Deoxycholate reduced calcium uptake by 16% (p less than 0.001). Combined culture supernatant and deoxycholate reduced calcium uptake by 39% (p less than 0.001) suggesting a potentiation of supernatant activity by deoxycholate. Culture supernatant and deoxycholate, both alone and combined, significantly reduced lactase, sucrase, and maltase activity. Electron microscopic evidence showed degeneration of microvilli, disruption of mitochondrial structure, and swelling of the endoplasmic reticulum after exposure of the intestinal loops to the supernatant or deoxycholate. Images Figure 2 Figure 3 Figure 4 PMID:1973395

  5. Characterization of Bacterial Communities in Venous Insufficiency Wounds by Use of Conventional Culture and Molecular Diagnostic Methods▿

    PubMed Central

    Tuttle, Marie S.; Mostow, Eliot; Mukherjee, Pranab; Hu, Fen Z.; Melton-Kreft, Rachael; Ehrlich, Garth D.; Dowd, Scot E.; Ghannoum, Mahmoud A.

    2011-01-01

    Microbial infections delay wound healing, but the effect of the composition of the wound microbiome on healing parameters is unknown. To better understand bacterial communities in chronic wounds, we analyzed debridement samples from lower-extremity venous insufficiency ulcers using the following: conventional anaerobic and aerobic bacterial cultures; the Ibis T5000 universal biosensor (Abbott Molecular); and 16S 454 FLX titanium series pyrosequencing (Roche). Wound debridement samples were obtained from 10 patients monitored clinically for at least 6 months, at which point 5 of the 10 sampled wounds had healed. Pyrosequencing data revealed significantly higher bacterial abundance and diversity in wounds that had not healed at 6 months. Additionally, Actinomycetales was increased in wounds that had not healed, and Pseudomonadaceae was increased in wounds that had healed by the 6-month follow-up. Baseline wound surface area, duration, or analysis by Ibis or conventional culture did not reveal significant differences between wounds that healed after 6 months and those that did not. Thus, pyrosequencing identified distinctive baseline characteristics of wounds that did not heal by the 6-month follow-up, furthering our understanding of potentially unique microbiome characteristics of chronic wounds. PMID:21880958

  6. No evidence for a culturable bacterial tetrodotoxin producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae) and Stylochoplana sp. (Platyhelminthes: Polycladida).

    PubMed

    Salvitti, Lauren R; Wood, Susanna A; McNabb, Paul; Cary, Stephen Craig

    2015-02-01

    Tetrodotoxin (TTX) is a potent neurotoxin found in the tissues of many taxonomically diverse organisms. Its origin has been the topic of much debate, with suggestions including endogenous production, acquisition through diet, and symbiotic bacterial synthesis. Bacterial production of TTX has been reported in isolates from marine biota, but at lower than expected concentrations. In this study, 102 strains were isolated from Pleurobranchaea maculata (Opisthobranchia) and Stylochoplana sp. (Platyhelminthes). Tetrodotoxin production was tested utilizing a recently developed sensitive method to detect the C9 base of TTX via liquid chromatography-mass spectrometry. Bacterial strains were characterized by sequencing a region of the 16S ribosomal RNA gene. To account for the possibility that TTX is produced by a consortium of bacteria, a series of experiments using marine broth spiked with various P. maculata tissues were undertaken. Sixteen unique strains from P. maculata and one from Stylochoplana sp. were isolated, representing eight different genera; Pseudomonadales, Actinomycetales, Oceanospirillales, Thiotrichales, Rhodobacterales, Sphingomonadales, Bacillales, and Vibrionales. Molecular fingerprinting of bacterial communities from broth experiments showed little change over the first four days. No C9 base or TTX was detected in isolates or broth experiments (past day 0), suggesting a culturable microbial source of TTX in P. maculata and Stylochoplana sp. is unlikely. PMID:25635464

  7. No Evidence for a Culturable Bacterial Tetrodotoxin Producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae) and Stylochoplana sp. (Platyhelminthes: Polycladida)

    PubMed Central

    Salvitti, Lauren R.; Wood, Susanna A.; McNabb, Paul; Cary, Stephen Craig

    2015-01-01

    Tetrodotoxin (TTX) is a potent neurotoxin found in the tissues of many taxonomically diverse organisms. Its origin has been the topic of much debate, with suggestions including endogenous production, acquisition through diet, and symbiotic bacterial synthesis. Bacterial production of TTX has been reported in isolates from marine biota, but at lower than expected concentrations. In this study, 102 strains were isolated from Pleurobranchaea maculata (Opisthobranchia) and Stylochoplana sp. (Platyhelminthes). Tetrodotoxin production was tested utilizing a recently developed sensitive method to detect the C9 base of TTX via liquid chromatography—mass spectrometry. Bacterial strains were characterized by sequencing a region of the 16S ribosomal RNA gene. To account for the possibility that TTX is produced by a consortium of bacteria, a series of experiments using marine broth spiked with various P. maculata tissues were undertaken. Sixteen unique strains from P. maculata and one from Stylochoplana sp. were isolated, representing eight different genera; Pseudomonadales, Actinomycetales, Oceanospirillales, Thiotrichales, Rhodobacterales, Sphingomonadales, Bacillales, and Vibrionales. Molecular fingerprinting of bacterial communities from broth experiments showed little change over the first four days. No C9 base or TTX was detected in isolates or broth experiments (past day 0), suggesting a culturable microbial source of TTX in P. maculata and Stylochoplana sp. is unlikely. PMID:25635464

  8. Identification of a New Marine Bacterial Strain SD8 and Optimization of Its Culture Conditions for Producing Alkaline Protease

    PubMed Central

    Cui, Hongxia; Yang, Muyang; Wang, Liping; Xian, Cory J.

    2015-01-01

    While much attention has been given to marine microorganisms for production of enzymes, which in general are relatively more stable and active compared to those from plants and animals, studies on alkaline protease production from marine microorganisms have been very limited. In the present study, the alkaline protease producing marine bacterial strain SD8 isolated from sea muds in the Geziwo Qinhuangdao sea area of China was characterized and its optimal culture conditions were investigated. Strain SD8 was initially classified to belong to genus Pseudomonas by morphological, physiological and biochemical characterizations, and then through 16S rDNA sequence it was identified to be likely Pseudomonas hibiscicola. In addition, the culture mediums, carbon sources and culture conditions of strain SD8 were optimized for maximum production of alkaline protease. Optimum enzyme production (236U/mL when cultured bacteria being at 0.75 mg dry weight/mL fermentation broth) was obtained when the isolate at a 3% inoculum size was grown in LB medium at 20 mL medium/100mL Erlenmeyer flask for 48h culture at 30°C with an initial of pH 7.5. This was the first report of strain Pseudomonas hibiscicola secreting alkaline protease, and the data for its optimal cultural conditions for alkaline protease production has laid a foundation for future exploration for the potential use of SD8 strain for alkaline protease production. PMID:26716833

  9. Identification of a New Marine Bacterial Strain SD8 and Optimization of Its Culture Conditions for Producing Alkaline Protease.

    PubMed

    Cui, Hongxia; Yang, Muyang; Wang, Liping; Xian, Cory J

    2015-01-01

    While much attention has been given to marine microorganisms for production of enzymes, which in general are relatively more stable and active compared to those from plants and animals, studies on alkaline protease production from marine microorganisms have been very limited. In the present study, the alkaline protease producing marine bacterial strain SD8 isolated from sea muds in the Geziwo Qinhuangdao sea area of China was characterized and its optimal culture conditions were investigated. Strain SD8 was initially classified to belong to genus Pseudomonas by morphological, physiological and biochemical characterizations, and then through 16S rDNA sequence it was identified to be likely Pseudomonas hibiscicola. In addition, the culture mediums, carbon sources and culture conditions of strain SD8 were optimized for maximum production of alkaline protease. Optimum enzyme production (236U/mL when cultured bacteria being at 0.75 mg dry weight/mL fermentation broth) was obtained when the isolate at a 3% inoculum size was grown in LB medium at 20 mL medium/100mL Erlenmeyer flask for 48h culture at 30°C with an initial of pH 7.5. This was the first report of strain Pseudomonas hibiscicola secreting alkaline protease, and the data for its optimal cultural conditions for alkaline protease production has laid a foundation for future exploration for the potential use of SD8 strain for alkaline protease production. PMID:26716833

  10. Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

    USGS Publications Warehouse

    Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J.P.; Ritter, Daniel J.; McIntosh, Jennifer C.; Clark, Arthur C.; Ruppert, Leslie F.; Cunningham, Alfred B.; Vinson, David S.; Orem, William H.; Fields, Matthew W.

    2016-01-01

    Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulic conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112 to 120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ13C values (−67‰ average), high alkalinity values (22 meq/kg average), relatively positive δ13C-DIC values (4‰ average), and no detectable higher chain hydrocarbons, NO3−, or SO42−. Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situbacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down

  11. Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

    PubMed Central

    2012-01-01

    Background Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-independent approaches performed in the AMD of Carnoulès (France) confirmed this low species richness. However, very little is known about the cultured bacteria in this ecosystem. The aims of the study were firstly to apply novel culture methods in order to access to the largest cultured bacterial diversity, and secondly to better define the robustness of the community for 3 important functions: As(III) oxidation, cellulose degradation and cobalamine biosynthesis. Results Despite the oligotrophic and acidic conditions found in AMDs, the newly designed media covered a large range of nutrient concentrations and a pH range from 3.5 to 9.8, in order to target also non-acidophilic bacteria. These approaches generated 49 isolates representing 19 genera belonging to 4 different phyla. Importantly, overall diversity gained 16 extra genera never detected in Carnoulès. Among the 19 genera, 3 were previously uncultured, one of them being novel in databases. This strategy increased the overall diversity in the Carnoulès sediment by 70% when compared with previous culture-independent approaches, as specific phylogenetic groups (e.g. the subclass Actinobacteridae or the order Rhizobiales) were only detected by culture. Cobalamin auxotrophy, cellulose degradation and As(III)-oxidation are 3 crucial functions in this ecosystem, and a previous meta- and proteo-genomic work attributed each function to only one taxon. Here, we demonstrate that other members of this community can also assume these functions, thus increasing the overall community robustness. Conclusions This work highlights that bacterial diversity in AMDs is much higher than previously envisaged, thus pointing out that the AMD system is functionally more robust than expected. The isolated bacteria

  12. Drastic changes in aquatic bacterial populations from the Cuatro Cienegas Basin (Mexico) in response to long-term environmental stress.

    PubMed

    Pajares, Silvia; Eguiarte, Luis E; Bonilla-Rosso, German; Souza, Valeria

    2013-12-01

    Understanding the changes of aquatic microbial community composition in response to changes in temperature and ultraviolet irradiation is relevant for predicting biogeochemical modifications in the functioning of natural microbial communities under global climate change scenarios. Herein we investigate shifts in the bacterioplankton composition in response to long-term changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with composite aquatic microbial communities from natural pools within the Cuatro Cienegas Basin (Mexican Chihuahuan desert) and were subject to different temperatures and UV conditions. 16S rRNA gene clone libraries were obtained from water samples at the mid-point (4 months) and the end of the experiment (8 months). An increase in bacterial diversity over time was found in the treatment of constant temperature and UV protection, which suggests that stable environments promote the establishment of complex and diverse bacterial community. Drastic changes in the phylogenetic bacterioplankton composition and structure were observed in response to fluctuating temperature and increasing UV radiation and temperature. Fluctuating temperature induced the largest decrease of bacterial richness during the experiment, indicating that frequent temperature changes drive the reduction in abundance of several species, most notably autotrophs. The long-term impact of these environmental stresses reduced diversity and selected for generalist aquatic bacterial populations, such as Porphyrobacter. These changes at the community level occur at an ecological time scale, suggesting that under global warming scenarios cascade effects on the food web are possible if the microbial diversity is modified. PMID:24072549

  13. Molecular Ecological Analysis of Fecal Bacterial Populations from Term Infants Fed Formula Supplemented with Selected Blends of Prebiotics▿

    PubMed Central

    Nakamura, Noriko; Gaskins, H. Rex; Collier, Chad T.; Nava, Gerardo M.; Rai, Deshanie; Petschow, Bryon; Russell, W. Michael; Harris, Cheryl; Mackie, Roderick I.; Wampler, Jennifer L.; Walker, D. Carey

    2009-01-01

    Supplementation of infant formulas with prebiotic ingredients continues the effort to mimic functional properties of human milk. In this double-blind, controlled, 28-day study, healthy term infants received control formula (control group; n = 25) or control formula supplemented with polydextrose (PDX) and galactooligosaccharide (GOS) (4 g/liter) (PG4 group; n = 27) or with PDX, GOS, and lactulose (LOS) (either 4 g/liter [PGL4 group; n = 27] or 8 g/liter [PGL8 group; n = 25]). A parallel breast-fed group (BF group) (n = 30) was included. Stool characteristics, formula tolerance, and adverse events were monitored. Fecal bacterial subpopulations were evaluated by culture-based selective enumeration (Enterobacteriaceae), quantitative real-time PCR (Clostridium clusters I, XI, and XIV, Lactobacillus, and Bifidobacterium), and fluorescence in situ hybridization (FISH) (Bifidobacterium). Fecal bacterial community profiles were examined by using 16S rRNA gene PCR-denaturing gradient gel electrophoresis. The daily stool consistency was significantly softer or looser in the BF group than in all of the groups that received formula. The formulas were well tolerated, and the incidences of adverse events did not differ among feeding groups. Few significant changes in bacterial subpopulations were observed at any time point. The bacterial communities were stable; individual profiles tended to cluster by subject rather than by group. Post hoc analysis, however, demonstrated that the bacterial community profiles for subjects in the BF, PG4, PGL4, and PGL8 groups that first received formula at a younger age were less stable than the profiles for subjects in the same groups that received formula at an older age, but there was no difference for the control group. These data indicate that formulas containing PDX, GOS, and LOS blends are more likely to influence gut microbes when administration is begun in early infancy and justify further investigation of the age-related effects of

  14. [Nonadhesive populations in cultures of mesenchymal stromal cells from hematopoietic organs in mouse and rat].

    PubMed

    Byeverova, E I; Bragina, E V; Molchanova, E A

    2008-01-01

    The study of adhesive properties of multipotent mesenchymal stromal cells evaluated from fibroblast colony-forming units in the bone marrow of adult mice and rats in populations of cells attached and unattached to plastic substrate after 2 h to 7 days in culture demonstrated both similarities and differences. The increase in the fibroblast colony-forming units in the adhesive population peaked on day 7 of in vitro culture in both cases; however, nearly no fibroblast colony-forming units were observed in the nonadhesive population from the mouse bone marrow in this period. Conversely, the number of colonies from the rat bone marrow nonadhesive population on day 7 of culture considerably increased, and this nonadhesive population in long-term culture became the source for subsequent nonadhesive subpopulations containing fibroblast colony-forming units. After 7 days of in vitro culture, the suspension of cells isolated from the liver of 17-day-old rat fetuses also contained a fraction of unattached fibroblast colony-forming units. In the nonadhesive subpopulations from the bone marrow and fetal liver, fibroblast colony-forming units were observed up to day 48 and 30, respectively. Stromal cell precursors of nonadhesive subpopulations from the rat bone marrow featured a period of colony formation reduced to 7 days (i.e., they were formed 1.5-2 times faster compared to the primary culture). The total number of fibroblast colony-forming units from all nonadhesive subpopulations was roughly 6 and 7.4 times that of the adhesive population of the primary culture from the bone marrow and fetal liver, respectively. Considering that the mammalian bone marrow remains the preferred source of mesenchymal stromal cells, using nonadhesive subpopulations in the presented culture system can considerably increase the yield of stromal precursor cells. PMID:19137707

  15. Enrichment and Molecular Characterization of a Bacterial Culture That Degrades Methoxy-Methyl Urea Herbicides and Their Aniline Derivatives

    PubMed Central

    El-Fantroussi, Said

    2000-01-01

    Soil treated with linuron for more than 10 years showed high biodegradation activity towards methoxy-methyl urea herbicides. Untreated control soil samples taken from the same location did not express any linuron degradation activity, even after 40 days of incubation. Hence, the occurrence in the field of a microbiota having the capacity to degrade a specific herbicide was related to the long-term treatment of the soil. The enrichment culture isolated from treated soil showed specific degradation activity towards methoxy-methyl urea herbicides, such as linuron and metobromuron, while dimethyl urea herbicides, such as diuron, chlorotoluron, and isoproturon, were not transformed. The putative metabolic intermediates of linuron and metobromuron, the aniline derivatives 3,4-dichloroaniline and 4-bromoaniline, were also degraded. The temperature of incubation drastically affected degradation of the aniline derivatives. Whereas linuron was transformed at 28 and 37°C, 3,4-dichloroaniline was transformed only at 28°C. Monitoring the enrichment process by reverse transcription-PCR and denaturing gradient gel electrophoresis (DGGE) showed that a mixture of bacterial species under adequate physiological conditions was required to completely transform linuron. This research indicates that for biodegradation of linuron, several years of adaptation have led to selection of a bacterial consortium capable of completely transforming linuron. Moreover, several of the putative species appear to be difficult to culture since they were detectable by DGGE but were not culturable on agar plates. PMID:11097876

  16. Biogenic selenium and tellurium nanoparticles synthesized by environmental microbial isolates efficaciously inhibit bacterial planktonic cultures and biofilms

    PubMed Central

    Zonaro, Emanuele; Lampis, Silvia; Turner, Raymond J.; Qazi, S. Junaid S.; Vallini, Giovanni

    2015-01-01

    The present study deals with Se0- and Te0-based nanoparticles bio-synthesized by two selenite- and tellurite-reducing bacterial strains, namely Stenotrophomonas maltophilia SeITE02 and Ochrobactrum sp. MPV1, isolated from polluted sites. We evidenced that, by regulating culture conditions and exposure time to the selenite and tellurite oxyanions, differently sized zero-valent Se and Te nanoparticles were produced. The results revealed that these Se0 and Te0 nanoparticles possess antimicrobial and biofilm eradication activity against Escherichia coli JM109, Pseudomonas aeruginosa PAO1, and Staphylococcus aureus ATCC 25923. In particular, Se0 nanoparticles exhibited antimicrobial activity at quite low concentrations, below that of selenite. Toxic effects of both Se0 and Te0 nanoparticles can be related to the production of reactive oxygen species upon exposure of the bacterial cultures. Evidence so far achieved suggests that the antimicrobial activity seems to be strictly linked to the dimensions of the nanoparticles: indeed, the highest activity was shown by nanoparticles of smaller sizes. In particular, it is worth noting how the bacteria tested in biofilm mode responded to the treatment by Se0 and Te0 nanoparticles with a susceptibility similar to that observed in planktonic cultures. This suggests a possible exploitation of both Se0 and Te0 nanoparticles as efficacious antimicrobial agents with a remarkable biofilm eradication capacity. PMID:26136728

  17. Weight-Loss Interventions for Hispanic Populations: The Role of Culture

    PubMed Central

    Lindberg, Nangel M.; Stevens, Victor J.; Halperin, Ruben O.

    2013-01-01

    In the United States, ethnic minorities are overrepresented among the overweight and obese population, with Hispanic individuals being among the groups most at risk for obesity and obesity-related disease and disability. Most weight-loss interventions designed for the general population have been less successful with individuals from ethnic minorities and there is a pressing need to develop more effective interventions for these groups. This paper examines the importance of culture in the development of “culturally competent” weight-loss interventions for ethnic minority populations, and discusses specific culturally mediated factors that should be considered in the design and implementation of treatment interventions. While specifically focusing on Hispanic populations, we also address issues of relevance to other multiethnic societies. PMID:23533725

  18. A Duplex PCR-Based Assay for Measuring the Amount of Bacterial Contamination in a Nucleic Acid Extract from a Culture of Free-Living Protists

    PubMed Central

    Marron, Alan O.; Akam, Michael; Walker, Giselle

    2013-01-01

    Background Cultures of heterotrophic protists often require co-culturing with bacteria to act as a source of nutrition. Such cultures will contain varying levels of intrinsic bacterial contamination that can interfere with molecular research and cause problems with the collection of sufficient material for sequencing. Measuring the levels of bacterial contamination for the purposes of molecular biology research is non-trivial, and can be complicated by the presence of a diverse bacterial flora, or by differences in the relative nucleic acid yield per bacterial or eukaryotic cell. Principal Findings Here we describe a duplex PCR-based assay that can be used to measure the levels of contamination from marine bacteria in a culture of loricate choanoflagellates. By comparison to a standard culture of known target sequence content, the assay can be used to quantify the relative proportions of bacterial and choanoflagellate material in DNA or RNA samples extracted from a culture. We apply the assay to compare methods of purifying choanoflagellate cultures prior to DNA extraction, to determine their effectiveness in reducing bacterial contamination. Together with measurements of the total nucleic acid concentration, the assay can then be used as the basis for determining the absolute amounts of choanoflagellate DNA or RNA present in a sample. Conclusions The assay protocol we describe here is a simple and relatively inexpensive method of measuring contamination levels in nucleic acid samples. This provides a new way to establish quantification and purification protocols for molecular biology and genomics in novel heterotrophic protist species. Guidelines are provided to develop a similar protocol for use with any protistan culture. This assay method is recommended where qPCR equipment is unavailable, where qPCR is not viable because of the nature of the bacterial contamination or starting material, or where prior sequence information is insufficient to develop q

  19. Population heterogeneity and dynamics in starter culture and lag phase adaptation of the spoilage yeast Zygosaccharomyces bailii to weak acid preservatives

    PubMed Central

    Stratford, Malcolm; Steels, Hazel; Nebe-von-Caron, Gerhard; Avery, Simon V.; Novodvorska, Michaela; Archer, David B.

    2014-01-01

    The food spoilage yeast Zygosaccharomyces bailii shows great resistance to weak-acid preservatives, including sorbic acid (2, 4-hexadienoic acid). That extreme resistance was shown to be due to population heterogeneity, with a small sub-population of cells resistant to a variety of weak acids, probably caused by a lower internal pH reducing the uptake of all weak acids. In the present paper, it was found that resistant cells were extremely rare in exponential cultures, but increased by up to 8000-fold in stationary phase. Inoculation of media containing sorbic acid with a population of Z. bailii cells gave rise to what appeared to be a prolonged lag phase, suggesting adaptation to the conditions before the cells entered the period of exponential growth. However, the apparent lag phase caused by sorbic acid was largely due to the time required for the resistant sub-population to grow to detectable levels. The slow growth rate of the sub-population was identical to that of the final total population. The non-resistant bulk population remained viable for 3 days but had lost viability by 6 days and, during that time, there was no indication of any development of resistance in the bulk population. The sub-population growing in sorbic acid showed very high population diversity in colony size and internal pH. After removal of sorbic acid, the population rapidly reverted back to the normal, largely non-resistant, population distribution. The data presented suggest that a reevaluation of the lag phase in microbial batch culture is required, at least for the resistance of Z. bailii to sorbic acid. Furthermore, the significance of phenotypic diversity and heterogeneity in microbial populations is discussed more broadly with potential relevance to bacterial “persisters”, natural selection and evolution. PMID:24813627

  20. In Vitro Study of the Effect of Cationic Biocides on Bacterial Population Dynamics and Susceptibility▿

    PubMed Central

    Moore, Louise E.; Ledder, Ruth G.; Gilbert, Peter; McBain, Andrew J.

    2008-01-01

    Cationic biocides (CBs) are widely used in domestic and public hygiene and to control biofouling and microbial contamination in industry. The increased use of biocides has led to concern regarding possible reductions in biocide effectiveness. Domestic drain microcosms were stabilized for 5 months and then exposed to polyhexamethylene biguanide (PHMB) at 0.1, 0.2, and 0.4g liter−1 over 6 months and characterized throughout by differential culture, together with eubacterial-specific PCR-denaturing gradient gel electrophoresis. Additionally, MICs and minimal bactericidal concentrations (MBCs) for bacteria previously isolated from a domestic drain (n = 18) and the human skin (n = 13) were determined before, during, and after escalating, sublethal exposure (14 passages) to two quaternary ammonium compounds (QAC1 and QAC2), the bisbiguanide chlorhexidine (CHX), and PHMB. Exposure of the drain microcosm to PHMB did not decrease the total viable count although significant (P < 0.01) decreases in recovery were observed for the gram-positive cocci with associated clonal expansion of pseudomonads (from ca. 0.1% of the population to ca. 10%). This clonal expansion was also manifested as elevations in bacteria that could grow in the presence of PHMB, CHX, and QAC1. Decreases in susceptibility (greater than twofold) occurred for 10/31 of the test bacteria for QAC1, 14/31 for QAC2, 10/31 for CHX, and 7/31 for PHMB. Exposure of microcosms to PHMB targeted gram-positive species and caused the clonal expansion of pseudomonads. In terms of prolonged-sublethal passage on CBs, exposure to all the biocides tested resulted in susceptibility decreases for a proportion of test bacteria, but refractory clones were not generated. PMID:18515475

  1. A comparison of culture-dependent and culture-independent techniques used to characterize bacterial communities on healthy and white plague-diseased corals of the Montastraea annularis species complex

    NASA Astrophysics Data System (ADS)

    Cook, G. M.; Rothenberger, J. P.; Sikaroodi, M.; Gillevet, P. M.; Peters, E. C.; Jonas, R. B.

    2013-06-01

    Diseases of hermatypic corals pose a global threat to coral reefs, and investigations of bacterial communities associated with healthy corals and those exhibiting signs of disease are necessary for proper diagnosis. One disease, commonly called white plague (WP), is characterized by acute tissue loss. This investigation compared the bacterial communities associated with healthy coral tissue ( N = 15), apparently healthy tissue on WP-diseased colonies ( N = 15), and WP-diseased tissues ( N = 15) from Montastraea annularis (species complex) colonies inhabiting a Bahamian reef. Aliquots of sediment ( N = 15) and water ( N = 15) were also obtained from the proximity of each coral colony sampled. Samples for culture-dependent analyses were inoculated onto one-half strength Marine Agar (½ MA) and Thiosulfate Citrate Bile Salts Sucrose Agar to quantify the culturable communities. Length heterogeneity PCR (LH-PCR) of the 16S rRNA gene characterized the bacterial operational taxonomic units (OTU) associated with lesions on corals exhibiting signs of a white plague-like disease as well as apparently healthy tissue from diseased and non-diseased conspecifics. Analysis of Similarity was conducted on the LH-PCR fingerprints, which indicated no significant difference in the composition of bacterial communities associated with apparently healthy and diseased corals. Comparisons of the 16S rRNA gene amplicons from cultured bacterial colonies (½ MA; N = 21) with all amplicons obtained from the whole coral-associated bacterial community indicated ≥39 % of coral-associated bacterial taxa could be cultured. Amplicons from these bacterial cultures matched amplicons from the whole coral-associated bacterial community that, when combined, accounted for >70 % total bacterial abundance. An OTU with the same amplicon length as Aurantimonas coralicida (313.1 bp), the reported etiological agent of WPII, was detected in relatively low abundance (<0.1 %) on all tissue types. These findings

  2. Culturable Aerobic and Facultative Anaerobic Intestinal Bacterial Flora of Black Cobra (Naja naja karachiensis) in Southern Pakistan

    PubMed Central

    Iqbal, Junaid; Sagheer, Mehwish; Tabassum, Nazneen; Siddiqui, Ruqaiyyah; Khan, Naveed Ahmed

    2014-01-01

    Using morphological analysis and biochemical testing, here for the first time, we determined the culturable gut bacterial flora (aerobes and facultative anaerobes) in the venomous Black Cobra (Naja naja karachiensis) from South Asia. The findings revealed that these snakes inhabit potentially pathogenic bacteria including Serratia marcescens, Pseudomonas aeruginosa, Shewanella putrefaciens, Aeromonas hydrophila, Salmonella sp., Moraxella sp., Bacillus sp., Ochrobactrum anthropi, and Providencia rettgeri. These findings are of concern, as injury from snake bite can result in wound infections and tissue necrosis leading to sepsis/necrotizing fasciitis and/or expose consumers of snake meat/medicine in the community to infections. PMID:25002979

  3. Culturable Aerobic and Facultative Anaerobic Intestinal Bacterial Flora of Black Cobra (Naja naja karachiensis) in Southern Pakistan.

    PubMed

    Iqbal, Junaid; Sagheer, Mehwish; Tabassum, Nazneen; Siddiqui, Ruqaiyyah; Khan, Naveed Ahmed

    2014-01-01

    Using morphological analysis and biochemical testing, here for the first time, we determined the culturable gut bacterial flora (aerobes and facultative anaerobes) in the venomous Black Cobra (Naja naja karachiensis) from South Asia. The findings revealed that these snakes inhabit potentially pathogenic bacteria including Serratia marcescens, Pseudomonas aeruginosa, Shewanella putrefaciens, Aeromonas hydrophila, Salmonella sp., Moraxella sp., Bacillus sp., Ochrobactrum anthropi, and Providencia rettgeri. These findings are of concern, as injury from snake bite can result in wound infections and tissue necrosis leading to sepsis/necrotizing fasciitis and/or expose consumers of snake meat/medicine in the community to infections. PMID:25002979

  4. Culturable bacterial flora associated with the dinoflagellate green Noctiluca miliaris during active and declining bloom phases in the Northern Arabian Sea.

    PubMed

    Basu, Subhajit; Deobagkar, Deepti D; Matondkar, S G Prabhu; Furtado, Irene

    2013-05-01

    A massive algal bloom of the dinoflagellate Noctiluca miliaris (green) was located in the Northern Arabian Sea by IRS-P4-2 (OCM-II) for microbiological studies, during two consecutive cruises of February-March 2009. Culturable bacterial load during bloom were ≈ 2-3-fold higher in comparison to non-bloom waters and ranged from 3.20 × 10(5) to 6.84 × 10(5) cfu ml(-1). An analysis of the dominant heterotrophs associated with Noctiluca bloom resulted in phylogenetic and a detailed metabolic characterization of 70 bacterial isolates from an overlapping active and declining bloom phase location near north-central Arabian Sea. The active phase flora was dominated by Gram-positive forms (70.59 %), a majority of which belonged to Bacillus (35.29 %) of Firmicutes. As the bloom declined, Gram-negative forms (61.11 %) emerged dominant, and these belonged to a diverse γ-proteobacterial population consisting of Shewanella (16.67 %) and equal fractions of a Cobetia-Pseudomonas-Psychrobacter-Halomonas population (36.11 %). A Unifrac-based principal coordinate analysis of partial 16S rDNA sequences showed significant differences among the active and declining phase flora and also with reported endocytic flora of Noctiluca (red). A nonparametric multidimensional scaling (NMDS) of antibiogram helped differentiation among closely related strains. The organic matter synthesized by N. miliaris appears to be quickly utilized and remineralized as seen from the high efficiency of isolates to metabolize various complex and simple C/N substrates such as carbohydrates, proteins/amino acids, lipids, sulfide production from organic matter, and solubilize phosphates. The ability of a large fraction of these strains (50-41.67 %) to further aerobically denitrify indicates their potential for nitrogen removal from these high-organic microniches of the Noctiluca bloom in the Arabian Sea, also known for high denitrification activity. The results indicate that culturable euphotic bacterial

  5. Biodegradation potential of pure and mixed bacterial cultures for removal of 4-nitroaniline from textile dye wastewater.

    PubMed

    Khalid, Azeem; Arshad, Muhammad; Crowley, David E

    2009-03-01

    Environmentally toxic aromatic amines including nitroanilines are commonly generated in dye contaminated wastewater in which azo dyes undergo degradation under anaerobic conditions. The aim of this study was to develop a process for biological treatment of 4-nitroaniline. Three bacteria identified as Acinetobacter sp., Citrobacter freundii and Klebsiella oxytoca were isolated from enrichment cultures of activated sludge on 4-nitroaniline, after which the isolates and the mixed culture were studied to determine optimal conditions for biodegradation. HPLC analyses showed the mixed culture was capable of complete removal of 100micromol/L of 4-nitroaniline within 72h under aerobic conditions. There was an inverse linear relationship (R(2)=0.96) between the rate of degradation (V) and 4-nitraoaniline concentrations [S] over 100-1000micromol/L. The bacterial culture was also capable of decolorizing structurally different azo dyes (Acid Red-88, Reactive Black-5, Direct Red-81, and Disperse Orange-3) and also degraded nitrobenzene. Our findings show that enrichment cultures from activated sludge can be effective for the removal of dyes and their toxic intermediates, and that treatment may best be accomplished using an anaerobic-aerobic process. PMID:19114284

  6. Decolourisation of Acid Orange 7 recalcitrant auto-oxidation coloured by-products using an acclimatised mixed bacterial culture.

    PubMed

    Bay, Hui Han; Lim, Chi Kim; Kee, Thuan Chien; Ware, Ismail; Chan, Giek Far; Shahir, Shafinaz; Ibrahim, Zaharah

    2014-03-01

    This study focuses on the biodegradation of recalcitrant, coloured compounds resulting from auto-oxidation of Acid Orange 7 (AO7) in a sequential facultative anaerobic-aerobic treatment system. A novel mixed bacterial culture, BAC-ZS, consisting of Brevibacillus panacihumi strain ZB1, Lysinibacillus fusiformis strain ZB2, and Enterococcus faecalis strain ZL bacteria were isolated from environmental samples. The acclimatisation of the mixed culture was carried out in an AO7 decolourised solution. The acclimatised mixed culture showed 98 % decolourisation within 2 h of facultative anaerobic treatment using yeast extract and glucose as co-substrate. Subsequent aerobic post treatment caused auto-oxidation reaction forming dark coloured compounds that reduced the percentage decolourisation to 73 %. Interestingly, further agitations of the mixed culture in the solution over a period of 48 h significantly decolourise the coloured compounds and increased the decolourisation percentage to 90 %. Analyses of the degradation compounds using UV-visible spectrophotometer, Fourier transform infrared spectroscopy (FTIR) and high performance liquid chromatography (HPLC) showed complete degradation of recalcitrant AO7 by the novel BAC-ZS. Phytotoxicity tests using Cucumis sativus confirmed the dye solution after post aerobic treatment were less toxic compared to the parent dye. The quantitative real-time PCR revealed that E. faecalis strain ZL was the dominant strain in the acclimatised mix culture. PMID:24293297

  7. Efficacy of a commercial probiotic relative to oxytetracycline as Gram-negative bacterial control agents in a rotifer (Brachionus plicatilis) batch culture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two trials were conducted to evaluate two gram-negative bacterial control strategies in batch cultures of the rotifer Brachionus plicatilis. In the first trial, rotifers at an initial density of 47/mL were cultured for 5 d and dosed with a 10-mg/L solution of either oxytetracycline or a commercial p...

  8. Coevolution of adaptive technology, maladaptive culture and population size in a producer–scrounger game

    PubMed Central

    Lehmann, Laurent; Feldman, Marcus W.

    2009-01-01

    Technology (i.e. tools, methods of cultivation and domestication, systems of construction and appropriation, machines) has increased the vital rates of humans, and is one of the defining features of the transition from Malthusian ecological stagnation to a potentially perpetual rising population growth. Maladaptations, on the other hand, encompass behaviours, customs and practices that decrease the vital rates of individuals. Technology and maladaptations are part of the total stock of culture carried by the individuals in a population. Here, we develop a quantitative model for the coevolution of cumulative adaptive technology and maladaptive culture in a ‘producer–scrounger’ game, which can also usefully be interpreted as an ‘individual–social’ learner interaction. Producers (individual learners) are assumed to invent new adaptations and maladaptations by trial-and-error learning, insight or deduction, and they pay the cost of innovation. Scroungers (social learners) are assumed to copy or imitate (cultural transmission) both the adaptations and maladaptations generated by producers. We show that the coevolutionary dynamics of producers and scroungers in the presence of cultural transmission can have a variety of effects on population carrying capacity. From stable polymorphism, where scroungers bring an advantage to the population (increase in carrying capacity), to periodic cycling, where scroungers decrease carrying capacity, we find that selection-driven cultural innovation and transmission may send a population on the path of indefinite growth or to extinction. PMID:19692409

  9. Coevolution of adaptive technology, maladaptive culture and population size in a producer-scrounger game.

    PubMed

    Lehmann, Laurent; Feldman, Marcus W

    2009-11-01

    Technology (i.e. tools, methods of cultivation and domestication, systems of construction and appropriation, machines) has increased the vital rates of humans, and is one of the defining features of the transition from Malthusian ecological stagnation to a potentially perpetual rising population growth. Maladaptations, on the other hand, encompass behaviours, customs and practices that decrease the vital rates of individuals. Technology and maladaptations are part of the total stock of culture carried by the individuals in a population. Here, we develop a quantitative model for the coevolution of cumulative adaptive technology and maladaptive culture in a 'producer-scrounger' game, which can also usefully be interpreted as an 'individual-social' learner interaction. Producers (individual learners) are assumed to invent new adaptations and maladaptations by trial-and-error learning, insight or deduction, and they pay the cost of innovation. Scroungers (social learners) are assumed to copy or imitate (cultural transmission) both the adaptations and maladaptations generated by producers. We show that the coevolutionary dynamics of producers and scroungers in the presence of cultural transmission can have a variety of effects on population carrying capacity. From stable polymorphism, where scroungers bring an advantage to the population (increase in carrying capacity), to periodic cycling, where scroungers decrease carrying capacity, we find that selection-driven cultural innovation and transmission may send a population on the path of indefinite growth or to extinction. PMID:19692409

  10. Batch culture enrichment of ANAMMOX populations from anaerobic and aerobic seed cultures.

    PubMed

    Suneethi, S; Joseph, Kurian

    2011-01-01

    Discharge of nitrate and ammonia rich wastewaters into the natural waters encourage eutrophication, and contribute to aquatic toxicity. Anaerobic ammonium oxidation process (ANAMMOX) is a novel biological nitrogen removal alternative to nitrification-denitrification, that removes ammonia using nitrite as the electron acceptor. The feasibility of enriching the ANAMMOX bacteria from the anaerobic digester sludge of a biomethanation plant treating vegetable waste and aerobic sludge from an activated sludge process treating domestic sewage is reported in this paper. ANAMMOX bacterial activity was monitored and established in terms of nitrogen transformations to ammonia, nitrite and nitrate along with formation of hydrazine and hydroxylamine. PMID:20729077

  11. Identification of Bacterial Populations in Drinking Water Using 16S rRNA-Based Sequence Analyses

    EPA Science Inventory

    Intracellular RNA is rapidly degraded in stressed cells and is more unstable outside of the cell than DNA. As a result, RNA-based methods have been suggested to study the active microbial fraction in environmental matrices. The aim of this study was to identify bacterial populati...

  12. Characterization of the Bacterial Community Associated with Larvae and Adults of Anoplophora chinensis Collected in Italy by Culture and Culture-Independent Methods

    PubMed Central

    Rizzi, Aurora; Crotti, Elena; Lupi, Daniela; Daffonchio, Daniele

    2013-01-01

    The wood-boring beetle Anoplophora chinensis Forster, native to China, has recently spread to North America and Europe causing serious damage to ornamental and forest trees. The gut microbial community associated with these xylophagous beetles is of interest for potential biotechnological applications in lignocellulose degradation and development of pest-control measures. In this study the gut bacterial community of larvae and adults of A. chinensis, collected from different host trees in North Italy, was investigated by both culture and culture-independent methods. Larvae and adults harboured a moderately diverse bacterial community, dominated by Proteobacteria, Actinobacteria, and Firmicutes. The gammaproteobacterial family Enterobacteriaceae (genera Gibbsiella, Enterobacter, Raoultella, and Klebsiella) was the best represented. The abundance of such bacteria in the insect gut is likely due to the various metabolic abilities of Enterobacteriaceae, including fermentation of carbohydrates derived from lignocellulose degradation and contribution to nitrogen intake by nitrogen-fixing activity. In addition, bacteria previously shown to have some lignocellulose-degrading activity were detected at a relatively low level in the gut. These bacteria possibly act synergistically with endogenous and fungal enzymes in lignocellulose breakdown. The detection of actinobacterial symbionts could be explained by a possible role in the detoxification of secondary plant metabolites and/or protection against pathogens. PMID:24069601

  13. Effect of dietary probiotic, prebiotic and synbiotic supplementation on performance, immune responses, intestinal morphology and bacterial populations in broilers.

    PubMed

    Salehimanesh, A; Mohammadi, M; Roostaei-Ali Mehr, M

    2016-08-01

    This study was conducted to investigate the effects of probiotic (Primalac), prebiotic (TechnoMos) and synbiotic (Primalac + TechnoMos) supplementation on performance, immune responses, intestinal morphology and bacterial populations of ileum in broilers. A total of 240 one-day-old broiler chicks were randomly divided into four treatment groups which included 60 birds. Control group did not receive any treatment. The chicks in the second, third and fourth groups were fed probiotic (0.9 g/kg), prebiotic (0.9 g/kg) and probiotic (0.9 g/kg) plus probiotic (0.9 g/kg; synbiotic), respectively, at entire period. Daily feed intake, daily weight gain and feed conversion ratio were evaluated. The birds were immunized by sheep red blood cell (SRBC) on days 12 and 29 of age and serum antibody titres were measured on days 28, 35 and 42. Newcastle vaccines administered on days 9, 18 and 27 to chicks and blood samples were collected on day 42. Intestinal morphometric assessment and enumeration of intestinal bacterial populations were performed on day 42. The results indicated that consumption of probiotic, prebiotic and synbiotic had no significant effect on daily feed intake, daily body weight gain, feed conversion ratio, carcass traits, intestinal morphology and bacterial populations of ileum (p > 0.05). Consumption of prebiotic increased total and IgM anti-SRBC titres on days 28 and 42 and antibody titre against Newcastle virus disease on day 42 (p < 0.05). Synbiotic increased only total anti-SRBC on day 28 (p < 0.05). It is concluded that consumption of prebiotic increased humoral immunity in broilers. Therefore, supplementation of diet with prebiotic for improvement of humoral immune responses is superior to synbiotic supplementation. PMID:26847817

  14. Bacterial concentration and diversity within repetitive aliquots collected from replicate continuous flow bioreactor cultures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: The aims of this study were to determine if: 1) aqueous and biofilm components within replicate, stabilized bioreactor communities initiated with chicken cecal material differed in diversity; 2) changes in bacterial diversity or diminished protective capabilities resulted from frozen glycerol ...

  15. The role of silicon in enhancing resistance to bacterial blight of hydroponic- and soil-cultured rice

    PubMed Central

    Song, Alin; Xue, Gaofeng; Cui, Peiyuan; Fan, Fenliang; Liu, Hongfang; Yin, Chang; Sun, Wanchun; Liang, Yongchao

    2016-01-01

    Here we report for the first time that bacterial blight of rice can be alleviated by silicon (Si) added. In both inoculated and uninoculated plants, shoot dry weight was significantly higher in the +Si plants than in the −Si plants. A soil-cultured trial showed that disease severity was 24.3% lower in the Si-amended plants than in the non-Si-amended plants. Plants that were switched from −Si to +Si nutrient solution and simultaneously inoculated with Xoo also exhibited the same high resistance to bacterial blight as the plants that were treated continuously with Si, with control efficiencies of 52.8 and 62.9%, respectively. Moreover, total concentrations of soluble phenolics and lignin in rice leaves were significantly higher in the +Si plants than in the −Si plants. Polyphenoloxidase (PPO) and phenylalanine ammonia-lyase (PAL) activities in rice leaves were observed to be higher in the +Si plants than in the −Si plants. The expression levels of Os03g0109600, Prla, Rcht2 and Lox2osPil, were also higher in +Si plants than in −Si plants post-inoculation during the experimental time. Addition of Si resulted in increased Pal transcription, and inhibited CatA and Os03g0126000 expression in the earlier and later stages of bacterial inoculation, respectively. PMID:27091552

  16. Suggested guidelines for using systemic antimicrobials in bacterial skin infections (1): diagnosis based on clinical presentation, cytology and culture.

    PubMed

    Beco, L; Guaguère, E; Lorente Méndez, C; Noli, C; Nuttall, T; Vroom, M

    2013-01-19

    Systemic antimicrobials are critically important in veterinary healthcare and resistance is a major concern. Antimicrobial stewardship will be important in maintaining clinical efficacy by reducing the development and spread of antimicrobial resistance. Bacterial skin infections are one of the most common reasons for using systemic antimicrobials in dogs and cats.Appropriate management of these infections is therefore crucial in any policy for responsible antimicrobial use. The goals of therapy are to confirm that an infection is present, identify the causative bacteria, select the most appropriate antimicrobial, ensure that the infection is treated correctly, and to identify and manage any underlying conditions. This is the first of two articles that will provide evidence-led guidelines to help practitioners address these issues. This article covers diagnosis, including descriptions of the different clinical presentations of surface, superficial and deep bacterial skin infections, how to perform and interpret cytology, and how to best use bacterial culture and sensitivity testing. The second article, to be published in a subsequent issue of Veterinary Record, will discuss therapy,including choice of drug and treatment regimens. PMID:23292951

  17. The role of silicon in enhancing resistance to bacterial blight of hydroponic- and soil-cultured rice.

    PubMed

    Song, Alin; Xue, Gaofeng; Cui, Peiyuan; Fan, Fenliang; Liu, Hongfang; Yin, Chang; Sun, Wanchun; Liang, Yongchao

    2016-01-01

    Here we report for the first time that bacterial blight of rice can be alleviated by silicon (Si) added. In both inoculated and uninoculated plants, shoot dry weight was significantly higher in the +Si plants than in the -Si plants. A soil-cultured trial showed that disease severity was 24.3% lower in the Si-amended plants than in the non-Si-amended plants. Plants that were switched from -Si to +Si nutrient solution and simultaneously inoculated with Xoo also exhibited the same high resistance to bacterial blight as the plants that were treated continuously with Si, with control efficiencies of 52.8 and 62.9%, respectively. Moreover, total concentrations of soluble phenolics and lignin in rice leaves were significantly higher in the +Si plants than in the -Si plants. Polyphenoloxidase (PPO) and phenylalanine ammonia-lyase (PAL) activities in rice leaves were observed to be higher in the +Si plants than in the -Si plants. The expression levels of Os03g0109600, Prla, Rcht2 and Lox2osPil, were also higher in +Si plants than in -Si plants post-inoculation during the experimental time. Addition of Si resulted in increased Pal transcription, and inhibited CatA and Os03g0126000 expression in the earlier and later stages of bacterial inoculation, respectively. PMID:27091552

  18. The effect of wheat prebiotics on the gut bacterial population and iron status of iron deficient broiler chickens

    PubMed Central

    2014-01-01

    Background Currently, there is a lot of interest in improving gut health, and consequently increasing Fe absorption, by managing the colonic microbial population. This is traditionally done by the consumption of probiotics, live microbial food supplements. However, an alternative, and often very effective approach, is the consumption of food ingredients known as prebiotics. Fructans and arabinoxylans are naturally occurring non-digestible oligosaccharides in wheat that exhibit prebiotic properties and may enhance intestinal iron (Fe) absorption. The aim of this study was to assess the effect of prebiotics from wheat on Fe bioavailability in vitro (Caco-2 cells) and in vivo (broiler chickens, Gallus gallus). Methods In the current study, the effect of intra-amniotic administration of wheat samples extracts at 17 d of embryonic incubation on the Fe status and possible changes in the bacterial population in intestinal content of broiler hatchlings were investigated. A group of 144 eggs were injected with the specified solution (1 ml per egg) into the amniotic fluid. Immediately after hatch (21 d) and from each treatment group, 10 chicks were euthanized and their small intestine, liver and cecum were removed for relative mRNA abundance of intestinal Fe related transporters, relative liver ferritin amounts and bacterial analysis of cecal content, respectively. Results The in vivo results are in agreement with the in vitro observations, showing no differences in the hatchling Fe status between the treatment groups, as Fe bioavailability was not increased in vitro and no significant differences were measured in the intestinal expression of DMT1, Ferroportin and DcytB in vivo. However, there was significant variation in relative amounts of bifidobacteria and lactobacilli in the intestinal content between the treatments groups, with generally more bifidobacteria being produced with increased prebiotic content. Conclusions In this study we showed that prebiotics naturally

  19. 16S rRNA gene sequencing is a non-culture method of defining the specific bacterial etiology of ventilator-associated pneumonia

    PubMed Central

    Xia, Li-Ping; Bian, Long-Yan; Xu, Min; Liu, Ying; Tang, Ai-Ling; Ye, Wen-Qin

    2015-01-01

    Ventilator-associated pneumonia (VAP) is an acquired respiratory tract infection following tracheal intubation. The most common hospital-acquired infection among patients with acute respiratory failure, VAP is associated with a mortality rate of 20-30%. The standard bacterial culture method for identifying the etiology of VAP is not specific, timely, or accurate in identifying the bacterial pathogens. This study used 16S rRNA gene metagenomic sequencing to identify and quantify the pathogenic bacteria in lower respiratory tract and oropharyngeal samples of 55 VAP patients. Sequencing of the 16S rRNA gene has served as a valuable tool in bacterial identification, particularly when other biochemical, molecular, or phenotypic identification techniques fail. In this study, 16S rRNA gene sequencing was performed in parallel with the standard bacterial culture method to identify and quantify bacteria present in the collected patient samples. Sequence analysis showed the colonization of multidrug-resistant strains in VAP secretions. Further, this method identified Prevotella, Proteus, Aquabacter, and Sphingomonas bacterial genera that were not detected by the standard bacterial culture method. Seven categories of bacteria, Streptococcus, Neisseria, Corynebacterium, Acinetobacter, Staphylococcus, Pseudomonas and Klebsiella, were detectable by both 16S rRNA gene sequencing and standard bacterial culture methods. Further, 16S rRNA gene sequencing had a significantly higher sensitivity in detecting Streptococcus and Pseudomonas when compared to standard bacterial culture. Together, these data present 16S rRNA gene sequencing as a novel VAP diagnosis tool that will further enable pathogen-specific treatment of VAP. PMID:26770469

  20. Population dynamics of Tisbe holothuriae (Copepoda; Harpacticoida) in exploited mass cultures

    NASA Astrophysics Data System (ADS)

    Gaudy, R.; Guerin, J. P.

    Three cultures of Tisbe holothuriae in 101 tanks were harvested each 7 or 10 to 12 days at a rate of 50%. The most frequently harvested culture showed the highest yield. At lower exploitation rates a higher rate of sea water renewal resulted in a higher production. In the cultures, variations in sex ratio, ovigerous rate, and number of eggs per sac contributed to a stabilization of the egg production. More frequent harvesting favoured the ovigerous rate and a higher renewal rate of the medium resulted in more eggs per sac. The growth rate of the population was estimated from calculated values for birth rate and death rate, and this estimate was compared with the observed growth rate. The quality of the sea water medium in mass cultures was investigated and discussed in its effects on population dynamics.

  1. Existence of both culturable and viable but non culturable (VNC) E. coli populations with distinct settling velocities in karst aquifer

    NASA Astrophysics Data System (ADS)

    Petit, F.; Ratajczak, M.; Massei, N.; Lafite, R.; Clermont, O.; Denamur, E.; Berthe, T.

    2012-12-01

    The karst aquifers are particularly vulnerable to contamination by faecal pathogens mainly during rainfall event. In groundwater, the fate of E. coli is dependent on their ability to overcome environmental stresses and on their association with particles. Moreover, some strains can survive leading to the emergence of a sub-population of E. coli which failed to grow on laboratory media, while they were still alive thus designated as viable but non culturable (VNC). The aim of this study was to investigate (i) the structure of culturable E. coli population based on the survival ability, the distribution in four main phylo-groups (A, B1, B2, D) and the phenotypic characteristics; and, (ii) the fate of culturable and VNC E. coli, according to their settling velocities. This work was carried out on a karstic workshop-site for which the microbial quality of water was impaired related to livestock density and septic tanks overflows. Particles characterisation was performed by estimation of their settling velocities combined with electronic microscopy observation, and solid phase cytometry (ChemScan®RDI) was carried out to quantify the viable E. coli, and thus VNC E. coli. In the karst, different populations of E. coli were coexisting related to their survival, their culturability, and their association to particles. At the sinkhole, during a rainfall event with pasture, E. coli rapidly losing their culturability after 2 days have been more frequently isolated. These isolates are mainly multiresistant to antibiotics and harbor several virulence factors. In the same time, a population of VNC E. coli (79%), associated to the "non settleable particles" (settling velocities ranging between 10-5 to 10-2 mm.s-1), mainly corresponding to colloids and organic or organo-mineral microflocs was injected in the karst system, probably corresponding to the runoff of attached-bacteria originating from cowpats. Once in the karst, the relative contribution of culturable and VNC E. coli

  2. Population Size and Cultural Evolution in Nonindustrial Food-Producing Societies

    PubMed Central

    Collard, Mark; Ruttle, April; Buchanan, Briggs; O’Brien, Michael J.

    2013-01-01

    Modeling work suggests that population size affects cultural evolution such that larger populations can be expected to have richer and more complex cultural repertoires than smaller populations. Empirical tests of this hypothesis, however, have yielded conflicting results. Here, we report a study in which we investigated whether the subsistence toolkits of small-scale food-producers are influenced by population size in the manner the hypothesis predicts. We applied simple linear and standard multiple regression analysis to data from 40 nonindustrial farming and pastoralist groups to test the hypothesis. Results were consistent with predictions of the hypothesis: both the richness and the complexity of the toolkits of the food-producers were positively and significantly influenced by population size in the simple linear regression analyses. The multiple regression analyses demonstrated that these relationships are independent of the effects of risk of resource failure, which is the other main factor that has been found to influence toolkit richness and complexity in nonindustrial groups. Thus, our study strongly suggests that population size influences cultural evolution in nonindustrial food-producing populations. PMID:24069153

  3. Speciation of vanadium in oilsand coke and bacterial culture by high performance liquid chromatography inductively coupled plasma mass spectrometry.

    PubMed

    Li, X Sherry; Glasauer, Susan; Le, X Chris

    2007-10-17

    A simple and sensitive method for the speciation of vanadium(III), (IV), and (V) was developed by using high performance liquid chromatography and inductively coupled plasma mass spectrometry (HPLC-ICPMS). The EDTA-complexed vanadium species were separated on a strong anion exchange column with an eluent containing 2 mM EDTA, 3% acetonitrile, and 80 mM ammonium bicarbonate at pH 6. Each analysis was complete in 5 min. The detection limits were 0.6, 0.7 and 1.0 microg L(-1) for V(III), V(IV), and V(V), respectively. The method was applied to coke pore water samples from an oilsand processing/upgrading site in Fort McMurray, Alberta, Canada and to Shewanella putrefaciens CN32 bacterial cultures incubated with V(V). In the coke pore water samples, V(IV) and V(V) were found to be the major species. For the first time, V(III) was detected in the bacterial cultures incubated with V(V). PMID:17936102

  4. Aerococcus christensenii native aortic valve subacute bacterial endocarditis (SBE) presenting as culture negative endocarditis (CNE) mimicking marantic endocarditis.

    PubMed

    Jose, Anita; Cunha, Burke A; Klein, Natalie C; Schoch, Paul E

    2014-01-01

    This is a case report of an adult who presented with apparent culture negative endocarditis (CNE) thought to be marantic endocarditis due to a B-cell lymphoproliferative disorder. This was a most perplexing case and was eventually diagnosed as subacute bacterial endocarditis (SBE) due to a rare slow growing organism. Against the diagnosis of SBE was the lack of fever, hepatomegaly, peripheral manifestations and microscopic hematuria. Also, against a diagnosis of SBE was another explanation for the patient's abnormal findings, e.g., elevated ferritin levels, elevated α1/α2 globulins on SPEP, an elevated alkaline phosphatase, flow cytometry showing B-lymphocytes expressing CD5, and a bone lesion in the right iliac. Findings compatible with both SBE and marantic endocarditis due to a B-cell lymphoproliferative disorder included an elevated ESR, and splenomegaly. Blood cultures eventually became positive during hospitalization. We report a case of native aortic valve (AV) subacute bacterial endocarditis (SBE) due to Aerococcus christensenii mimicking marantic endocarditis due to a B-cell lymphoproliferative disorder. To the best of our knowledge, this is the first reported case of native AV SBE due to A. christensenii presenting as marantic endocarditis. PMID:24341951

  5. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

    PubMed Central

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V.; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A.; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N.; Golyshina, Olga V.; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R.; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I.; Golyshin, Peter N.; Yakimov, Michail M.; Daffonchio, Daniele; Ferrer, Manuel

    2015-01-01

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills. PMID:26119183

  6. Blood culture confirmed bacterial sepsis in neonates in a North Indian tertiary care center: changes over the last decade.

    PubMed

    Sundaram, Venkataseshan; Kumar, Praveen; Dutta, Sourabh; Mukhopadhyay, Kanya; Ray, Pallab; Gautam, Vikas; Narang, Anil

    2009-01-01

    The spectrum of organisms causing sepsis is different in developing countries. Data on the recent trends of organisms causing sepsis are limited. This study was conducted in a tertiary care neonatal unit in Northern India. All inborn babies with blood-culture-positive sepsis from 1995 to 2006 were divided into two epochs, viz. 1995 to 1998 (epoch I) and 2001 to 2006 (epoch II). Organisms were grouped into early (<72 h) and late onset (> or =72 h) sepsis groups. The overall incidence of sepsis, the incidence of sepsis stratified by weight groups, the organism profile on different days of life, sepsis-related mortality and pathogen-specific case fatality rate were calculated and compared between the two epochs. Out of 34,362 live births during the study period, organisms were isolated in 1,491 neonates. Out of these, 89% had bacterial sepsis. The incidence of neonatal bacterial sepsis increased from epoch I to epoch II (35.8/1,000 versus 40.1/1,000 live births, P<0.05). The incidence of early onset sepsis (EOS) did not change between the epochs, but the incidence of late onset sepsis (LOS) increased from 12 to 16.5 per 1,000 live births (P<0.001). The incidence of bacterial sepsis decreased significantly in the 1,000- to 1,999-g birth weight groups. Klebsiella pneumoniae and Enterobacter aerogenes decreased, whereas Staphylococcus aureus increased in incidence during epoch II. Non-fermenting Gram-negative bacilli emerged as a newly identified pathogen during epoch II. Sepsis-associated mortality decreased from 42 to 20%. The incidence of bacterial sepsis has decreased significantly in 1,000- to 1,999-g infants, with a significant reduction in sepsis-related mortality. New organisms have emerged in recent years. The organism profile in recent years has changed, with a significant overlap of organisms causing EOS and LOS. PMID:19168958

  7. Defining the estimated core genome of bacterial populations using a Bayesian decision model.

    PubMed

    van Tonder, Andries J; Mistry, Shilan; Bray, James E; Hill, Dorothea M C; Cody, Alison J; Farmer, Chris L; Klugman, Keith P; von Gottberg, Anne; Bentley, Stephen D; Parkhill, Julian; Jolley, Keith A; Maiden, Martin C J; Brueggemann, Angela B

    2014-08-01

    The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance. PMID:25144616

  8. Direct identification of clinically relevant bacterial and yeast microcolonies and macrocolonies on solid culture media by Raman spectroscopy.

    PubMed

    Espagnon, Isabelle; Ostrovskii, Denis; Mathey, Raphaël; Dupoy, Mathieu; Joly, Pierre L; Novelli-Rousseau, Armelle; Pinston, Frédéric; Gal, Olivier; Mallard, Frédéric; Leroux, Denis F

    2014-02-01

    Decreasing turnaround time is a paramount objective in clinical diagnosis. We evaluated the discrimination power of Raman spectroscopy when analyzing colonies from 80 strains belonging to nine bacterial and one yeast species directly on solid culture medium after 24-h (macrocolonies) and 6-h (microcolonies) incubation. This approach, that minimizes sample preparation and culture time, would allow resuming culture after identification to perform downstream antibiotic susceptibility testing. Correct identification rates measured for macrocolonies and microcolonies reached 94.1% and 91.5%, respectively, in a leave-one-strain-out cross-validation mode without any correction for possible medium interference. Large spectral differences were observed between macrocolonies and microcolonies, that were attributed to true biological differences. Our results, conducted on a very diversified panel of species and strains, were obtained by using simple and robust sample preparation and preprocessing procedures, while still confirming published results obtained by using more complex elaborated protocols. Instrumentation is simplified by the use of 532-nm laser excitation yielding a Raman signal in the visible range. It is, to our knowledge, the first side-by-side full classification study of microorganisms in the exponential and stationary phases confirming the excellent performance of Raman spectroscopy for early species-level identification of microorganisms directly from an agar culture. PMID:24522809

  9. Effects of premilking udder preparation on bacterial population, sediment, and iodine residue in milk.

    PubMed

    Galton, D M; Petersson, L G; Merrill, W G; Bandler, D K; Shuster, D E

    1984-11-01

    Udder preparations that wet both udder surfaces and teats had the highest standard plate count in milk compared with methods that wet teats only. Physical action of cleaning teats with a dry towel lowered bacterial count compared with preparations wetting both udder surfaces and teats. Methods resulting in lowest bacterial counts were the use of water hose, wet towel, or premilking disinfectant teat dip followed by drying with paper towels. Counts of coliform and Staphylococcus sp. followed similar trends. In most comparisons, addition of udder wash sanitizer was of marginal or no benefit. Standard plate count of teat rinses after udder preparation confirmed the benefit of cleaning and drying teats. Physical manipulation of teats during cleaning was essential for lowering sediment in milk. Drying of teats with a paper towel for at least 10 s after dipping with a 1% iodophor disinfectant dip was essential for reducing iodine residue. Both premilking and postmilking disinfectant teat dipping with a 1% iodophor teat dip caused higher iodine residue in milk than premilking disinfectant dip with subsequent drying. A .5% iodophor teat dip contributed less iodine in milk than a 1% iodophor teat dip. Premilking udder preparation affects bacterial count, sediment, and iodine residue in milk. PMID:6520268

  10. The metabolism of neonicotinoid insecticide thiamethoxam by soil enrichment cultures, and the bacterial diversity and plant growth-promoting properties of the cultured isolates.

    PubMed

    Zhou, Guang-Can; Wang, Ying; Ma, Yuan; Zhai, Shan; Zhou, Ling-Yan; Dai, Yi-Jun; Yuan, Sheng

    2014-01-01

    A soil enrichment culture (SEC) rapidly degraded 96% of 200 mg L(-1) neonicotinoid insecticide thiamethoxam (TMX) in MSM broth within 30 d; therefore, its metabolic pathway of TMX, bacterial diversity and plant growth-promoting rhizobacteria (PGPR) activities of the cultured isolates were studied. The SEC transformed TMX via the nitro reduction pathway to form nitrso, urea metabolites and via cleavage of the oxadiazine cycle to form a new metabolite, hydroxyl CLO-tri. In addition, 16S rRNA gene-denaturing gradient gel electrophoresis analysis revealed that uncultured rhizobacteria are predominant in the SEC broth and that 77.8% of the identified bacteria belonged to uncultured bacteria. A total of 31 cultured bacterial strains including six genera (Achromobacter, Agromyces, Ensifer, Mesorhizobium, Microbacterium and Pseudoxanthomonas) were isolated from the SEC broth. The 12 strains of Ensifer adhaerens have the ability to degrade TMX. All six selected bacteria showed PGPR activities. E. adhaerens TMX-23 and Agromyces mediolanus TMX-25 produced indole-3-acetic acid, whereas E. adhaerens TMX-23 and Mesorhizobium alhagi TMX-36 are N2-fixing bacteria. The six-isolated microbes were tolerant to 200 mg L(-1) TMX, and the growth of E. adhaerens was significantly enhanced by TMX, whereas that of Achromobacter sp. TMX-5 and Microbacterium sp.TMX-6 were enhanced slightly. The present study will help to explain the fate of TMX in the environment and its microbial degradation mechanism, as well as to facilitate future investigations of the mechanism through which TMX enhances plant vigor. PMID:24762175

  11. Usefulness of inflammatory biomarkers in discriminating between bacterial and aseptic meningitis in hospitalized children from a population with low vaccination coverage

    PubMed Central

    Wysocki, Jacek; Avonts, Dirk; Januszkiewicz-Lewandowska, Danuta; Michalak, Michal

    2016-01-01

    Introduction Neisseria meningitidis and Streptococcus pneumoniae are the most frequent pathogens responsible for meningitis beyond the neonatal period. Aseptic meningitis is a disabling condition, but bacterial meningitis if left untreated is 100% fatal. The aim of the study was to analyze the usefulness of biochemical and hematological parameters in distinguishing between bacterial and non-bacterial meningitis in children with meningitis from a population with low rates of vaccination against S. pneumoniae and N. meningitidis. Material and methods This study is a retrospective chart review of children hospitalized with meningitis. In patients with aseptic and bacterial meningitis the following parameters were compared: C-reactive protein, D-dimers, fibrinogen, glucose level, and leukocyte level, and in cerebrospinal fluid, protein, glucose, and leukocyte concentrations were analyzed. Number of points in the Bacterial Meningitis Score (BMS) was calculated. The predictive value of each parameter to distinguish between bacterial and aseptic meningitis was evaluated. Results In total, 129 patients were included in the study: 65 diagnosed with bacterial meningitis and 64 with aseptic meningitis. Bacterial and aseptic meningitis were statistically significantly different based on each analyzed parameter (p < 0.000001). Among children with aseptic meningitis 42 (66%) scored 0 points in the BMS, while all the children with bacterial meningitis had at least one point. Conclusions In children with meningitis inflammatory biomarkers differ statistically significantly depending on the etiology – bacterial or aseptic. Serum concentration of C-reactive protein higher than 80 mg/dl is a useful marker of bacterial etiology of meningitis. A high Bacterial Meningitis Score is indicative for bacterial meningitis. PMID:27186188

  12. Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil

    PubMed Central

    Weber, Sabine; Stubner, Stephan; Conrad, Ralf

    2001-01-01

    Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), and Acidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly

  13. Culturable bacterial endophytes isolated from Mangrove tree (Rhizophora apiculata Blume) enhance seedling growth in Rice

    PubMed Central

    Deivanai, Subramanian; Bindusara, Amitraghata Santhanam; Prabhakaran, Guruswamy; Bhore, Subhash Janardhan

    2014-01-01

    Background: Endophytic bacteria do have several potential applications in medicine and in other various sectors of biotechnology including agriculture. Bacterial endophytes need to be explored for their potential applications in agricultural biotechnology. One of the potential applications of bacterial endophytes in agricultural is to enhance the growth of the agricultural crops. Hence, this study was undertaken to explore the plant growth promoting potential application of bacterial endophytes. Objective: The objective of this study was to examine the effect of endophytic bacteria from mangrove tree (Rhizophora apiculata Blume) for their efficacy in promoting seedling growth in rice. Materials and Methods: Eight endophytic bacterial isolates (EBIs) isolated from twig and petiole tissues of the mangrove were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequence homology. Separately, surface sterilized paddy seeds were treated with cell-free broth and cell suspension of the EBIs. Rice seedlings were analyzed by various bioassays and data was recorded. Results: The gene sequences of the isolates were closely related to two genera namely, Bacillus and Pantoea. Inoculation of EBIs from R. apiculata with rice seeds resulted in accelerated root and shoot growth with significant increase in chlorophyll content. Among the isolates, Pantoea ananatis (1MSE1) and Bacillus amyloliquefaciens (3MPE1) had shown predominance of activity. Endophytic invasion was recognized by the non-host by rapid accumulation of reactive oxygen species (ROS) and was counteracted by the production of hydrogen peroxide (H2O2) and lipid peroxide. The results demonstrated that EBIs from mangrove tree can increase the fitness of the rice seedlings under controlled conditions. Conclusion: These research findings could be useful to enhance the seedling growth and could serve as foundation in further research on enhancing the growth of the rice crop using endophytic bacteria. PMID

  14. Culturable bacterial microflora associated with nectarine fruit and their potential for control of brown rot.

    PubMed

    Janisiewicz, Wojciech J; Buyer, Jeffrey S

    2010-06-01

    Microflora of fruit surfaces have been the best source of antagonists against fungi causing postharvest decay of fruit. However, there is little information on microflora colonizing surfaces of fruits other than grape, apple, and citrus. We characterized bacterial microflora on nectarine fruit surfaces from the early stage of development until harvest. Identification of bacterial strains was made using MIDI (fatty acid methyl ester analysis) and Biolog systems. Biolog identified 35% and MIDI 53% of the strains. Thus results from MIDI were used to determine the frequency of occurrence of genera and species. The most frequently occurring genera were Curtobacterium (21.31%), followed by Pseudomonas (19.99%), Microbacterium (13.57%), Clavibacter (9.69%), Pantoea (6.59%), and Enterobacter (4.26%). The frequency of isolations of some bacteria - for example, the major pseudomonads (Pseudomonas syringae, Pseudomonas putida, and Pseudomonas savastanoi) or Pantoea agglomerans - tended to decline as fruit developed. As Pseudomonas declined, Curtobacterium became more dominant. Time of isolation was a significant factor in the frequency of occurrence of different bacteria, indicating succession of the genera. Throughput screening of the bacterial strains against Monilinia fructicola on nectarine fruit resulted in the detection of strains able to control brown rot. The 10 best-performing antagonistic strains were subjected to secondary screening. Four strains reduced decay severity by more than 50% (51.7%-91.4% reduction) at the high pathogen inoculum concentration of 105 conidia/mL. PMID:20657618

  15. Assessment of Bacterial Communities in Thirteen Species of Laboratory-Cultured Domestic Mites (Acari: Acaridida).

    PubMed

    Hubert, Jan; Kopecky, Jan; Sagova-Mareckova, Marketa; Nesvorna, Marta; Zurek, Ludek; Erban, Tomas

    2016-08-01

    House dust mites (HDMs) and stored-product mites (SPMs) of various species inhabit human homes and stored agricultural products. These mites are carriers and hosts of microorganisms that enable their survival. The bacteriome from 13 species of SPMs and HDMs was analyzed and compared by 454 pyrosequencing of partial 16S rRNA gene amplicons. Altogether 128,052 sequences were obtained and assigned to 71 operational taxonomic units (OTUs) at the 97% identity level. The number of sequences in the OTUs between species of mites ranged from 6 to 31 in the individual mite species. We did not find any significant effect of diet or evolutionary origin of mites or their interaction on the composition of the mite bacteriome. In mite species with low bacterial diversity, the bacterial communities were dominated by potential symbiotic or parasitic bacteria, i.e., Cardinium in Dermatophagoides farinae (Hughes, 1961) and Aeroglyphus robustus (Banks 1906) and the enteric bacteria Erwinia in Blomia tropicalis Van Bronswijk, de Cock & Oshima, 1974 and Xenorhabdus in Tyroborus lini (Oudemans, 1924). Among the bacterial species identified, Staphylococcus, Bacillus, Kocuria, Brevibacterium, Corynebacterium, and Brachybacterium likely serve as food sources for the mites. The domestic acaridid mites carried high numbers of various bacteria that are potential threats to human health. These results contribute to the general understanding of the ecology of mite adaptation to human-made habitats. PMID:27122496

  16. Comparison of PCR-DGGE and selective plating methods for monitoring the dynamics of a mixed culture population in synthetic brewery wastewater.

    PubMed

    Tam, Kawai; Yang, Ching-Hong; Matsumoto, Mark R; Crowley, David E; Sheppard, John D

    2005-01-01

    Enrichment of an activated sludge inoculum in synthetic brewery wastewater, which included glucose, maltose, and ethanol, was conducted in batch experiments to identify the dominant microbes present, to determine methodologies capable of monitoring the mixed culture population dynamics, and to determine the consortium's substrate degradation behavior. These results and methodologies were subsequently used in the determination of the population dynamics of suspended and attached microorganisms in a sequencing batch system in the second part of this research work. The three-membered microbial community comprised two bacterial and one fungal species that were identified as Acinetobacter sp., Enterobacter sp., and Candida sp. PCR-DGGE and plating on selective media were used to track the population dynamics of the consortium during the degradation of different substrates in synthetic wastewater containing glucose, maltose, and ethanol. Enterobacter sp. could degrade glucose and maltose but not ethanol, whereas Acinetobacter and Candida could degrade all three carbon sources. In buffered batch mixed culture experiments, Enterobacter was the predominant bacterium until the sugar concentrations decreased to levels that enabled Acinetobacter and Candida to degrade ethanol. PCR-DGGE was effective for detecting the dominant species, but culture-based methods were more accurate for monitoring the population dynamics of these microorganisms during growth in the wastewater medium. PMID:15932247

  17. Correlations between bacterial populations and process parameters in four full-scale anaerobic digesters treating sewage sludge.

    PubMed

    Shin, Seung Gu; Koo, Taewoan; Lee, Joonyeob; Han, Gyuseong; Cho, Kyungjin; Kim, Woong; Hwang, Seokhwan

    2016-08-01

    Process parameters and bacterial populations were investigated in four full-scale anaerobic digesters treating sewage sludge. Although the four digesters were operated under similar conditions, digesters A and B had higher pH (7.2-7.4) and lipid removal efficiencies (>50%) than C and D (pH 6.1-6.4; average lipid removal <16%). Bacterial richness, diversity, and evenness were higher in digesters C and D. Among the top-populated genera, ten (group I) were more abundant in digesters A and/or B; they were putative syntrophic fatty acid or protein/amino acid-utilizers. In contrast, fifteen others (group II) were less abundant in A and/or B and included potentially dormant/dead cells originated from activated sludge. Despite the overall richness trend, the presence of the 25 genera in groups I/II was greater in digesters A and B (24) than in C and D (17); this observation suggests that group I bacteria might be essential in AD of sewage sludge. PMID:27209453

  18. Lactic Acid Bacterial Starter Culture with Antioxidant and γ-Aminobutyric Acid Biosynthetic Activities Isolated from Flatfish-Sikhae Fermentation.

    PubMed

    Won, Yeong Geol; Yu, Hyun-Hee; Chang, Young-Hyo; Hwang, Han-Joon

    2015-12-01

    The aim of this study is to select a lactic acid bacterial strain as a starter culture for flatfish-Sikhae fermentation and to evaluate its suitability for application in a food system. Four strains of lactic acid bacteria isolated from commercial flatfish-Sikhae were identified and selected as starter culture candidates through investigation of growth rates, salt tolerance, food safety, and functional properties such as antioxidative and antimicrobial activities. The fermentation properties of the starter candidates were also examined in food systems prepared with these strains (candidate batch) in comparison with a spontaneous fermentation process without starter culture (control batch) at 15°C. The results showed that the candidate YG331 batch had better fermentation properties such as viable cell count, pH, and acidity than the other experimental batches, including the control batch. The results are expressed according to selection criteria based on a preliminary sensory evaluation and physiochemical investigation. Also, only a small amount of histamine was detected with the candidate YG331 batch. The radical scavenging activity of the candidate batches was better compared with the control batch, and especially candidate YG331 batch showed the best radical scavenging activity. Also, we isolated another starter candidate (identified as Lactobacillus brevis PM03) with γ-aminobutyric acid (GABA)-producing activity from commercial flatfish-Sikhae products. The sensory scores of the candidate YG331 batch were better than those of the other experimental batches in terms of flavor, color, and overall acceptance. In this study, we established selection criteria for the lactic acid bacterial starter for the flatfish-Sikhae production and finally selected candidate YG331 as the most suitable starter. PMID:26348620

  19. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    ERIC Educational Resources Information Center

    Delpech, Roger

    2009-01-01

    This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

  20. Identification of Common Bacterial Pathogens Causing Meningitis in Culture-Negative Cerebrospinal Fluid Samples Using Real-Time Polymerase Chain Reaction

    PubMed Central

    2016-01-01

    Background. Meningitis is a serious communicable disease with high morbidity and mortality rates. It is an endemic disease in Egypt caused mainly by Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. In some settings, bacterial meningitis is documented depending mainly on positive cerebrospinal fluid (CSF) culture results or CSF positive latex agglutination test, missing the important role of prior antimicrobial intake which can yield negative culture and latex agglutination test results. This study aimed to utilize molecular technology in order to diagnose bacterial meningitis in culture-negative CSF samples. Materials and Methods. Forty culture-negative CSF samples from suspected cases of bacterial meningitis were examined by real-time polymerase chain reaction (real-time PCR) for the presence of lytA, bexA, and ctrA genes specific for Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, respectively. Results. Positive real-time PCR results for Streptococcus pneumoniae were detected in 36 (90%) of culture-negative CSF samples while no positive results for Haemophilus influenzae or Neisseria meningitidis were detected. Four (10%) samples were negative by real-time PCR for all tested organisms. Conclusion. The use of molecular techniques as real-time PCR can provide a valuable addition to the proportion of diagnosed cases of bacterial meningitis especially in settings with high rates of culture-negative results. PMID:27563310

  1. Identification of Common Bacterial Pathogens Causing Meningitis in Culture-Negative Cerebrospinal Fluid Samples Using Real-Time Polymerase Chain Reaction.

    PubMed

    Khater, Walaa Shawky; Elabd, Safia Hamed

    2016-01-01

    Background. Meningitis is a serious communicable disease with high morbidity and mortality rates. It is an endemic disease in Egypt caused mainly by Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. In some settings, bacterial meningitis is documented depending mainly on positive cerebrospinal fluid (CSF) culture results or CSF positive latex agglutination test, missing the important role of prior antimicrobial intake which can yield negative culture and latex agglutination test results. This study aimed to utilize molecular technology in order to diagnose bacterial meningitis in culture-negative CSF samples. Materials and Methods. Forty culture-negative CSF samples from suspected cases of bacterial meningitis were examined by real-time polymerase chain reaction (real-time PCR) for the presence of lytA, bexA, and ctrA genes specific for Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, respectively. Results. Positive real-time PCR results for Streptococcus pneumoniae were detected in 36 (90%) of culture-negative CSF samples while no positive results for Haemophilus influenzae or Neisseria meningitidis were detected. Four (10%) samples were negative by real-time PCR for all tested organisms. Conclusion. The use of molecular techniques as real-time PCR can provide a valuable addition to the proportion of diagnosed cases of bacterial meningitis especially in settings with high rates of culture-negative results. PMID:27563310

  2. Frequency of genes in aromatic and aliphatic hydrocarbon biodegradation pathways within bacterial populations from Alaskan sediments.

    PubMed

    Sotsky, J B; Greer, C W; Atlas, R M

    1994-11-01

    A significant proportion of the naturally occurring hydrocarbon-degrading populations within Alaskan sediments affected by the Exxon Valdez oil spill had both the xylE and alkB genes and could convert hexadecane and naphthalene to carbon dioxide; a greater proportion of the population had xylE than had alkB, reflecting the composition of the residual oil at the time of sampling; nearly equal populations with xylE alone, alkB alone, and xylE + alkB genes together were found after exposure to fresh crude oil; populations with xylE lacking alkB increased after enrichment on naphthalene. Thus, the genotypes of hydrocarbon-degrading populations reflected the composition of the hydrocarbons to which they were exposed. PMID:7804909

  3. Composition and Diversity Analysis of the Gut Bacterial Community of the Oriental Armyworm, Mythimna separata, Determined by Culture-Independent and Culture-Dependent Techniques

    PubMed Central

    He, Cai; Nan, Xiaoning; Zhang, Zhengqing; Li, Menglou

    2013-01-01

    The intestinal bacteria community structure and diversity of the Oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae), was studied by analysis of a 16S rDNA clone library, denaturing gradient gel electrophoresis,and culture-dependent techniques. The 16S rDNA clone library revealed a bacterial community diversity comprising Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes and Proteobacteria, among which Escherichia coli (Migula) (Enterobacteriales: Enterobacteriaceae) was the dominant bacteria. The intestinal bacteria isolated by PCR-denaturing gradient gel electrophoresis were classified to Firmicutes, Proteobacteria, and Gracilicutes, and E. coli was again the dominant bacteria. The culture-dependent technique showed that the intestinal bacteria belonged to Firmicutes and Actinobacteria, and Staphylococcus was the dominant bacteria. The intestinal bacteria of M. separata were widely distributed among the groups Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes, Proteobacteria, and Gracilicutes. 16S rDNA clone library, denaturing gradient gel electrophoresis, and culture-dependent techniques should be integrated to obtain precise results in terms of the microbial community and its diversity. PMID:24773514

  4. Bench Test for the Detection of Bacterial Contamination in Platelet Concentrates Using Rapid and Cultural Detection Methods with a Standardized Proficiency Panel

    PubMed Central

    Vollmer, Tanja; Knabbe, Cornelius; Geilenkeuser, Wolf-Jochen; Schmidt, Michael; Dreier, Jens

    2015-01-01

    Summary Background The most frequent infectious complication in transfusion therapy in developed countries is related to the bacterial contamination of platelet concentrates (PCs). Rapid and cultural screening methods for bacterial detection in platelets are available, but external performance evaluation, especially of rapid methods, has been difficult to realize so far. Here we summarize the results of three individual collaborative trials using an external quality assessment program (EQAP) for the application of current rapid and cultural screening methods. Methods Three different modules were available for the detection of bacterial contamination: module 1: rapid methods, module 2: culture methods, module 3: bacterial identification methods. The sample set-up included up to six different bacterial strains, 1-2 negative samples and 4-6 positive samples with stabilized bacterial cell counts (approximately 103/104/105 CFU/ml). Time schedule for testing was limited (module 1: 6 h, module 2 and 3: 7 days). Results Samples of module 1 were analyzed with two different rapid methods (BactiFlow, NAT). The results of the three individual collaborative trials showed that all participants detected the negative samples with both assays correctly. Samples spiked with 104 to 105 CFU/ml of bacteria obtained positive results with both rapid screening methods, whereas samples spiked with only 103 CFU/ml disclosed a lower number of correctly identified positive results by NAT (86.6-93.8% sensitivity) compared to BactiFlow (100% sensitivity). The results for modules 2 and 3 revealed a 100% diagnostic sensitivity and specificity in all three collaborative trials. Conclusion This proficiency panel facilitates the verification of the analytical sensitivity of rapid and cultural bacterial detection systems under controlled routine conditions. The concept of samples provided in this EQAP has three main advantages: i) samples can be examined by both rapid and culture methods, ii) the

  5. Improved statistical analysis of low abundance phenomena in bimodal bacterial populations.

    PubMed

    Reinhard, Friedrich; van der Meer, Jan Roelof

    2013-01-01

    Accurate detection of subpopulation size determinations in bimodal populations remains problematic yet it represents a powerful way by which cellular heterogeneity under different environmental conditions can be compared. So far, most studies have relied on qualitative descriptions of population distribution patterns, on population-independent descriptors, or on arbitrary placement of thresholds distinguishing biological ON from OFF states. We found that all these methods fall short of accurately describing small population sizes in bimodal populations. Here we propose a simple, statistics-based method for the analysis of small subpopulation sizes for use in the free software environment R and test this method on real as well as simulated data. Four so-called population splitting methods were designed with different algorithms that can estimate subpopulation sizes from bimodal populations. All four methods proved more precise than previously used methods when analyzing subpopulation sizes of transfer competent cells arising in populations of the bacterium Pseudomonas knackmussii B13. The methods' resolving powers were further explored by bootstrapping and simulations. Two of the methods were not severely limited by the proportions of subpopulations they could estimate correctly, but the two others only allowed accurate subpopulation quantification when this amounted to less than 25% of the total population. In contrast, only one method was still sufficiently accurate with subpopulations smaller than 1% of the total population. This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R. PMID:24205184

  6. Diversity and Partitioning of Bacterial Populations within the Accessory Nidamental Gland of the Squid Euprymna scolopes

    PubMed Central

    Collins, Andrew J.; LaBarre, Brenna A.; Wong Won, Brian S.; Shah, Monica V.; Heng, Steven; Choudhury, Momena H.; Haydar, Shahela A.; Santiago, Jose

    2012-01-01

    Microbial consortia confer important benefits to animal and plant hosts, and model associations are necessary to examine these types of host/microbe interactions. The accessory nidamental gland (ANG) is a female reproductive organ found among cephalopod mollusks that contains a consortium of bacteria, the exact function of which is unknown. To begin to understand the role of this organ, the bacterial consortium was characterized in the Hawaiian bobtail squid, Euprymna scolopes, a well-studied model organism for symbiosis research. Transmission electron microscopy (TEM) analysis of the ANG revealed dense bacterial assemblages of rod- and coccus-shaped cells segregated by morphology into separate, epithelium-lined tubules. The host epithelium was morphologically heterogeneous, containing ciliated and nonciliated cells with various brush border thicknesses. Hemocytes of the host's innate immune system were also found in close proximity to the bacteria within the tubules. A census of 16S rRNA genes suggested that Rhodobacterales, Rhizobiales, and Verrucomicrobia bacteria were prevalent, with members of the genus Phaeobacter dominating the consortium. Analysis of 454-shotgun sequencing data confirmed the presence of members of these taxa and revealed members of a fourth, Flavobacteria of the Bacteroidetes phylum. 16S rRNA fluorescent in situ hybridization (FISH) revealed that many ANG tubules were dominated by members of specific taxa, namely, Rhodobacterales, Verrucomicrobia, or Cytophaga-Flavobacteria-Bacteroidetes, suggesting symbiont partitioning to specific host tubules. In addition, FISH revealed that bacteria, including Phaeobacter species from the ANG, are likely deposited into the jelly coat of freshly laid eggs. This report establishes the ANG of the invertebrate E. scolopes as a model to examine interactions between a bacterial consortium and its host. PMID:22504817

  7. Cultural Relevance and Working with Inner City Youth Populations to Achieve Civic Engagement

    ERIC Educational Resources Information Center

    Ward, Shakoor; Webster, Nicole

    2011-01-01

    This article helps Extension professionals consider the cultural relevant needs of inner city residents in hopes of achieving ongoing civic engagement and appropriate program activities in these communities. Having a deep understanding of how the various dimensions of marginalized community life among inner city populations affect participation in…

  8. Teaching Population Growth Using Cultures of Vinegar Eels, "Turbatrix aceti" (Nematoda)

    ERIC Educational Resources Information Center

    Wallace, Robert L.

    2005-01-01

    A simple laboratory exercise is presented that follows the population growth of the common vinegar eel, "Turbatrix aceti" (Nematoda), in a microcosm using a simple culture medium. It lends itself to an exercise in a single semester course. (Contains 4 figures.)

  9. Parental Opinion Concerning School Sexuality Education in a Culturally Diverse Population in the USA

    ERIC Educational Resources Information Center

    Heller, Janet R.; Johnson, Helen L.

    2013-01-01

    This study aimed to expand upon previous research related to parental opinion concerning school sexuality education by sampling a culturally diverse, low-income population that has been traditionally under-represented in the literature. A total of 191 parents attending an urban community college completed a written questionnaire about what topics…

  10. Impact of the freeze-drying process on product appearance, residual moisture content, viability, and batch uniformity of freeze-dried bacterial cultures safeguarded at culture collections.

    PubMed

    Peiren, Jindrich; Hellemans, Ann; De Vos, Paul

    2016-07-01

    In this study, causes of collapsed bacterial cultures in glass ampoules observed after freeze-drying were investigated as well as the influence of collapse on residual moisture content (RMC) and viability. Also, the effect of heat radiation and post freeze-drying treatments on the RMC was studied. Cake morphologies of 21 bacterial strains obtained after freeze-drying with one standard protocol could be classified visually into four major types: no collapse, porous, partial collapse, and collapse. The more pronounced the collapse, the higher residual moisture content of the freeze-dried product, ranging from 1.53 % for non-collapsed products to 3.62 % for collapsed products. The most important cause of collapse was the mass of the inserted cotton plug in the ampoule. Default cotton plugs with a mass between 21 and 30 mg inside the ampoule did not affect the viability of freeze-dried Aliivibrio fischeri LMG 4414(T) compared to ampoules without cotton plugs. Cotton plugs with a mass higher than 65 mg inside the ampoule induced a full collapsed product with rubbery look (melt-back) and decreasing viability during storage. Heat radiation effects in the freeze-drying chamber and post freeze-drying treatments such as exposure time to air after freeze-drying and manifold drying time prior to heat sealing of ampoules influenced the RMC of freeze-dried products. To produce uniform batches of freeze-dried bacterial strains with intact cake structures and highest viabilities, inserted cotton plugs should not exceed 21 mg per ampoule. Furthermore, heat radiation effects should be calculated in the design of the primary drying phase and manifold drying time before heat sealing should be determined as a function of exposure time to air. PMID:26875878

  11. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    PubMed

    Harris, Jordan Lee; Balci, Yilmaz

    2015-01-01

    Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship. PMID:25815838

  12. Response of single bacterial cells to stress gives rise to complex history dependence at the population level.

    PubMed

    Mathis, Roland; Ackermann, Martin

    2016-04-12

    Most bacteria live in ever-changing environments where periods of stress are common. One fundamental question is whether individual bacterial cells have an increased tolerance to stress if they recently have been exposed to lower levels of the same stressor. To address this question, we worked with the bacterium Caulobacter crescentus and asked whether exposure to a moderate concentration of sodium chloride would affect survival during later exposure to a higher concentration. We found that the effects measured at the population level depended in a surprising and complex way on the time interval between the two exposure events: The effect of the first exposure on survival of the second exposure was positive for some time intervals but negative for others. We hypothesized that the complex pattern of history dependence at the population level was a consequence of the responses of individual cells to sodium chloride that we observed: (i) exposure to moderate concentrations of sodium chloride caused delays in cell division and led to cell-cycle synchronization, and (ii) whether a bacterium would survive subsequent exposure to higher concentrations was dependent on the cell-cycle state. Using computational modeling, we demonstrated that indeed the combination of these two effects could explain the complex patterns of history dependence observed at the population level. Our insight into how the behavior of single cells scales up to processes at the population level provides a perspective on how organisms operate in dynamic environments with fluctuating stress exposure. PMID:26960998

  13. Response of single bacterial cells to stress gives rise to complex history dependence at the population level

    PubMed Central

    Mathis, Roland; Ackermann, Martin

    2016-01-01

    Most bacteria live in ever-changing environments where periods of stress are common. One fundamental question is whether individual bacterial cells have an increased tolerance to stress if they recently have been exposed to lower levels of the same stressor. To address this question, we worked with the bacterium Caulobacter crescentus and asked whether exposure to a moderate concentration of sodium chloride would affect survival during later exposure to a higher concentration. We found that the effects measured at the population level depended in a surprising and complex way on the time interval between the two exposure events: The effect of the first exposure on survival of the second exposure was positive for some time intervals but negative for others. We hypothesized that the complex pattern of history dependence at the population level was a consequence of the responses of individual cells to sodium chloride that we observed: (i) exposure to moderate concentrations of sodium chloride caused delays in cell division and led to cell-cycle synchronization, and (ii) whether a bacterium would survive subsequent exposure to higher concentrations was dependent on the cell-cycle state. Using computational modeling, we demonstrated that indeed the combination of these two effects could explain the complex patterns of history dependence observed at the population level. Our insight into how the behavior of single cells scales up to processes at the population level provides a perspective on how organisms operate in dynamic environments with fluctuating stress exposure. PMID:26960998

  14. eSalud: designing and implementing culturally competent ehealth research with latino patient populations.

    PubMed

    Victorson, David; Banas, Jennifer; Smith, Jeremiah; Languido, Lauren; Shen, Elaine; Gutierrez, Sandra; Cordero, Evelyn; Flores, Lucia

    2014-12-01

    eHealth is characterized by technology-enabled processes, systems, and applications that expedite accurate, real-time health information, feedback, and skill development to advance patient-centered care. When designed and applied in a culturally competent manner, eHealth tools can be particularly beneficial for traditionally marginalized ethnic minority groups, such as Latinos, a group that has been identified as being at the forefront of emerging technology use in the United States. In this analytic overview, we describe current eHealth research that has been conducted with Latino patient populations. In addition, we highlight cultural and linguistic factors that should be considered during the design and implementation of eHealth interventions with this population. With increasing disparities in preventive care information, behaviors, and services, as well as health care access in general, culturally competent eHealth tools hold great promise to help narrow this gap and empower communities. PMID:25320901

  15. eSalud: Designing and Implementing Culturally Competent eHealth Research With Latino Patient Populations

    PubMed Central

    Banas, Jennifer; Smith, Jeremiah; Languido, Lauren; Shen, Elaine; Gutierrez, Sandra; Cordero, Evelyn; Flores, Lucia

    2014-01-01

    eHealth is characterized by technology-enabled processes, systems, and applications that expedite accurate, real-time health information, feedback, and skill development to advance patient-centered care. When designed and applied in a culturally competent manner, eHealth tools can be particularly beneficial for traditionally marginalized ethnic minority groups, such as Latinos, a group that has been identified as being at the forefront of emerging technology use in the United States. In this analytic overview, we describe current eHealth research that has been conducted with Latino patient populations. In addition, we highlight cultural and linguistic factors that should be considered during the design and implementation of eHealth interventions with this population. With increasing disparities in preventive care information, behaviors, and services, as well as health care access in general, culturally competent eHealth tools hold great promise to help narrow this gap and empower communities. PMID:25320901

  16. Effects of bacterial contamination of media on the diagnosis of Tritrichomonas foetus by culture and real-time PCR.

    PubMed

    Clothier, Kristin A; Villanueva, Michelle; Torain, Andrea; Hult, Cynthia; Wallace, Rachel

    2015-03-15

    The venereal pathogen Tritrichomonas foetus causes early embryonic death and abortion in cattle. With no approved treatment, control involves detection of infected animals and their removal from the herd. Culture is the traditional diagnostic method; standard media are formulated to support protozoal growth while suppressing competing organisms which may prevent microscopic recognition of T. foetus. Real-time PCR increases diagnostic sensitivity and specificity over culture but requires intact T. foetus DNA for detection. The purposes of this study were 1) to evaluate the effects of resident preputial bacteria that are not suppressed by antimicrobials in a commercial culture medium (InPouch™) on T. foetus detection by culture and PCR, and 2) to determine the performance of a laboratory-prepared culture medium on T. foetus detection by culture and PCR in samples with and without this bacterial contamination. A known concentration of one of three different strains of T. foetus inoculated into InPouch™ (IP) or modified Diamonds-Plastridge media (DPM) were co-incubated with a smegma culture media (CONTAM) for 24h and examined microscopically for the presence of identifiable T. foetus. PCR was performed on IP samples to determine if CONTAM also affected T. foetus DNA detection. A PCR protocol was then validated in DPM that performed similarly to the established IP PCR method. IP and DPM with CONTAM were spiked with serial dilutions that mimic field infections of one of four T. foetus strains and evaluated by real-time PCR; cycles to threshold (Ct) values and "positive" classification were compared between media. T. foetus motility and morphology as well as media pH were severely altered in IP samples with CONTAM compared to those without as well as to DPM medium with and without CONTAM (P<0.0001). PCR testing demonstrated significantly greater Ct values were for T. foetus DNA (P<0.001) in IP contaminated with smegma bacteria compared to those without. When using T

  17. Bacterial diversity associated with populations of Glossina spp. from Cameroon and distribution within the Campo sleeping sickness focus.

    PubMed

    Geiger, Anne; Fardeau, Marie-Laure; Njiokou, Flobert; Joseph, Manon; Asonganyi, Tazoacha; Ollivier, Bernard; Cuny, Gérard

    2011-10-01

    Tsetse flies were sampled in three villages of the Campo sleeping sickness focus in South Cameroon. The aim of this study was to investigate the flies' gut bacterial composition using culture-dependent techniques. Out of the 32 flies analyzed (27 Glossina palpalis palpalis, two Glossina pallicera, one Glossina nigrofusca, and two Glossina caliginea), 17 were shown to be inhabited by diverse bacteria belonging to the Proteobacteria, the Firmicutes, or the Bacteroidetes phyla. Phylogenetic analysis based on 16S rRNA gene sequences indicated the presence of 16 bacteria belonging to the genera Acinetobacter (4), Enterobacter (4), Enterococcus (2), Providencia (1), Sphingobacterium (1), Chryseobacterium (1), Lactococcus (1), Staphylococcus (1), and Pseudomonas (1). Using identical bacterial isolation and identification processes, the diversity of the inhabiting bacteria analyzed in tsetse flies sampled in Cameroon was much higher than the diversity found previously in flies collected in Angola. Furthermore, bacterial infection rates differed greatly between the flies from the three sampling areas (Akak, Campo Beach/Ipono, and Mabiogo). Last, the geographic distribution of the different bacteria was highly uneven; two of them identified as Sphingobacterium spp. and Chryseobacterium spp. were only found in Mabiogo. Among the bacteria identified, several are known for their capability to affect the survival of their insect hosts and/or insect vector competence. In some cases, bacteria belonging to a given genus were shown to cluster separately in phylogenetic trees; they could be novel species within their corresponding genus. Therefore, such investigations deserve to be pursued in expanded sampling areas within and outside Cameroon to provide greater insight into the diverse bacteria able to infect tsetse flies given the severe human and animal sickness they transmit. PMID:21387098

  18. An obligatory bacterial mutualism in a multi-drug environment exhibits strong oscillatory population dynamics

    NASA Astrophysics Data System (ADS)

    Conwill, Arolyn; Yurtsev, Eugene; Gore, Jeff

    2014-03-01

    A common mechanism of antibiotic resistance in bacteria involves the production of an enzyme that inactivates the antibiotic. By inactivating the antibiotic, resistant cells can protect other cells in the population that would otherwise be sensitive to the drug. In a multidrug environment, an obligatory mutualism arises because populations of different strains rely on each other to breakdown antibiotics in the environment. Here, we experimentally track the population dynamics of two E. coli strains in the presence of two different antibiotics: ampicillin and chloramphenicol. Together the strains are able to grow in antibiotic concentrations that inhibit growth of either one of the strains alone. Although mutualisms are often thought to stabilize population dynamics, we observe strong oscillatory dynamics even when there is long-term coexistence between the two strains. We expect that our results will provide insight into the evolution of antibiotic resistance and, more generally, the evolutionary origin of phenotypic diversity, cooperation, and ecological stability.

  19. DIFFERENTIAL RESPONSE TO BACTERIAL CHALLENGE IN POPULATIONS OF FUNDULUS HETERCLITUS FROM CLEAN AND POLLUTED SITES

    EPA Science Inventory

    Mummichogs (Fundulus heteroclitus) indigenous to an urban estuarine Superfund site in New Bedford Harbor (NBH, MA, USA) contain extremely high concentrations of the local contaminants, polychlorinated biphenyls (PCBs). These fish populations apparently persist due to an inherited...

  20. Spatial Heterogeneity of Bacterial Populations along an Environmental Gradient at a Shallow Submarine Hydrothermal Vent near Milos Island (Greece)

    PubMed Central

    Sievert, Stefan M.; Brinkhoff, Thorsten; Muyzer, Gerard; Ziebis, Wiebke; Kuever, Jan

    1999-01-01

    The spatial heterogeneity of bacterial populations at a shallow-water hydrothermal vent in the Aegean Sea close to the island of Milos (Greece) was examined at two different times by using acridine orange staining for total cell counts, cultivation-based techniques, and denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments. Concurrent with measurements of geochemical parameters, samples were taken along a transect from the center of the vent to the surrounding area. Most-probable-number (MPN) counts of metabolically defined subpopulations generally constituted a minor fraction of the total cell counts; both counting procedures revealed the highest cell numbers in a transition zone from the strongly hydrothermally influenced sediments to normal sedimentary conditions. Total cell counts ranged from 3.2 × 105 cells ml−1 in the water overlying the sediments to 6.4 × 108 cells g (wet weight) of sediment−1. MPN counts of chemolithoautotrophic sulfur-oxidizing bacteria varied between undetectable and 1.4 × 106 cells g−1. MPN counts for sulfate-reducing bacteria and dissimilatory iron-reducing bacteria ranged from 8 to 1.4 × 105 cells g−1 and from undetectable to 1.4 × 106 cells g−1, respectively. DGGE revealed a trend from a diverse range of bacterial populations which were present in approximately equal abundance in the transition zone to a community dominated by few populations close to the center of the vent. Temperature was found to be an important parameter in determining this trend. However, at one sampling time this trend was not discernible, possibly due to storm-induced disturbance of the upper sediment layers. PMID:10473383

  1. Light Suppresses Bacterial Population through the Accumulation of Hydrogen Peroxide in Tobacco Leaves Infected with Pseudomonas syringae pv. tabaci

    PubMed Central

    Cheng, Dan-Dan; Liu, Mei-Jun; Sun, Xing-Bin; Zhao, Min; Chow, Wah S.; Sun, Guang-Yu; Zhang, Zi-Shan; Hu, Yan-Bo

    2016-01-01

    Pseudomonas syringae pv. tabaci (Pst) is a hemibiotrophic bacterial pathogen responsible for tobacco wildfire disease. Although considerable research has been conducted on the tobacco plant’s tolerance to Pst, the role of light in the responses of the photosystems to Pst infection is poorly understood. This study aimed to elucidate the underlying mechanisms of the reduced photosystem damage in tobacco leaves due to Pst infection under light conditions. Compared to dark conditions, Pst infection under light conditions resulted in less chlorophyll degradation and a smaller decline in photosynthetic function. Although the maximal quantum yield of photosystem II (PSII) and the activity of the photosystem I (PSI) complex decreased as Pst infection progressed, damage to PSI and PSII after infection was reduced under light conditions compared to dark conditions. Pst was 17-fold more abundant in tobacco leaves under dark compared to light conditions at 3 days post inoculation (dpi). Additionally, H2O2 accumulated to a high level in tobacco leaves after Pst infection under light conditions; although to a lesser extent, H2O2 accumulation was also significant under dark conditions. Pretreatment with H2O2 alleviated chlorotic lesions and decreased Pst abundance in tobacco leaves at 3 dpi under dark conditions. MV pretreatment had the same effects under light conditions, whereas 3-(3,4-dichlorophenyl)-1,1-dimethylurea pretreatment aggravated chlorotic lesions and increased the Pst population. These results indicate that chlorotic symptoms and the size of the bacterial population are each negatively correlated with H2O2 accumulation. In other words, light appears to suppress the Pst population in tobacco leaves through the accumulation of H2O2 during infection. PMID:27148334

  2. Light Suppresses Bacterial Population through the Accumulation of Hydrogen Peroxide in Tobacco Leaves Infected with Pseudomonas syringae pv. tabaci.

    PubMed

    Cheng, Dan-Dan; Liu, Mei-Jun; Sun, Xing-Bin; Zhao, Min; Chow, Wah S; Sun, Guang-Yu; Zhang, Zi-Shan; Hu, Yan-Bo

    2016-01-01

    Pseudomonas syringae pv. tabaci (Pst) is a hemibiotrophic bacterial pathogen responsible for tobacco wildfire disease. Although considerable research has been conducted on the tobacco plant's tolerance to Pst, the role of light in the responses of the photosystems to Pst infection is poorly understood. This study aimed to elucidate the underlying mechanisms of the reduced photosystem damage in tobacco leaves due to Pst infection under light conditions. Compared to dark conditions, Pst infection under light conditions resulted in less chlorophyll degradation and a smaller decline in photosynthetic function. Although the maximal quantum yield of photosystem II (PSII) and the activity of the photosystem I (PSI) complex decreased as Pst infection progressed, damage to PSI and PSII after infection was reduced under light conditions compared to dark conditions. Pst was 17-fold more abundant in tobacco leaves under dark compared to light conditions at 3 days post inoculation (dpi). Additionally, H2O2 accumulated to a high level in tobacco leaves after Pst infection under light conditions; although to a lesser extent, H2O2 accumulation was also significant under dark conditions. Pretreatment with H2O2 alleviated chlorotic lesions and decreased Pst abundance in tobacco leaves at 3 dpi under dark conditions. MV pretreatment had the same effects under light conditions, whereas 3-(3,4-dichlorophenyl)-1,1-dimethylurea pretreatment aggravated chlorotic lesions and increased the Pst population. These results indicate that chlorotic symptoms and the size of the bacterial population are each negatively correlated with H2O2 accumulation. In other words, light appears to suppress the Pst population in tobacco leaves through the accumulation of H2O2 during infection. PMID:27148334

  3. RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel

    PubMed Central

    Lawley, Blair; Munro, Karen; Sims, Ian M.; Lee, Julian; Butts, Christine A.; Roy, Nicole

    2014-01-01

    Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope (13C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [13C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect 13C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the 13C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA–stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism. PMID:24487527

  4. The Population Structure of Antibiotic-Producing Bacterial Symbionts of Apterostigma dentigerum Ants: Impacts of Coevolution and Multipartite Symbiosis

    PubMed Central

    Caldera, Eric J.; Currie, Cameron R.

    2016-01-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured (FST = 0.39) and dispersal-limited (i.e., significant isolation by distance; r = 0.517, P = .05) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., ρ/θ = 0.028 in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species (r = 0.67, P = .02), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a specialized mutualistic association than with recently

  5. The population structure of antibiotic-producing bacterial symbionts of Apterostigma dentigerum ants: impacts of coevolution and multipartite symbiosis.

    PubMed

    Caldera, Eric J; Currie, Cameron R

    2012-11-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured ([Formula: see text]) and dispersal-limited (i.e., significant isolation by distance; [Formula: see text], [Formula: see text]) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., [Formula: see text] in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species ([Formula: see text], [Formula: see text]), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a

  6. Pyrosequencing analyses of endophytic bacterial populations in tomato leaves infected by ‘Candidatus Liberibacter solanacearum’

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Candidatus Liberibacter solanacearum’ (CLso) is associated with zebra Chip (ZC) disease of potato. The bacterium is currently not culturable and commonly maintained in plant hosts for characterization. In this study, CLso was graft-transmitted to tomato plants. A maximum of over 200-fold increase i...

  7. Defined bacterial culture development for methane generation from lactose. [Streptococcus lactis; Clostridium formicoaceticum; Methanococcus mazei

    SciTech Connect

    Yang, S.T.; Tang, I.C.; Okos, M.R.

    1988-06-20

    The defined microbial cultures for methane generation from lactose were investigated. A mixed culture consisting of homolactic (Streptococcus lactis), homoacetic (Clostridium formicoaceticum), and acetate-utilizing methanogenic (Methanococcus mazei) bacteria was used to convert lactose and whey permeate to methane at mesophilic temperatures (35-37/sup 0/C) and a pH around 7.0. Lactose was first converted to lactic acid by S. lactis, then to acetic acid by C. formicoaceticum, and finally to methane and CO/sub 2/ by M. mazei. About 5.3 mol methane were obtained from each mole of lactose consumed, and the conversion of acetate to methane was the rate-limiting step for this mixed-culture fermentation.

  8. Response of endophytic bacterial communities in banana tissue culture plantlets to Fusarium wilt pathogen infection.

    PubMed

    Lian, Jie; Wang, Zifeng; Zhou, Shining

    2008-04-01

    Endophytic bacteria reside within plant hosts without having pathogenic effects, and various endophytes have been found to functionally benefit plant disease suppressive ability. In this study, the influence of banana plant stress on the endophytic bacterial communities, which was achieved by infection with the wilt pathogen Fusarium oxysporum f. sp. cubense, was examined by cultivation-independent denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA directly amplified from plant tissue DNA. Community analysis clearly demonstrated increased bacterial diversity in pathogen-infected plantlets compared to that in control plantlets. By sequencing, bands most similar to species of Bacillus and Pseudomonas showed high density in the pathogen-treated pattern. In vitro screening of the isolates for antagonistic activity against Fusarium wilt pathogen acquired three strains of endophytic bacteria which were found to match those species that obviously increased in the pathogen infection process; moreover, the most inhibitive strain could also interiorly colonize plantlets and perform antagonism. The evidence obtained from this work showed that antagonistic endophytic bacteria could be induced by the appearance of a host fungal pathogen and further be an ideal biological control agent to use in banana Fusarium wilt disease protection. PMID:18497482

  9. Antibiotic resistance among cultured bacterial isolates from bioethanol fermentation facilities across the United States.

    PubMed

    Murphree, Colin A; Heist, E Patrick; Moe, Luke A

    2014-09-01

    Bacterial contamination of fuel ethanol fermentations by lactic acid bacteria (LAB) can have crippling effects on bioethanol production. Producers have had success controlling bacterial growth through prophylactic addition of antibiotics to fermentors, yet concerns have arisen about antibiotic resistance among the LAB. Here, we report on mechanisms used by 32 LAB isolates from eight different US bioethanol facilities to persist under conditions of antibiotic stress. Minimum inhibitory concentration assays with penicillin, erythromycin, and virginiamycin revealed broad resistance to each of the antibiotics as well as high levels of resistance to individual antibiotics. Phenotypic assays revealed that antibiotic inactivation mechanisms contributed to the high levels of individual resistances among the isolates, especially to erythromycin and virginiamycin, yet none of the isolates appeared to use a β-lactamase. Biofilm formation was noted among the majority of the isolates and may contribute to persistence under low levels of antibiotics. Nearly all of the isolates carried at least one canonical antibiotic resistance gene and many carried more than one. The erythromycin ribosomal methyltransferase (erm) gene class was found in 19 of 32 isolates, yet a number of these isolates exhibit little to no resistance to erythromycin. The erm genes were present in 15 isolates that encoded more than one antibiotic resistance mechanism, suggestive of potential genetic linkages. PMID:24748439

  10. Impact of heterogeneity within cultured cells on bacterial invasion: analysis of Pseudomonas aeruginosa and Salmonella enterica serovar typhi entry into MDCK cells by using a green fluorescent protein-labelled cystic fibrosis transmembrane conductance regulator receptor.

    PubMed

    Gerçeker, A A; Zaidi, T; Marks, P; Golan, D E; Pier, G B

    2000-02-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride ion channel that also serves as a receptor for entry of Pseudomonas aeruginosa and Salmonella enterica serovar Typhi into epithelial cells. To evaluate heterogeneity in CFTR protein expression in cultured cells and the effect of heterogeneity on internalization of different P. aeruginosa and serovar Typhi strains, we used two-color flow cytometry and confocal laser microscopy to study bacterial uptake by Madin-Darby canine kidney (MDCK) type I epithelial cells stably expressing a green fluorescent protein (GFP)-CFTR fusion construct (MDCK-GFP-CFTR cells). We found a strong correlation between cell size and GFP-CFTR protein expression, with 60 to 70% of cells expressing low levels of GFP-CFTR protein, 20 to 30% expressing intermediate levels, and <10% expressing high levels. The cells were sorted into low-, intermediate-, or high-level producers of CFTR protein; in vitro growth of each sorted population yielded the same distribution of CFTR protein expression as that in the original population. Cells expressing either low or high levels of CFTR protein internalized bacteria poorly; maximal bacterial uptake occurred in the cells expressing intermediate levels of CFTR protein. Treatment of MDCK cells with sodium butyrate markedly enhanced the production of CFTR protein without increasing cell size; butyrate treatment also increased the proportion of cells with internalized bacteria. However, there were fewer bacteria per butyrate-treated cell and, for P. aeruginosa, there was an overall decrease in the total level of bacterial uptake. The most highly ingested bacterial strains were internalized by fewer total MDCK-GFP-CFTR cells, indicating preferential bacterial uptake by a minority of epithelial cells within a given culture. Confocal fluorescence microscopy showed that P. aeruginosa and serovar Typhi induced cytoplasmic accumulation of CFTR protein close to the plasma membrane where the

  11. Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices.

    PubMed

    Xia, Ye; DeBolt, Seth; Dreyer, Jamin; Scott, Delia; Williams, Mark A

    2015-01-01

    Plants have a diverse internal microbial biota that has been shown to have an important influence on a range of plant health attributes. Although these endophytes have been found to be widely occurring, few studies have correlated agricultural production practices with endophyte community structure and function. One agricultural system that focuses on preserving and enhancing soil microbial abundance and biodiversity is organic farming, and numerous studies have shown that organically managed system have increased microbial community characteristics. Herein, the diversity and specificity of culturable bacterial endophytes were evaluated in four vegetable crops: corn, tomato, melon, and pepper grown under organic or conventional practices. Endophytic bacteria were isolated from surface-sterilized shoot, root, and seed tissues and sequence identified. A total of 336 bacterial isolates were identified, and grouped into 32 species and five phyla. Among these, 239 isolates were from organically grown plants and 97 from those grown conventionally. Although a diverse range of bacteria were documented, 186 were from the Phylum Firmicutes, representing 55% of all isolates. Using the Shannon diversity index, we observed a gradation of diversity in tissues, with shoots and roots having a similar value, and seeds having the least diversity. Importantly, endophytic microbial species abundance and diversity was significantly higher in the organically grown plants compared to those grown using conventional practices, potentially indicating that organic management practices may increase endophyte presence and diversity. The impact that these endophytes could have on plant growth and yield was evaluated by reintroducing them into tomato plants in a greenhouse environment. Of the bacterial isolates tested, 61% were found to promote tomato plant growth and 50-64% were shown to enhance biomass accumulation, illustrating their potential agroecosystem application. PMID:26217348

  12. Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices

    PubMed Central

    Xia, Ye; DeBolt, Seth; Dreyer, Jamin; Scott, Delia; Williams, Mark A.

    2015-01-01

    Plants have a diverse internal microbial biota that has been shown to have an important influence on a range of plant health attributes. Although these endophytes have been found to be widely occurring, few studies have correlated agricultural production practices with endophyte community structure and function. One agricultural system that focuses on preserving and enhancing soil microbial abundance and biodiversity is organic farming, and numerous studies have shown that organically managed system have increased microbial community characteristics. Herein, the diversity and specificity of culturable bacterial endophytes were evaluated in four vegetable crops: corn, tomato, melon, and pepper grown under organic or conventional practices. Endophytic bacteria were isolated from surface-sterilized shoot, root, and seed tissues and sequence identified. A total of 336 bacterial isolates were identified, and grouped into 32 species and five phyla. Among these, 239 isolates were from organically grown plants and 97 from those grown conventionally. Although a diverse range of bacteria were documented, 186 were from the Phylum Firmicutes, representing 55% of all isolates. Using the Shannon diversity index, we observed a gradation of diversity in tissues, with shoots and roots having a similar value, and seeds having the least diversity. Importantly, endophytic microbial species abundance and diversity was significantly higher in the organically grown plants compared to those grown using conventional practices, potentially indicating that organic management practices may increase endophyte presence and diversity. The impact that these endophytes could have on plant growth and yield was evaluated by reintroducing them into tomato plants in a greenhouse environment. Of the bacterial isolates tested, 61% were found to promote tomato plant growth and 50–64% were shown to enhance biomass accumulation, illustrating their potential agroecosystem application. PMID:26217348

  13. Synchrony in human, mouse and bacterial cell cultures--a comparison

    NASA Technical Reports Server (NTRS)

    Helmstetter, Charles E.; Thornton, Maureen; Romero, Ana; Eward, K. Leigh

    2003-01-01

    Growth characteristics of synchronous human MOLT-4, human U-937 and mouse L1210 cultures produced with a new minimally-disturbing technology were compared to each other and to synchronous Escherichia coli B/r. Based on measurements of cell concentrations during synchronous growth, synchrony persisted in similar fashion for all cells. Cell size and DNA distributions in the mammalian cultures also progressed synchronously and reproducibly for multiple cell cycles. The results demonstrate that unambiguous multi-cycle synchrony, critical for verifying the absence of significant growth imbalances induced by the synchronization procedure, is feasible with these cell lines, and possibly others.

  14. Are variations in rates of attending cultural activities associated with population health in the United States?

    PubMed Central

    Wilkinson, Anna V; Waters, Andrew J; Bygren, Lars Olov; Tarlov, Alvin R

    2007-01-01

    Background Population studies conducted in Sweden have revealed an association between attendance at cultural activities and health. Using data from US residents, we examined whether the association could be observed in the US. Methods Participants in the current study included 1,244 individuals who participated in the 1998 General Social Survey. Results A significant association between cultural activities and self-reported health (SRH) was observed, even after controlling for age, gender, marital status, race, number of children, subjective social class, employment status, household income, and educational attainment. Specifically, the more cultural activities people reported attending, the better was their SRH. Conclusion The data confirm that an association between cultural activity and health is present in a US sample. The data do not mean that the association is causal, but they suggest that further longitudinal research is warranted. PMID:17764546

  15. Proteins dominate in the surface layers formed on materials exposed to extracellular polymeric substances from bacterial cultures.

    PubMed

    Yang, Yi; Wikieł, Agata J; Dall'Agnol, Leonardo T; Eloy, Pierre; Genet, Michel J; Moura, José J G; Sand, Wolfgang; Dupont-Gillain, Christine C; Rouxhet, Paul G

    2016-01-01

    The chemical compositions of the surface conditioning layers formed by different types of solutions (from isolated EPS to whole culture media), involving different bacterial strains relevant for biocorrosion were compared, as they may influence the initial step in biofilm formation. Different substrata (polystyrene, glass, steel) were conditioned and analyzed by X-ray photoelectron spectroscopy. Peak decomposition and assignment were validated by correlations between independent spectral data and the ubiquitous presence of organic contaminants on inorganic substrata was taken into account. Proteins or peptides were found to be a major constituent of all conditioning layers and polysaccharides were not present in appreciable concentrations; the proportion of nitrogen which may be due to DNA was lower than 15%. There was no significant difference between the compositions of the adlayers formed from different conditioning solutions, except for the adlayers produced with tightly bound EPS extracted from D. alaskensis. PMID:26769222

  16. Cultured C2C12 cell lines as a model for assessment of bacterial attachment to bovine primary muscle cells.

    PubMed

    Zulfakar, Siti Shahara; White, Jason D; Ross, Tom; Tamplin, Mark L

    2013-06-01

    The mechanisms of bacterial attachment to meat tissues need to be understood to enhance meat safety interventions. However, little is known about attachment of foodborne pathogens to meat muscle cells. In this study, attachment of six Escherichia coli and two Salmonella strains to primary bovine muscle cells and a cultured muscle cell line, C2C12, was measured, including the effect of temperature. At 37°C, all but one strain (EC623) attached to C2C12 cells, whereas only five of eight strains (M23Sr, H10407, EC473, Sal1729a and Sal691) attached to primary cells. At 10 °C, two strains (H10407 and EC473) attached to C2C12 cells, compared to four strains (M23Sr, EC614, H10407 and Sal1729a) of primary cells. Comparing all strains at both temperatures, EC614 displayed the highest CFU per C2C12 cell (4.60±2.02CFU/muscle cell at 37 °C), whereas greater numbers of M23Sr attached per primary cell (51.88±39.43CFU/muscle cell at 37 °C). This study indicates that primary bovine muscle cells may provide a more relevant model system to study bacterial attachment to beef carcasses compared to cell lines such as C2C12. PMID:23501253

  17. Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing.

    PubMed

    Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen

    2015-01-01

    Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods. PMID:24950754

  18. The Weak Shall Inherit: Bacteriocin-Mediated Interactions in Bacterial Populations

    PubMed Central

    Majeed, Hadeel; Lampert, Adam; Ghazaryan, Lusine; Gillor, Osnat

    2013-01-01

    Background Evolutionary arms race plays a major role in shaping biological diversity. In microbial systems, competition often involves chemical warfare and the production of bacteriocins, narrow-spectrum toxins aimed at killing closely related strains by forming pores in their target’s membrane or by degrading the target’s RNA or DNA. Although many empirical and theoretical studies describe competitive exclusion of bacteriocin-sensitive strains by producers of bacteriocins, the dynamics among producers are largely unknown. Methodology/Principal findings We used a reporter-gene assay to show that the bacterial response to bacteriocins’ treatment mirrors the inflicted damage Potent bacteriocins are lethal to competing strains, but at sublethal doses can serve as strong inducing agents, enhancing their antagonists’ bacteriocin production. In contrast, weaker bacteriocins are less toxic to their competitors and trigger mild bacteriocin expression. We used empirical and numerical models to explore the role of cross-induction in the arms race between bacteriocin-producing strains. We found that in well-mixed, unstructured environments where interactions are global, producers of weak bacteriocins are selectively advantageous and outcompete producers of potent bacteriocins. However, in spatially structured environments, where interactions are local, each producer occupies its own territory, and competition takes place only in “no man’s lands” between territories, resulting in much slower dynamics. Conclusion/Significance The models we present imply that producers of potent bacteriocins that trigger a strong response in neighboring bacteriocinogenic strains are doomed, while producers of weak bacteriocins that trigger a mild response in bacteriocinogenic strains flourish. This counter-intuitive outcome might explain the preponderance of weak bacteriocin producers in nature. However, the described scenario is prolonged in spatially structured environments thus

  19. [Comparison of the adaptive potential for Rhizobium leguminosarum bv. viceae nodule bacterial populations isolated in natural ecosystems and agrocenoses].

    PubMed

    Kurchak, O N; Provorov, N A; Simarov, B V

    2011-04-01

    Polymorphism analysis was performed in Rhizobium leguminosarum bv. viceae populations isolated from geographically distant regions of Ukraine and Middle Asia. Examination of cultural, biochemical, and symbiotic traits revealed interpopulation differences, which were attributed to the difference in conditions between natural ecosystems and agrocenoses. Vetch has high species diversity and is not cultivated in Middle Asia, and the corresponding rhizobial population displayed higher genetic diversity and higher polymorphism of adaptive traits ensuring saprophytic development in soil and the rhizosphere, including melanin synthesis (35%) and active exopolysaccharide production (90%). Strains of the Ukrainian population had a lower exopolysaccharide production (10%), did not produce melanin, had higher herbicide resistance, and utilized glucose and succinate (main components of plant root exudation) as carbon sources. Strains capable of efficient symbiosis with Vicia villosa Roth. had a higher frequency in the Middle Asian than in the Ukrainian population, especially among strains isolated from soil (80 and 35%, respectively). In addition, strains of the Middle Asian population better competed for nodulation. It was assumed that the formation of rhizobial populations in vetch cultivation regions (Ukraine) is aimed at adaptation to ectosymbiotic (rhizospheric) interactions with plants and anthropogenic stress factors, while strains of the vetch original center (Middle Asia) are mostly adapted to the endosymbiotic interaction and to natural edaphic stress factors. PMID:21675237

  20. Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices.

    PubMed

    Battini, Fabio; Cristani, Caterina; Giovannetti, Manuela; Agnolucci, Monica

    2016-02-01

    Arbuscular Mycorrhizal Fungi (AMF) live in symbiosis with most crop plants and represent essential elements of soil fertility and plant nutrition and productivity, facilitating soil mineral nutrient uptake and protecting plants from biotic and abiotic stresses. These beneficial services may be mediated by the dense and active spore-associated bacterial communities, which sustain diverse functions, such as the promotion of mycorrhizal activity, biological control of soilborne diseases, nitrogen fixation, and the supply of nutrients and growth factors. In this work, we utilised culture-dependent methods to isolate and functionally characterize the microbiota strictly associated to Rhizophagus intraradices spores, and molecularly identified the strains with best potential plant growth promoting (PGP) activities by 16S rDNA sequence analysis. We isolated in pure culture 374 bacterial strains belonging to different functional groups-actinobacteria, spore-forming, chitinolytic and N2-fixing bacteria-and screened 122 strains for their potential PGP activities. The most common PGP trait was represented by P solubilization from phytate (69.7%), followed by siderophore production (65.6%), mineral P solubilization (49.2%) and IAA production (42.6%). About 76% of actinobacteria and 65% of chitinolytic bacteria displayed multiple PGP activities. Nineteen strains with best potential PGP activities, assigned to Sinorhizobium meliloti, Streptomyces spp., Arthrobacter phenanthrenivorans, Nocardiodes albus, Bacillus sp. pumilus group, Fictibacillus barbaricus and Lysinibacillus fusiformis, showed the ability to produce IAA and siderophores and to solubilize P from mineral phosphate and phytate, representing suitable candidates as biocontrol agents, biofertilisers and bioenhancers, in the perspective of targeted management of beneficial symbionts and their associated bacteria in sustainable food production systems. PMID:26805620

  1. Simplified extraction of bisphenols from bacterial culture suspensions and solid matrices.

    PubMed

    Im, Jeongdae; Yip, Dan; Lee, Jaejin; Löffler, Frank E

    2016-07-01

    We demonstrate the utility of a simple and fast methanol extraction method that achieves similar bisphenols recovery efficiencies from microbial culture suspensions and sediment material than more laborious and costly extraction procedures. The methanol extraction method may have broad application for the rapid analysis of hydrophobic compounds in biodegradation studies. PMID:27179438

  2. Enumerating Virus-Like Particles and Bacterial Populations in the Sinuses of Chronic Rhinosinusitis Patients Using Flow Cytometry.

    PubMed

    Carlson-Jones, Jessica A P; Paterson, James S; Newton, Kelly; Smith, Renee J; Dann, Lisa M; Speck, Peter; Mitchell, James G; Wormald, Peter-John

    2016-01-01

    There is increasing evidence to suggest that the sinus microbiome plays a role in the pathogenesis of chronic rhinosinusitis (CRS). However, the concentration of these microorganisms within the sinuses is still unknown. We show that flow cytometry can be used to enumerate bacteria and virus-like particles (VLPs) in sinus flush samples of CRS patients. This was achieved through trialling 5 sample preparation techniques for flow cytometry. We found high concentrations of bacteria and VLPs in these samples. Untreated samples produced the highest average bacterial and VLP counts with 3.3 ± 0.74 x 107 bacteria ml-1 and 2.4 ± 1.23 x 109 VLP ml-1 of sinus flush (n = 9). These counts were significantly higher than most of the treated samples (p < 0.05). Results showed 103 and 104 times inter-patient variation for bacteria and VLP concentrations. This wide variation suggests that diagnosis and treatment need to be personalised and that utilising flow cytometry is useful and efficient for this. This study is the first to enumerate bacterial and VLP populations in the maxillary sinus of CRS patients. The relevance of enumeration is that with increasing antimicrobial resistance, antibiotics are becoming less effective at treating bacterial infections of the sinuses, so alternative therapies are needed. Phage therapy has been proposed as one such alternative, but for dosing, the abundance of bacteria is required. Knowledge of whether phages are normally present in the sinuses will assist in gauging the safety of applying phage therapy to sinuses. Our finding, that large numbers of VLP are frequently present in sinuses, indicates that phage therapy may represent a minimally disruptive intervention towards the nasal microbiome. We propose that flow cytometry can be used as a tool to assess microbial biomass dynamics in sinuses and other anatomical locations where infection can cause disease. PMID:27171169

  3. The effects of a probiotic yeast on the bacterial diversity and population structure in the rumen of cattle.

    PubMed

    Pinloche, Eric; McEwan, Neil; Marden, Jean-Philippe; Bayourthe, Corinne; Auclair, Eric; Newbold, C Jamie

    2013-01-01

    It has been suggested that the ability of live yeast to improve milk yield and weight gain in cattle is because the yeast stimulates bacterial activity within the rumen. However it remains unclear if this is a general stimulation of all species or a specific stimulation of certain species. Here we characterised the change in the bacterial population within the rumen of cattle fed supplemental live yeast. Three cannulated lactating cows received a daily ration (24 kg/d) of corn silage (61% of DM), concentrates (30% of DM), dehydrated alfalfa (9% of DM) and a minerals and vitamins mix (1% of DM). The effect of yeast (BIOSAF SC 47, Lesaffre Feed Additives, France; 0.5 or 5 g/d) was compared to a control (no additive) in a 3 × 3 Latin square design. The variation in the rumen bacterial community between treatments was assessed using Serial Analysis of V1 Ribosomal Sequence Tag (SARST-V1) and 454 pyrosequencing based on analysis of the 16S rRNA gene. Compared to the control diet supplementation of probiotic yeast maintained a healthy fermentation in the rumen of lactating cattle (higher VFA concentration [high yeast dose only], higher rumen pH, and lower Eh and lactate). These improvements were accompanied with a shift in the main fibrolytic group (Fibrobacter and Ruminococcus) and lactate utilising bacteria (Megasphaera and Selenomonas). In addition we have shown that the analysis of short V1 region of 16s rRNA gene (50-60 bp) could give as much phylogenetic information as a longer read (454 pyrosequencing of 250 bp). This study also highlights the difficulty of drawing conclusions on composition and diversity of complex microbiota because of the variation caused by the use of different methods (sequencing technology and/or analysis). PMID:23844101

  4. Enumerating Virus-Like Particles and Bacterial Populations in the Sinuses of Chronic Rhinosinusitis Patients Using Flow Cytometry

    PubMed Central

    Carlson-Jones, Jessica A. P.; Paterson, James S.; Newton, Kelly; Smith, Renee J.; Dann, Lisa M.; Speck, Peter; Mitchell, James G.; Wormald, Peter-John

    2016-01-01

    There is increasing evidence to suggest that the sinus microbiome plays a role in the pathogenesis of chronic rhinosinusitis (CRS). However, the concentration of these microorganisms within the sinuses is still unknown. We show that flow cytometry can be used to enumerate bacteria and virus-like particles (VLPs) in sinus flush samples of CRS patients. This was achieved through trialling 5 sample preparation techniques for flow cytometry. We found high concentrations of bacteria and VLPs in these samples. Untreated samples produced the highest average bacterial and VLP counts with 3.3 ± 0.74 x 107 bacteria ml-1 and 2.4 ± 1.23 x 109 VLP ml-1 of sinus flush (n = 9). These counts were significantly higher than most of the treated samples (p < 0.05). Results showed 103 and 104 times inter-patient variation for bacteria and VLP concentrations. This wide variation suggests that diagnosis and treatment need to be personalised and that utilising flow cytometry is useful and efficient for this. This study is the first to enumerate bacterial and VLP populations in the maxillary sinus of CRS patients. The relevance of enumeration is that with increasing antimicrobial resistance, antibiotics are becoming less effective at treating bacterial infections of the sinuses, so alternative therapies are needed. Phage therapy has been proposed as one such alternative, but for dosing, the abundance of bacteria is required. Knowledge of whether phages are normally present in the sinuses will assist in gauging the safety of applying phage therapy to sinuses. Our finding, that large numbers of VLP are frequently present in sinuses, indicates that phage therapy may represent a minimally disruptive intervention towards the nasal microbiome. We propose that flow cytometry can be used as a tool to assess microbial biomass dynamics in sinuses and other anatomical locations where infection can cause disease. PMID:27171169

  5. Interaction between stocking density and settlement on population dynamics in suspended mussel culture

    NASA Astrophysics Data System (ADS)

    Cubillo, Alhambra M.; Fuentes-Santos, Isabel; Labarta, Uxío

    2015-01-01

    Population dynamics on mussels growing on suspended culture depend mainly on the balance of several processes: mortality and/or dislodgements from the ropes, recruitment and growth. The negative effect of overcrowding on mussel growth and survival has been widely studied. Other works have addressed the effect of population size on recruitment on bottom beds. This study aims to provide insight into the processes underlying population dynamics. To this purpose, we analyzed the effect of stocking density on mussel growth, survival and seed settlement, and the post-settlement interaction between adults and recruits in suspended culture. The temporal pattern of the variables involved in population dynamics was fitted by GAM models, which in contrast with parametric models does not assume any prior relationships between variables. Our results show that mussel growth and survival depend on a trade-off between competition for resources at high densities and the risk of great settlements in less crowded adult mussel populations. Intracohort competition increased with stocking density, while seed settlement, which increases the risk of mussel dislodgements and leads to intercohort competition, was higher at moderate stocking densities. Post-settlement competitive pressures were driven by total population density and size composition. Both intracohort competition in adults and asymmetric competition between adults and recruits increase with higher adult-recruit ratios. All these density-dependent processes should be considered in future management strategies and research experimental designs.

  6. Statistical Evaluation of Electronic and Plate Counts for Estimating Bacterial Populations

    PubMed Central

    Mountney, G. J.; O'malley, J.

    1966-01-01

    Bacteria from cultures of Staphylococcus aureus, Pseudomonas geniculata, and Rhodotorula glutenis were counted by use of an electronic counter and by plate counts from broth cultures at selected periods from 0 to 24 hr. Variations in the two methods were noted, and the results were compared after calculating correlations, coefficients of variation, and nested analyses of variance. It was not possible to determine the absolute accuracy of the two methods; however, the precision of the results obtained with an electronic counter was better than that obtained with plate counting. It appears that electronic counting, because of ease and convenience, provides better comparative counts at a particular stage of growth, especially during the early stages of the growth period, whereas plate counting yields the best results in determining growth curves. PMID:16349683

  7. a Paradox in Life Thermodynamics:. the Long-Term Survival of Bacterial Populations

    NASA Astrophysics Data System (ADS)

    Carnazza, S.; Guglielmino, S.; Nicolò, M.; Santoro, F.; Oliveri, F.

    2008-04-01

    Pseudomonas aeruginosa is an ubiquitous bacterium that, due to its high metabolic versatility, is able to persist for prolonged periods of time. It is the ethiological agent of cystic fibrosis and is involved in urinary infections, conjunctivitis, otitis and pneumonia. We present the results of a batch culture of P. aeruginosa inoculated in LB medium and monitored weekly for a period of 24 months during which no more nutrients are added. A mathematical model suitable to describe the experimental viability data is given.

  8. Diagnosis of bacterial pulmonary infections with quantitative protected catheter cultures obtained during bronchoscopy.

    PubMed Central

    Pollock, H M; Hawkins, E L; Bonner, J R; Sparkman, T; Bass, J B

    1983-01-01

    Quantitative bacteriology was performed on specimens collected by protected catheter fiberoptic bronchoscopy from 172 patients. Of the patients who had pneumonia, 75 of 78 (96%) had one or more species present at greater than or equal to 10(3) CFU/ml, whereas 2 of 35 (6%) control patients had organisms present in that quantity. In addition, 66% of the control specimens yielded no isolates by this technique. All of the 11 patients with bronchitis had greater than or equal to 10(3) CFU/ml. Quantitative bacteriology revealed high levels of colonization in patients without infection and endobronchial structural disease. The data suggest that bacterial counts of greater than or equal to 10(3) CFU/ml in suspended secretions collected with a protected catheter brush were diagnostic of the bacteriological etiology of lower respiratory tract infections in patients without endobronchial structural abnormalities. PMID:6339545

  9. Effects of gamma-irradiation before and after cooking on bacterial population and sensory quality of Dakgalbi

    NASA Astrophysics Data System (ADS)

    Yoon, Young Min; Park, Jong-Heum; Lee, Ji-Hye; Park, Jae-Nam; Park, Jin-Kyu; Sung, Nak-Yun; Song, Beom-Seok; Kim, Jae-Hun; Yoon, Yohan; Gao, Meixu; Yook, Hong-Sun; Lee, Ju-Woon

    2012-08-01

    The purpose of this study was to compare the effect of gamma irradiation on the total bacterial population and the sensory quality of Dakgalbi irradiated before and after cooking. Fresh chicken meat was cut into small pieces and used to prepare Dakgalbi. For the preparation of Dakgalbi cooked with gamma-irradiated chicken meat and sauce (IBC), raw chicken meat and Dakgalbi sauce were irradiated and then stir-fried. For the preparation of Dakgalbi irradiated after cooking with raw chicken meat and sauce (IAC), raw chicken meat and Dakgalbi sauce were first cooked and subsequently irradiated. Under the accelerated storage condition of 35 °C for 7 days, bacteria in IBC were below the detection limit (1 log CFU/g) on day 1 but were detected on day 2 and gradually increased hereafter. In IAC, on the other hand, bacteria were not detected at all. Evaluation of sensory quality also decreased on both samples. However, IAC showed a better trend. Our results indicate that IAC protocol was a more effective method for reducing bacterial growth in Dakgalbi.

  10. BACTERIAL POPULATION SHIFTS IN THE RUMEN OF LACTATING DAIRY COWS WITHIN AND ACROSS FEEDING CYCLES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While species composition of the ruminal microflora is thought to change during the feeding cycle due to variations in feed intake and ruminal environmental conditions, no studies have systematically characterized these purported population shifts. We used PCR amplification and automated ribosomal ...

  11. Bacterial populations within copper mine tailings: long-term effects of amendment with Class A biosolids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study evaluates the effect of surface application of dried Class A biosolids on microbial populations within copper mine tailings. Methods and Results: Mine tailing sites were established at ASARCO Mission Mine close to Sahuarita, Arizona. Site 1 (Dec. 1998) was amended with 248 tons ha-1 of C...

  12. Dynamics of Adaptation and Diversification: A 10,000-Generation Experiment with Bacterial Populations

    NASA Astrophysics Data System (ADS)

    Lenski, Richard E.; Travisano, Michael

    1994-07-01

    We followed evolutionary change in 12 populations of Escherichia coli propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences of the uniqueness of evolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drift) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms.

  13. Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal.

    PubMed

    Venkatachalam, Siddarthan; Gowdaman, Vasudevan; Prabagaran, Solai Ramatchandirane

    2015-04-01

    Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills. PMID:25204748

  14. Detection of Group A Streptococcus from Pharyngeal Swab Samples by Bacterial Culture Is Challenged by a Novel mariPOC Point-of-Care Test

    PubMed Central

    Koskinen, Janne O.; Brandt, Annika; Muotiala, Anna; Liukko, Viivi; Soittu, Sari; Meriluoto, Siiri; Vesalainen, Marika; Huovinen, Pentti; Irjala, Kerttu

    2015-01-01

    mariPOC is a novel point-of-care test system for rapid detection of respiratory tract infections. We compared the performance of the mariPOC test to that of bacterial culture for detecting group A streptococcus (GAS) in 219 pharyngitis patients (ages 1–64 years) and 109 healthy asymptomatic controls (ages 19–69 years). In addition, 42 patient samples were analyzed by quantitative PCR (qPCR). Of the 219 pharyngeal patient samples, 32 were positive in a GAS bacterial culture (prevalence 15%) and 65 (30%) in the mariPOC test. The amount of GAS in samples reported positive by the mariPOC test and negative by culture was, on average, 10-fold less than that of those positive in both methods. This indicated that the negative results in bacterial cultures were due to lower sensitivity. The qPCR results were positive and in line with the mariPOC results in 43% of the discordant samples studied. Two GAS culture-positive samples were negative by the mariPOC test. The prevalences of GAS in the control subjects were 2% and 6% by culture and mariPOC results, respectively. We conclude that the mariPOC antigen detection test is more sensitive than the conventional bacterial culture for the detection of GAS among symptomatic pharyngitis patients. The higher prevalence of GAS by the mariPOC test among symptomatic patients was probably not due to carriership, since among the control patients, the difference in the prevalence of GAS by the mariPOC test and culture was not nearly as high, 15% versus 4%, respectively. Clinical trials are needed to show the clinical importance of our findings. PMID:25903570

  15. A new spectrophotometric method for quantification of potassium solubilized by bacterial cultures.

    PubMed

    Rajawat, Mahendra Vikram Singh; Singh, Surender; Saxena, Anil Kumar

    2014-03-01

    A new spectrophotometric method was developed for the quantification of potassium in the culture broth supernatant of K-solubilizing bacteria. The standard curve of potassium with the new method, which is based on the measurement of cobalt, showed a regression coefficient (R2) of 0.998. The quantification values of potassium obtained with flame photometric method and the newly developed method showed a significant correlation (r) of 0.978. The new method depends on the precipitation of sodium cobaltinitrite with solubilized potassium in liquid medium as potassium sodium cobaltinitrite, which develops bluish green colour by the addition of conc. HCl. The intensity of developed colour can be recorded at 623 nm. This method involves less number of steps, is easy and time saving, and can be used for the reliable estimation of available potassium in culture broth supernatant of K-solubilizing bacteria. PMID:24669669

  16. Variations of culturable thermophilic microbe numbers and bacterial communities during the thermophilic phase of composting.

    PubMed

    Li, Rong; Li, Linzhi; Huang, Rong; Sun, Yifei; Mei, Xinlan; Shen, Biao; Shen, Qirong

    2014-06-01

    Composting is a process of stabilizing organic wastes through the degradation of biodegradable components by microbial communities under controlled conditions. In the present study, genera and species diversities, amylohydrolysis, protein and cellulose degradation abilities of culturable bacteria in the thermophilic phase of composting of cattle manure with plant ash and rice bran were investigated. The number of culturable thermophilic bacteria and actinomyces decreased with the increasing temperature. At the initiation and end of the thermophilic phase, genera and specie diversities and number of bacteria possessing degradation abilities were higher than during the middle phase. During the thermophilic composting phase, Bacillus, Geobacillus and Ureibacillus were the dominant genera, and Geobacillus thermodenitrificans was the dominant species. In later thermophilic phases, Geobacillus toebii and Ureibacillus terrenus were dominant. Bacillus, at the initiation, and Ureibacillus and Geobacillus, at the later phase, contributed the multiple degradation abilities. These data will facilitate the control of composting in the future. PMID:24415499

  17. Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation†

    PubMed Central

    Brodie, Eoin L.; DeSantis, Todd Z.; Joyner, Dominique C.; Baek, Seung M.; Larsen, Joern T.; Andersen, Gary L.; Hazen, Terry C.; Richardson, Paul M.; Herman, Donald J.; Tokunaga, Tetsu K.; Wan, Jiamin M.; Firestone, Mary K.

    2006-01-01

    Reduction of soluble uranium U(VI) to less-soluble uranium U(IV) is a promising approach to minimize migration from contaminated aquifers. It is generally assumed that, under constant reducing conditions, U(IV) is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To determine if changes in microbial community composition were a factor in U(IV) reoxidation, we employed a high-density phylogenetic DNA microarray (16S microarray) containing 500,000 probes to monitor changes in bacterial populations during this remediation process. Comparison of the 16S microarray with clone libraries demonstrated successful detection and classification of most clone groups. Analysis of the most dynamic groups of 16S rRNA gene amplicons detected by the 16S microarray identified five clusters of bacterial subfamilies responding in a similar manner. This approach demonstrated that amplicons of known metal-reducing bacteria such as Geothrix fermentans (confirmed by quantitative PCR) and those within the Geobacteraceae were abundant during U(VI) reduction and did not decline during the U(IV) reoxidation phase. Significantly, it appears that the observed reoxidation of uranium under reducing conditions occurred despite elevated microbial activity and the consistent presence of metal-reducing bacteria. High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner. PMID:16957256

  18. Prolonging culture to 15 days improves bacterial detection in bone and joint infections.

    PubMed

    Drago, L; De Vecchi, E; Cappelletti, L; Vassena, C; Toscano, M; Bortolin, M; Mattina, R; Romanò, C L

    2015-09-01

    Since the optimal incubation period of cultures for diagnosis of bone and joint infections is still a matter of debate, the present study aimed to evaluate the effects of different incubation periods (5 and 15 days) on microbial isolation. Samples from 387 patients with bone and joint infections (including prosthetic ones) were analyzed from March 2012 to February 2014. In 197 patients (51 %) growth was obtained within 48 hrs, while in 124 (32 %) and 66 (17 %) patients cultures yielded positive results within and after 5 days of incubation, respectively. Of 449 microorganisms isolated, 247 grew within 48 hrs, 131 within the first 5 days of incubation while 71 were isolated after 5 days. Staphylococcus aureus was the most frequently isolated pathogen within 48 hrs, while Propionibacteria were prevalently isolated after 5 days of incubation. Interestingly, about 25 % of microorganisms isolated after 5 days of incubation were coagulase-negative staphylococci. Extending incubation period of broth cultures improves isolation rates of pathogens involved in bone and joint infections thus improving management of these infections. PMID:26054716

  19. Diverse UV-B resistance of culturable bacterial community from high-altitude wetland water.

    PubMed

    Zenoff, Veronica Fernández; Heredia, Judith; Ferrero, Marcela; Siñeriz, Faustino; Farías, María Eugenia

    2006-05-01

    Isolation of most ultraviolet B (UV-B)-resistant culturable bacteria that occur in the habitat of Laguna Azul, a high-altitude wetland [4554 m above sea level (asl)] from the Northwestern Argentinean Andes, was carried out by culture-based methods. Water from this environment was exposed to UV-B radiation under laboratory conditions during 36 h, at an irradiance of 4.94 W/m2. It was found that the total number of bacteria in water samples decreased; however, most of the community survived long-term irradiation (312 nm) (53.3 kJ/m2). The percentage of bacteria belonging to dominant species did not vary significantly, depending on the number of UV irradiation doses. The most resistant microbes in the culturable community were Gram-positive pigmented species (Bacillus megaterium [endospores and/or vegetative cells], Staphylococcus saprophyticus, and Nocardia sp.). Only one Gram-negative bacterium could be cultivated (Acinetobacter johnsonii). Nocardia sp. that survived doses of 3201 kJ/m2 were the most resistant bacteria to UV-B treatment. This study is the first report on UV-B resistance of a microbial community isolated from high-altitude extreme environments, and proposes a method for direct isolation of UV-B-resistant bacteria from extreme irradiated environments. PMID:16604419

  20. Robustness of an aerobic metabolically vinyl chloride degrading bacterial enrichment culture.

    PubMed

    Zhao, He-Ping; Schmidt, Kathrin R; Lohner, Svenja; Tiehm, Andreas

    2011-01-01

    Degradation of the lower chlorinated ethenes is crucial to the application of natural attenuation or in situ bioremediation on chlorinated ethene contaminated sites. Recently, within mixtures of several chloroethenes as they can occur in contaminated groundwater inhibiting effects on aerobic chloroethene degradation have been shown. The current study demonstrated that metabolic vinyl chloride (VC) degradation by an enrichment culture originating from groundwater was not affected by an equimolar concentration (50 μM) of cis-1,2-dichloroethene (cDCE). Only cDCE concentrations at a ratio of 2.4:1 (initial cDCE to VC concentration) caused minor inhibition of VC degradation. Furthermore, the degradation of VC was not affected by the presence of trans-1,2-dichloroethene (tDCE), 1,1-dichloroethene (1,1-DCE), trichloroethene (TCE), and tetrachloroethene (PCE) in equimolar concentrations (50 μM). Only cDCE and tDCE were cometabolically degraded in small amounts. The VC-degrading culture demonstrated a broad pH tolerance from 5 to 9 with an optimum between 6 and 7. Results also showed that the culture could degrade VC concentrations up to 1,800 μM (110 mg/L). PMID:22020471

  1. Collective Bacterial Dynamics Revealed Using a Three-Dimensional Population-Scale Defocused Particle Tracking Technique

    PubMed Central

    Wu, Mingming; Roberts, John W.; Kim, Sue; Koch, Donald L.; DeLisa, Matthew P.

    2006-01-01

    An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming Escherichia coli cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type Escherichia coli strain RP437 as well as for isogenic derivatives that display smooth swimming due to a cheA deletion (strain RP9535) or incessant tumbling behavior due to a cheZ deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria. PMID:16820497

  2. Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon.

    PubMed

    Hernández, Marcela; Dumont, Marc G; Yuan, Quan; Conrad, Ralf

    2015-03-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. PMID:25616793

  3. Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

    NASA Technical Reports Server (NTRS)

    Ortega, Maya C.

    2011-01-01

    Stromatolites are layered sedimentary structures resulting from microbial mat communities that remove carbon dioxide from their environment and biomineralize it as calcium carbonate. Although prevalent in the fossil record, stromatolites are rare in the modem world and are only found in a few locations including Highbome Cay in the Bahamas. The stromatolites found at this shallow marine site are analogs to ancient microbial mat ecosystems abundant in the Precambrian period on ancient Earth. To understand how stromatolites form and develop, it is important to identify what microorganisms are present in these mats, and how these microbes contribute to geological structure. These results will provide insight into the molecular and geochemical processes of microbial communities that prevailed on ancient Earth. Since stromatolites are formed by lithifying microbial mats that are able to mineralize calcium carbonate, understanding the biological mechanisms involved may lead to the development of carbon sequestration technologies that will be applicable in human spaceflight, as well as improve our understanding of global climate and its sustainability. The objective of my project was to analyze the archaeal and bacterial dIversity in stromatolites from Highborn Cay in the Bahamas. The first step in studying the molecular processes that the microorganisms carry out is to ascertain the microbial complexity within the mats, which includes identifying and estimating the numbers of different microbes that comprise these mats.

  4. Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

    PubMed Central

    Hernández, Marcela; Yuan, Quan; Conrad, Ralf

    2015-01-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with 13CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with 13C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the “Spartobacteria” and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. PMID:25616793

  5. Biodegradation of Various Aromatic Compounds by Enriched Bacterial Cultures: Part A-Monocyclic and Polycyclic Aromatic Hydrocarbons.

    PubMed

    Oberoi, Akashdeep Singh; Philip, Ligy; Bhallamudi, S Murty

    2015-08-01

    Present study focused on the screening of bacterial consortium for biodegradation of monocyclic aromatic hydrocarbon (MAH) and polycyclic aromatic hydrocarbons (PAHs). Target compounds in the present study were naphthalene, acenaphthene, phenanthrene (PAHs), and benzene (MAH). Microbial consortia enriched with the above target compounds were used in screening experiments. Naphthalene-enriched consortium was found to be the most efficient consortium, based on its substrate degradation rate and its ability to degrade other aromatic pollutants with significantly high efficiency. Substrate degradation rate with naphthalene-enriched culture followed the order benzene > naphthalene > acenaphthene > phenanthrene. Chryseobacterium and Rhodobacter were discerned as the predominant species in naphthalene-enriched culture. They are closely associated to the type strain Chryseobacterium arthrosphaerae and Rhodobacter maris, respectively. Single substrate biodegradation studies with naphthalene (PAH) and benzene (MAH) were carried out using naphthalene-enriched microbial consortium (NAPH). Phenol and 2-hydroxybenzaldehyde were identified as the predominant intermediates during benzene and naphthalene degradation, respectively. Biodegradation of toluene, ethyl benzene, xylene, phenol, and indole by NAPH was also investigated. Monod inhibition model was able to simulate biodegradation kinetics for benzene, whereas multiple substrate biodegradation model was able to simulate biodegradation kinetics for naphthalene. PMID:26054614

  6. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

    SciTech Connect

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; Trimble, William; Meyer, Folker; Guglielmini, Julien; Rocha, Eduardo P. C.; Polz, Martin F.

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells. Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.

  7. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

    DOE PAGESBeta

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; Trimble, William; Meyer, Folker; Guglielmini, Julien; Rocha, Eduardo P. C.; Polz, Martin F.

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells.more » Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.« less

  8. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

    PubMed Central

    Phillips, Robyn L.; Gifford, Danna R.; MacLean, R. Craig

    2016-01-01

    There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale. However, bottlenecking had a profound impact on the genes involved in antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions. PMID:27466449

  9. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution.

    PubMed

    Vogwill, Tom; Phillips, Robyn L; Gifford, Danna R; MacLean, R Craig

    2016-07-27

    There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale. However, bottlenecking had a profound impact on the genes involved in antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions. PMID:27466449

  10. Further evidence for the regulation of bacterial populations in soil by protozoa.

    PubMed

    Habte, M; Alexander, M

    1977-06-20

    After the addition to soil of large numbers of a cowpea Rhizobium strain, the population declined steadily until the numbers reached about 10(7)/g, and the protozoa rose to about 10(4)/g. When indigenous protozoa were suppressed by the addition of actidione to the soil, the density of the test rhizobium did not fall initially, but its abundance declined to about 10(7)/g when actidione-resistant protozoa arose in significant numbers. The addition to actidione-treated soil of an antibiotic-resistant strain of Paramecium led to a rapid decrease in the population of the rhizobium, the density reaching essentially the same value as in soil receiving neither the drug nor the paramecia. The same changes occurred with Xanthomonas campestris as test prey except that its numbers fell to about 10(5)/g of soil. These data provide further evidence for the key role of protozoa in controlling the abundance of populations of certain bacteria introduced into soil. PMID:879960

  11. A Locked Nucleic Acid (LNA)-Based Real-Time PCR Assay for the Rapid Detection of Multiple Bacterial Antibiotic Resistance Genes Directly from Positive Blood Culture

    PubMed Central

    Zhu, Lingxiang; Shen, Dingxia; Zhou, Qiming; Li, Zexia; Fang, Xiangdong; Li, Quan-Zhen

    2015-01-01

    Bacterial strains resistant to various antibiotic drugs are frequently encountered in clinical infections, and the rapid identification of drug-resistant strains is highly essential for clinical treatment. We developed a locked nucleic acid (LNA)-based quantitative real-time PCR (LNA-qPCR) method for the rapid detection of 13 antibiotic resistance genes and successfully used it to distinguish drug-resistant bacterial strains from positive blood culture samples. A sequence-specific primer-probe set was designed, and the specificity of the assays was assessed using 27 ATCC bacterial strains and 77 negative blood culture samples. No cross-reaction was identified among bacterial strains and in negative samples, indicating 100% specificity. The sensitivity of the assays was determined by spiking each bacterial strain into negative blood samples, and the detection limit was 1–10 colony forming units (CFU) per reaction. The LNA-qPCR assays were first applied to 72 clinical bacterial isolates for the identification of known drug resistance genes, and the results were verified by the direct sequencing of PCR products. Finally, the LNA-qPCR assays were used for the detection in 47 positive blood culture samples, 19 of which (40.4%) were positive for antibiotic resistance genes, showing 91.5% consistency with phenotypic susceptibility results. In conclusion, LNA-qPCR is a reliable method for the rapid detection of bacterial antibiotic resistance genes and can be used as a supplement to phenotypic susceptibility testing for the early detection of antimicrobial resistance to allow the selection of appropriate antimicrobial treatment and to prevent the spread of resistant isolates. PMID:25775001

  12. Three-dimensional characterization of bacterial microcolonies on solid agar-based culture media.

    PubMed

    Drazek, Laurent; Tournoud, Maud; Derepas, Frédéric; Guicherd, Maryse; Mahé, Pierre; Pinston, Frédéric; Veyrieras, Jean-Baptiste; Chatellier, Sonia

    2015-02-01

    For the last century, in vitro diagnostic process in microbiology has mainly relied on the growth of bacteria on the surface of a solid agar medium. Nevertheless, few studies focused in the past on the dynamics of microcolonies growth on agar surface before 8 to 10h of incubation. In this article, chromatic confocal microscopy has been applied to characterize the early development of a bacterial colony. This technology relies on a differential focusing depth of the white light. It allows one to fully measure the tridimensional shape of microcolonies more quickly than classical confocal microscopy but with the same spatial resolution. Placing the device in an incubator, the method was able to individually track colonies growing on an agar plate, and to follow the evolution of their surface or volume. Using an appropriate statistical modeling framework, for a given microorganism, the doubling time has been estimated for each individual colony, as well as its variability between colonies, both within and between agar plates. A proof of concept led on four bacterial strains of four distinct species demonstrated the feasibility and the interest of the approach. It showed in particular that doubling times derived from early tri-dimensional measurements on microcolonies differed from classical measurements in micro-dilutions based on optical diffusion. Such a precise characterization of the tri-dimensional shape of microcolonies in their late-lag to early-exponential phase could be beneficial in terms of in vitro diagnostics. Indeed, real-time monitoring of the biomass available in a colony could allow to run well established microbial identification workflows like, for instance, MALDI-TOF mass-spectrometry, as soon as a sufficient quantity of material is available, thereby reducing the time needed to provide a diagnostic. Moreover, as done for pre-identification of macro-colonies, morphological indicators such as three-dimensional growth profiles derived from

  13. Variability in Beta-Adrenergic Receptor Population in Cultured Chicken Muscle Cells

    NASA Technical Reports Server (NTRS)

    Young, Ronald B; Bridge, Kristin Y.; Vaughn, Jeffrey R.

    1998-01-01

    Investigations into expression of the beta-adrenergic receptor (bAR) in chicken skeletal muscle cells in culture were initiated because several beta-adrenergic receptor agonists are known to increase skeletal muscle protein deposition in avian and mammalian species. During initial attempts to study the bAR population on the surface of chicken skeletal muscle cells, we observed a high degree of variability that was later found to be the result of using different batches of horse serum in the cell culture media. The separation between total binding and nonspecific binding in cells grown in two serum samples was approximately two-fold The number of nuclei within multinucleated myotubes was not significantly different in cells grown in the two serum samples. To investigate whether these two sera had an effect on coupling efficiency between bAR population and cAMP production, the ability of these cells to synthesize cAMP was also assessed. Despite the two-fold difference in receptor population, the ability of these cells to synthesize cAMP was not significantly different. Because of the possible link between bAR population and muscle protein, we also determined if the quantity of the major skeletal muscle protein, myosin, was affected by conditions that so drastically affected the bAR population. The quantity of myosin heavy chain was not significantly different.

  14. Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches

    PubMed Central

    Pascual, Javier; Blanco, Silvia; García-López, Marina; García-Salamanca, Adela; Bursakov, Sergey A.; Genilloud, Olga; Bills, Gerald F.; Ramos, Juan L.; van Dillewijn, Pieter

    2016-01-01

    Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit. PMID:26741495

  15. Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches.

    PubMed

    Pascual, Javier; Blanco, Silvia; García-López, Marina; García-Salamanca, Adela; Bursakov, Sergey A; Genilloud, Olga; Bills, Gerald F; Ramos, Juan L; van Dillewijn, Pieter

    2016-01-01

    Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit. PMID:26741495

  16. Characterization of certain bacterial strains for potential use as starter or probiotic cultures in dairy products.

    PubMed

    Monteagudo-Mera, A; Caro, I; Rodríguez-Aparicio, L B; Rúa, J; Ferrero, M A; García-Armesto, M R

    2011-08-01

    The present work was aimed at characterizing 12 strains of lactic acid bacteria (LAB) to obtain improved potential starter or probiotic cultures that could be used for making dairy products from ewe's milk and cow's milk. Eight strains with antimicrobial properties, isolated from ewe's milk and from cheese made from ewe's and/or cow's milk, were studied. They were identified as Enterococcus faecalis (five strains), Lactococcus lactis subsp. cremoris, Leuconostoc mesenteroides, and Lactobacillus paracasei subsp. paracasei (one strain of each species). Additionally, four strains were obtained from the American Type Culture Collection: Lactobacillus casei 393 (isolated from cheese), L. lactis subsp. lactis 11454 (origin nonspecified and a producer of nisin), and two strains isolated from human feces (L. paracasei subsp. paracasei 27092 and Lactobacillus rhamnosus 53103, antibacterial agent producer). All E. faecalis strains showed at least one virulence factor (either hemolysin or gelatinase), which emphasizes the importance of these studies in this species. Both L. lactis strains and most Lactobacillus spp. were good acidifiers in ewe's milk and cow's milk at 30°C. High β-galactosidase activity, as well as aminopeptidase activities that favor the development of desirable flavors in cheese, were detected in all Lactobacillus spp. strains. Furthermore, L. rhamnosus ATCC 53103 showed α-fucosidase activity (thought to help colonization of the intestine) and lack of α-glucosidase activity (a trait considered positive for diabetic and obese humans). This last enzymatic activity was also lacking in L. lactis ATCC 11454. L. mesenteroides was the only strain D(2)-lactic acid producer. The selection of any particular strain for probiotic or dairy cultures should be performed according to the technological and/or functional abilities needed. PMID:21819671

  17. Biodegradation of Methyl tert-Butyl Ether by a Bacterial Pure Culture

    PubMed Central

    Hanson, Jessica R.; Ackerman, Corinne E.; Scow, Kate M.

    1999-01-01

    A bacterial strain, PM1, which is able to utilize methyl tert-butyl ether (MTBE) as its sole carbon and energy source, was isolated from a mixed microbial consortium in a compost biofilter capable of degrading MTBE. Initial linear rates of MTBE degradation by 2 × 106 cells ml−1 were 0.07, 1.17, and 3.56 μg ml−1 h−1 for initial concentrations of 5, 50, and 500 μg MTBE ml−1, respectively. When incubated with 20 μg of uniformly labeled [14C]MTBE ml−1, strain PM1 converted 46% to 14CO2 and 19% to 14C-labeled cells within 120 h. This yield is consistent with the measurement of protein accumulation at different MTBE concentrations from which was estimated a biomass yield of 0.18 mg of cells mg MTBE−1. Strain PM1 was inoculated into sediment core material collected from a contaminated groundwater plume at Port Hueneme, California, in which there was no evidence of MTBE degradation. Strain PM1 readily degraded 20 μg of MTBE ml−1 added to the core material. The rate of MTBE removal increased with additional inputs of 20 μg of MTBE ml−1. These results suggest that PM1 has potential for use in the remediation of MTBE-contaminated environments. PMID:10543787

  18. Artificial caries produced by different oral bacterial cultures incubated with bovine dental enamel.

    PubMed

    Gallagher, I H; Pearce, E I; Cutress, T W

    1983-01-01

    Early caries-like lesions were formed in enamel incubated in glucose broths inoculated with different cultures of oral bacteria. Analysis of the broths by gas chromatography revealed, after appropriate incubation, the presence of lactic, succinic, formic, acetic, propionic, isobutyric, n-butyric, isovaleric or n-caproic or mixtures of these acid catabolites. Subsurface lesions formed with all acids and mixtures providing that the terminal pH dropped less than or equal to 5.6. However, the processes conformed in part only with the idealized simple diffusion phenomenon for caries formation, indicating the presence of other factors which could affect the production of lesions in biological systems. PMID:6349592

  19. 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. PMID:26296728

  20. 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 chang