WorldWideScience

Sample records for culturable bacterial populations

  1. Effect of isolate of ruminal fibrolytic bacterial culture supplementation on fibrolytic bacterial population and survivability of inoculated bacterial strain in lactating Murrah buffaloes

    Directory of Open Access Journals (Sweden)

    Brishketu Kumar

    2013-02-01

    Full Text Available Aim: The present study was conducted to evaluate the effect of bacterial culture supplementation on ruminal fibrolytic bacterial population as well as on survivability of inoculated bacterial strain in lactating Murrah buffaloes kept on high fibre diet. Materials and Methods: Fibrolytic bacterial strains were isolated from rumen liquor of fistulated Murrah buffaloes and live bacterial culture were supplemented orally in treatment group of lactating Murrah buffaloes fed on high fibre diet to see it's effect on ruminal fibrolytic bacterial population as well as to see the effect of survivability of the inoculated bacterial strain at three different time interval in comparison to control group. Results: It has been shown by real time quantification study that supplementation of bacterial culture orally increases the population of major fibre degrading bacteria i.e. Ruminococcus flavefaciens, Ruminococcus albus as well as Fibrobacter succinogenes whereas there was decrease in secondary fibre degrading bacterial population i.e. Butyrivibrio fibrisolvens over the different time periods. However, the inoculated strain of Ruminococcus flavefaciens survived significantly over the period of time, which was shown in stability of increased inoculated bacterial population. Conclusion: The isolates of fibrolytic bacterial strains are found to be useful in increasing the number of major ruminal fibre degrading bacteria in lactating buffaloes and may act as probiotic in large ruminants on fibre-based diets. [Vet World 2013; 6(1.000: 14-17

  2. Behaviour of marine oil-degrading bacterial populations in a continuous culture system

    Digital Repository Service at National Institute of Oceanography (India)

    Mohandass, C.; David, J.J.; Nair, S.; LokaBharathi, P.A.; Chandramohan, D.

    In pursuit of developing an oil-degrading microbial consortium, we used the principle of "plasmid assisted molecular breeding" (PAMB) in a continuous culture system. Three marine bacteria, Pseudomonas putida, Brevibacterium epidermidis...

  3. Bacterial cell culture

    OpenAIRE

    sprotocols

    2014-01-01

    ### Materials 1. Glass culture tubes with metal caps and labels - Growth medium, from media room or customized - Glass pipette tubes - Parafilm ### Equipment 1. Vortexer - Fireboy or Bunsen burner - Motorized pipette - Micropipettes and sterile tips ### Procedure For a typical liquid culture, use 5 ml of appropriate medium. The amount in each tube does not have to be exact if you are just trying to culture cells for their precious DNA. 1. Streak an a...

  4. Characterization by culture-dependent and culture-1 independent methods of the 2 bacterial population of suckling-lamb packaged in different atmospheres

    NARCIS (Netherlands)

    Oses, S.M.; Diez, A.M.; Melero, B.; Luning, P.A.; Jaime, I.; Rovira, J.

    2013-01-01

    This study offers insight into the dynamics of bacterial populations in fresh cuts of suckling lamb under four different atmospheric conditions: air (A), and three Modified Atmosphere Packaging (MAP) environments, 15%O2/30%CO2/55%N2 (C, commercial), 70%O2/30%CO2 (O), and 15%O2/85%CO2 (H) for 18

  5. Exometabolomic Profiling of Bacterial Cultures

    DEFF Research Database (Denmark)

    Honoré, Anders Hans

    as the application into other food matrices. The scope of the thesis was to develop and apply a chromatography mass spectrometry based metabolomic footprint workflow for the investigation of the mechanisms behind the antifungal properties of a co‐culture, consisting of Lactobacillus paracasei (LAB A...... chromatography/mass spectrometry (GC/MS). Data from the untargeted LC/MS analysis was processed using feature selection and subsequent multivariate data analysis. The antifungal properties of the co‐culture were composed of several components when fermented in the model system. The major contribution came from......Selected bacterial cultures are used on an industrial scale for biopreservation of fresh fermented dairy products. The selected cultures provide efficient inhibition of yeasts and molds and serve as an alternative to the use of purified or synthetic antimicrobials. Despite the fact that numerous...

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

    Science.gov (United States)

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Bacterial computing with engineered populations.

    Science.gov (United States)

    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. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  8. Diversity of aquatic bacterial populations

    International Nuclear Information System (INIS)

    Teska, J.D.

    1988-01-01

    A study was designed to evaluate the feasibility of adapting the automated Quantum II for the identification of bacterial fish pathogens. Optimal incubation conditions were determined for each of the species used, and, by using a Chi-square goodness of fit test, it was shown that isolates could be sorted into like-species groups with a Ward's hierarchical cluster analysis technique. In a second study, population profiles, growth kinetics, and transformation kinetics were evaluated for bacteria isolated from 4 aquatic environments located in the southeastern United States. Gradual long-term accumulation of organic acids in the waters of the Okefenokee Swamp, located in southeast Georgia and northeast Florida, has resulted in acidic water ranging from pH 3.5 to 4.5. A study was designed to evaluate the metabolic efficiency of surface-water gram-negative nonfermentative bacteria and ascertain whether aquatic bacterial populations exhibit adaptation to the low pH conditions. Using the computerized AMBIS the uptake and incorporation of 35 S-methionine into bacterial proteins under 5 levels of pH was quantitated for each of the test organisms

  9. Exploring bacterial infections: theoretical and experimental studies of the bacterial population dynamics and antibiotic treatment

    Science.gov (United States)

    Shao, Xinxian

    Bacterial infections are very common in human society. Thus extensive research has been conducted to reveal the molecular mechanisms of the pathogenesis and to evaluate the antibiotics' efficacy against bacteria. Little is known, however, about the population dynamics of bacterial populations and their interactions with the host's immune system. In this dissertation, a stochatic model is developed featuring stochastic phenotypic switching of bacterial individuals to explain the single-variant bottleneck discovered in multi strain bacterial infections. I explored early events in a bacterial infection establishment using classical experiments of Moxon and Murphy on neonatal rats. I showed that the minimal model and its simple variants do not work. I proposed modifications to the model that could explain the data quantitatively. The bacterial infections are also commonly established in physical structures, as biofilms or 3-d colonies. In contrast, most research on antibiotic treatment of bacterial infections has been conducted in well-mixed liquid cultures. I explored the efficacy of antibiotics to treat such bacterial colonies, a broadly applicable method is designed and evaluated where discrete bacterial colonies on 2-d surfaces were exposed to antibiotics. I discuss possible explanations and hypotheses for the experimental results. To verify these hypotheses, we investigated the dynamics of bacterial population as 3-d colonies. We showed that a minimal mathematical model of bacterial colony growth in 3-d was able to account for the experimentally observed presence of a diffusion-limited regime. The model further revealed highly loose packing of the cells in 3-d colonies and smaller cell sizes in colonies than plancktonic cells in corresponding liquid culture. Further experimental tests of the model predictions have revealed that the ratio of the cell size in liquid culture to that in colony cultures was consistent with the model prediction, that the dead cells

  10. Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing

    DEFF Research Database (Denmark)

    Masoud, Wafa Mahmoud Hasan; Takamiya, Monica K Wik; Vogensen, Finn Kvist

    2011-01-01

    ripening. Other bacteria like Corynebacterium, Halomonas, Pediococcus, Micrococcus and Staphylococcus, which were encountered in some cheese samples at low percentages compared with the total bacterial populations, were only detected by pyrosequencing. 16S rRNA gene pyrosequencing is an efficient method...

  11. Heterotrophic bacterial populations in tropical sandy beaches

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, S.; LokaBharathi, P.A.

    Distribution pattern of heterotrophic bacterial flora of three sandy beaches of the west coast of India was studied. The population in these beaches was microbiologically different. Population peaks of halotolerant and limnotolerant forms were...

  12. Exometabolomic Profiling of Bacterial Cultures

    DEFF Research Database (Denmark)

    Honoré, Anders Hans

    compounds have been identified as antifungal based on a strategy of bioassay guided fractionation, the factors for antifungal effect remain unexplained. Lack of understanding about the mechanism(s) responsible for the effect restricts development of new cultures with antifungal properties as well...... (LC/MS) instrumentation and a combination of methods selected based on expected compound classes in the exometabolome (paper I). In order to extend the coverage of the exometabolome, low molecular weight and volatile compounds were analyzed after pre‐derivatisation or headspace sampling by gas...... the LAB A cells which produced diacetyl, either secreted or formed by oxidative decarboxylation of secreted acetolactate (manuscript IV). Production of diacetyl occurred without any perturbation of the system by mold hyphae, but was enhanced by the presence of PAB A ferments. Presence of live LAB A cells...

  13. Determination of Bacterial Growth in Culture Media

    International Nuclear Information System (INIS)

    Elly Ellyna Rashid; Shariza Hanim Zainal Abidin; Mok, P.S.

    2015-01-01

    Bacteria is one of the important microorganism in our daily life. Bacteria provides human beings with products in the field of medical, industry, food, agriculture and others. Determination of bacteria growth is important so that we can enjoy the most benefit from it. Spread-plate method is one of the methods to obtain the bacterial counts. Agar plates, such as Nutrient Agar or Plate Count Agar are usually used for this purpose. Bacterial culture will be diluted first before being spread on the agar plate and incubated at specific temperature. The number of bacteria in colony-forming unit (CFU) will be counted the next day. The count will be used to determine the bacterial growth. (author)

  14. Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin.

    Science.gov (United States)

    Medina, Daniel; Walke, Jenifer B; Gajewski, Zachary; Becker, Matthew H; Swartwout, Meredith C; Belden, Lisa K

    2017-01-01

    One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads ( Anaxyrus americanus ) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media, (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting

  15. Population bottlenecks promote cooperation in bacterial biofilms.

    Directory of Open Access Journals (Sweden)

    Michael A Brockhurst

    2007-07-01

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

  16. Culturable endophytic bacterial communities associated with field-grown soybean.

    Science.gov (United States)

    de Almeida Lopes, K B; Carpentieri-Pipolo, V; Oro, T H; Stefani Pagliosa, E; Degrassi, G

    2016-03-01

    Assess the diversity of the culturable endophytic bacterial population associated with transgenic and nontransgenic soybean grown in field trial sites in Brazil and characterize them phenotypically and genotypically focusing on characteristics related to plant growth promotion. Endophytic bacteria were isolated from roots, stems and leaves of soybean cultivars (nontransgenic (C) and glyphosate-resistant (GR) transgenic soybean), including the isogenic BRS133 and BRS245RR. Significant differences were observed in bacterial densities in relation to genotype and tissue from which the isolates were obtained. The highest number of bacteria was observed in roots and in GR soybean. Based on characteristics related to plant growth promotion, 54 strains were identified by partial 16S rRNA sequence analysis, with most of the isolates belonging to the species Enterobacter ludwigii and Variovorax paradoxus. Among the isolates, 44·4% were able to either produce indoleacetic acid (IAA) or solubilize phosphates, and 9·2% (all from GR soybean) presented both plant growth-promoting activities. The results from this study indicate that the abundance of endophytic bacterial communities of soybean differs between cultivars and in general it was higher in the transgenic cultivars than in nontransgenic cultivars. BRS 245 RR exhibited no significant difference in abundance compared to nontransgenic BRS133. This suggests that the impact of the management used in the GR soybean fields was comparable with the impacts of some enviromental factors. However, the bacterial endophytes associated to GR and nontransgenic soybean were different. The soybean-associated bacteria showing characteristics related to plant growth promotion were identified as belonging to the species Pantoea agglomerans and Variovorax paradoxus. Our study demonstrated differences concerning compostion of culturable endophytic bacterial population in nontransgenic and transgenic soybean. © 2016 The Society for Applied

  17. Synchronization and survival of connected bacterial populations

    Science.gov (United States)

    Gokhale, Shreyas; Conwill, Arolyn; Ranjan, Tanvi; Gore, Jeff

    Migration plays a vital role in controlling population dynamics of species occupying distinct habitat patches. While local populations are vulnerable to extinction due to demographic or environmental stochasticity, migration from neighboring habitat patches can rescue these populations through colonization of uninhabited regions. However, a large migratory flux can synchronize the population dynamics in connected patches, thereby enhancing the risk of global extinction during periods of depression in population size. Here, we investigate this trade-off between local rescue and global extinction experimentally using laboratory populations of E. coli bacteria. Our model system consists of co-cultures of ampicillin resistant and chloramphenicol resistant strains that form a cross-protection mutualism and exhibit period-3 oscillations in the relative population density in the presence of both antibiotics. We quantify the onset of synchronization of oscillations in a pair of co-cultures connected by migration and demonstrate that period-3 oscillations can be disturbed for moderate rates of migration. These features are consistent with simulations of a mechanistic model of antibiotic deactivation in our system. The simulations further predict that the probability of survival of connected populations in high concentrations of antibiotics is maximized at intermediate migration rates. We verify this prediction experimentally and show that survival is enhanced through a combination of disturbance of period-3 oscillations and stochastic re-colonization events.

  18. Culture´Contribution to Democracy: Culture, nationalisme and Populism

    DEFF Research Database (Denmark)

    Duelund, Peter

    2018-01-01

    Developments on culture, populism and democracy in Europe. Reasons to populism?   Is populism a new phenomenon? Populism as catch-all label? Common indicators of populism How to deal with populists? Proposal to a comparative COE study on populism......Developments on culture, populism and democracy in Europe. Reasons to populism?   Is populism a new phenomenon? Populism as catch-all label? Common indicators of populism How to deal with populists? Proposal to a comparative COE study on populism...

  19. Bacterial Population Genetics in a Forensic Context

    Energy Technology Data Exchange (ETDEWEB)

    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

  20. Bacterial Pneumonia in Elderly Japanese Populations

    Directory of Open Access Journals (Sweden)

    Naoya Miyashita

    2018-01-01

    Full Text Available Bacterial pneumonia is one of the most important infectious diseases in terms of incidence, effect on quality of life, mortality, and impact on society. Pneumonia was the third leading cause of death in Japan in 2011. In 2016, 119 650 Japanese people died of pneumonia, 96% of whom were aged 65 years and above. The symptoms of pneumonia in elderly people are often atypical. Aspiration pneumonia is seen more frequently than in young people because of swallowing dysfunction in the elderly. The mortality rate is also higher in the elderly than in young people. In Japan, the population is aging at an unprecedented rate, and pneumonia in the elderly will be increasingly important in medicine and medical economics in the future. To manage pneumonia in the elderly, it is important to accurately evaluate its severity, administer appropriate antibiotic treatment, and implement effective preventive measures.

  1. Dynamics of genome rearrangement in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Aaron E Darling

    2008-07-01

    represent the 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.

  2. Early Bacterial Cultures from Open Fractures - Differences Before ...

    African Journals Online (AJOL)

    multiruka1

    hours after injury, had antiseptic wound dressing, had received antibiotics, presented with contamination from the gastrointestinal or genitourinary injuries or were known to have diabetes, peripheral vascular disease or immunosuppression. Informed consent was obtained. Early Bacterial Cultures from Open Fractures -.

  3. Ascitic Fluid Culture In Cirrhotic Patients With Spontaneous Bacterial Peritonitis

    International Nuclear Information System (INIS)

    Sajjad, M.; Khan, Z.A.; Khan, M.S.

    2016-01-01

    Objective: To determine the frequency and compare the culture yield of bacterial isolation by conventional and blood culture BACTEC bottle techniques in cirrhotic patients with spontaneous bacterial peritonitis (SBP). Study Design: Cross-sectional comparative study. Place and Duration of Study: Pathology Department, Bannu Medical College, Bannu, KPK, from January 2012 to December 2013. Methodology: Paracentesis of 20 ml of ascitic fluid tapped from cirrhotic patients with SBP was carried out by a single technologist. The analysis included differential leukocyte count (DLC), while 5 ml each of the fluid was inoculated into conventional culture media and BACTEC blood culture bottle. All the data were analysed on (SPSS) version 16 to determine frequencies with percentages and mean values with standard deviation. Chi-square test was used for comparing the yield of conventional and blood culture bottle methods. P-value was considered significant if < 0.05. Results: In 105 cases of ascitic fluid analyses, 27 (25.72 percent) had positive ascitic fluid culture whereas 78 (74.28 percent) had negative ascitic fluid culture. Ascitic fluid culture was positive in 6 cases by conventional culture media and in 27 cases by BACTEC culture bottle media (p < 0.001). Bacterial isolation was obtained by both culture methods in 6 cases (p < 0.001). Conclusion: Direct bedside inoculation of ascitic fluid by BACTEC culture bottle method has better yield as compared to conventional culture method. (author)

  4. Enrichment of an Endosulfan-Degrading Mixed Bacterial Culture

    OpenAIRE

    Sutherland, Tara D.; Horne, Irene; Lacey, Michael J.; Harcourt, Rebecca L.; Russell, Robyn J.; Oakeshott, John G.

    2000-01-01

    An endosulfan-degrading mixed bacterial culture was enriched from soil with a history of endosulfan exposure. Enrichment was obtained by using the insecticide as the sole source of sulfur. Chemical hydrolysis was minimized by using strongly buffered culture medium (pH 6.6), and the detergent Tween 80 was included to emulsify the insecticide, thereby increasing the amount of endosulfan in contact with the bacteria. No growth occurred in control cultures in the absence of endosulfan. Degradatio...

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

    Science.gov (United States)

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

    2012-10-16

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

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

    International Nuclear Information System (INIS)

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

    1995-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

    A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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

    Science.gov (United States)

    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

  9. Comparison of culture and PCR methods in the diagnosis of bacterial meningitis.

    Science.gov (United States)

    Başpınar, Emel Ödemiş; Dayan, Saim; Bekçibaşı, Muhammed; Tekin, Recep; Ayaz, Celal; Deveci, Özcan; Hoşoğlu, Salih

    Our aim in this study is to compare the standard culture method with the multiplex PCR and the Speed-Oligo ® Bacterial Meningitis Test (SO-BMT) - a hybridization-based molecular test method - during the CSF examination of the patients with the pre-diagnosis of acute bacterial meningitis. For the purposes of this study, patients with acute bacterial meningitis treated at the Dicle University Medical Faculty Hospital, Infectious Diseases and Clinical Microbiology Clinic between December 2009 and April 2012 were retrospectively evaluated. The diagnosis of bacterial meningitis was made based on the clinical findings, laboratory test anomalies, CSF analysis results, and the radiological images. Growth was observed in the CSF cultures of 10 out of the 57 patients included in the study (17.5%) and Streptococcus pneumoniae was isolated in all of them. The CSF samples of 34 patients (59.6%) were positive according to the SO-BMT and S. pneumoniae was detected in 33 of the samples (97.05%), while Neisseria meningitidis was found in 1 sample (2.95%). In a total of 10 patients, S. pneumoniae was both isolated in the CSF culture and detected in the SO-BMT. The culture and the SO-BMT were negative in 23 of the CSF samples. There was no sample in which the CSF culture was positive although the SO-BMT was negative. While SO-BMT seems to be a more efficient method than bacterial culturing to determine the pathogens that most commonly cause bacterial meningitis in adults, further studies conducted on larger populations are needed in order to assess its efficiency and uses. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  10. Effect of a Bacterial Grass Culture on the Plant Growth and Disease Control in Tomato

    Directory of Open Access Journals (Sweden)

    Yong Seong Lee

    2017-12-01

    Full Text Available This study aimed to investigate the plant growth-promoting and biocontrol potential of a grass culture with Paenibacillus ehimensis KWN8 on tomato. For this experiment, treatments of a chemical fertilizer (F, a bacterial grass culture (G, a 1/3 volume of G plus 2/3 F (GF, and F plus a synthetic fungicide (FSf were applied to tomato leaves and roots. The result showed that the severity of Alternariasolani and Botrytiscinerea symptoms were significantly reduced after the application of the bacterial grass culture (G and GF and FSf. In addition, root mortality in G and GF was lower compared to F. Tomato plants treated with G or GF had better vegetative growth and yield compared to F. Application of G affected the fungal and bacterial populations in the soil. In conclusion, treatment with a bacterial grass culture decreased disease severity and increased tomato growth parameters. However, there were no statistically significant correlations between disease occurrence and tomato yields. This experiment presents the possibility to manage diseases of tomato in an environmentally friendly manner and to also increase the yield of tomato by using a grass culture broth containing P. ehimensis KWN38.

  11. Population Bottlenecks Promote Cooperation in Bacterial Biofilms

    OpenAIRE

    Brockhurst, Michael A.

    2007-01-01

    Population bottlenecks are assumed to play a key role in the maintenance of social traits in microbes. Ecological parameters such as colonisation or disturbances can favour cooperation through causing population bottlenecks that enhance genetic structuring (relatedness). However, the size of the population bottleneck is likely to play a crucial role in determining the success of cooperation. Relatedness is likely to increase with decreasing bottleneck size thus favouring the evolution of coop...

  12. Characterization of Cellulolytic Bacterial Cultures Grown in Different Substrates

    Directory of Open Access Journals (Sweden)

    Mohamed Idris Alshelmani

    2013-01-01

    Full Text Available 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.

  13. Measurement of Behavioral Evolution in Bacterial Populations

    Science.gov (United States)

    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

  14. Abundance of three bacterial populations in selected streams

    Science.gov (United States)

    O.A. Olapade; X. Gao; L.G. LEff

    2005-01-01

    The population sizes of three bacterial species, Acinetobacter calcoaceticw, Burkholderia cepacia, and Pseudomonas putida, were examined in water and sediment from nine streams in different parts of the United States using fluorescent in situ hybridization (FISH). Population sizes were determined from three sites (upstream,...

  15. The analysis of bacterial culture in radiation mucositis

    International Nuclear Information System (INIS)

    Wen Zunbei; Su Deqing; Liang Yuxue

    2006-01-01

    Objective: To investigate pathogen dose existing or not in patients with radiation mucositis. Methods: From Juanary 2004 to August 2005, from 46 patients with radiation mucositis some pharynx secretion were taken for culture. Then they were treated with antibiotics selected by the cultured results and gargle. Results: 5 patients with grade 0 of radiation mucositis were with no cultured pathogen, and the results of some other patients with radiation mucositis include 8 cases of epiphyte, 1 cases of p. vulgaris and 3 cases of Staphylococcus. the positive rate is 29.2% (12/41); Conclusion: Some patients with radiation mucositis do exist pathogen, and we must slect antibiotics by the bacterial cultured results. (authors)

  16. Oviposition Attractancy of Bacterial Culture Filtrates: response of Culex quinquefasciatus

    Directory of Open Access Journals (Sweden)

    S Poonam

    2002-04-01

    Full Text Available Oviposition attractants could be used for monitoring as well as controlling mosquitoes by attracting them to lay eggs at chosen sites. In the present study, culture filtrates of seven bacterial species were tested for their attractancy against gravid females of Culex quinquefasciatus. When their oviposition active indices (OAI were studied, the culture filtrates of Bacillus cereus and Pseudomonas fluorescens exhibited oviposition attractancy (OAI = >0.3 at 100 ppm and the OAI were respectively 0.70 and 0.47. Culture filtrates of B. thuringiensis var. israelensis (wild type, B. t. var. israelensis (mutant and B. sphaericus showed attractancy at 2000 ppm with OAI of respectively 0.71, 0.59 and 0.68. However, the OAI of B. megaterium as well as Azospirillum brasilense was 0.13 (at 2000 ppm, which was less than 0.3 required to be considered them as attractants. When the oviposition attractancy of the bacterial culture filtrates were compared with that of a known oviposition attractant, p-cresol (at 10 ppm, the culture filtrates of B. t. var. israelensis (wild type and B. cereus were found to be more active than p-cresol, respectively with 64.2 and 54.3% oviposition.

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

    Science.gov (United States)

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

    2013-12-01

    culture-dependent methods. The use of pyrosequencing allowed for the identification of low abundance bacteria in leaf salad vegetables not detected by culture-dependent methods. The presence of a range of bacterial populations as endophytes presents an interesting phenomenon as these microorganisms cannot be removed by washing and are thus ingested during salad consumption.

  18. Bayesian modeling of bacterial growth for multiple populations

    OpenAIRE

    Palacios, Ana Paula; Marín, J. Miguel; Quinto, Emiliano J.; Wiper, Michael P.

    2014-01-01

    Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this study, we develop two models to describe bacterial growth for multiple populations under both equal and different environmental conditions. Firstly, a semi-parametric model based on the Gompertz equation is proposed. Assuming that the parameters of the Gomp...

  19. Bayesian modelling of bacterial growth for multiple populations

    OpenAIRE

    Palacios, Ana Paula; Marín Díazaraque, Juan Miguel; Quinto, Emiliano; Wiper, Michael Peter

    2012-01-01

    Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this study, we develop two models to describe bacterial growth for multiple populations under both equal and different environmental conditions. Firstly, a semi-parametric model based on the Gompertz equation is proposed. Assuming that the parameters of the Gomp...

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

    International Nuclear Information System (INIS)

    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 14 CO 2 from mineralized 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Foght, J.M.; Westlake, D.W.S. (Univ. of Alberta, Edmonton (Canada)); Gutnick, D.L. (Tel Aviv Univ., Ramat Aviv (Israel))

    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.

  2. Enrichment of an endosulfan-degrading mixed bacterial culture.

    Science.gov (United States)

    Sutherland, T D; Horne, I; Lacey, M J; Harcourt, R L; Russell, R J; Oakeshott, J G

    2000-07-01

    An endosulfan-degrading mixed bacterial culture was enriched from soil with a history of endosulfan exposure. Enrichment was obtained by using the insecticide as the sole source of sulfur. Chemical hydrolysis was minimized by using strongly buffered culture medium (pH 6.6), and the detergent Tween 80 was included to emulsify the insecticide, thereby increasing the amount of endosulfan in contact with the bacteria. No growth occurred in control cultures in the absence of endosulfan. Degradation of the insecticide occurred concomitant with bacterial growth. The compound was both oxidized and hydrolyzed. The oxidation reaction favored the alpha isomer and produced endosulfate, a terminal pathway product. Hydrolysis involved a novel intermediate, tentatively identified as endosulfan monoaldehyde on the basis of gas chromatography-mass spectrometry and chemical derivatization results. The accumulation and decline of metabolites suggest that the parent compound was hydrolyzed to the putative monoaldehyde, thereby releasing the sulfite moiety required for growth. The monoaldehyde was then oxidized to endosulfan hydroxyether and further metabolized to (a) polar product(s). The cytochrome P450 inhibitor, piperonyl butoxide, did not prevent endosulfan oxidation or the formation of other metabolites. These results suggest that this mixed culture is worth investigating as a source of endosulfan-hydrolyzing enzymes for use in enzymatic bioremediation of endosulfan residues.

  3. Biodegradation of dibenzothiophenes by pure and mixed bacterial cultures

    Energy Technology Data Exchange (ETDEWEB)

    Kropp, K.G.; Fedorak, P.M.; Saftic, S. [Alberta Univ., Edmonton, AB (Canada). Dept. of Biochemistry; Anderson, J.T. [University of Munster, Dept. of Analytical Chemistry, Munster (Germany)

    1996-05-01

    Studies of the biotransformation of compounds such as alkyl-dibenzothiophenes in petroleum were performed in an effort to clarify the feasibility of bioremediation in environmental cleanup. Dibenzothiophene (DBT) has been used as a model compound for studies of microbial metabolism of aromatic sulfur heterocycles, but studies on the biodegradation of alkylated DBTs were hampered because they are not commercially available. The transformation of dimethylDBTs by mixed oil-degrading bacterial cultures were studied with the aromatic fraction of Prudhoe Bay crude oil as the growth substrate. Many metabolites from the bacterial oxidation of methyl and dimethylDBTs were identified. The accumulation of these metabolites suggests that loss of a compound from an environment could be due to partial oxidation rather than complete biodegradation. 36 refs., 1 tab., 12 figs.

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

    Science.gov (United States)

    McGarvey, J A; Franco, R B; Palumbo, J D; Hnasko, R; Stanker, L; Mitloehner, F M

    2013-06-01

    To describe, at high resolution, the bacterial population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their bacterial population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in bacterial diversity. In-depth 16S rRNA gene sequence analysis revealed significant bacterial population structure changes during ensiling and again during exposure to air. This in-depth description of the bacterial population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes. © 2013 The Society for Applied Microbiology No claim to US Government works.

  5. Metabolic competition as a driver of bacterial population structure.

    Science.gov (United States)

    Watkins, Eleanor R; Maiden, Martin Cj; Gupta, Sunetra

    2016-10-01

    Understanding the processes whereby diversity arises and is maintained in pathogen populations is pivotal for designing disease control interventions. A particular problem is the maintenance of strain structure in bacterial pathogen populations despite frequent genetic exchange. Although several theoretical frameworks have been put forward to explain this widespread phenomenon, few have focused on the role of genes encoding metabolic functions, despite an increasing recognition of their importance in pathogenesis and transmission. In this article, we review the literature for evidence of metabolic niches within the host and discuss theoretical frameworks which examine ecological interactions between metabolic genes. We contend that metabolic competition is an important phenomenon which contributes to the maintenance of population structure and diversity of many bacterial pathogens.

  6. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    International Nuclear Information System (INIS)

    Cherrier, J.

    2005-01-01

    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 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 2 was used as the indicator of hydrocarbon degradation and (delta) 13 C analysis of the resultant CO 2 was used to evaluate the source of the respired CO 2 (i.e. petroleum hydrocarbons or the pinfish cometabolite). Results from these time

  7. Atypical bacterial pneumonia in the HIV-infected population.

    Science.gov (United States)

    Head, Breanne M; Trajtman, Adriana; Rueda, Zulma V; Vélez, Lázaro; Keynan, Yoav

    2017-01-01

    Human immunodeficiency virus (HIV)-infected individuals are more susceptible to respiratory tract infections by other infectious agents (viruses, bacteria, parasites, and fungi) as their disease progresses to acquired immunodeficiency syndrome. Despite effective antiretroviral therapy, bacterial pneumonia (the most frequently occurring HIV-associated pulmonary illness) remains a common cause of morbidity and mortality in the HIV-infected population. Over the last few decades, studies have looked at the role of atypical bacterial pneumonia (i.e. pneumonia that causes an atypical clinical presentation or responds differently to typical therapeutics) in association with HIV infection. Due to the lack of available diagnostic strategies, the lack of consideration, and the declining immunity of the patient, HIV co-infections with atypical bacteria are currently believed to be underreported. Thus, following an extensive database search, this review aimed to highlight the current knowledge and gaps regarding atypical bacterial pneumonia in HIV. The authors discuss the prevalence of Chlamydophila pneumoniae , Mycoplasma pneumoniae , Coxiella burnetii , Legionella species and others in the HIV-infected population as well as their clinical presentation, methods of detection, and treatment. Further studies looking at the role of these microbes in association with HIV are required. Increased knowledge of these atypical bacteria will lead to a more rapid diagnosis of these infections, resulting in an improved quality of life for the HIV-infected population.

  8. Culture and population: a theoretical perspective.

    Science.gov (United States)

    Mann, R S

    1983-12-01

    Social scientists, and especially anthropologists, have failed to provide the type of cultural information needed to develop effective strategies for increasing family planning acceptance among India's rural ethnic and tribal groups. Anthropologists have provided detailed description of the social behavior and of the material culture of these diverse groups, but they have not furnished information on the mental or emic aspects of their cultures. Effective program strategies must be tailored to the underlying cultural codes which govern, organize, and integrate the observed behavior of these groups. Knowledge of the cultural codes, or cognitive maps of the culture, permits an outsider to understand why individuals in specific cultures behave the way they do and how the diverse aspects of observed behavior are interconnected. Strategies developed on the basis of observed behavior often fail to effect change because they are based on false assumptions about how the culture operates. A technique, componential analysis, for ascertaining the underlying code or cognitive map of a culture was developed during the 1950s, and this approach should be more widely applied in anthropological investigations in India. An approach for developing effective population and family planning programs should include: 1) strengthening the academic training of anthropologists and preparing them to undertake microlevel research aimed at delineating the cognitive maps of India's ethnic communities, 2) using the cognitive maps derived from investigations to develop program strategies, 3) assigning specific tasks to the various organizations and agencies involved in family planning in accordance with the cultural requirements of the target population, 4) coordinating the tasks of the different organizations, and 5) conducting ongoing evaluation research to assess the effectiveness of the programs and to detect weak program components which need to be brought more into line with the cognitive

  9. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Science.gov (United States)

    Müller, Maren Stella; Scheu, Stefan; Jousset, Alexandre

    2013-01-01

    Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  10. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Directory of Open Access Journals (Sweden)

    Maren Stella Müller

    Full Text Available Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG, pyrrolnitrin (PRN and hydrogen cyanide (HCN in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks, as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  11. The Importance of Bacterial Culture to Food Microbiology in the Age of Genomics.

    Science.gov (United States)

    Gill, Alexander

    2017-01-01

    Culture-based and genomics methods provide different insights into the nature and behavior of bacteria. Maximizing the usefulness of both approaches requires recognizing their limitations and employing them appropriately. Genomic analysis excels at identifying bacteria and establishing the relatedness of isolates. Culture-based methods remain necessary for detection and enumeration, to determine viability, and to validate phenotype predictions made on the bias of genomic analysis. The purpose of this short paper is to discuss the application of culture-based analysis and genomics to the questions food microbiologists routinely need to ask regarding bacteria to ensure the safety of food and its economic production and distribution. To address these issues appropriate tools are required for the detection and enumeration of specific bacterial populations and the characterization of isolates for, identification, phylogenetics, and phenotype prediction.

  12. Improved yield of minimal proportional sample volume platelet bacterial culture.

    Science.gov (United States)

    Kamel, Hany; Townsend, Mary; Bravo, Marjorie; Vassallo, Ralph R

    2017-10-01

    Reports of septic transfusion reactions (STRs) after transfusion of culture-negative platelets (PLTs) justify more effective prevention strategies. Pathogen reduction technologies or performance of additional point-of-issue testing are proposed strategies to enhance safety through Day 5 of storage. Trima leukoreduced apheresis PLTs (APs) were collected during two study periods (45 and 31 months) using standard procedures, with target settings adjusted during the second period to maintain split rate after increased culture volume. Primary testing for bacterial contamination was performed using BacT/ALERT 3D with sampling from the mother bag 24 to 36 hours after collection. Two culture approaches were compared: in Period A, an 8-mL sample in one aerobic culture bottle (CB), and in Period B a minimal proportional sample volume (PSV) of at least 3.8% of mother bag volume into one to three aerobic CBs (7-10 mL per bottle). In Periods A and B, 188,389 and 159,098 AP collections were tested, respectively. The true-positive (TP) rate in Period A was 0.90 per 10,000 collections and in Period B was 1.83 per 10,000 (p collections, was significantly higher than that of Period A, 3.66 per 10,000. One contaminated collection resulting in STR(s) was reported in each study period. Implementation of PSV was operationally successful and did not impact the AP split rate. Proportional sample volume improved the sensitivity of primary testing and identified collections that could have escaped detection had only a single bottle with 8- to 10-mL volume been used. PSV may represent another approach to enhanced PLT safety for 5-day storage without a requirement for secondary testing. © 2017 AABB.

  13. Effect of lidocaine 2% on bacterial culture of bronchial fluid

    International Nuclear Information System (INIS)

    Samet, M.; Meybodi, F.A.A.; Mokarianpour, T.; Fallah, T.; Mongabadi, F.D.; Ayatollahi, J.; Shahcherghi, S.H.; Yazdi, M.H.A

    2017-01-01

    Objective:To evaluate the action of 2% lidocaine on the culture results of bronchial fluid in patients suspected of having lower respiratory tract infections. Study Design:Cross-sectional analytical study. Place and Duration of Study:Shahid Sadoughi Hospital, Yazd, Iran, from November 2014 to November 2015. Methodology:Patients suspected of lower respiratory tract infections referred to bronchoscopy unit of the Hospital were included. Those with incomplete questionnaire and bronchoscopy contraindication were excluded. Bronchial fluid was aspirated before and after local application of 2% lidocaine and cultured, according to the suspected clinical diagnosis. Finally, statistical analysis was performed using SPSS software, version 17.0. For statistical comparisons, McNemar's test was used. Level of significance was kept at p <0.05. Results:The mean age of the study population was 51.83 +-15.93 with a range of 25 - 80 years. Out of 130 patients, 60 patients had positive culture results. Nineteen (31.7%) cases had positive culture for tuberculosis and 41 (63.3%) cases had positive results for other bacteria before intervention that did not change after using 2% lidocaine (p=1). In 70 (53.84%) cases, results were negative before and after use of 2% lidocaine. Conclusion:No significant difference was found between culture results before and after the use of lidocaine. Therefore, lidocaine can be used during bronchoscopy to increase patient tolerance. (author)

  14. Nonlinear Stochastic Modelling of Antimicrobial resistance in Bacterial Populations

    DEFF Research Database (Denmark)

    Philipsen, Kirsten Riber

    an important role for the evolution of resistance. When growing under stressed conditions, such as in the presence of antibiotics, mutators are considered to have an advantages in comparison to non-mutators. This has been supported by a mathematical model for competing growth between a mutator and a non......This thesis applies mathematical modelling and statistical methods to investigate the dynamics and mechanisms of bacterial evolution. More specifically it is concerned with the evolution of antibiotic resistance in bacteria populations, which is an increasing problem for the treatment of infections...... in humans and animals. To prevent the evolution and spread of resistance, there is a need for further understanding of its dynamics. A grey-box modelling approach based on stochastic differential equations is the main and innovative method applied to study bacterial systems in this thesis. Through...

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

    Science.gov (United States)

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

    2014-09-01

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

  16. Detecting rare gene transfer events in bacterial populations

    Directory of Open Access Journals (Sweden)

    Kaare Magne Nielsen

    2014-01-01

    Full Text Available 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.

  17. Cultural sexual selection in monogamous human populations.

    Science.gov (United States)

    Nakahashi, Wataru

    2017-06-01

    In humans, both sexes sometimes show peculiar mating preferences that do not appear to increase their fitness either directly or indirectly. As humans may transmit their preferences and target culturally, and these may be artificially modifiable, I develop theoretical models where a preference and/or a trait are culturally transmitted with a restriction of the trait modification. I assume a monogamous population where some individuals fail to find a mate, and this affects the preference and the trait in the next time step. I show that a strong aversion to, or high tolerance of, failed individuals are necessary for the evolution of irrational preferences that neither seek good genes nor any direct benefit. This evolution is more likely to occur when the preference and/or the trait are cultural rather than genetic. These results may partly explain why humans sometimes show mating preferences for exaggerated physical and cultural traits.

  18. Culture -independent Pathogenic Bacterial Communities in Bottled Mineral Water

    Directory of Open Access Journals (Sweden)

    Hamdy A. Hassan

    2015-08-01

    Full Text Available Bottled mineral water (BMW is an alternative to mains water and consider it to be better and safer. Access to safe BMW from the bacteria involving potential health hazard is essential to health. Cultivation-independent technique PCR-based single-strand conformation polymorphism (SSCP for genetic profiling of PCR-amplified 16S rRNA genes was performed using Com primer set targeting the 16S rRNA genes for detection of pathogenic bacteria in bottled mineral water from the final product of six factories for bottled mineral drinking water in Wadi El-natron region- Egypt. These factories use often ozone technology to treat large quantities of water because of its effectiveness in purifying and conditioning water. A total of 27 single products were isolated from the profiles by PCR re-amplification and cloning. Sequence analysis of 27 SSCP bands revealed that the 16S rRNA sequences were clustered into seven operational taxonomic units (OTUs and the compositions of the communities of the six samples were all common. The results showed that most communities from phyla Alphaproteobacteria and certainly in the Sphingomonas sp. Culture-independent approaches produced complementary information, thus generating a more accurate view for the bacterial community in the BMW, particularly in the disinfection step, as it constitutes the final barrier before BMW distribution to the consumer

  19. Culture-proven bacterial keratitis in a Malaysian general hospital.

    Science.gov (United States)

    Hooi, S H; Hooi, S T

    2005-12-01

    One hundred patients (101 eyes) with culture-proven bacterial keratitis were treated in the Department of Ophthalmology, Hospital Sultanah Aminah, Johor Bahru, over a 4-year period. The majority of patients was male (63%), Malay (60%), from the Johor Bahru district (62%) and aged between 41 to 50 years (20%). The ocular predisposing factors were ocular trauma (41 eyes), ocular surface disease (28 eyes) and contact lens wear (26 eyes). The corneal ulcers were mainly large (50.5%), central (59.4%) and colonized by Gram-negative bacteria (78.1%). The most frequently isolated microorganisms were Pseudomonas aeruginosa (67 eyes), Staphylococcus aureus (12 eyes), Acinetobacter baumanii (6 eyes), Klebsiella pneumoniae (5 eyes), Corynebacterium sp. (3 eyes:) and Streptococcus pneumonliae (3 eyes). Twelve eyes (11.8%) had polymicrobial infection. A good visual outcome occurred in 52.5% of eyes analysed. Prognostic factors for visual outcome include presenting Snellen visual acuity, time to presentation after onset of ocular symptoms, ocular predisposing factor, corneal ulcer location and corneal ulcer size.

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

    Science.gov (United States)

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

    2015-02-01

    Microbial spoilage of meat is a complex event to which many different bacterial populations can contribute depending on the temperature of storage and packaging conditions. The spoilage can derive from microbial development and consumption of meat nutrients by bacteria with a consequent release of undesired metabolites. The volatile organic compounds (VOCs) that are generated during meat storage can have an olfactory impact and can lead to rejection of the product when their concentration increase significantly as a result of microbial development. The VOCs most commonly identified in meat during storage include alcohols, aldehydes, ketones, fatty acids, esters and sulfur compounds. In this review, the VOCs found in fresh meat during storage in specific conditions are described together with the possible bacterial populations responsible of their production. In addition, on the basis of the data available in the literature, the sensory impact of the VOCs and their dynamics during storage is discussed to highlight their possible contribution to the spoilage of meat. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Dynamics of adaptive immunity against phage in bacterial populations

    Science.gov (United States)

    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. Perfil de susceptibilidade a antimicrobianos de bactérias isoladas em diferentes sistemas de cultivo de tilápia-do-nilo (Oreochromis niloticus Profile of antimicrobial resistance in bacterial populations recovered from different Nile tilapia (Oreochromis niloticus culture systems

    Directory of Open Access Journals (Sweden)

    D.O. Carneiro

    2007-08-01

    Full Text Available Caracterizaram-se as populações bacterianas isoladas de três sistemas de cultivo de tilápias, sem utilização prévia de antimicrobianos. No sistema 1 usou-se tanque de alvenaria com arraçoamento, no sistema 2, tanque de terra com arraçoamento e no sistema 3, tanque de terra com adubação orgânica. Posteriormente, foi verificado o perfil qualitativo de resistência a antimicrobianos de 98 amostras bacterianas. Membros da família Vibrionaceae predominaram nos três sistemas analisados. Observou-se elevado número de bactérias resistentes principalmente à ampicilina e à eritromicina. Bactérias resistentes à norfloxacina e à gentamicina não foram freqüentes e cerca de 50% das amostras dos isolados bacterianos foram resistentes à tetraciclina. Dentre as amostras testadas, 96% apresentaram resistência simultânea a dois ou mais antimicrobianos (MAR>0,2. O índice MAR médio para os três sistemas de criação foi 0,4, e foram mesmo considerados fontes de risco para disseminação de bactérias resistentes.Bacterial populations from different tilapia culture system with no antimicrobial use were characterized. Concret pond and commercial feed, land pond and commercial feed, and land pond and animal manure were used in systems I, II and III, respectively. Ninety-eight bacterial strains were subjected to sensitivity testing. Members of Vibrionaceae were the most prevalent in all systems analysed. The most bacterial strains were resistant to ampicillin and erithromicin, but resistance to norfloxacin and gentamicin were uncommon. A half to bacterial isolates was resistant to tetracycline. From the 98 bacterial isolates, 96% were resistant to two or more antimicrobials. The multiple antimicrobial resistance index was determined and it was similar for all systems analyzed (Mar= 0.4, indicating a high risk source for multiple antibiotic resistance.

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

    Directory of Open Access Journals (Sweden)

    Leilei Qu

    2016-01-01

    Full Text Available 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.

  4. Bacterial population solitary waves can defeat rings of funnels

    International Nuclear Information System (INIS)

    Morris, Ryan J; Phan, Trung V; Austin, Robert H; Black, Matthew; Bos, Julia A; Lin, Ke-Chih; Kevrekidis, Ioannis G

    2017-01-01

    We have constructed a microfabricated circular corral for bacteria made of rings of concentric funnels which channel motile bacteria outwards via non-hydrodynamic interactions with the funnel walls. Initially bacteria do move rapidly outwards to the periphery of the corral. At the edge, nano-slits allow for the transport of nutrients into the device while keeping the bacteria from escaping. After a period of time in which the bacteria increase their cell density in this perimeter region, they are then able to defeat the physical constrains of the funnels by launching back-propagating collective waves. We present the basic data and some nonlinear modeling which can explain how bacterial population waves propagate through a physical funnel, and discuss possible biological implications. (paper)

  5. The population and evolutionary dynamics of homologous gene recombination in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Bruce R Levin

    2009-08-01

    Full Text Available In bacteria, recombination is a rare event, not a part of the reproductive process. Nevertheless, recombination -- broadly defined to include the acquisition of genes from external sources, i.e., horizontal gene transfer (HGT -- plays a central role as a source of variation for adaptive evolution in many species of bacteria. Much of niche expansion, resistance to antibiotics and other environmental stresses, virulence, and other characteristics that make bacteria interesting and problematic, is achieved through the expression of genes and genetic elements obtained from other populations of bacteria of the same and different species, as well as from eukaryotes and archaea. While recombination of homologous genes among members of the same species has played a central role in the development of the genetics and molecular biology of bacteria, the contribution of homologous gene recombination (HGR to bacterial evolution is not at all clear. Also, not so clear are the selective pressures responsible for the evolution and maintenance of transformation, the only bacteria-encoded form of HGR. Using a semi-stochastic simulation of mutation, recombination, and selection within bacterial populations and competition between populations, we explore (1 the contribution of HGR to the rate of adaptive evolution in these populations and (2 the conditions under which HGR will provide a bacterial population a selective advantage over non-recombining or more slowly recombining populations. The results of our simulation indicate that, under broad conditions: (1 HGR occurring at rates in the range anticipated for bacteria like Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, and Bacillus subtilis will accelerate the rate at which a population adapts to environmental conditions; (2 once established in a population, selection for this capacity to increase rates of adaptive evolution can maintain bacteria-encoded mechanisms of recombination and prevent

  6. Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp.

    Directory of Open Access Journals (Sweden)

    Cécile Clavaud

    Full Text Available 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.

  7. Rapid radiorespirometric method for the estimation of bacterial counts of cellulomonas cultures

    International Nuclear Information System (INIS)

    Jakubick-Neradova, V.

    1975-01-01

    The determination of bacterial counts in cultures of Cellulomonas species C-72-4 by a radiorespirometric technique was twenty times faster than the conventional method. A linear correlation was found between the bacterial counts and the 14 CO 2 metabolized from labelled glucose added to the cellulose medium. (orig.) [de

  8. Costs and benefits of bacterial culturing and pathogen reduction in the Netherlands

    NARCIS (Netherlands)

    Janssen, M.P.; van der Poel, C.L.; Buskens, E.; Bonneux, L.; Bonsel, G.J.; van Hout, B.A.

    2006-01-01

    BACKGROUND: Bacterial contamination is a life-threatening risk of blood transfusion, especially with platelet (PLT) transfusions. Bacterial culturing (BCU) of PLTs as well as pathogen reduction (PRT) reduce the likelihood of such contamination. The cost-effectiveness (CE) of these interventions was

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  11. Cultural competency and recovery within diverse populations.

    Science.gov (United States)

    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.

  12. Evaluation of various pesticides-degrading pure bacterial cultures ...

    African Journals Online (AJOL)

    Due to the intensive use of pesticides within the greenhouse-rose production, remediation of polluted soils has become a hot topic for researchers in recent decades. Several bacterial strains having the ability to utilize various pesticides as a sole source of carbon and energy were isolated from pesticidecontaminated soils ...

  13. Bacterial profile of dentine caries and the impact of pH on bacterial population diversity.

    Directory of Open Access Journals (Sweden)

    Nima Kianoush

    Full Text Available 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.

  14. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations

    OpenAIRE

    Nikolic, Nela; Schreiber, Frank; Dal Co, Alma; Kiviet, Daniel J.; Bergmiller, Tobias; Littmann, Sten; Kuypers, Marcel M. M.; Ackermann, Martin

    2017-01-01

    Author summary This study addresses a fundamental question in bacterial metabolism: do all individuals in a clonal population express the same metabolic functions, or do individuals specialize on different metabolic functions and assimilate different substrates? Reports about stochastic gene expression in bacterial populations raise the possibility that transcriptional differences between individuals translate into different metabolic behaviors, but the prevalence and magnitude of such effect...

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

    Science.gov (United States)

    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...

  16. Evaluation of a PCR for detection of Actinobacillus pleuropneumoniae in mixed bacterial cultures from tonsils

    DEFF Research Database (Denmark)

    Gram, T.; Ahrens, Peter; Nielsen, J.P.

    1996-01-01

    strains of A. lignieresii. The lower detection limit of the PCR test was 10(3) A. pleuropneumoniae CFU/PCR test tube and was not affected by addition of 10(6) E. coli CFU/PCR test tube. Mixed bacterial cultures from tonsils of 101 pigs from 9 different herds were tested by culture and by PCR using four...

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

    Directory of Open Access Journals (Sweden)

    Yalda Khosravi

    2014-01-01

    Full Text Available 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.

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

    Science.gov (United States)

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

    2017-09-01

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

  19. Diversity of Hindgut Bacterial Population in Subterranean Termite, Reticulitermes flavipes

    Science.gov (United States)

    Olanrewaju Raji; Dragica Jeremic-Nikolic; Juliet D. Tang

    2017-01-01

    The termite hindgut contains a bacterial community that symbiotically aids in digestion of cellulosic materials. For this paper, a species survey of bacterial hindgut symbionts in termites collected from Saucier, Mississippi was examined. Two methods were tested for optimal genetic material isolation. Genomic DNA was isolated from the hindgut luminal contents of five...

  20. Compositional stability of a salivary bacterial population against supragingival microbiota shift following periodontal therapy.

    Directory of Open Access Journals (Sweden)

    Wataru Yamanaka

    Full Text Available 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.

  1. Molecular approaches for viable bacterial population and transcriptional analyses in a rodent model of dental caries

    Science.gov (United States)

    Klein, Marlise I.; Scott-Anne, Kathleen M.; Gregoire, Stacy; Rosalen, Pedro L.; Koo, Hyun

    2012-01-01

    SUMMARY Culturing methods are the primary approach for microbiological analysis of plaque-biofilms in rodent models of dental caries. In this study, we developed strategies for isolation of DNA and RNA from in vivo formed plaque-biofilms to analyze the viable bacterial population and gene expression. Plaque-biofilm samples from rats were treated with propidium monoazide to isolate DNA from viable cells, and the purified DNA was used to quantify total bacteria and S. mutans population via qPCR and specific primers; the same samples were also analyzed by colony forming unit (CFU) counting. In parallel, RNA was isolated from plaque-biofilm samples (from same animals) and used for transcriptional analyses via RT-qPCR. The viable population of both S. mutans and total bacteria assessed by qPCR were positively correlated with the CFU data (P0.8). However, the qPCR data showed higher bacterial cell counts, particularly for total bacteria (vs. CFU). Moreover, S. mutans proportion in the plaque-biofilm determined by qPCR analysis showed strong correlation with incidence of smooth-surface caries (P=0.0022, r=0.71). The purified RNAs presented high RNA integrity numbers (>7), which allowed measurement of the expression of genes that are critical for S. mutans virulence (e.g. gtfB and gtfC). Our data show that the viable microbial population and the gene expression can be analyzed simultaneously, providing a global assessment of the infectious aspect of the disease dental caries. Our approach could enhance the value of the current rodent model in further understanding the pathophysiology of this disease and facilitating the exploration of novel anti-caries therapies. PMID:22958384

  2. Population-based surveillance for bacterial meningitis in China, September 2006-December 2009.

    Science.gov (United States)

    Li, Yixing; Yin, Zundong; Shao, Zhujun; Li, Manshi; Liang, Xiaofeng; Sandhu, Hardeep S; Hadler, Stephen C; Li, Junhong; Sun, Yinqi; Li, Jing; Zou, Wenjing; Lin, Mei; Zuo, Shuyan; Mayer, Leonard W; Novak, Ryan T; Zhu, Bingqing; Xu, Li; Luo, Huiming

    2014-01-01

    During September 2006-December 2009, we conducted active population and sentinel laboratory-based surveillance for bacterial meningitis pathogens, including Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae type b, in 4 China prefectures. We identified 7,876 acute meningitis and encephalitis syndrome cases, including 6,388 among prefecture residents. A total of 833 resident cases from sentinel hospitals met the World Health Organization case definition for probable bacterial meningitis; 339 of these cases were among children bacterial meningitis in 74 of 3,391 tested cases. The estimated annual incidence (per 100,000 population) of probable bacterial meningitis ranged from 1.84 to 2.93 for the entire population and from 6.95 to 22.30 for children bacterial meningitis cases in China, but more complete laboratory testing is needed to better define the epidemiology of the disease in this country.

  3. Population-based Surveillance for Bacterial Meningitis in China, September 2006–December 2009

    Science.gov (United States)

    Li, Yixing; Yin, Zundong; Shao, Zhujun; Li, Manshi; Liang, Xiaofeng; Sandhu, Hardeep S.; Hadler, Stephen C.; Li, Junhong; Sun, Yinqi; Li, Jing; Zou, Wenjing; Lin, Mei; Zuo, Shuyan; Mayer, Leonard W.; Novak, Ryan T.; Zhu, Bingqing; Xu, Li

    2014-01-01

    During September 2006–December 2009, we conducted active population and sentinel laboratory–based surveillance for bacterial meningitis pathogens, including Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae type b, in 4 China prefectures. We identified 7,876 acute meningitis and encephalitis syndrome cases, including 6,388 among prefecture residents. A total of 833 resident cases from sentinel hospitals met the World Health Organization case definition for probable bacterial meningitis; 339 of these cases were among children bacterial meningitis in 74 of 3,391 tested cases. The estimated annual incidence (per 100,000 population) of probable bacterial meningitis ranged from 1.84 to 2.93 for the entire population and from 6.95 to 22.30 for children bacterial meningitis cases in China, but more complete laboratory testing is needed to better define the epidemiology of the disease in this country. PMID:24377388

  4. Effect of Spiritist "passe" (Spiritual healing) on growth of bacterial cultures.

    Science.gov (United States)

    Lucchetti, Giancarlo; de Oliveira, Renata Ferreira; Gonçalves, Juliane Piasseschi de Bernardin; Ueda, Suely Mitoi Ykko; Mimica, Lycia Mara Jenne; Lucchetti, Alessandra Lamas Granero

    2013-12-01

    Biofield therapies are approaches that harness energy fields to influence the human body. These therapies encompass Reiki, Qigong, Therapeutic Touch, Johrei and Spiritist "passe", among others. The aim of this study was to evaluate bacterial growth in two groups of cultures subjected to biofield therapy (Spiritist "passe" and laying on of hands (LOH)) in four situations (no intention, intention to inhibit bacterial growth, intention to promote growth, and influence of a negative factor) and compare them with a "no LOH/no treatment" group. Bacterial cultures (Escherichia coli ATCC) were randomized and allocated into three groups: Spiritist "passe", "LOH", and "no LOH". Bacterial growth was assessed using the McFarland Nephelometer Scale. A One-way ANOVA was performed to determine group differences in bacterial growth at 48h, and at 1 week after each situation. A total of 11 Spiritist "passe" healers, 10 LOH laymen and "no LOH" tubes were assessed. Under the intention to inhibit bacterial growth condition, statistically significant differences were found between the Spiritist "passe" and "no LOH" Groups (p=0.002 after 48h, and p=0.008 after one week) and also between the Spiritist "passe" and "LOH" Groups (p=0.005 after 48h, and p=0.009 after one week). No statistically significant difference was detected for the other situations tested (no intention, intention to promote growth and influence of a negative factor). We concluded that Spiritist "passe" effectively inhibited growth in bacterial cultures compared to LOH with intention or no LOH. Further studies comparing different intentions and types of LOH in cultures of cells and microorganisms are warranted. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. The impact of overcrowding on the bacterial contamination of blood cultures in the ED.

    Science.gov (United States)

    Lee, Ching-Chi; Lee, Nan-Yao; Chuang, Ming-Che; Chen, Po-Lin; Chang, Chia-Ming; Ko, Wen-Chien

    2012-07-01

    This study aims to determine the risk factors associated with the bacterial contamination of blood cultures among adults visiting the emergency department (ED). Clinical variables and medical records of adults with bacterial growth of blood cultures in the ED as well as the degree of ED crowding, between August 2007 and July 2008, were prospectively collected. Of the 11 491 adults who underwent blood culture sampling, the medical records of 558 (4.86%) eligible patients with bacterial growth in their blood cultures were analyzed. Most patients (366, or 3.19%) had true bacteremia, whereas 192 (1.67%) were regarded as contaminated. In multivariate analyses, ED overcrowding (scoring was based on a National Emergency Department Overcrowding Study [NEDOCS] score ≥ 100 points) was independently associated with blood culture contamination (odds ratio [OR], 1.58; P = .04). In contrast, other medical comorbidities, such as liver cirrhosis (OR, 0.31; P = .02), thrombocytopenia (100 mg/L; OR, 0.24; P overcrowded (60-100), overcrowded (100-140), severely overcrowded (140-180), and dangerously overcrowded (180-200), there was a strong correlation between blood culture contamination rates and the degrees of ED crowding (γ = 0.99, P overcrowding may have an adverse impact on the quality of clinical care, including increasing the risk of blood culture contamination. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Bacterial diversity determination using culture-dependent and culture-independent methods

    Directory of Open Access Journals (Sweden)

    M. Ghiasian

    2017-04-01

    Full Text Available Mud volcanoes are taken into consideration by geologists and oil industry experts have given their association with oil and gas reserves and methane greenhouse gas production in hydrosphere and atmosphere. Gomishan mud volcano phenomenon in the southeastern edge of the Caspian Sea, given its oil and gas resources, has been studied by some geologists in terms of geology and tectonics but not in terms of microbiology. Accordingly, it seems necessary to study this phenomenon from the perspective of microbiology in order to identify prokaryotes living in this area. Prokaryotes diversity in Mud volcano has been studied by cultivation techniques, fluorescence in situ hybridization, and denaturing gradient gel electrophoresis of PCR-amplified fragments of 16S rRNA genes. Total cell abundance in the mud volcano from 1×101-6×101per milliliter was determined by 4', 6-diamidino-2-phenylindole direct count. The detectable proportion of Archaea to Bacteria in the community by FISH was one to five. High viable counts (1 – 3 × 106 were obtained in culture media. A total of 122 isolates were obtained, 46 colonies were selected based on primarily morphological and physiological traits, and their 16S rRNA sequences were determined. The isolated genera included Halomonas (20%, Arthrobacter (5%, Kocuria (5%, Thalassobacillus (5%, Marinobacter (20%, Paracoccus (5%, Roseovarius (5%, Jeotgalicoccus (5%, Bacillus (15%, and Staphylococcus (15%. Regarding DGGE analysis, selected bands were obtained from the gels, reamplified and sequenced. Overall, 75% of the bacterial sequences were related to Rahnella and 25% related to Serratia.

  7. Seasonal effect on the bacterial and fungal population of an oilfield ...

    African Journals Online (AJOL)

    Seasonal effect on the bacterial and fungal populations of an oilfield wastewater – polluted soil was investigated for a period of 12 months. Many bacterial and fungal species were present in the soil and the wastewater of the area investigated. Some of the organisms occurred in both the soil and oilfield wastewater while ...

  8. Factors Associated With Conjunctival Bacterial Culture Positivity In ...

    African Journals Online (AJOL)

    The associated risk factors with conjunctival culture positivity in patients scheduled for cataract surgery were: age 50 years and above (p value=0.004, risk ratio 1.4), male gender (p value=0.032, risk ratio 1.6) and low literacy level (p value=0.031, risk ratio 1.8). It was recommended that elderly, male and illiterate patients ...

  9. Bacterial populations concomitant with Sclerotium rolfsii sclerotia in ...

    African Journals Online (AJOL)

    SARAH

    2015-09-30

    Sep 30, 2015 ... J. Appl. Biosci. Bacterial communities concomitant with sclerotia. 8708. Table 4 : Soil chemical characteristics before and after flooding in the greenhouse and fielda. Redox potential Eh (mV)b,c. Electrical conductivity (µS m-1)c. Treatments. 1 DAF. 15 DAF. 30 DAF before after. Greenhouse experiment.

  10. Petroleum-hydrocarbon utilization by native bacterial population ...

    African Journals Online (AJOL)

    Two Nigerian crude oils (Bonny light and Escravos blend) were exposed to the wastewater canal via oil impregnated membrane filters (0.45 μm diameter) for 21 days in a microcosm experiment. Bacterial petroleum-hydrocarbon utilizers were later harvested from both the millipore membrane filters and laboratory ...

  11. Vulnerable populations: cultural and spiritual direction.

    Science.gov (United States)

    Quest, Tammie E; Franks, Nicole M

    2006-08-01

    Cultural, spiritual, and religious diversity of emergency department patients is increasing while that of emergency physicians in particular remains predominantly homogeneous. With a discordance of cultural, race, and ethnicity exist, in the case of ethical conflict -resolution becomes that much more difficult. Patients may feel vulnerable when their emergency care provider does not understand his or her cultural, spiritual, and religious uniqueness as it relates to the patient-doctor interaction and health care decision making. This review will examine (1) language differences; (2) cultural, religious, and spiritual differences between patient and provider; (3) differing explanatory models of disease between patient and provider; and (4) diverse bioethical models of decision making of differing cultures in an effort to reduce vulnerabilities.

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

    Digital Repository Service at National Institute of Oceanography (India)

    Khandeparker, L.; Anil, A; Naik, S.D.; Gaonkar, C.C.

    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...

  13. Blood culture bottles are superior to lysis-centrifugation tubes for bacteriological diagnosis of spontaneous bacterial peritonitis.

    OpenAIRE

    Siersema, P D; de Marie, S; van Zeijl, J H; Bac, D J; Wilson, J H

    1992-01-01

    The conventional method of ascitic fluid culturing was compared with the bedside inoculation of ascites into blood culture bottles and into lysis-centrifugation tubes. The conventional culture method was compared with the blood culture bottle method in 31 episodes of spontaneous bacterial peritonitis (SBP). Cultures were positive with the conventional culture method in 11 (35%) episodes and with the blood culture bottle method in 26 (84%) episodes (P less than 0.001). The lysis-centrifugation...

  14. Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

    KAUST Repository

    Herrera Sarrias, Marcela

    2017-05-02

    Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

  15. The impact of natural transformation on adaptation in spatially structured bacterial populations

    OpenAIRE

    Moradigaravand, Danesh; Engelstädter, Jan

    2014-01-01

    Background Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. Results In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on ...

  16. Discrepancy between growth of Coccidioides immitis in bacterial blood culture media and a radiometric growth index

    International Nuclear Information System (INIS)

    Ampel, N.M.; Wieden, M.A.

    1988-01-01

    Spherules of Coccidioides immitis grew readily after inoculation in vented trypticase soy broth, biphasic brain heart infusion media, and aerobic tryptic soy broth bottles used in a radiometric system (BACTEC). However, visible growth was not accompanied by a significant radiometric growth index. Growth of C. immitis can be visually detected in routine bacterial blood culture media while the radiometric growth index remains negative

  17. Comparison of Genotyping Helicobacter pylori Directly from Biopsy Specimens and Genotyping from Bacterial Cultures

    OpenAIRE

    Park, Chang-Young; Kwak, Minjung; Gutierrez, Oscar; Graham, David Y.; Yamaoka, Yoshio

    2003-01-01

    PCR for vacA and cagA genotypes of Helicobacter pylori using DNA isolated from infected gastric biopsy specimens was approximately equal to genotyping using bacterial DNA from cultures. Inconsistent results were associated with low H. pylori density in biopsies. A higher proportion of mixed infection was found when biopsies were used.

  18. Bacterial incorporation of tritiated thymidine and populations of bacteriophagous fauna in the rhizosphere of wheat

    DEFF Research Database (Denmark)

    Christensen, Henrik; Griffiths, Bryan; Christensen, Søren

    1992-01-01

    Bacterial and microfaunal populations, and bacterial productivity measured by tritiated thymidine (3HTdr) incorporation, in the rhizosphere of wheat seedlings were measured. Soil from planted pots was fractionated into rhizosphere and non-rhizosphere (bulk) soil, while unplanted soil was taken from...... pots without plants. Total bacterial counts and biovolume did not differ between fractions but viable (plate) counts were 8 times higher in the rhizosphere compared to bulk and unplanted soil. 3HTdr was incorporated at a constant rate with low variability in bulk or unplanted soil. In rhizosphere soil...... 3HTdr incorporation was lower than in bulk or unplanted soils and showed high variability. The populations of bacterial-feeding protozoa and nematodes indicated that rhizosphere bacterial activity was actually 3–4 times greater in rhizosphere than bulk soil in accordance with the results...

  19. Bacterial enteropathogens associated with diarrhea in a rural population of Haiti

    Directory of Open Access Journals (Sweden)

    Jackson JC

    2011-09-01

    Full Text Available John C Jackson, Anthony L Farone, Mary B Farone Biology Department, Middle Tennessee State University, Murfreesboro, Tennessee, USA Purpose: Diarrheal disease is one of the leading causes of morbidity in developing countries. To further understand the epidemiology of diarrheal disease among a rural population surrounding Robillard, Haiti, fecal swabs from patients with diarrhea were screened for the presence of enteropathogenic bacteria. Patients and methods: Fecal swabs were collected from 34 patients with signs and symptoms of diarrhea and stored in BBLTM Cary-Blair transport medium (Becton, Dickinson and Company, Sparks, MD until transit to the USA. Swab material was inoculated on to different enrichment and selective agars for incubation. Fermenting and nonfermenting bacteria that grew on the enteric selection media were identified by the BBLTM CrystalTM Enteric/Nonferementing Identification system (Becton, Dickinson and Company. Organisms identified as Escherichia coli were further screened for the presence of virulence factors by polymerase chain reaction (PCR. Results: Of 34 patients, no Campylobacter, Shigella, Salmonella, or Vibrio spp. were isolated from swabs transported to the USA for culture. Of 73 E. coli isolates cultured from the swabs, one enteropathogenic strain of E. coli was identified by multiplex PCR. Escherichia fergusonii and Cronobacter sakazakii, both potential gastrointestinal pathogens, were also isolated from patient stools. Conclusion: This study was undertaken to determine if bacterial enteropathogens could be detected in the stools of patients suffering from diarrhea or dysentery and, in the absence of sufficient facilities, rectal swabs could be transported to the USA for culture. Although several genera of overt enteropathogens were not detected, one enteropathogenic E. coli and other pathogenic enterobacteriaceae were successfully cultured and identified. Keywords: Escherichia, Cronobacter, diarrheagenic, stool

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

    Science.gov (United States)

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2014-10-01

    The organophosphate pesticide chlorpyrifos (CP) has been used extensively since the 1960s for insect control. However, its toxic effects on mammals and persistence in environment necessitate its removal from contaminated sites, biodegradation studies of CP-degrading microbes are therefore of immense importance. Samples from a Pakistani agricultural soil with an extensive history of CP application were used to prepare enrichment cultures using CP as sole carbon source for bacterial community analysis and isolation of CP metabolizing bacteria. Bacterial community analysis (denaturing gradient gel electrophoresis) revealed that the dominant genera enriched under these conditions were Pseudomonas, Acinetobacter and Stenotrophomonas, along with lower numbers of Sphingomonas, Agrobacterium and Burkholderia. Furthermore, it revealed that members of Bacteroidetes, Firmicutes, α- and γ-Proteobacteria and Actinobacteria were present at initial steps of enrichment whereas β-Proteobacteria appeared in later steps and only Proteobacteria were selected by enrichment culturing. However, when CP-degrading strains were isolated from this enrichment culture, the most active organisms were strains of Acinetobacter calcoaceticus, Pseudomonas mendocina and Pseudomonas aeruginosa. These strains degraded 6-7.4 mg L(-1) day(-1) of CP when cultivated in mineral medium, while the consortium of all four strains degraded 9.2 mg L(-1) day(-1) of CP (100 mg L(-1)). Addition of glucose as an additional C source increased the degradation capacity by 8-14 %. After inoculation of contaminated soil with CP (200 mg kg(-1)) disappearance rates were 3.83-4.30 mg kg(-1) day(-1) for individual strains and 4.76 mg kg(-1) day(-1) for the consortium. These results indicate that these organisms are involved in the degradation of CP in soil and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

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

    Science.gov (United States)

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

    2016-12-18

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

    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. (letter)

  3. Design Factors Affect User Experience for Different Cultural Populations

    Science.gov (United States)

    Chu, Sauman

    2016-01-01

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

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

    Science.gov (United States)

    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.

  5. Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community.

    Directory of Open Access Journals (Sweden)

    Naomi F Montalvo

    Full Text Available 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.

  6. Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community.

    Science.gov (United States)

    Montalvo, Naomi F; Davis, Jeanette; 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.

  7. Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds

    Science.gov (United States)

    Wang, Hui; Zhang, Shuangfei; Pratush, Amit; Ye, Xueying; Xie, Jinli; Wei, Huan; Sun, Chongran; Hu, Zhong

    2018-01-01

    The phylogenetic diversity of bacterial communities in response to environmental disturbances such as organic pollution has been well studied, but little is known about the way in which organic contaminants influence the acclimation of functional bacteria. In the present study, tolerance assays for bacterial communities from the sediment in the Pearl River Estuary were conducted with the isolation of functional bacteria using pyrene and different estrogens as environmental stressors. Molecular ecological networks and phylogenetic trees were constructed using both 16S rRNA gene sequences of cultured bacterial strains and 16S rRNA gene-based pyrosequencing data to illustrate the successions of bacterial communities and their acclimations to the different organic compounds. A total of 111 bacterial strains exhibiting degradation and endurance capabilities in response to the pyrene estrogen-induced stress were successfully isolated and were mainly affiliated with three orders, Pseudomonadales, Vibrionales, and Rhodobacterales. Molecular ecological networks and phylogenetic trees showed various adaptive abilities of bacteria to the different organic compounds. For instance, some bacterial OTUs could be found only in particular organic compound-treated groups while some other OTUs could tolerate stresses from different organic compounds. Furthermore, the results indicated that some new phylotypes were emerged under stresses of different organic pollutions and these new phylotypes could adapt to the contaminated environments and contribute significantly to the microbial community shifts. Overall, this study demonstrated a crucial role of the community succession and the acclimation of functional bacteria in the adaptive responses to various environmental disturbances. PMID:29520254

  8. Seasonal changes in the heavy metal resistant bacterial population ...

    African Journals Online (AJOL)

    Seasonal changes and the contribution of industrial effluent discharges to the population of heavy metal – resistant bacteria (HMRB) in the river water and sediment of the New Calabar River, were examined. On exposure of river water microflora to 2µg of heavy metals, the HMRB population ranged from 55 to 78% in the ...

  9. The impact of natural transformation on adaptation in spatially structured bacterial populations.

    Science.gov (United States)

    Moradigaravand, Danesh; Engelstädter, Jan

    2014-06-20

    Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.

  10. Molecular Ecology of Bacterial Populations in Environmental Hazardous Chemical Control

    Science.gov (United States)

    1991-11-30

    and performance during engineering implementation and an increased regulatory requirement for bioprocess "credibility." With these technical...Reactor Figure 1. A schematic drawing of the bioreactor system for on-line studies of naphthalene degradation and light production by bioluminescent...shown). Competitive maintenance of engineered and wild type strains: The mixed culture results indicate that factors other than competition for

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

    Science.gov (United States)

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

    2016-01-01

    Purpose To describe the trends in pathogens and antibacterial resistance of corneal culture isolates in infectious keratitis during a period of 13 years at Hadassah-Hebrew University Medical Center. Methods A Retrospective analysis of bacterial corneal isolates was performed during the months of January 2002 to December 2014 at Hadassah Hebrew University Medical Center. Demographics, microbiological data and antibiotic resistance and sensitivity were collected. Results A total of 943 corneal isolates were analyzed during a 13 year period. A total of 415 positive bacterial cultures and 37 positive fungal cultures were recovered, representing 48% of the total cultures. The Annual incidence was 34.78 ± 6.54 cases. The most common isolate was coagulase-negative staphylococcus (32%), which had a significant decrease in trend throughout the study period (APC = -8.1, p = 0.002). Methicillin-resistant Staphylococcus aureus (MRSA) appears to have a decrease trend (APC = -31.2, P = 0.5). There was an increase in the resistance trend of coagulase-negative staphylococci to penicillin (APC = 5.0, P = keratitis. There was no significant change in the annual incidence of cases of bacterial keratitis seen over the past 13 years. Keratitis caused by MRSA appeared to decrease in contrast to the reported literature. PMID:27893743

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

    Directory of Open Access Journals (Sweden)

    Michael Politis

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

  13. Bacterial meningitis in patients with HIV: A population-based prospective study.

    Science.gov (United States)

    van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

    2016-03-01

    We studied occurrence, disease course, and prognosis of community-acquired bacterial meningitis in HIV-infected adults in the Netherlands. We performed a nationwide, prospective cohort study. Patients over 16 years old with bacterial meningitis were included. Data on patient history, symptoms and signs on admission, laboratory findings, radiologic examination, treatment, and outcome were collected prospectively. For HIV-positive patients additional information was collected retrospectively. From March 2006 to December 2013, 1354 episodes of community-acquired meningitis were included in the cohort. Thirteen patients were HIV-infected (1.0%). The annual incidence of bacterial meningitis was 8.3-fold higher (95%CI 4.6-15.1, P bacterial meningitis as compared to the general population despite cART therapy. Clinical presentation and outcome of patients with acute bacterial meningitis with and without HIV are similar. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  14. Use of nasopharyngeal culture to determine appropriateness of antibiotic therapy in acute bacterial rhinosinusitis.

    Science.gov (United States)

    Lee, Stella; Woodbury, Kristin; Ferguson, Berrylin J

    2013-04-01

    Rhinosinusitis is one of the top 5 diagnoses for which an antibiotic is prescribed, often without a clear bacterial etiology. This study evaluated whether nasopharyngeal culture and gram stain could serve as a surrogate for endoscopically obtained middle meatal cultures in directing appropriate therapy for acute bacterial rhinosinusitis (ABRS). This study also investigated the utility of a rapid sinus test screen in differentiating bacterial from nonbacterial rhinosinusitis. Thirty-one adult patients met inclusion criteria for ABRS. Samples were obtained from both the middle meatus and nasopharynx for Gram stain and culture. Nasal mucous samples were tested with a rapid sinus test strip measuring pH, levels of protein, nitrites, and leukocyte esterase. Sixty-one percent (61%) of nasopharyngeal and 48% of middle meatal samples grew pathogenic bacteria. The concordance rate was 84% between the 2 sites (p = 0.0006). The following pathogenic organisms were detected: Moraxella catarrhalis, Streptococcus pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, and Staphylococcus aureus. For nasopharyngeal samples, reliance on Gram stain alone exhibited a sensitivity of 31% and specificity of 100% and, similarly, for middle meatus samples, 47% and 93%, respectively. The rapid sinus test revealed a sensitivity of 83% and specificity of 7%. Nasopharyngeal and middle meatal cultures exhibited high concordance for pathogenic bacteria. Gram stain exhibited moderate sensitivity and excellent specificity. Nasopharyngeal cultures could provide a viable method, especially in a primary care setting, for determining the appropriateness of antibiotic therapy. The rapid sinus test's lack of specificity precluded its utility in the differentiation between bacterial and nonbacterial rhinosinusitis. © 2013 ARS-AAOA, LLC.

  15. Bacterial communities differ among Drosophila melanogaster populations and affect host resistance against parasitoids

    NARCIS (Netherlands)

    Chaplinska, Mariia; Gerritsma, Sylvia; Dini-Andreote, Francisco; Falcao Salles, Joana; Wertheim, Bregje

    2016-01-01

    In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population

  16. Do wild chimpanzee populations develop diverse cultures? [Latest Thinking

    OpenAIRE

    Boesch, C.

    2017-01-01

    Humans pride themselves on having extensive and diverse cultures. However, cultures can also be observed in animals. The research presented in this video aims at understanding the cultures of wild chimpanzee populations in several African countries and how they differ from each other. As chimpanzees avoid human contact, CHRISTOPHE BOESCH explains, the research team conducted the study by setting up camera traps to catch chimpanzee behavior on video. Forty locations were carefully selected to ...

  17. Diagnosis and Management of Bacterial Meningitis in the Paediatric Population: A Review

    Directory of Open Access Journals (Sweden)

    Catherine L. Tacon

    2012-01-01

    Full Text Available Paediatric bacterial meningitis is a neurological emergency which, despite advances in medical management, still has a significant morbidity and mortality. Over recent decades new vaccines have led to a change in epidemiology of the disease; however, it remains a condition that requires a high index of suspicion, prompt diagnosis, and early management in the emergency department. New laboratory techniques and clinical tools are aiding the diagnosis of bacterial meningitis, yet some controversies still exist in its management. This paper outlines the changing epidemiology of the disease, current diagnostic techniques as well as controversies and advances in the management of bacterial meningitis in the paediatric population.

  18. Genetic drift suppresses bacterial conjugation in spatially structured populations

    OpenAIRE

    Freese, Peter D.; Korolev, Kirill S.; Jimenez, Jose I.; Chen, Irene A.

    2014-01-01

    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 ag...

  19. Microbiology and visual outcomes of culture-positive bacterial endophthalmitis in Oxford, UK.

    Science.gov (United States)

    Gupta, A; Orlans, H O; Hornby, S J; Bowler, I C J W

    2014-11-01

    To review the microbiology of culture-positive cases of bacterial endophthalmitis, and to correlate this with visual outcomes. Case notes were reviewed for culture-positive cases of bacterial endophthalmitis over a period from November 1999 to June 2012. Cases were identified retrospectively using a local database. The Fisher exact test was used for statistical analysis. Of the 47 cases of culture-positive bacterial endophthalmitis identified, 81 % occurred postoperatively, 11 % followed intravitreal injection, 6 % had an endogenous source and 2 % followed ocular trauma. Eighty-seven percent of bacteria cultured were Gram-positive. The most commonly identified organisms were coagulase-negative Staphylococci (47 %) and Streptococcus spp. (30 %). Patients were treated with intravitreal vancomycin and either amikacin or ceftazidime. All Gram-negative isolates were sensitive to aminoglycosides and ceftazidime, and all Gram-positive isolates were vancomycin-sensitive. Final visual acuity (VA) was 6/12 or better in 41 % of cases and counting fingers (CF) or worse in 30 %. Endophthalmitis caused by Streptococcus spp. was associated with a poorer final VA (OR for CF or worse = 14.9, P < 0.01). Cases caused by coagulase-negative Staphylococci had a better visual outcome (OR for VA of 6/12 or better = 5.7, P = 0.013). Five eyes were eviscerated or enucleated. Infection with Haemophilus influenzae was strongly associated with this outcome (OR = 57, P < 0.01). Over the time period of this study there was no evidence of emerging resistance to empirical antibiotics which are commonly used for the treatment of bacterial endophthalmitis. Infection with coagulase-negative Staphylococci was associated with a good visual outcome, whilst infection with Streptococcus spp. or Haemophilus influenzae was associated with a poor visual outcome.

  20. Radiation Sterilization of Two Commonly Culture Media Used for Bacterial Growth

    International Nuclear Information System (INIS)

    El-Hifnawi, H.N.

    2008-01-01

    Radiation sterilization of culture media used for the cultivation of bacteria by Co-60 gamma ray was investigated. Nutrient agar and tryptone glucose yeast extract (TGY) media widely used for the propagation of bacteria were sterilized with 15 kGy dose gamma radiation. Seven different bacterial species were grown as well on the radiation sterilized media as on media sterilized by autoclaving in a conventional way

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

    Science.gov (United States)

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

    2015-06-11

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

  2. Diagnosis of spontaneous bacterial peritonitis: Role of tween 80 and triton X in ascitic fluid cultures

    Directory of Open Access Journals (Sweden)

    Iyer R

    2009-01-01

    Full Text Available A patient with alcoholic cirrhosis of the liver, portal hypertension with hepatic encephalopathy and spontaneous bacterial peritonitis (SBP was admitted in an obtunded condition. Attempts at delineating the aetiology of the SBP using conventional cultures as well as automated systems were not successful. The use of non-anionic surfactant agents such as Tween 80-incorporated blood agar and Triton X treatment of the specimens facilitated the growth of Klebsiella pneumoniae from the ascitic fluid, which otherwise would have been concluded to represent culture-negative neutrocytic ascites. Thus, the use of the aforementioned agents could be explored in elucidating the aetiology of body cavity infections when conventional methods fail.

  3. Seasonal Effect on the Bacterial and Fungal Population of an

    African Journals Online (AJOL)

    ... the microbial densities. llowcver, fungal counts l showed somewhat seasonahpollutant effect in two locationsv The chemical constituents of the wastewater are relatively of low toxicity and hence had no toxic effects on the soil microbial population Seasonal variations showed that the drier seasons supported large active ...

  4. Application of Biomaterials and Inkjet Printing to Develop Bacterial Culture System

    Directory of Open Access Journals (Sweden)

    Tithimanan Srimongkon

    2015-01-01

    Full Text Available We created an automated bioassay system based on inkjet printing. Compared to conventional manual bacterial culture systems our printing approach improves the quality as well as the processing speed. A hydrophobic/hydrophilic pattern as a container supporting a culture medium was built on filter paper using a toluene solution of polystyrene for hydrophobization, followed by toluene printing to create several hydrophilic areas. As culture media we used a novel poly(vinyl alcohol based hydrogel and a standard calcium alginate hydrogel. The poly(vinyl alcohol hydrogel was formed by physical crosslinking poly(vinyl alcohol with adipic acid dihydrazide solutions. The conditions of poly(vinyl alcohol gelation were optimized for inkjet printability and the optimum mixture ratio was determined. The calcium alginate hydrogel was formed by chemical reaction between sodium alginate and CaCl2 solutions. Together with nutrients both hydrogel solutions were successfully printed on paper by means of the modified inkjet printer. The amount of each solution was demanded simply by outputting CMYK values. In the last step bacterial cells were printed on both hydrogel media. For both media we achieved a stable bacteria growth which was confirmed by microscopical imaging of the developed bacterial colonies.

  5. Case Study: A Novel Bacterial Contamination in Cell Culture Production--Leptospira licerasiae.

    Science.gov (United States)

    Chen, Joseph; Bergevin, Jesse; Kiss, Robert; Walker, Gordon; Battistoni, Todd; Lufburrow, Patricia; Lam, Harry; Vinther, Anders

    2012-01-01

    Leptospira licerasiae, a novel bacterial contaminant found in Genentech cell culture manufacturing operations, poses a challenge to current microbial control strategies in upstream cell culture processes, as this microorganism is fully capable of passing through 0.1 μm sterilizing-grade filtration and is not detectable by standard microbiological methods described in major pharmaceutical compendia for microbial screening and quantification required for release of raw materials, in-process intermediates, and finished products in biopharmaceutical production. The root cause investigation was greatly aided by the genetic identification of the contaminant and subsequent confirmation by cultural method and real-time polymerase chain reaction assay from the affected product batches. The purpose of this case study is to share knowledge on the novel contaminant, L. licerasiae, and potential routes of contamination in the cell culture manufacturing environment from a series of investigations involving root cause analysis, impact assessments, risk assessment, and global corrective and preventative action, as well as to provide guidance on the detection and prevention of Leptospira contamination with the intent to aid the industry to continually improve microbial control strategies for the benefit of patients. Leptospira licerasiae, a novel bacterial contaminant found in cell culture manufacturing operations, poses a challenge to current microbial control strategies in upstream cell culture processes because this microorganism is capable of passing through 0.1 μm sterilizing-grade membrane filters and is not detectable by standard microbiological methods used in biopharmaceutical production. The root cause investigation was greatly aided by the genetic identification of the contaminant and subsequent confirmation by cultural method and real-time polymerase chain reaction assay from the affected product batches. The purpose of this case study is to share knowledge on the

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

    Science.gov (United States)

    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.

  7. Population change and socio-cultural values.

    Science.gov (United States)

    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

  8. Bacterial diversity in a nonsaline alkaline environment: heterotrophic aerobic populations.

    Science.gov (United States)

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

    2004-12-01

    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 alpha-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.

  9. Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations

    Science.gov (United States)

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

    Science.gov (United States)

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

    2013-11-01

    Ceftaroline, the active form of ceftaroline fosamil, is a broad-spectrum cephalosporin antibiotic. A population pharmacokinetic (PPK) model for ceftaroline was developed in NONMEM® using data from 185 healthy subjects and 92 patients with acute bacterial skin and skin structure infection (ABSSSI). Data from 128 patients with community-acquired bacterial pneumonia (CABP) were used for external model validation. Healthy subjects received 50-2,000 mg ceftaroline fosamil via intravenous (IV) infusion over 1 hour or intramuscular (IM) injection q12h or q24h. ABSSSI and CABP patients received 600 mg of ceftaroline fosamil IV over 1 hour q12h. A three-compartment model with zero-order IV or parallel first-order IM input and first-order elimination described ceftaroline fosamil PK. A two-compartment model with first-order conversion of prodrug to ceftaroline and parallel linear and saturable elimination described ceftaroline PK. Creatinine clearance was the primary determinant of ceftaroline exposure. Good agreement between the observed data and both population (r(2)  = 0.93) and individual post-hoc (r(2)  = 0.98) predictions suggests the PPK model can adequately approximate ceftaroline PK using covariate information. Such a PPK model can evaluate dose adjustments for patients with renal impairment and generate ceftaroline exposures for use in pharmacokinetic-pharmacodynamic assessments of efficacy in patients with ABSSSI or CABP. © 2013, The American College of Clinical Pharmacology.

  11. Acid-suppression medications and bacterial gastroenteritis: a population-based cohort study.

    Science.gov (United States)

    Wei, Li; Ratnayake, Lasantha; Phillips, Gabby; McGuigan, Chris C; Morant, Steve V; Flynn, Robert W; Mackenzie, Isla S; MacDonald, Thomas M

    2017-06-01

    To investigate whether acid-suppression medicines (ASMs) increase the risk of bacterial gastroenteritis. A population-based, propensity-score matched cohort study using a record-linkage database in Tayside, UK. The study consisted of 188 323 exposed to ASMs (proton-pump inhibitors and histamine-2 receptor antagonists) and 376 646 controls (a propensity-score matched cohort from the rest of population who were not exposed to ASMs) between 1999 and 2013. The main outcome measure was a positive stool test for Clostridium difficile, Campylobacter, Salmonella, Shigella or Escherichia coli O157. The association between ASMs and risk of bacterial gastroenteritis was assessed by a Cox regression model. There were 22 705 positive test results (15 273 C. difficile [toxin positive], 6590 Campylobacter, 852 Salmonella, 129 Shigella and 193 E. coli O157, not mutually exclusive) with a total of 5 729 743 person-years follow up time in Tayside, 1999-2013. The adjusted hazard ratios for culture positive diarrhoea for the proton-pump inhibitors and histamine-2 receptor antagonists exposed vs. unexposed cohort were 2.72 (95% confidence interval [CI] 2.33, 3.17) during follow-up time for samples submitted from the community and 1.28 (95% CI 1.08, 1.52) for samples submitted from hospitals. Compared with the unexposed cohort, patients in the exposed group had increased risks of C. difficile and Campylobacter [adjusted hazard ratios of 1.70 (95% CI 1.28, 2.25), 3.71 (95% CI 3.04, 4.53) for community samples, and 1.42 (95% CI 1.17, 1.71), 4.53 (95% CI 1.75, 11.8) for hospital samples, respectively]. The results suggest that community prescribed ASMs were associated with increased rates of C. difficile and Campylobacter positive gastroenteritis in both the community and hospital settings. © 2017 The Authors. British Journal of Clinical Pharmacology published by John Wiley & Sons Ltd on behalf of British Pharmacological Society.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. Metagenomic analysis of two important, but difficult to culture soil borne bacterial phyla, the Acidobacteria and the Verrucomicrobia

    NARCIS (Netherlands)

    Kielak, A.M.

    2010-01-01

    Based on phylogenetic marker genes, such as 16S rRNA genes, it is clear that numerous bacterial lineages exist that appear to be quite common in the environment, yet poorly characterized and underrepresented in culture. Two of the most common bacterial phyla in soils that fall into this category are

  15. Repeatability of differential goat bulk milk culture and associations with somatic cell count, total bacterial count, and standard plate count

    NARCIS (Netherlands)

    Koop, G.; Dik, N.; Nielen, M.; Lipman, L.J.A.

    2010-01-01

    The aims of this study were to assess how different bacterial groups in bulk milk are related to bulk milk somatic cell count (SCC), bulk milk total bacterial count (TBC), and bulk milk standard plate count (SPC) and to measure the repeatability of bulk milk culturing. On 53 Dutch dairy goat farms,

  16. Influence of copper on Euplotes sp. and associated bacterial population

    Directory of Open Access Journals (Sweden)

    Guilherme Oliveira Andrade da Silva

    2014-05-01

    Full Text Available The influence of copper on the ciliate Euplotes sp. and associated bacteria isolated from sediment samples of Guanabara Bay were investigated in bioassays. This region is highly affected by heavy metals such as copper, from solid waste constantly dumped in the bay and other sources such as industrial effluents, antifouling paints, atmospheric deposition and urban drainage, and even today there are few data on the metal toxicity to the ecosystem of the Bay of Guanabara. Bioassays were conducted to estimate the LC50-24 h of copper, in order to determine the concentration of metal bearing 50% of the population mortality. The results indicated that the concentrations of 0.05 and 0.009 mg L-1 presented no toxicity to Euplotes sp. The associated bacteria are tolerant to copper concentrations used in bioassays, and suggest that they could be used as a potential agent in the bioremediation of areas affected by copper.

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

    Directory of Open Access Journals (Sweden)

    Amy Apprill

    Full Text Available 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

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

    Science.gov (United States)

    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

  19. Effect of dietary monensin on the bacterial population structure of dairy cattle colonic contents.

    Science.gov (United States)

    McGarvey, Jeffery A; Hamilton, Scott W; DePeters, Edward J; Mitloehner, Frank M

    2010-02-01

    To determine the effect of monensin, a carboxylic polyether ionophore antibiotic, on the bacterial population structure of dairy cattle colonic contents, we fed six lactating Holstein cows a diet containing monensin (600 mg day(-1)) or an identical diet without monensin. Fresh waste samples were taken directly from the animals once a month for 3 months and assayed for their bacterial population structure via 16S rRNA gene sequence analysis. In total 6,912 16S rRNA genes were examined, comprising 345 and 315 operational taxonomic units (OTUs) from the monensin fed and control animals, respectively. Coverage estimates of the OTUs identified were 87.6% for the monensin fed and 88.3% for the control colonic content derived library. Despite this high level of coverage, no significant difference was found between the libraries down to the genus level. Thus we concluded that although monensin is believed to increase milk production in dairy cattle by altering the bacterial population structure within the bovine gastrointestinal tract, we were unable to identify any significant difference in the bacterial population structure of the colonic contents of monensin fed vs. the control dairy cattle, down to the genus level.

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

    Directory of Open Access Journals (Sweden)

    Thomas E Gorochowski

    Full Text Available 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.

  1. Response of Vancomycin according to Steroid Dosage in Pediatric Patients with Culture-Proven Bacterial Meningitis.

    Science.gov (United States)

    Lee, Shin Ae; Kim, Jin Kyu; Jo, Dae Sun; Kim, Sun Jun

    2017-12-01

    This study aimed to evaluate the efficacy of combined vancomycin and steroid therapy for the treatment of culture-proven bacterial meningitis in pediatric patients. We identified a total of 86 pediatric patients with culture-positive cerebrospinal fluid who were treated at our facility between 2005 and 2015. Ten of these patients (5 boys and 5 girls) received first-line treatment with vancomycin as the initial form of therapy. All cultured bacteria were sensitive to vancomycin. We retrospectively analyzed these cases to examine the relationship between concomitant steroid dosage and antibiotic treatment effectiveness. Nine of the 10 patients included in our analysis received steroid treatment. Of these, 3 received high-dose steroid therapy and 6 received low-dose steroid therapy. Five patients did not respond to vancomycin, including all 3 patients in the high-dose steroid group and 2 patients in the low-dose steroid group. Our analysis confirmed that the response rate to vancomycin treatment was significantly reduced in accordance with steroid dosage (P = 0.035). Patients who did not to respond to vancomycin with concomitant high-dose steroid administration improved clinically after the substitution of vancomycin with teicoplanin. The use of steroids, especially in high doses, may impair the effectiveness of vancomycin for treating bacterial meningitis in pediatric patients. Physicians should be cautious when administering concomitant steroid therapy and should carefully monitor the steroid dosage. Copyright © 2017 by The Korean Society of Infectious Diseases and Korean Society for Chemotherapy

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

    Science.gov (United States)

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

    2014-12-01

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

  3. Bacterial Meningitis in Patients using Immunosuppressive Medication: a Population-based Prospective Nationwide Study.

    Science.gov (United States)

    van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

    2017-06-01

    We studied occurrence, presentation, disease course, effect of adjunctive dexamethasone, and prognosis of bacterial meningitis in patients using immunosuppressive medication. Patients were selected from our nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 1, 2006 through October 31, 2014. Eighty-seven of 1447 episodes (6 %) of bacterial meningitis occurred in patients using immunosuppressive medication, and consisted of corticosteroids in 82 %. Patients with bacterial meningitis using immunosuppressive medication were less likely to present with headache (P = 0.02) or neck stiffness (P = 0.005), as compared those not on immunosuppressive medication. In 46 % of episodes CSF leukocyte count was below 1000/mm 3 . CSF cultures revealed S. pneumoniae in 41 % and L. monocytogenes in 40 % of episodes. Outcome was unfavorable in 39 of 87 episodes (45 %) and death occurred in 22 of 87 episodes (25 %). Adjunctive dexamethasone was administered in 52 of 87 (60 %) episodes, and mortality tended to be lower in those on adjunctive dexamethasone therapy as compared to those without dexamethasone therapy (10 of 52 [19 %] vs 12 of 35 [34 %], P = 0.14). We conclude that bacterial meningitis in patients using immunosuppressive medication is likely to present with atypical clinical and laboratory features, and is often caused by atypical bacteria, mainly L. monocytogenes. Adjunctive dexamethasone is widely prescribed in these patients and was not associated with harm in this study.

  4. The presence of embedded bacterial pure cultures in agar plates stimulate the culturability of soil bacteria

    DEFF Research Database (Denmark)

    Burmølle, Mette; Johnsen, Kaare; Abu Al-Soud, Waleed Mohamad Abdel F

    2009-01-01

    cultures in between two layers of agar. Plates containing either embedded Pseudomonas putida or Arthrobacter globiformis resulted in higher numbers of CFUs of soil bacteria (21% and 38%, respectively) after 833 h of incubation, compared to plates with no embedded strain. This indicates a stimulatory effect...... homology to known sequenced isolates in GenBank were recovered from plates with embedded strains than from those without, which indicate a higher number of potential novel soil isolates. This approach for cultivation is therefore a feasible alternative or supplement to traditional cultivation on agar...

  5. Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population.

    Science.gov (United States)

    Qi, Z; Cao, H; Jiang, H; Zhao, J; Tang, Z

    2016-01-01

    To use microarrays to detect 11 selected bacteria in infected root canals, revealing bacterial combinations that are associated with clinical symptoms and signs of primary endodontic infections in a Chinese population. DNA was extracted from 90 samples collected from the root canals of teeth with primary endodontic infections in a Chinese population, and the 16S rRNA gene was amplified by polymerase chain reaction (PCR). The PCR products were hybridized to microarrays containing specific oligonucleotide probes targeting 11 species, and the arrays were screened with a confocal laser scanner. Pearson's chi-squared test and cluster analysis were performed to investigate the associations between the bacterial combinations and clinical symptoms and signs using SAS 8.02. Seventy-seven samples (86%) yielded at least one of the 11 target species. Parvimonas micra (56%), Porphyromonas endodontalis (51%), Tannerella forsythia (48%), Prevotella intermedia (44%) and Porphyromonas gingivalis (37%) were the most prevalent taxa and were often concomitant. The following positive associations were found between the bacterial combinations and clinical features: P. endodontalis and T. forsythia with abscess; P. gingivalis and P. micra with sinus tract; P. gingivalis and P. endodontalis or P. micra and P. endodontalis with abscess and sinus tract; and the combination of P. endodontalis, P. micra, T. forsythia and P. gingivalis with sinus tract (P endodontic origin with bacterial synergism in a Chinese population. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  6. Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations.

    Science.gov (United States)

    Kühn, I; Allestam, G; Stenström, T A; Möllby, R

    1991-01-01

    A simple, automated microplate system for biochemical characterization of water isolates can be used to obtain fingerprints of the bacterial flora from various water samples. Mathematical models for calculating the diversities and similarities between bacterial populations are described for such fingerprints. The diversity may give information on whether an indigenous or allochthonous flora is present, and the similarities between bacterial populations, as calculated by using a population similarity coefficient (Sp), may indicate contaminations between different water samples. The system was demonstrated on coliform bacterial populations from various water samples, with or without suspected intercontamination. For unrelated water samples, the Sps were close to 0, whereas repeated samples of the same source showed Sps of 0.64 to 0.74. The Sp values from several water samples were also clustered to form a dendrogram, thus indicating the relative similarities between the bacterial populations to confirm suspected common sources of pollution. PMID:1781680

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

    Directory of Open Access Journals (Sweden)

    Jason Karslake

    2016-10-01

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

  8. Bacterial diversity associated with wild caught Anopheles mosquitoes from Dak Nong Province, Vietnam using culture and DNA fingerprint.

    Science.gov (United States)

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

    2015-01-01

    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. 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. 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. 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.

  9. Bacterial diversity associated with wild caught Anopheles mosquitoes from Dak Nong Province, Vietnam using culture and DNA fingerprint.

    Directory of Open Access Journals (Sweden)

    Chung Thuy Ngo

    Full Text Available 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.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.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.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.

  10. Green mitigation strategy for cultural heritage: bacterial potential for biocide production.

    Science.gov (United States)

    Silva, Mara; Rosado, Tânia; Teixeira, Dora; Candeias, António; Caldeira, Ana Teresa

    2017-02-01

    Several biosurfactants with antagonistic activity are produced by a variety of microorganisms. Lipopeptides (LPPs) produced by some Bacillus strains, including surfactin, fengycin and iturin are synthesized nonribosomally by mega-peptide synthetase (NRPS) units and they are particularly relevant as antifungal agents. Characterisation, identification and evaluation of the potentials of several bacterial isolates were undertaken in order to establish the production of active lipopeptides against biodeteriogenic fungi from heritage assets. Analysis of the iturin operon revealed four open reading frames (ORFs) with the structural organisation of the peptide synthetases. Therefore, this work adopted a molecular procedure to access antifungal potential of LPP production by Bacillus strains in order to exploit the bioactive compounds synthesis as a green natural approach to be applied in biodegraded cultural heritage context. The results reveal that the bacterial strains with higher antifungal potential exhibit the same morphological and biochemical characteristics, belonging to the genera Bacillus. On the other hand, the higher iturinic genetic expression, for Bacillus sp. 3 and Bacillus sp. 4, is in accordance with the culture antifungal spectra. Accordingly, the adopted methodology combining antifungal screening and molecular data is represent a valuable tool for quick identification of iturin-producing strains, constituting an effective approach for confirming the selection of lipopeptides producer strains.

  11. Enrichment and optimization of anaerobic bacterial mixed culture for conversion of syngas to ethanol.

    Science.gov (United States)

    Singla, Ashish; Verma, Dipti; Lal, Banwari; Sarma, Priyangshu M

    2014-11-01

    The main aim of the present study was to enrich anaerobic mixed bacterial culture capable of producing ethanol from synthesis gas fermentation. Screening of thirteen anaerobic strains together with enrichment protocol helped to develop an efficient mixed culture capable of utilizing syngas for ethanol production. Physiological and operational parameters were optimized for enhanced ethanol production. The optimized value of operational parameters i.e. initial media pH, incubation temperature, initial syngas pressure, and agitation speed were 6.0±0.1, 37°C, 2kgcm(-2) and 100rpm respectively. Under these conditions ethanol and acetic acid production by the selected mixed culture were 1.54gL(-1) and 0.8gL(-1) respectively. Furthermore, up-scaling studies in semi-continuous fermentation mode further enhanced ethanol and acetic acid production up to 2.2gL(-1) and 0.9gL(-1) respectively. Mixed culture TERI SA1 was efficient for ethanol production by syngas fermentation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Effect of Single Bacterial Starter Culture on Odour Reduction During Controlled Fermentation of Cassava Tubers for Foofoo Production

    OpenAIRE

    Henshaw, E. E.; Ikpoh, I. S

    2010-01-01

    Effects of single bacterial starter culture on odour reduction during controlled fermentation of cassava tubers for foofoo production were investigated. Pure cultures were used to ferment cassava tubers in water for 96 h. The cultures used include Bacillus subtilis, Klebsiela sp., Lactobacillus plantarum and Leuconostoc mesenteroides. L. plantarum exhibited the highest acid producing ability, decreasing the pH of the Cassava tubers from 6.2 to 3.68 with a corresponding increase in total titra...

  13. Enrichment and characterization of chlorinated organophosphate ester-degrading mixed bacterial cultures.

    Science.gov (United States)

    Takahashi, Shouji; Kawashima, Koji; Kawasaki, Manami; Kamito, Jun; Endo, Yusuke; Akatsu, Kumiko; Horino, Sadatoshi; Yamada, Ryo-Hei; Kera, Yoshio

    2008-07-01

    Chlorinated organophosphate ester (OPE)-degrading enrichment cultures were obtained using tris(2-chloroethyl) phosphate (TCEP) or tris(1,3-dichloro-2-propyl) phosphate (TDCPP) as the sole phosphorus source. In cultures with 46 environmental samples, significant TCEP and TDCPP degradation was observed in 10 and 3 cultures, respectively, and successive subcultivation markedly increased their degradation rates. 67E and 45D stable enrichment cultures obtained with TCEP and TDCPP, respectively, completely degraded 20 muM of the respective compounds within 6 h and also the other, although the degradation rate of TCEP by 45D was relatively slow. We confirmed chloride ion generation on degradation in both cases and the generation of 2-chloroethanol (2-CE) and 1,3-dichloro-2-propanol (1,3-DCP) as metabolites of TCEP and TDCPP, respectively. 67E and 45D also showed dehalogenation ability toward 2-CE and 1,3-DCP, respectively. Addition of inorganic phosphate did not significantly influence their ability to degrade the chlorinated OPEs but markedly increased their dehalogenation ability, which was maximum at 0.2 mM of inorganic phosphate and decreased at a higher concentration. Denaturing gradient gel electrophoresis analysis showed that dominant bacteria in 67E are related to Acidovorax spp. and Sphingomonas spp. and those in 45D are Acidovorax spp., Aquabacterium spp., and Sphingomonas spp. This analysis indicated the relationship of the Sphingomonas- and Acidovorax-related bacteria with the cleavage of the phosphoester bond and dehalogenation, respectively, in both cultures. This is the first report on bacterial enrichment cultures capable of degrading both TCEP and TDCPP.

  14. COMPARATIVE EVALUATION OF CULTURE MEDIA FOR PATHOGEN ISOLATION OF PURULENT BACTERIAL MENINGITIS

    Directory of Open Access Journals (Sweden)

    Ya. V. Podkopaev

    2016-01-01

    Full Text Available The State Research Center for Applied Microbiology and Biotechnology has designed two nutrient media — chocolate agar and PBM-agar to isolate pathogens of purulent bacterial meningitis (PBM. In our previous research using collected microbial strains the media were shown to be highly susceptible and to provide the growth of Neisseria meningiti-dis, Streptococcus pneumoniae and Haemophilus influenzae strains, when inoculated with microbial suspensions containing single cells. When isolating Haemophilus influenzae, meningococci, and pneumococci the use of selective additives in both media assures selective isolation of required microorganisms, inhibiting contaminants. The objective of this research was to assess the media in bacteriological tests of clinical samples collected from the upper and lower respiratory tract in humans. The bacteriological plating of throat smear specimens (n = 90 from children and adults at the age of 0 to 66 with disorder of the upper respiratory tract on chocolate agar, PBM-agar and on a control medium in the absence of selective additives resulted in the equal amount of microbial cultures isolated. Of 154 isolated cultures 2, 23 and 9 were attributed to Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae, respectively. The plating of throat smears (n = 10 from healthy people at the age of 30 to 55 on the analyzable and control media in the presence of additives allowed us to selectively isolate Haemophilus influenzae and Streptococcus pneumoniae cultures without a quantitative loss, with contaminants inhibited. By their growth characteristics chocolate agar and PBM-agar were highly competitive with reference media being used in clinical practice for isolating main causative agents of purulent bacterial meningitis.

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

    Science.gov (United States)

    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

    2014-06-01

    To determine the efficacy and safety of azithromycin 1.5% eye drops in a paediatric population with purulent bacterial conjunctivitis. 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. 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. 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. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  16. Supplemental Dietary Inulin of Variable Chain Lengths Alters Intestinal Bacterial Populations in Young Pigs123

    Science.gov (United States)

    Patterson, Jannine K.; Yasuda, Koji; Welch, Ross M.; Miller, Dennis D.; Lei, Xin Gen

    2010-01-01

    Previously, we showed that supplementation of diets with short-chain inulin (P95), long-chain inulin (HP), and a 50:50 mixture of both (Synergy 1) improved body iron status and altered expression of the genes involved in iron homeostasis and inflammation in young pigs. However, the effects of these 3 types of inulin on intestinal bacteria remain unknown. Applying terminal restriction fragment length polymorphism analysis, we determined the abundances of luminal and adherent bacterial populations from 6 segments of the small and large intestines of pigs (n = 4 for each group) fed an iron-deficient basal diet (BD) or the BD supplemented with 4% of P95, Synergy 1, or HP for 5 wk. Compared with BD, all 3 types of inulin enhanced (P inulin on bacterial populations in the lumen contents were found. Meanwhile, all 3 types of inulin suppressed the less desirable bacteria Clostridium spp. and members of the Enterobacteriaceae in the lumen and mucosa of various gut segments. Our findings suggest that the ability of dietary inulin to alter intestinal bacterial populations may partially account for its iron bioavailability-promoting effect and possibly other health benefits. PMID:20980641

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    Chaplinska, Mariia; Gerritsma, Sylvia; Dini-Andreote, Francisco; Falcao Salles, Joana; Wertheim, Bregje

    2016-01-01

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

  19. Diagnosis of common bacterial causes of urethritis in men by Gram stain, culture and multiplex PCR.

    Science.gov (United States)

    Jahan, F; Shamsuzzaman, S M; Akter, S

    2014-12-01

    Urethritis is one of the most important causes of morbidity and mortality in developing countries. The aim of this study was to detect common bacterial causes of urethritis in men by Gram stain, culture and multiplex PCR.185 male patients who presented at the Skin and venereal clinic of the Dhaka Medical College, Bangladesh with clinical symptoms suggestive of urethritis were enrolled in this study. Urethral discharges were tested for detection of Neisseria gonorrhoeae by Gram stain, culture and PCR. Multiplex PCR assay was done to detect DNA of Chlamydia trachomatis, Ureaplasma urealyticum and Mycoplasma genitalium. Out of 185 participants, 30.27% and 14.6% were infected by Neisseria gonorrhoeae and Chlamydia trachomatis respectively. None of the individuals was found positive for either Ureaplasma urealyticum or Mycoplasma genitalium. Among the Neisseria gonorrhoeae positive patients 27.57% were positive from Gram stain, 26.49% were culture positive, 30.27% were positive by PCR (p<0.001). 32.65% of the Neisseria gonorrhoeae isolates were penicillinase producers and 83.67% were susceptible to ceftriaxone. Considering culture as the gold standard, the sensitivity and specificity of PCR for the detection of Neisseria gonorrhoeae was 100%, and 94.85% respectively with an accuracy of 96.22%. 3.73% of the 134 smear negative and 5.15% of the 136 culture negative samples were positive by PCR. PCR was the most sensitive and rapid method for the diagnosis of urethritis. Multiplex PCR may be a useful approach to laboratory diagnosis of urethritis in men for its high sensitivity and specificity.

  20. Bacterial Cellulose Shifts Transcriptome and Proteome of Cultured Endothelial Cells Towards Native Differentiation.

    Science.gov (United States)

    Feil, Gerhard; Horres, Ralf; Schulte, Julia; Mack, Andreas F; Petzoldt, Svenja; Arnold, Caroline; Meng, Chen; Jost, Lukas; Boxleitner, Jochen; Kiessling-Wolf, Nicole; Serbest, Ender; Helm, Dominic; Kuster, Bernhard; Hartmann, Isabel; Korff, Thomas; Hahne, Hannes

    2017-09-01

    Preserving the native phenotype of primary cells in vitro is a complex challenge. Recently, hydrogel-based cellular matrices have evolved as alternatives to conventional cell culture techniques. We developed a bacterial cellulose-based aqueous gel-like biomaterial, dubbed Xellulin, which mimics a cellular microenvironment and seems to maintain the native phenotype of cultured and primary cells. When applied to human umbilical vein endothelial cells (HUVEC), it allowed the continuous cultivation of cell monolayers for more than one year without degradation or dedifferentiation. To investigate the impact of Xellulin on the endothelial cell phenotype in detail, we applied quantitative transcriptomics and proteomics and compared the molecular makeup of native HUVEC, HUVEC on collagen-coated Xellulin and collagen-coated cell culture plastic (polystyrene).Statistical analysis of 12,475 transcripts and 7831 proteins unveiled massive quantitative differences of the compared transcriptomes and proteomes. K -means clustering followed by network analysis showed that HUVEC on plastic upregulate transcripts and proteins controlling proliferation, cell cycle and protein biosynthesis. In contrast, HUVEC on Xellulin maintained, by and large, the expression levels of genes supporting their native biological functions and signaling networks such as integrin, receptor tyrosine kinase MAP/ERK and PI3K signaling pathways, while decreasing the expression of proliferation associated proteins. Moreover, CD34-an endothelial cell differentiation marker usually lost early during cell culture - was re-expressed within 2 weeks on Xellulin but not on plastic. And HUVEC on Xellulin showed a significantly stronger functional responsiveness to a prototypic pro-inflammatory stimulus than HUVEC on plastic.Taken together, this is one of the most comprehensive transcriptomic and proteomic studies of native and propagated HUVEC, which underscores the importance of the morphology of the cellular

  1. Value of bacterial culture of vaginal swabs in diagnosis of vaginal infections

    Directory of Open Access Journals (Sweden)

    Nenadić Dane

    2015-01-01

    Full Text Available Bacground/Aim. Vaginal and cervical swab culture is still very common procedure in our country’s everyday practice whereas simple and rapid diagnostic methods have been very rarely used. The aim of this study was to show that the employment of simple and rapid diagnostic tools [vaginal fluid wet mount microscopy (VFWMM, vaginal pH and potassium hydroxide (KOH test] offers better assessment of vaginal environment than standard microbiologic culture commonly used in Serbia. Methods. This prospective study included 505 asymptomatic pregnant women undergoing VFWMM, test with 10% KOH, determination of vaginal pH and standard culture of cervicovaginal swabs. Combining findings from the procedures was used to make diagnoses of bacterial vaginosis (BV and vaginitis. In addition, the number of polymorphonuclear leukocytes (PMN was determined in each sample and analyzed along with other findings. Infections with Candida albicans and Trichomonas vaginalis were confirmed or excluded by microscopic examination. Results. In 36 (6% patients cervicovaginal swab cultures retrieved several aerobes and facultative anaerobes, whereas in 52 (11% women Candida albicans was isolated. Based on VFWMM findings and clinical criteria 96 (19% women had BV, 19 (4% vaginitis, and 72 (14% candidiasis. Of 115 women with BV and vaginitis, pH 4.5 was found in 5, and of 390 with normal findings 83 (21% had vaginal pH 4.5. Elevated numbers of PMN were found in 154 (30% women - in 83 (54% of them VFWMM was normal. Specificity and sensitivity of KOH test and vaginal pH determination in defining pathological vaginal flora were 95% and 81%, and 79% and 91%, respectively. Conclusion. Cervicovaginal swab culture is expensive but almost non-informative test in clinical practice. The use of simpler and rapid methods as vaginal fluid wet mount microscopy, KOH test and vaginal pH offers better results in diagnosis, and probably in the treatment and prevention of sequels of vaginal

  2. Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil

    DEFF Research Database (Denmark)

    Rasmussen, Lasse Dam; Sørensen, S. J.

    2001-01-01

    This study investigates the effect of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. The changes in diversity were monitored in soil microcosms, enriched with 25 mug Hg(II) g(-1) soil, over a period of 3 months...... by purification of total soil DNA and amplification of bacterial 16S rDNA fragments by polymerase chain reaction. Concentrations of bioavailable and total mercury were measured throughout the experiment. The effect on the culturable heterotrophic and genetic diversity was very similar, showing an immediate...... analysed by Shannon-Weaver indices, functional diversity was found to increase almost immediately after mercury addition and to remain at a level higher than the control soil for the rest of the experiment. The fraction of culturable heterotrophic bacteria increased from 1% to 10% of the total bacterial...

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

    Science.gov (United States)

    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.

  4. 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

    Directory of Open Access Journals (Sweden)

    Shanivarsanthe Leelesh Ramya

    2016-06-01

    Full Text Available Abstract 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 2.32 µmol/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 0.26 µmol/min/mg protein. Apart from the insect esterases, bacterial carboxylesterase may aid in the degradation of insecticides in DBM.

  5. Bacterial meningitis in hematopoietic stem cell transplant recipients: a population-based prospective study.

    Science.gov (United States)

    van Veen, K E B; Brouwer, M C; van der Ende, A; van de Beek, D

    2016-11-01

    We performed a nationwide prospective cohort study on the epidemiology and clinical features of community-acquired bacterial meningitis. Patients with a medical history of autologous or allogeneic hematopoietic stem cell transplantation (HSCT) were identified from the cohort performed from March 2006 to October 2014. Fourteen of 1449 episodes (1.0%) of bacterial meningitis occurred in patients with a history of HSCT. The incidence of bacterial meningitis in HSCT recipients was 40.4 per 100 000 patients per year (95% confidence interval (CI) 23.9-62.2), which is 30-fold (95% CI 18-51; Pmeningitis were infected with a serotype included in the 23-valent pneumococcal polysaccharide vaccine, of whom four developed meningitis despite vaccination. In conclusion, HSCT recipients have a substantially increased risk compared with the general population of acquiring bacterial meningitis, which is mostly due to S. pneumoniae, and disease is associated with high mortality and morbidity. Vaccination is important to prevent disease although vaccine failures did occur.

  6. Characterization of metabolically active bacterial populations in subseafloor Nankai Trough sediments above, within and below the sulfate-methane transition zone

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    Heath J. Mills

    2012-04-01

    Full Text Available 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 (IODP Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate-methane transition zone (SMTZ, which was observed approximately 20 meters below the seafloor (mbsf. Small subunit ribosomal RNA (SSU rRNA 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 meters 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

  7. Sensitivity, specificity and predictive value of blood cultures from cattle clinically suspected of bacterial endocarditis

    DEFF Research Database (Denmark)

    Houe, Hans; Eriksen, L.; Jungersen, Gregers

    1993-01-01

    This study investigated the number of blood culture-positive cattle among 215 animals clinically suspected of having bacterial endocarditis. For animals that were necropsied, the sensitivity, specificity and predictive value of the diagnosis of endocarditis were calculated on the basis...... of the isolation of the causative bacteria from blood. Furthermore, it was investigated whether the glutaraldehyde coagulation time, total leucocyte count, per cent neutrophil granulocytes, pulse rate and duration of disease could help to discriminate endocarditis from other diseases. Among 138 animals necropsied...... the sensitivity, specificity and predictive value of blood cultivation were 70.7 per cent, 93.8 per cent and 89.1 per cent, respectively. None of the other measurements could be used to discriminate between endocarditis and non-endocarditis cases....

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2007-09-01

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

  10. Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants.

    Science.gov (United States)

    Hadapad, Ashok B; Prabhakar, Chandra S; Chandekar, Snehal C; Tripathi, Jyoti; Hire, Ramesh S

    2016-06-01

    The microbiota plays an important role in insect development and fitness. Understanding the gut microbiota composition is essential for the development of pest management strategies. Midgut bacteria were isolated from nine wild B. cucurbitae populations collected from different agroecological zones of India. These isolates were further studied for attractant potential of fruit fly adults, and the chemical constituents in the supernatants of gut bacteria were analysed. Twenty-six bacterial isolates belonging to the families Enterobacteriaceae, Bacillaceae, Micrococcaceae and Staphylococcaceae were isolated and identified on the basis of 16S rRNA gene sequence analysis. The dominant species in the midgut of melon fly were from the genera Enterobacter (34.6%), Klebsiella (19.2%), Citrobacter (7.7%), Bacillus (15.4%) and Providencia (7.7%), and 3.8% each of Micrococcus, Staphylococcus, Leclercia and Exiguobacterium. Bactrocera cucurbitae and B. dorsalis adults were significantly attracted to bacterial whole cell cultures and their supernatants in the fruit fly attraction bioassays. Bacillus cereus, Enterobacter, Klebsiella, Citrobacter and Providencia species attracted both male and females of Bactrocera species. The supernatants of Klebsiella, Citrobacter and Providencia species attracted a significantly greater number of females than males. The most abundant chemical constituents in supernatants of K. oxytoca and C. freundii were 3-methyl-1-butanol, 2-phenylethanol, butyl isocyanatoacetate, 2-methyl-1-propanol and 3-hydroxy-2-butanone, as identified by gas chromatography-mass spectrometry. The bacterial endosymbionts associated with melon fly exhibited attractant potential which could facilitate eco-friendly insect control strategies. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  11. Variability of Caltha palustris L. populations in garden culture

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    Krystyna Falińska

    2014-01-01

    Full Text Available On the basis of studies performed in the experimental garden the character of the variability of Caltha palustris L. populations is described. Individuals were bred under uniform conditions from diaspores of meadow, springwood, flood-plain forest and alder forest populations. The results obtained allow to evaluate the hypothesis concerning the ecological preference of cytotypes (S m i t 1967, 1968 and the somewhat different ecological requirements of two subspecies: C. palustris ssp. palustris and C. palustris ssp. cornuta. It was found that each population includes individuals with different cytotypes. The situation is similar as far as subspecies are concerned, distinguished on the basis of fruit morphology (Fig. 1. It should be stressed, however, that, investigations of many years duration raised serious doubts as to the diagnostic value of fruit morphology (Figs. 2, 3. On the basis of the preserved differences between the populations in shoot habitus, reproduction and phenology in garden culture, a springwood and an alder forest ecotype were distinguished. Meadow and flood-plain populations exhibited a transitional character with certain similarities both to the alder forest and to the springwood populations.

  12. Bacterial meningitis

    NARCIS (Netherlands)

    Roos, Karen L.; van de Beek, Diederik

    2010-01-01

    Bacterial meningitis is a neurological emergency. Empiric antimicrobial and adjunctive therapy should be initiated as soon as a single set of blood cultures has been obtained. Clinical signs suggestive of bacterial meningitis include fever, headache, meningismus, vomiting, photophobia, and an

  13. CHROMagar COL-APSE: a selective bacterial culture medium for the isolation and differentiation of colistin-resistant Gram-negative pathogens

    DEFF Research Database (Denmark)

    Abdul Momin, Muhd Haziq F; Bean, David C; Hendriksen, Rene S.

    2017-01-01

    Purpose. A selective chromogenic culture medium for the laboratory isolation and differentiation of colistin resistant Acinetobacter, Pseudomonas, Stenotrophomonas and Enterobacteriaceae spp. (CHROMagar COL-APSE) was developed, evaluated and compared to an existing selective bacterial culture...

  14. [Characterization of bacterial diversity in the Shengli-S12 oil reservoir by culture-dependent and culture-independent methods].

    Science.gov (United States)

    Yuan, Sangqing; Xue, Yanfen; Wang, Weidong; Li, Ximing; Ma, Yanhe

    2008-08-01

    Examining bacterial diversity in an oil reservoir of Shengli oil field by both culture-independent molecular technique and enrichment method. The heterotrophic bacteria, hydrocarbon-degrading bacteria and sulfate-reducing bacteria were enriched from S12-4 oil-well samples by the corresponding media. Then the genomic DNAs of the enrichments were extracted and the 16S rRNA gene clone libraries were constructed. The phylogenetic analysis revealed that the bacterial 16S rRNA gene clone libraries of the 3 enrichments were dominated by clones of Thermotoga, Thermaerobacter and Thermotoga, respectively. Sequences of the other co-dominant clones observed only in the enrichments of hydrocarbon-degrading bacteria and sulfate-reducing bacteria were, respectively, associated with Marinobacter and Moorella. The uncultured 16S rRNA gene library was also generated directly from total DNA of S12-4 oil-well samples by bacterial primer set. Sequence analysis of this bacterial library indicated that a large percentage of clones were highly related to the genus Pseudomonas and the dominant species emerging in the enrichment samples had a very low content in the tested oil reservoir. The significant difference of the bacterial composition between the samples obtained from independent-culture method and enrichment method implies that the specialized nutrient may lead to a distinctive selection of dominant organisms. Through culture-dependent and culture-independent methods, we acquired important information on the bacterial diversity of ShengLi oil reservoir. These results may expand our understanding of the microbial diversity of oil reservoir and provide useful information for MEOR(microbial enhancement of oil recovery).

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

    Science.gov (United States)

    Mohammadkazemi, Faranak; Azin, Mehrdad; Ashori, Alireza

    2015-03-06

    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. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Jyoti Kumar

    2015-09-01

    Full Text Available 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 r

  17. Liquid-liquid extraction and liquid chromatography-mass spectrometry detection of curcuminoids from bacterial culture medium.

    Science.gov (United States)

    Tan, Suryani; Rupasinghe, Thusitha W T; Tull, Dedreia L; Augustin, Mary Ann; Gras, Sally L

    2015-04-15

    Liquid chromatography-mass spectrometry (LC-MS) has been used to detect polyphenolic curcuminoids found in turmeric but studies of metabolism by bacterial and mammalian cells in vitro are compromised by poor recovery from the culture medium. We report a liquid-liquid extraction procedure with ethyl acetate and use LC-MS to quantify extracted curcuminoids. Ethyl acetate allows recoveries of ∼ 80-86% of curcuminoids from the bacterial growth medium, bacterial cell lysate and combined bacterial cell and growth medium matrices; a clear improvement over acetonitrile where recoveries were ∼ 25-66%. This optimised method will enable studies of curcuminoid metabolism and may be applicable to other hydrophobic polyphenolic compounds. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    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 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 (0.07 ± 0.41) (P < 0.05). There was an increase in CLA detection with increasing

  19. Identifying the bacterial community on the surface of Intralox belting in a meat boning room by culture-dependent and culture-independent 16S rDNA sequence analysis.

    Science.gov (United States)

    Brightwell, Gale; Boerema, Jackie; Mills, John; Mowat, Eilidh; Pulford, David

    2006-05-25

    We examined the bacterial community present on an Intralox conveyor belt system in an operating lamb boning room by sequencing the 16S ribosomal DNA (rDNA) of bacteria extracted in the presence or absence of cultivation. RFLP patterns for 16S rDNA clone library and cultures were generated using HaeIII and MspI restriction endonucleases. 16S rDNA amplicons produced 8 distinct RFLP pattern groups. RFLP groups I-IV were represented in the clone library and RFLP groups I and V-VIII were represented amongst the cultured isolates. Partial DNA sequences from each RFLP group revealed that all group I, II and VIII representatives were Pseudomonas spp., group III were Sphingomonas spp., group IV clones were most similar to an uncultured alpha proteobacterium, group V was similar to a Serratia spp., group VI with an Alcaligenes spp., and group VII with Microbacterium spp. Sphingomonads were numerically dominant in the culture-independent clone library and along with the group IV alpha proteobacterium were not represented amongst the cultured isolates. Serratia, Alcaligenes and Microbacterium spp. were only represented with cultured isolates. Pseudomonads were detected by both culture-dependent (84% of isolates) and culture-independent (12.5% of clones) methods and their presence at high frequency does pose the risk of product spoilage if transferred onto meat stored under aerobic conditions. The detection of sphingomonads in large numbers by the culture-independent method demands further analysis because sphingomonads may represent a new source of meat spoilage that has not been previously recognised in the meat processing environment. The 16S rDNA collections generated by both methods were important at representing the diversity of the bacterial population associated with an Intralox conveyor belt system.

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

    Science.gov (United States)

    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.

  1. BACTERIAL POPULATION DYNAMICS IN WASTE OILY EMULSIONS FROM THE METAL-PROCESSING INDUSTRY

    Directory of Open Access Journals (Sweden)

    Paweł Kaszycki

    2014-07-01

    Full Text Available Oil-containing wastewaters are regarded as main industrial pollutants of soil and water environments. They can occur as free-floating oil, unstable or stable oil-in-water (O/W emulsions, and in the case of extreme organic load, as water-in-oil (W/O emulsions. In this study two types of oily effluents, a typical O/W emulsion marked as E1 and a W/O emulsion E2, both discharged by local metal processing plants were examined to test their toxicity to microbial communities and the ability to serve as nutrient sources for bacterial growth. The organic contaminant load of the samples was evaluated on the basis of chemical oxygen demand (COD parameter values and was equal to 48 200 mg O2·dm-3 and >300 000 mg O2·dm-3 for E1 and E2, respectively.Both emulsions proved to be non toxic to bacterial communities and were shown to contain biodiverse autochthonous microflora consisting of several bacterial strains adapted to the presence of xenobiotics (the total of 1.36 · 106 CFU·cm-3 and 1.72 · 105 CFU·cm-3 was determined for E1 and E2, respectively. These indigenous bacteria as well as exogenously inoculated specialized allochthonous microorganisms were biostimulated so as to proliferate within the wastewater environment whose organic content served as the only source of carbon. The most favorable cultivation conditions were determined as fully aerobic growth at the temperature of 25 ºC. In 9 to 18 day-tests, autochthonous as well as bioaugmented allochthonous bacterial population dynamics were monitored. For both emulsions tested there was a dramatic increase (up to three orders of magnitude in bacterial frequency, as compared to the respective initial values. The resultant high biomass densities suggest that the effluents are susceptible to bioremediation. A preliminary xenobiotic biodegradation test confirmed that mixed auto- and allochthonous bacterial consortia obtained upon inoculation of the samples with microbiocenoses preselected for efficient

  2. Bacterial meningitis in Finland, 1995-2014: a population-based observational study.

    Science.gov (United States)

    Polkowska, Aleksandra; Toropainen, Maija; Ollgren, Jukka; Lyytikäinen, Outi; Nuorti, J Pekka

    2017-06-06

    Bacterial meningitis remains an important cause of morbidity and mortality worldwide. Its epidemiological characteristics, however, are changing due to new vaccines and secular trends. Conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae (10-valent) were introduced in 1986 and 2010 in Finland. We assessed the disease burden and long-term trends of five common causes of bacterial meningitis in a population-based observational study. A case was defined as isolation of S. pneumoniae , Neisseria meningitidis , Streptococcus agalactiae , Listeria monocytogenes or H. influenzae from cerebrospinal fluid and reported to national, population-based laboratory surveillance system during 1995-2014. We evaluated changes in incidence rates (Poisson or negative binomial regression), case fatality proportions (χ 2 ) and age distribution of cases (Wilcoxon rank-sum). During 1995-2014, S. pneumoniae and N. meningitidis accounted for 78% of the total 1361 reported bacterial meningitis cases. H. influenzae accounted for 4% of cases (92% of isolates were non-type b). During the study period, the overall rate of bacterial meningitis per 1 00 000 person-years decreased from 1.88 cases in 1995 to 0.70 cases in 2014 (4% annual decline (95% CI 3% to 5%). This was primarily due to a 9% annual reduction in rates of N. meningitidis (95% CI 7% to 10%) and 2% decrease in S. pneumoniae (95% CI 1% to 4%). The median age of cases increased from 31 years in 1995-2004 to 43 years in 2005-2014 (p=0.0004). Overall case fatality proportion (10%) did not change from 2004 to 2009 to 2010-2014. Substantial decreases in bacterial meningitis were associated with infant conjugate vaccination against pneumococcal meningitis and secular trend in meningococcal meningitis in the absence of vaccination programme. Ongoing epidemiological surveillance is needed to identify trends, evaluate serotype distribution, assess vaccine impact and develop future vaccination strategies

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

    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

  5. Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations

    Science.gov (United States)

    Logsdon, Michelle M.; Aldridge, Bree B.

    2018-01-01

    Model bacteria, such as E. coli and B. subtilis, tightly regulate cell cycle progression to achieve consistent cell size distributions and replication dynamics. Many of the hallmark features of these model bacteria, including lateral cell wall elongation and symmetric growth and division, do not occur in mycobacteria. Instead, mycobacterial growth is characterized by asymmetric polar growth and division. This innate asymmetry creates unequal birth sizes and growth rates for daughter cells with each division, generating a phenotypically heterogeneous population. Although the asymmetric growth patterns of mycobacteria lead to a larger variation in birth size than typically seen in model bacterial populations, the cell size distribution is stable over time. Here, we review the cellular mechanisms of growth, division, and cell cycle progression in mycobacteria in the face of asymmetry and inherent heterogeneity. These processes coalesce to control cell size. Although Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) utilize a novel model of cell size control, they are similar to previously studied bacteria in that initiation of DNA replication is a key checkpoint for cell division. We compare the regulation of DNA replication initiation and strategies used for cell size homeostasis in mycobacteria and model bacteria. Finally, we review the importance of cellular organization and chromosome segregation relating to the physiology of mycobacteria and consider how new frameworks could be applied across the wide spectrum of bacterial diversity. PMID:29619019

  6. EFFECT OF REFINED PETROLEUM PRODUCTS CONTAMINATION ON BACTERIAL POPULATION AND PHYSICOCHEMICAL CHARACTERISTICS OF CULTIVATED AGRICULTURAL SOIL

    Directory of Open Access Journals (Sweden)

    Adewale Sogo Olalemi

    2012-10-01

    Full Text Available An investigation into the effect of refined petroleum products contamination on bacterial population and physicochemical characteristics of cultivated agricultural soil was carried out. The soil samples obtained from the Teaching and Research Farm, Obakekere, Federal University of Technology, Akure, Ondo State were contaminated with varying volumes of petrol, diesel and kerosene. The results revealed higher bacterial populations in uncontaminated soils than contaminated soils. The counts of bacteria ranged from 3.0 × 105 to 5.0 × 105 cfu/g in uncontaminated soils and 1.0 × 105 to 3.0 × 105 cfu/g in contaminated soils. The isolated bacteria were identified as Bacillus subtilis, Flavobacterium lutescens, Micrococcus luteus, Corynebacterium variabilis, Pseudomonas fluorescens. The contamination had no significant effect on pH, potassium, sodium, organic carbon and nitrogen content of the soils, while the moisture, calcium, phosphorus and magnesium content of the contaminated soils were significantly different (P < 0.05 compared with the uncontaminated soils. The ability of Bacillus subtilis, Flavobacterium lutescens, Micrococcus luteus, and Pseudomonas fluorescens to utilize the refined petroleum products suggest that these bacteria had potential to bioremediate petroleum contaminated soils.

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

    Science.gov (United States)

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

    2016-12-01

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

  8. Impact of bioremediation treatments on the biodegradation of buried oil and predominant bacterial populations

    International Nuclear Information System (INIS)

    Swannell, R.P.J.; Mitchell, D.J.; Waterhouse, J.C.; Miskin, I.P.; Head, I.M.; Petch, S.; Jones, D.M.; Willis, A.; Lee, K.; Lepo, J.E.

    2000-01-01

    The feasibility of using mineral fertilizers as a bioremediation treatment for oil buried in fine sediments was tested in field trials at a site in the south-west of England. The plots were divided into three blocks of four treatments including untreated, fertilized, oiled unfertilized and oiled fertilized plots. The changes in residual hydrocarbons were monitored to study the biodegradation of Arabian Light Crude Oil which is known to have a high portion of biodegradable components. Samples were extracted at random points at intervals of 0, 42 and 101 days. The analysis process identified a range of aliphatic and aromatic hydrocarbons, as well as a range of geochemical biomarkers. The final results suggested that the oil in the fertilized plots was more degraded than in the oiled, unfertilized control plots. Three way, factorial analysis of variance was used to analyse the data from the oiled fertilized and oiled unfertilized plots. No significant effect of treatment on the degradation of aromatic hydrocarbons was observed. The results also showed that oil treatment and treatment with oil and fertilizer increased the abundance of hydrocarbon-degrading bacterial population. One significant observation was that different bacterial populations were stimulated in response to oil alone and a bioremediation treatment. It was concluded that the addition of inorganic fertilizers to the oiled oxic fine sediment substantially enhanced the level of biodegradation compared to untreated oiled sediment. Bioremediation is a feasible treatment for oil spills where the oil is buried in fine sediment. 14 refs., 1 tab., 4 figs

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

    Science.gov (United States)

    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.

  10. Detection of bacterial species involved in perimplantitis concerned with cultural and RT-PCR

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    Marcello Gatti

    2010-06-01

    Full Text Available Dental implants offer new treatment options for edentulous either partially or completely, now represent a viable alternative to conventional fixed protheses. Dental implants are colonized by a flora dominated by Gram-positive facultative aerobic, while in patients with bone loss and formation of pockets peri-implant diseases was found a significant difference in the composition of microflora, bacteria, Gram-negative anaerobes in particular Fusobacterium spp., Treponema denticola (Spirochetes, Tannerella forsythensis, Aggregatibacter actinomycetemcomitans, Prevotella intermedia as interim black-pigmented bacteria, Porphyromonas gingivalis, often in high concentrations. Aims. The purpose of this study was to identify those at risk of perimplantitis using 2 techniques: RT-PCR examination of trade and culture. The results were compared taking into consideration the advantages and disadvantages of both methods. Materials and methods.We studied 24 patients (14 women and 10 men, aged, women between 43 and 76 years, with an average of 63.8 + / - 10.9 years, men between 45 and 88 years with a average of 64.3 years + / - 12.5 years. Was performed a double levy of sub-gingival plaque at multiple sites that had an implant CAL (clinical attachment level> 4mm in order to assess the microbiological identification with the two techniques: Examining culture and Real-Time PCR of Commerce ( Gum-Sunstar that identifies 4 bacterial species: A. actinomycetemcomitans (A.a., P.gingivalis (P.g., T.forsythensis (T.f., and T.denticola (T.d.. Results. All patients studied were positive to both tests with charger high: the consideration of tenure, with CFU / ml > 105, was positive in 66.6% of samples by:T.f., and P.g., in 12.5% for A.a., while T.d. not been sought by examining culture, the RT-PCR was positive, with high loads, in 95.8% of samples for T.f., in 79.1% for P.g., in 12.5% for A.a. and 20.8% for T.d.The test crop showed the presence of even P.intermedia in 91

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

    Science.gov (United States)

    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.

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

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    Gbenga Adedeji Adewumi

    2013-01-01

    Full Text Available 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 sixteen 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, Staphylococcus 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 Bacillus subtilis and its variants from food-borne pathogens such as Bacillus 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  15. Dynamic Changes in Bacterial Population and Corresponding Exoenzyme Activity in Response to a Tropical Phytoplankton Bloom Chattonella marina

    Directory of Open Access Journals (Sweden)

    Anit M. Thomas

    2014-01-01

    Full Text Available The raphidophyte Chattonella marina (Subrahmanyan Hara & Chihara bloom which causes lethal effects on marine ecosystem has been reported intermittently from Indian waters. In the present study, periodic samplings were made in a Chattonella marina bloom area, off Mahe, on 27 and 29 October and 1 November 2011 (in different phases of the bloom to assess the associated bacterial population and their exoenzyme activity. Microbial community composition of Chattonella marina bloom revealed a twentyfold increase in bacterial load over the nonbloom area. The bacterial genera, Micrococcus, Flavobacterium, Vibrio, and Pseudomonas, increased significantly during the declining phase of the bloom. An assessment of the extracellular enzyme production also showed a marked increase in percentage of bacterial strains, potent in protease production, suggesting the possible role of proteolytic bacteria in bloom crash. This study reveals the bacterial community succession during the bloom and indicates that bacteria play an important role in bloom regulation.

  16. Lethal Consequences of Overcoming Metabolic Restrictions Imposed on a Cooperative Bacterial Population.

    Science.gov (United States)

    Goo, Eunhye; Kang, Yongsung; Lim, Jae Yun; Ham, Hyeonheui; Hwang, Ingyu

    2017-02-28

    Quorum sensing (QS) controls cooperative activities in many Proteobacteria In some species, QS-dependent specific metabolism contributes to the stability of the cooperation. However, the mechanism by which QS and metabolic networks have coevolved to support stable public good cooperation and maintenance of the cooperative group remains unknown. Here we explored the underlying mechanisms of QS-controlled central metabolism in the evolutionary aspects of cooperation. In Burkholderia glumae , the QS-dependent glyoxylate cycle plays an important role in cooperativity. A bifunctional QS-dependent transcriptional regulator, QsmR, rewired central metabolism to utilize the glyoxylate cycle rather than the tricarboxylic acid cycle. Defects in the glyoxylate cycle caused metabolic imbalance and triggered high expression of the stress-responsive chaperonin GroEL. High-level expression of GroEL in glyoxylate cycle mutants interfered with the biosynthesis of a public resource, oxalate, by physically interrupting the oxalate biosynthetic enzyme ObcA. Under such destabilized cooperativity conditions, spontaneous mutations in the qsmR gene in glyoxylate cycle mutants occurred to relieve metabolic stresses, but these mutants lost QsmR-mediated pleiotropy. Overcoming the metabolic restrictions imposed on the population of cooperators among glyoxylate cycle mutants resulted in the occurrence and selection of spontaneous qsmR mutants despite the loss of other important functions. These results provide insight into how QS bacteria have evolved to maintain stable cooperation via QS-mediated metabolic coordination. IMPORTANCE We address how quorum sensing (QS) has coevolved with metabolic networks to maintain bacterial sociality. We found that QS-mediated metabolic rewiring is critical for sustainable bacterial cooperation in Burkholderia glumae The loss of the glyoxylate cycle triggered the expression of the stress-responsive molecular chaperonin GroEL. Excessive biosynthesis of Gro

  17. Biodegradation of γ-hexachlorocyclohexane by transgenic hairy root cultures of Cucurbita moschata that accumulate recombinant bacterial LinA.

    Science.gov (United States)

    Nanasato, Yoshihiko; Namiki, Sayuri; Oshima, Masao; Moriuchi, Ryota; Konagaya, Ken-Ichi; Seike, Nobuyasu; Otani, Takashi; Nagata, Yuji; Tsuda, Masataka; Tabei, Yutaka

    2016-09-01

    γ-HCH was successfully degraded using LinA-expressed transgenic hairy root cultures of Cucurbita moschata . Fusing an endoplasmic reticulum-targeting signal peptide to LinA was essential for stable accumulation in the hairy roots. The pesticide γ-hexachlorocyclohexane (γ-HCH) is a persistent organic pollutant (POP) that raises public health and environmental pollution concerns worldwide. Although several isolates of γ-HCH-degrading bacteria are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the bacterial survival rate. Cucurbita species incorporate significant amounts of POPs from soils compared with other plant species. Here, we describe a novel bioremediation strategy that combines the bacterial degradation of γ-HCH and the efficient uptake of γ-HCH by Cucurbita species. We produced transgenic hairy root cultures of Cucurbita moschata that expressed recombinant bacterial linA, isolated from the bacterium Sphingobium japonicum UT26. The LinA protein was accumulated stably in the hairy root cultures by fusing an endoplasmic reticulum (ER)-targeting signal peptide to LinA. Then, we demonstrated that the cultures degraded more than 90 % of γ-HCH (1 ppm) overnight and produced the γ-HCH metabolite 1,2,4-trichlorobenzene, indicating that LinA degraded γ-HCH. These results indicate that the gene linA has high potential for phytoremediation of environmental γ-HCH.

  18. A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies.

    Science.gov (United States)

    Korolev, Kirill S; Xavier, João B; Nelson, David R; Foster, Kevin R

    2011-10-01

    It is widely accepted that population-genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on- and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatiogenetic patterns in colony biofilms of both species are accurately described by an extension of the one-dimensional stepping-stone model. We use one empirical measure, genetic diversity at the colony periphery, to parameterize our models and show that we can then accurately predict another key variable: the degree of short-range cell migration along an edge. Moreover, the model allows us to estimate other key parameters, including effective population size (density) at the expansion frontier. While our experimental system is a simplification of natural microbial community, we argue that it constitutes proof of principle that the spatial models of population genetics can quantitatively capture organismal evolution.

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

    Science.gov (United States)

    Mao, Junwen; Lu, Ting

    2016-01-05

    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. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Comparison of the diagnostic performance of bacterial culture of nasopharyngeal swab and bronchoalveolar lavage fluid samples obtained from calves with bovine respiratory disease.

    Science.gov (United States)

    Capik, Sarah F; White, Brad J; Lubbers, Brian V; Apley, Michael D; DeDonder, Keith D; Larson, Robert L; Harhay, Greg P; Chitko-McKown, Carol G; Harhay, Dayna M; Kalbfleisch, Ted S; Schuller, Gennie; Clawson, Michael L

    2017-03-01

    OBJECTIVE To compare predictive values, extent of agreement, and gamithromycin susceptibility between bacterial culture results of nasopharyngeal swab (NPS) and bronchoalveolar lavage fluid (BALF) samples obtained from calves with bovine respiratory disease (BRD). ANIMALS 28 beef calves with clinical BRD. PROCEDURES Pooled bilateral NPS samples and BALF samples were obtained for bacterial culture from calves immediately before and at various times during the 5 days after gamithromycin (6 mg/kg, SC, once) administration. For each culture-positive sample, up to 12 Mannheimia haemolytica, 6 Pasteurella multocida, and 6 Histophilus somni colonies underwent gamithromycin susceptibility testing. Whole-genome sequencing was performed on all M haemolytica isolates. For paired NPS and BALF samples collected 5 days after gamithromycin administration, the positive and negative predictive values for culture results of NPS samples relative to those of BALF samples and the extent of agreement between the sampling methods were determined. RESULTS Positive and negative predictive values of NPS samples were 67% and 100% for M haemolytica, 75% and 100% for P multocida, and 100% and 96% for H somni. Extent of agreement between results for NPS and BALF samples was substantial for M haemolytica (κ, 0.71) and H somni (κ, 0.78) and almost perfect for P multocida (κ, 0.81). Gamithromycin susceptibility varied within the same sample and between paired NPS and BALF samples. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated culture results of NPS and BALF samples from calves with BRD should be interpreted cautiously considering disease prevalence within the population, sample collection relative to antimicrobial administration, and limitations of diagnostic testing methods.

  1. Worldwide populations of the aphid Aphis craccivora are infected with diverse facultative bacterial symbionts.

    Science.gov (United States)

    Brady, Cristina M; Asplen, Mark K; Desneux, Nicolas; Heimpel, George E; Hopper, Keith R; Linnen, Catherine R; Oliver, Kerry M; Wulff, Jason A; White, Jennifer A

    2014-01-01

    Facultative bacterial endosymbionts can play an important role in the evolutionary trajectory of their hosts. Aphids (Hemiptera: Aphididae) are infected with a wide variety of facultative endosymbionts that can confer ecologically relevant traits, which in turn may drive microevolutionary processes in a dynamic selective environment. However, relatively little is known about how symbiont diversity is structured in most aphid species. Here, we investigate facultative symbiont species richness and prevalence among world-wide populations of the cowpea aphid, Aphis craccivora Koch. We surveyed 44 populations of A. craccivora, and detected 11 strains of facultative symbiotic bacteria, representing six genera. There were two significant associations between facultative symbiont and aphid food plant: the symbiont Arsenophonus was found at high prevalence in A. craccivora populations collected from Robinia sp. (locust), whereas the symbiont Hamiltonella was almost exclusively found in A. craccivora populations from Medicago sativa (alfalfa). Aphids collected from these two food plants also had divergent mitochondrial haplotypes, potentially indicating the formation of specialized aphid lineages associated with food plant (host-associated differentiation). The role of facultative symbionts in this process remains to be determined. Overall, observed facultative symbiont prevalence in A. craccivora was lower than that of some other well-studied aphids (e.g., Aphis fabae and Acyrthosiphon pisum), possibly as a consequence of A. craccivora's almost purely parthenogenetic life history. Finally, most (70 %) of the surveyed populations were polymorphic for facultative symbiont infection, indicating that even when symbiont prevalence is relatively low, symbiont-associated phenotypic variation may allow population-level evolutionary responses to local selection.

  2. Antimicrobial activity of endophytic bacterial populations isolated from medical plants of Iran.

    Science.gov (United States)

    Beiranvand, Maryam; Amin, Mansour; Hashemi-Shahraki, Abdolrazag; Romani, Bizhan; Yaghoubi, Sajad; Sadeghi, Parisa

    2017-02-01

    Endophytic actinobacteria colonize inside the plant tissues without causing damages to the host plant. Since these microorganisms colonize in the different parts of plants and can stop plant disease, they have been applied as biological agents for controlling human diseases. The aim of this study was molecular identification and measuring the antimicrobial activity of endophytic Actinomycete s isolated from medicinal plants of Iran. The total of 23 medicinal plant samples were collected, sterilized, and crushed. Small pieces of the crushed samples were then cultured directly on three selective media. Grown colonies were identified by 16S rRNA gene sequencing method. Each isolate was cultured in TSB medium and then antimicrobial compound was extracted using ethyl acetate and tested against the target bacteria. Sixteen out of 23 bacterial isolates (69%) exhibited antimicrobial activity against the selected pathogenic bacteria, such as Bacillus cereus, Staphylococcus aureus, Bacillus subtilis, Klebsiella pneumoniae, Citrobacter freundii, Proteus mirabilis, Shigella flexneri and Escherichia coli. Our Study showed a high phylogenetic diversity and the potent antibiotic activity of endophytic bacteria in medicinal plants of Iran.

  3. Antimicrobial activity of endophytic bacterial populations isolated from medical plants of Iran

    Science.gov (United States)

    Beiranvand, Maryam; Amin, Mansour; Hashemi-Shahraki, Abdolrazag; Romani, Bizhan; Yaghoubi, Sajad; Sadeghi, Parisa

    2017-01-01

    Background and Objectives: Endophytic actinobacteria colonize inside the plant tissues without causing damages to the host plant. Since these microorganisms colonize in the different parts of plants and can stop plant disease, they have been applied as biological agents for controlling human diseases. The aim of this study was molecular identification and measuring the antimicrobial activity of endophytic Actinomycetes isolated from medicinal plants of Iran. Materials and Methods: The total of 23 medicinal plant samples were collected, sterilized, and crushed. Small pieces of the crushed samples were then cultured directly on three selective media. Grown colonies were identified by 16S rRNA gene sequencing method. Each isolate was cultured in TSB medium and then antimicrobial compound was extracted using ethyl acetate and tested against the target bacteria. Results: Sixteen out of 23 bacterial isolates (69%) exhibited antimicrobial activity against the selected pathogenic bacteria, such as Bacillus cereus, Staphylococcus aureus, Bacillus subtilis, Klebsiella pneumoniae, Citrobacter freundii, Proteus mirabilis, Shigella flexneri and Escherichia coli. Conclusion: Our Study showed a high phylogenetic diversity and the potent antibiotic activity of endophytic bacteria in medicinal plants of Iran. PMID:28775818

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

    Science.gov (United States)

    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

  5. Red Sea Acropora hemprichii Bacterial Population Dynamics under Adverse Anthropogenic Conditions

    KAUST Repository

    Lizcano, Javier

    2012-08-01

    Reef-building corals are cornerstones of life in the oceans. Understanding their interactions with microorganisms and their surrounding physicochemical conditions is important to comprehend reef functioning and ultimately protect coral reef ecosystems. Corals associate with a complex and specific array of microorganisms that supposedly affect their physiology and therefore can significantly determine the condition of a coral ecosystem. As environmental conditions may shape bacterial diversity and ecology in the coral symbiosis, ecosystem changes might have unfavorable consequences for the holobiont, to date poorly understood. Here, we were studying microbial community changes in A. hemprichii as a consequence of simulated eutrophication and overfishing over a period of 16 weeks by using in situ caging and slow release fertilizer treatments in an undisturbed Red Sea reef (22.18ºN, 38.57ºW). We used 16S rDNA amplicon sequencing to evaluate the individual and combined effects of overnutrification and fishing pressure, two of the most common local threats to coral reefs. With our data we hope to better understand bacterial population dynamics under anthropogenic influences and its role in coral resilience. Projecting further, this data will be useful to better predict the consequences of human activity on reef ecosystems.

  6. Culturable bacterial endophytes isolated from Mangrove tree (Rhizophora apiculata Blume) enhance seedling growth in Rice

    OpenAIRE

    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 endophyt...

  7. Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil

    DEFF Research Database (Denmark)

    Rasmussen, Lasse Dam; Sørensen, S. J.

    2001-01-01

    This study investigates the effect of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. The changes in diversity were monitored in soil microcosms, enriched with 25 mug Hg(II) g(-1) soil, over a period of 3 months...... by purification of total soil DNA and amplification of bacterial 16S rDNA fragments by polymerase chain reaction. Concentrations of bioavailable and total mercury were measured throughout the experiment. The effect on the culturable heterotrophic and genetic diversity was very similar, showing an immediate...... decrease after mercury addition but then slowly increasing throughout the entire experimental period. Pre-exposure levels were not reached within the time span of this investigation. The DGGE band pattern indicated that a shift in the community structure was responsible for recovered diversity. When...

  8. Effect of bacterial population density on germination wheat seeds and dynamics of simple artificial ecosystems

    Science.gov (United States)

    Somova, L. A.; Pechurkin, N. S.; Sarangova, A. B.; Pisman, T. I.

    Effect of the size of rhizospheric bacterial populations on germination of seeds and development of simple terrestrial "wheat plants - rhizospheric microorganisms - artificial soil" and "wheat plants - artificial soil" systems has been studied. Experiments demonstrated that within specify ranges in the inoculate, the rhizospheric bacteria are capable of increasing the yield of germinated seeds and stimulate the growth of plantlets. Germination of seeds inoculated with bacteria was either stimulated, or inhibited or remained at control levels depending on the amount of bacteria. Plant biomass growth and total photoassimilation has been found to depend on the amount of bacteria on the plant roots: the higher the amount of bacteria on plant roots, the smaller is the biomass of plants but the total photoassimilation is, higher. Thus, depending on the amount of bacteria on the roots of plants the system either increases the biomass of plants or increases the total photoassimilation, i.e. "pumps" carbon through itself involving bacteria.

  9. Effect of buctril super (Bromoxynil herbicide on soil microbial biomass and bacterial population

    Directory of Open Access Journals (Sweden)

    Zafar Abbas

    2014-02-01

    Full Text Available The present study aimed to evaluate the effect of bromoxynil herbicide on soil microorganisms, with the hypothesis that this herbicide caused suppression in microbial activity and biomass by exerting toxic effect on them. Nine sites of Punjab province (Pakistan those had been exposed to bromoxynil herbicide for about last ten years designated as soil 'A' were surveyed in 2011 and samples were collected and analyzed for Microbial Biomass Carbon (MBC, Biomass Nitrogen (MBN, Biomass Phosphorus (MBP and bacterial population. Simultaneously, soil samples from the same areas those were not exposed to herbicide designated as soil 'B' were taken. At all the sites MBC, MBN and MBP ranged from 131 to 457, 1.22 to 13.1 and 0.59 to 3.70 µg g-1 in the contaminated soils (Soil A, which was 187 to 573, 1.70 to 14.4 and 0.72 to 4.12 µg g-1 in the soils without contamination (soil B. Bacterial population ranged from 0.67 to 1.84x10(8 and 0.87 to 2.37x10(8 cfu g-1 soil in the soils A and B, respectively. Bromoxynil residues ranged from 0.09 to 0.24 mg kg-1 at all the sites in soil A. But no residues were detected in the soil B. Due to lethal effect of bromoxynil residues on the above parameters, considerable decline in these parameters was observed in the contaminated soils. Results depicted that the herbicide had left toxic effects on soil microbial parameters, thus confirmed that continuous use of this herbicide affected the quality of soil and sustainable crop production.

  10. Effectiveness of oxytetracycline in reducing the bacterial load in rohu fish (Labeo rohita, Hamilton) under laboratory culture condition

    OpenAIRE

    Syed Ariful Haque; Md. Shaheed Reza; Md. Rajib Sharker; Md. Mokhlasur Rahman; Md. Ariful Islam

    2014-01-01

    Objective: To observe the effectiveness of most widely used antibiotic, oxytetracycline (OTC) in reducing the bacterial load in rohu fish under artificial culture condition in the laboratory. Methods: The experiment was conducted in the Faculty Fisheries, Bangladesh Agricultural University, Mymensingh-2202. The fish were reared in 8 aquaria where fish in 5 aquaria were used for replication of the treatment (experimental group) and fish in remaining 3 aquaria were considered...

  11. Cyanuric acid biodegradation by a mixed bacterial culture of Agrobacterium tumefaciens and Acinetobacter sp. in a packed bed biofilm reactor.

    Science.gov (United States)

    Galíndez-Nájera, S P; Llamas-Martínez, M A; Ruiz-Ordaz, N; Juárez-Ramírez, C; Mondragón-Parada, M E; Ahuatzi-Chacón, D; Galíndez-Mayer, J

    2009-02-01

    Cyanuric acid (1,3,5-triazine-2,4,6-triol [OOOT]) is a common biodegradation byproduct of triazinic herbicides, frequently accumulated in soils or water when supplementary carbon sources are absent. A binary bacterial culture able to degrade OOOT was selected through a continuous selection process accomplished in a chemostat fed with a mineral salt (MS) medium containing cyanuric acid as the sole carbon and nitrogen source. By sequence comparison of their 16S rDNA amplicons, bacterial strains were identified as Agrobacterium tumefaciens, and Acinetobacter sp. When the binary culture immobilized in a packed bed reactor (PBR) was fed with MS medium containing OOOT (50 mg L(-1)), its removal efficiencies were about 95%; when it was fed with OOOT plus glucose (120 mg L(-1)) as a supplementary carbon source, its removal efficiencies were closer to 100%. From sessile cells, attached to PBR porous support, or free cells present in the outflowing medium, DNA was extracted and used for Random Amplification of Polymorphic DNA analysis. Electrophoretic patterns obtained were compared to those of pure bacterial strains, a clear predominance of A. tumefaciens in PBR was observed. Although in continuous suspended cell culture, a stable binary community could be maintained, the attachment capability of A. tumefaciens represented a selective advantage over Acinetobacter sp. in the biofilm reactor, favoring its predominance in the porous stone support.

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

    Science.gov (United States)

    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. © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

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

    Directory of Open Access Journals (Sweden)

    Guillaume eMinard

    2015-09-01

    Full Text Available The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the 21st 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.

  14. Radiation resistance of bacterial populations, isolated from the environment of the radiation sterilization plant type JS-6900, Debrecen

    International Nuclear Information System (INIS)

    Gazso, L.; Igali, S.; Daroczy, E.

    1978-01-01

    The radiation resistance of bacterial populations isolated from the air of an industrial sterilization plant loaded with an activity of 250000 Ci was investigated before loading and a year after loading with 60 Co. The mean D 10 value of the 23 strains isolated before loading was 73 krad with a maximum of 173 krad. The mean D 10 value of the 26 strains isolated a year after loading was 32 krad with a maximum of 156 krad. It was not possible to detect any increase in radiation resistance of bacterial populations isolated from the irradiation room after one year of running radiation sterilization of disposable medical supplies. (author)

  15. Food additives reduce lactic acid bacterial growth in culture medium and in meat products, increasing product shelf life

    Directory of Open Access Journals (Sweden)

    Cleonice Mendes Pereira Sarmento

    2015-12-01

    Full Text Available The uncontrolled growth of lactic acid bacteria (LAB in meat and meat products leads to product spoilage, and thus shortens product shelf life. Although food additives are known to decrease LAB growth, this effect has not been analyzed in detail. Here, a detailed analysis was performed of the effects of sodium chloride, sodium polyphosphate, sodium lactate, sodium nitrite/nitrate, and garlic on the growth of the Lactobacillus plantarum in culture medium. The results were used to design and test experimental formulations of meat products. Initially, the effect of food additives on L. plantarum was evaluated using a Fractional Factorial Design (FFD, followed by a Central Composite Rotatable Design (CCRD. The Modified Gompertz Model was adjusted to the growth curves to determine the Kinetic parameters of bacterial growth (logarithmic increase in the population, specific growth rate, and lag phase extension. Higher sodium lactate and sodium chloride levels had a negative impact on L. plantarum growth parameters (p?0.05. Therefore, we designed experimental formulations of mortadella and smoked pork sausages containing 4% sodium lactate (w w-1 and 2.4-3.5% sodium chloride (w w-1, and determined LAB growth from samples of stored products produced according to these formulations, in order to determine product shelf life. There was an increased lag phase of LAB growth for most experimental formulations. Also, the experimental smoked pork sausages had a longer shelf life, which was increased by at least 22 days, suggesting that the proposed formulation, with higher than standard lactate concentration, increased the product’s shelf life.

  16. Clinical Value of Assessing Cytokine Levels for the Differential Diagnosis of Bacterial Meningitis in a Pediatric Population.

    Science.gov (United States)

    Ye, Qing; Shao, Wen-Xia; Shang, Shi-Qiang; Shen, Hong-Qiang; Chen, Xue-Jun; Tang, Yong-Min; Yu, Yong-Lin; Mao, Jian-Hua

    2016-03-01

    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 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.

  17. A Culture-Independent Approach to Enrich Endophytic Bacterial Cells from Sugarcane Stems for Community Characterization.

    Science.gov (United States)

    Dos-Santos, Carlos M; de Souza, Daniel G; Balsanelli, Eduardo; Cruz, Leonardo Magalhães; de Souza, Emanuel M; Baldani, José I; Schwab, Stefan

    2017-08-01

    Bacterial endophytes constitute a very diverse community and they confer important benefits which help to improve agricultural yield. Some of these benefits remain underexplored or little understood, mainly due to the bottlenecks associated with the plant feature, a low number of endophytic bacterial cells in relation to the plant, and difficulties in accessing these bacteria using cultivation-independent methods. Enriching endophytic bacterial cells from plant tissues, based on a non-biased, cultivation-independent physical enrichment method, may help to circumvent those problems, especially in the case of sugarcane stems, which have a high degree of interfering factors, such as polysaccharides, phenolic compounds, nucleases, and fibers. In the present study, an enrichment approach for endophytic bacterial cells from sugarcane lower stems is described. The results demonstrate that the enriched bacterial cells are suitable for endophytic community characterization. A community analysis revealed the presence of previously well-described but also novel endophytic bacteria in sugarcane tissues which may exert functions such as plant growth promotion and biological control, with a predominance of the Proteobacterial phylum, but also Actinobacteria, Bacteroidetes, and Firmicutes, among others. In addition, by comparing the present and literature data, it was possible to list the most frequently detected bacterial endophyte genera in sugarcane tissues. The presented enrichment approach paves the way for improved future research toward the assessment of endophytic bacterial community in sugarcane and other biofuel crops.

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

    Science.gov (United States)

    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, Π(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.

  19. The type VI secretion system impacts bacterial invasion and population dynamics in a model intestinal microbiota

    Science.gov (United States)

    Logan, Savannah L.; Shields, Drew S.; Hammer, Brian K.; Xavier, Joao B.; Parthasarathy, Raghuveer

    Animal gastrointestinal tracts are home to a diverse community of microbes. The mechanisms by which microbial species interact and compete in this dense, physically dynamic space are poorly understood, limiting our understanding of how natural communities are assembled and how different communities could be engineered. Here, we focus on a physical mechanism for competition: the type VI secretion system (T6SS). The T6SS is a syringe-like organelle used by certain bacteria to translocate effector proteins across the cell membranes of target bacterial cells, killing them. Here, we use T6SS+ and T6SS- strains of V. cholerae, the pathogen that causes cholera in humans, and light sheet fluorescence microscopy for in vivo imaging to show that the T6SS provides an advantage to strains colonizing the larval zebrafish gut. Furthermore, we show that T6SS+ bacteria can invade and alter an existing population of a different species in the zebrafish gut, reducing its abundance and changing the form of its population dynamics. This work both demonstrates a mechanism for altering the gut microbiota with an invasive species and explores the processes controlling the stability and dynamics of the gut ecosystem. Research Corporation, Gordon and Betty Moore Foundation, and the Simons Foundation.

  20. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques

    Science.gov (United States)

    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

  1. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques

    Directory of Open Access Journals (Sweden)

    Siele Ceuppens

    2015-08-01

    Full Text Available 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.

  2. Following an imaginary Campylobacter population from farm to fork and beyond: a bacterial perspective.

    Science.gov (United States)

    Wassenaar, T M

    2011-09-01

    It has been known for decades that poultry meat is the most common single source for campylobacteriosis, yet the problem has not been solved. This review identifies some of the reasons why our attempts to reduce the incidence of this pathogen have largely failed. Based on the literature, the events a virtual population of Campylobacter may encounter, from growing in the gut of a broiler to eventually infecting humans and causing disease, are reviewed. Most steps in the farm-to-fork process are well studied, though there are gaps in our knowledge about survival and spread of Campylobacter populations before they enter the farm. Key events in the farm-to-fork chain that are suitable targets for prevention and control, to reduce food-borne campylobacteriosis, are indicated. Novel insights into the pathogenic mechanism responsible for disease in humans are summarized, which hypothesize that an overactive immune response is the reason for the typical inflammatory diarrhoea. A role of genetic microheterogeneity within a clonal population in this chain of events is being proposed here. The human host is not necessary for the survival of the bacterial species, nor have these bacteria specifically evolved to cause disease in that host. More likely, the species evolved for a commensal life in birds, and human disease can be considered as collateral damage owing to an unfortunate host-microbe interaction. The indirect environmental burden that results from poultry production should not be ignored as it may pose a diffuse, but possibly significant risk factor for disease. © 2011 The Author. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

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

    OpenAIRE

    Radzki, W.; Gutierrez Ma?ero, F. J.; Algar, E.; Lucas Garc?a, J. A.; Garc?a-Villaraco, A.; Ramos Solano, B.

    2013-01-01

    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 toma...

  4. Respiratory bacterial culture from two sequential bronchoalveolar lavages of the same lobe in children with chronic cough.

    Science.gov (United States)

    Hare, K M; Marsh, R L; Smith-Vaughan, H C; Bauert, P; Chang, A B

    2015-11-01

    Identification of bacteria causing lower-airway infections is important to determine appropriate antimicrobial therapy. Flexible bronchoscopy with bronchoalveolar lavage (BAL) is used to obtain lower-airway specimens in young children. The first lavage (lavage-1) is typically used for bacterial culture. However, no studies in children have compared the detection of cultivable bacteria from sequential lavages of the same lobe. BAL fluid was collected from two sequential lavages of the same lobe in 79 children enrolled in our prospective studies of chronic cough. The respiratory bacteria Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Haemophilus parainfluenzae were isolated and identified using standard published methods. H. influenzae was differentiated from Haemophilus haemolyticus using PCR assays. Lower-airway infection was defined as ≥ 104 c.f.u. ml- 1 BAL fluid. We compared cultivable bacteria from lavage-1 with those from the second lavage (lavage-2) using the κ statistic. Lower-airway infections by any pathogen were detected in 46% of first lavages and 39% of second lavages. Detection was similar in both lavages for all pathogens; the κ statistic was 0.7-0.8 for all bacteria except H. parainfluenzae. Of all infections detected in either lavage, 90% were detected in lavage-1 and 78  in lavage-2. However, culture of lavage-2 identified infections that would have been missed in 8% of children, including infections by additional Streptococcus pneumoniae serotypes. Our findings support the continued use of lavage-1 for bacterial culture; however, culture of lavage-2 may yield additional identifications of bacterial pathogens in lower-airway infections.

  5. Effectiveness of oxytetracycline in reducing the bacterial load in rohu fish (Labeo rohita, Hamilton under laboratory culture condition

    Directory of Open Access Journals (Sweden)

    Syed Ariful Haque

    2014-04-01

    Full Text Available Objective: To observe the effectiveness of most widely used antibiotic, oxytetracycline (OTC in reducing the bacterial load in rohu fish under artificial culture condition in the laboratory. Methods: The experiment was conducted in the Faculty Fisheries, Bangladesh Agricultural University, Mymensingh-2202. The fish were reared in 8 aquaria where fish in 5 aquaria were used for replication of the treatment (experimental group and fish in remaining 3 aquaria were considered as a control (Control group. OTC was fed to the fish in the experimental aquarium at the rate of 2 g/kg through diet twice daily whereas fish reared under control condition was given feed without antibiotic for 20 d and bacterial content in the aquarium water, gills, skin and intestine of fish were estimated at every alternative day after onset of the experiment. Results: Rearing the fish with OTC treated feed resulted in gradual decrease of bacterial load in the aquarium water, gills, intestine and skin of the fish whereas the content remain unchanged or little increased in the control group. Water quality parameters such as dissolved oxygen, pH and total hardness were within the suitable range in the experimental aquarium but not in control aquaria throughout the experimental period. Conclusions: These results suggest that OTC could be a potential antibiotic to reduce the bacterial load in fish and can be used commercially for maintaining the fish health in aquarium conditions.

  6. No evidence for a culturable bacterial tetrodotoxin producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae) and Stylochoplana sp. (Platyhelminthes: Polycladida).

    Science.gov (United States)

    Salvitti, Lauren R; Wood, Susanna A; McNabb, Paul; Cary, Stephen Craig

    2015-01-28

    Tetrodotoxin (TTX) is a potent neurotoxin found in the tissues of many taxonomically diverse organisms. Its origin has been the topic of much debate, with suggestions including endogenous production, acquisition through diet, and symbiotic bacterial synthesis. Bacterial production of TTX has been reported in isolates from marine biota, but at lower than expected concentrations. In this study, 102 strains were isolated from Pleurobranchaea maculata (Opisthobranchia) and Stylochoplana sp. (Platyhelminthes). Tetrodotoxin production was tested utilizing a recently developed sensitive method to detect the C9 base of TTX via liquid chromatography-mass spectrometry. Bacterial strains were characterized by sequencing a region of the 16S ribosomal RNA gene. To account for the possibility that TTX is produced by a consortium of bacteria, a series of experiments using marine broth spiked with various P. maculata tissues were undertaken. Sixteen unique strains from P. maculata and one from Stylochoplana sp. were isolated, representing eight different genera; Pseudomonadales, Actinomycetales, Oceanospirillales, Thiotrichales, Rhodobacterales, Sphingomonadales, Bacillales, and Vibrionales. Molecular fingerprinting of bacterial communities from broth experiments showed little change over the first four days. No C9 base or TTX was detected in isolates or broth experiments (past day 0), suggesting a culturable microbial source of TTX in P. maculata and Stylochoplana sp. is unlikely.

  7. No Evidence for a Culturable Bacterial Tetrodotoxin Producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae and Stylochoplana sp. (Platyhelminthes: Polycladida

    Directory of Open Access Journals (Sweden)

    Lauren R. Salvitti

    2015-01-01

    Full Text Available 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.

  8. Agreement between microscopic examination and bacterial culture of bile samples for detection of bactibilia in dogs and cats with hepatobiliary disease.

    Science.gov (United States)

    Pashmakova, Medora B; Piccione, Julie; Bishop, Micah A; Nelson, Whitney R; Lawhon, Sara D

    2017-05-01

    OBJECTIVE To evaluate the agreement between results of microscopic examination and bacterial culture of bile samples from dogs and cats with hepatobiliary disease for detection of bactibilia. DESIGN Cross-sectional study. ANIMALS 31 dogs and 21 cats with hepatobiliary disease for which subsequent microscopic examination and bacterial culture of bile samples was performed from 2004 through 2014. PROCEDURES Electronic medical records of included dogs and cats were reviewed to extract data regarding diagnosis, antimicrobials administered, and results of microscopic examination and bacterial culture of bile samples. Agreement between these 2 diagnostic tests was assessed by calculation of the Cohen κ value. RESULTS 17 (33%) dogs and cats had bactibilia identified by microscopic examination of bile samples, and 11 (21%) had bactibilia identified via bacterial culture. Agreement between these 2 tests was substantial (percentage agreement [positive and negative results], 85%; κ = 0.62; 95% confidence interval, 0.38 to 0.89) and improved to almost perfect when calculated for only animals that received no antimicrobials within 24 hours prior to sample collection (percentage agreement, 94%; κ = 0.84; 95% confidence interval, 0.61 to 1.00). CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that agreement between microscopic examination and bacterial culture of bile samples for detection of bactibilia is optimized when dogs and cats are not receiving antimicrobials at the time of sample collection. Concurrent bacterial culture and microscopic examination of bile samples are recommended for all cats and dogs evaluated for hepatobiliary disease.

  9. Detrimental effects of commercial zinc oxide and silver nanomaterials on bacterial populations and performance of wastewater systems

    Science.gov (United States)

    Mboyi, Anza-vhudziki; Kamika, Ilunga; Momba, MaggyN. B.

    2017-08-01

    The widespread use of commercial nanomaterials (NMs) in consumer products has raised environmental concerns as they can enter and affect the efficiency of the wastewater treatment plants. In this study the effect of various concentrations of zinc oxide NMs (nZnO) and silver NMs (nAg) on the selected wastewater bacterial species (Bacillus licheniformis, Brevibacillus laterosporus and Pseudomonas putida) was ascertained at different pH levels (pH 2, 7 and 10). Lethal concentrations (LC) of NMs and parameters such as chemical oxygen demand (COD) and dissolved oxygen (DO) were taken into consideration to assess the performance of a wastewater batch reactor. Bacterial isolates were susceptible to varying concentrations of both nZnO and nAg at pH 2, 7 and 10. It was found that a change in pH did not significantly affect the toxicity of test NMs towards target bacterial isolates. All bacterial species were significantly inhibited (p 0.05) in COD removal in the presence of increasing concentrations of NMs, which resulted in increasing releases of COD. Noticeably, there was no significant difference (p > 0.05) in the decrease in DO uptake in the presence of increasing NM concentrations for all bacterial isolates. The toxic effects of the target NMs on bacterial populations in wastewater may negatively impact the performance of biological treatment processes and may thus affect the efficiency of wastewater treatment plants in producing effluent of high quality.

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

    Science.gov (United States)

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

    2016-07-25

    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.

  11. Mass culture strategy for bacterial yeast co-culture for degradation of petroleum hydrocarbons in marine environment.

    Science.gov (United States)

    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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Identification of a New Marine Bacterial Strain SD8 and Optimization of Its Culture Conditions for Producing Alkaline Protease

    Science.gov (United States)

    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

  13. Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

    Directory of Open Access Journals (Sweden)

    Delavat François

    2012-09-01

    Full Text Available Abstract 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

  14. Yeast and bacterial diversity along a transect in an acidic, As-Fe rich environment revealed by cultural approaches.

    Science.gov (United States)

    Delavat, François; Lett, Marie-Claire; Lièvremont, Didier

    2013-10-01

    Acid mine drainages (AMDs) are often thought to harbour low biodiversity, yet little is known about the diversity distribution along the drainages. Using culture-dependent approaches, the microbial diversity from the Carnoulès AMD sediment was investigated for the first time along a transect showing progressive environmental stringency decrease. In total, 20 bacterial genera were detected, highlighting a higher bacterial diversity than previously thought. Moreover, this approach led to the discovery of 16 yeast species, demonstrating for the first time the presence of this important phylogenetic group in this AMD. All in all, the location of the microbes along the transect helps to better understand their distribution in a pollution gradient. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. On fermionic models of a closed ecosystem with application to bacterial populations

    Directory of Open Access Journals (Sweden)

    Rosa Di Salvo

    2016-09-01

    Full Text Available This paper deals with the application of operatorial techniques of quantum physics to a theoretical model of closed ecosystems. The model is built by using fermionic operators whose evolution is ruled by a self--adjoint Hamiltonian operator. Adopting Heisenberg--like dynamics, we consider either linear or nonlinear models with the aim of describing the long-term survival of bacterial populations; the introduction of effective dissipative mechanisms is also considered. Moreover, a variant of linear models through the introduction of additional rules acting periodically on the system is proposed. Specifically, the evolution in a time interval is obtained by gluing the evolutions in a finite set of adjacent subintervals. In each subinterval the Hamiltonian is time independent, but the values of the parameters entering the Hamiltonian may be changed by the rules at the end of a subinterval on the basis of the actual state of the system. Within this context, a new approach is provided in order to obtain reliable results, without increasing the computational cost of the numerical integration of the differential equations involved.

  16. High-pressure processing applied to cooked sausages: bacterial populations during chilled storage.

    Science.gov (United States)

    Yuste, J; Pla, R; Capellas, M; Ponce, E; Mor-Mur, M

    2000-08-01

    Vacuum-packaged cooked sausages were pressurized at 500 MPa for 5 or 15 min at mild temperature (65 degrees C) and later stored at 2 and 8 degrees C for 18 weeks. Counts of aerobic mesophiles and psychrotrophs, lactic acid bacteria, enterobacteria, Baird-Parker microbiota, and Listeria spp. were determined 1 day and 3, 6, 9, 12, 15, and 18 weeks after treatment and compared with those of cooked sausages treated at 80 to 85 degrees C for 40 min. Pressurization generated reductions of about 4 log CFU/g in psychrotrophs and lactic acid bacteria. Enterobacteria and Listeria proved the most pressure sensitive; insignificant or no growth was detected throughout the study. Heat treatment inactivated psychrotrophs and enterobacteria similarly to pressure treatment. Listeria monocytogenes and enterotoxigenic Staphylococcus aureus were not found in treated samples. In general, there was no significant difference in counts of any bacterial populations either among treatments or between storage temperatures. High-pressure processing at mild temperature is an effective preservation method that can replace heat pasteurization applied to some cooked meat and poultry products after packaging.

  17. Visualizing the response of a gut bacterial population to antibiotic perturbations

    Science.gov (United States)

    Schlomann, Brandon; Wiles, Travis; Guillemin, Karen; Parthasarathy, Raghuveer

    Each of our intestines is home to a vast ecosystem composed of trillions of bacteria in a dynamic environment. Bacterial communities face fluctuations in nutrient influx, invasions by new microbes, physical disturbances from peristalsis, and, perhaps, the arrival of antibiotic drugs. Metagenomic profiling has shown that antibiotic treatments can cause major changes in the composition of species present in the gut, at timescales shorter than a day. How this happens is unknown, as these dynamics have never been observed directly. I'll present recent work that addresses this by using well-defined microbial communities in a model organism, the zebrafish. Light Sheet Fluorescence Microscopy is used to image a commensal species of Vibrioresponding to antibiotic perturbations in the guts of live, larval fish. We find that sub-lethal concentrations of different classes of antibiotics induce similar physical responses in Vibrio, namely filamentation and reduction of motility. The arrested bacteria then aggregate and can be ejected via peristalsis, resulting in large population collapses. These observations suggest that antibiotics can cause large disruptions to gut ecosystems even in low concentrations, and that physical processes may be important drivers of response dynamics.

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

    Science.gov (United States)

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

    2017-04-01

    Bacteria live in dynamic systems where selection pressures can alter rapidly, forcing adaptation to the prevailing conditions. In particular, bacteriophages and antibiotics of anthropogenic origin are major bacterial stressors in many environments. We previously observed that populations of the bacterium Pseudomonas fluorescens SBW25 exposed to the lytic bacteriophage SBW25Φ2 and a noninhibitive concentration of the antibiotic streptomycin (coselection) achieved higher levels of phage resistance compared to populations exposed to the phage alone. In addition, the phage became extinct under coselection while remaining present in the phage alone environment. Further, phenotypic tests indicated that these observations might be associated with increased mutation rate under coselection. In this study, we examined the genetic causes behind these phenotypes by whole-genome sequencing clones isolated from the end of the experiments. We were able to identify genetic factors likely responsible for streptomycin resistance, phage resistance and hypermutable (mutator) phenotypes. This constitutes genomic evidence in support of the observation that while the presence of phage did not affect antibiotic resistance, the presence of antibiotic affected phage resistance. We had previously hypothesized an association between mutators and elevated levels of phage resistance under coselection. However, our evidence regarding the mechanism was inconclusive, as although with phage mutators were only found under coselection, additional genomic evidence was lacking and phage resistance was also observed in nonmutators under coselection. More generally, our study provides novel insights into evolution between univariate and multivariate selection (here two stressors), as well as the potential role of hypermutability in natural communities. © 2016 John Wiley & Sons Ltd.

  19. Diversity of bacterial communities that colonize the filter units used for controlling plant pathogens in soilless cultures.

    Science.gov (United States)

    Renault, David; Vallance, Jessica; Déniel, Franck; Wery, Nathalie; Godon, Jean Jacques; Barbier, Georges; Rey, Patrice

    2012-01-01

    In recent years, increasing the level of suppressiveness by the addition of antagonistic bacteria in slow filters has become a promising strategy to control plant pathogens in the recycled solutions used in soilless cultures. However, knowledge about the microflora that colonize the filtering columns is still limited. In order to get information on this issue, the present study was carried out over a 4-year period and includes filters inoculated or not with suppressive bacteria at the start of the filtering process (two or three filters were used each year). After 9 months of filtration, polymerase chain reaction (PCR)-single strand conformation polymorphism analyses point out that, for the same year of experiment, the bacterial communities from control filters were relatively similar but that they were significantly different between the bacteria-amended and control filters. To characterize the changes in bacterial communities within the filters, this microflora was studied by quantitative PCR, community-level physiological profiles, and sequencing 16SrRNA clone libraries (filters used in year 1). Quantitative PCR evidenced a denser bacterial colonization of the P-filter (amended with Pseudomonas putida strains) than control and B-filter (amended with Bacillus cereus strains). Functional analysis focused on the cultivable bacterial communities pointed out that bacteria from the control filter metabolized more carbohydrates than those from the amended filters whose trophic behaviors were more targeted towards carboxylic acids and amino acids. The bacterial communities in P- and B-filters both exhibited significantly more phylotype diversity and markedly distinct phylogenetic compositions than those in the C-filter. Although there were far fewer Proteobacteria in B- and P-filters than in the C-filter (22% and 22% rather than 69% of sequences, respectively), the percentages of Firmicutes was much higher (44% and 55% against 9%, respectively). Many Pseudomonas

  20. An EPA pilot study characterizing fungal and bacterial populations at homes after flooding events at the Martin Peña Channel community-Puerto Rico

    Science.gov (United States)

    The overall objective of this program is to characterize fungal and bacterial populations in the MPC residences in San Juan, Puerto Rico, following flooding events. These profiles will be generated by comparing the fungal and bacterial populations in two groups of residences: hom...

  1. Some aspects of the culture, population dynamics and reproductive ...

    African Journals Online (AJOL)

    The effectiveness of using freshwater Chlorella, mixed algae, lettuce leaves and supplemental baker's yeast for the culture of freshwater rotifer, Brachionus calyciflorus were evaluated every two days for 18 days culture period. Rotifers raised without yeast attained maximum density of 100 - 152 inds.ml-1 after 6 days of ...

  2. Symbiotic nitrogen-fixing bacterial populations trapped from soils under agroforestry systems in the Western Amazon

    Directory of Open Access Journals (Sweden)

    Paula Marcela Duque Jaramillo

    2013-12-01

    Full Text Available Cowpea (Vigna unguiculata is an important grain-producing legume that can forego nitrogen fertilization by establishing an efficient symbiosis with nitrogen-fixing bacteria. Although inoculating strains have already been selected for this species, little is known about the genotypic and symbiotic diversity of native rhizobia. Recently, Bradyrhizobium has been shown to be the genus most frequently trapped by cowpea in agricultural soils of the Amazon region. We investigated the genetic and symbiotic diversity of 148 bacterial strains with different phenotypic and cultural properties isolated from the nodules of the trap species cowpea, which was inoculated with samples from soils under agroforestry systems from the western Amazon. Sixty non-nodulating strains indicated a high frequency of endophytic strains in the nodules. The 88 authenticated strains had varying symbiotic efficiency. The SPAD (Soil Plant Analysis Development index (indirect measurement of chlorophyll content was more efficient at evaluating the contribution of symbiotic N2-fixation than shoot dry matter under axenic conditions. Cowpea-nodulating bacteria exhibited a high level of genetic diversity, with 68 genotypes identified by BOX-PCR. Sequencing of the 16S rRNA gene showed a predominance of the genus Bradyrhizobium, which accounted for 70 % of all strains sequenced. Other genera identified were Rhizobium, Ochrobactrum, Paenibacillus, Bosea, Bacillus, Enterobacter, and Stenotrophomonas. These results support the promiscuity of cowpea and demonstrate the high genetic and symbiotic diversity of rhizobia in soils under agroforestry systems, with some strains exhibiting potential for use as inoculants. The predominance of Bradyrhizobium in land uses with different plant communities and soil characteristics reflects the adaptation of this genus to the Amazon region.

  3. Controlling the diversity of cell populations in a stem cell culture

    NARCIS (Netherlands)

    Heo, Inha; Clevers, Hans

    2015-01-01

    Culturing intestinal stem cells into 3D organoids results in heterogeneous cell populations, reflecting the in vivo cell type diversity. In a recent paper published in Nature, Wang et al. established a culture condition for a highly homogeneous population of intestinal stem cells.

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

    Science.gov (United States)

    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…

  5. Microbial population analysis of the salivary glands of ticks; a possible strategy for the surveillance of bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Yongjin Qiu

    Full Text Available 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

  6. Characterization of the rate and temperature sensitivities of bacterial remineralization of dissolved organic phosphorus by natural populations

    Directory of Open Access Journals (Sweden)

    Angelicque E. White

    2012-08-01

    Full Text Available Production, transformation, and degradation are the principal components of the cycling of dissolved organic matter (DOM in marine systems. Heterotrophic Bacteria (and Archaea play a large part in this cycling via enzymatic decomposition and intracellular transformations of organic material to inorganic carbon (C, nitrogen (N , and phosphorus (P. The rate and magnitude of inorganic nutrient regeneration from DOM is related to the elemental composition and lability of DOM substrates as well as the nutritional needs of the mediating organisms. While many previous efforts have focused on C and N cycling of DOM, less is known in regards to the controls of organic P utilization and remineralization by natural populations of bacteria. In order to constrain the relative time scales and degradation of select dissolved organic P (DOP compounds we have conducted a series of experiments focused on (1 assessment of the short-term lability of a range of DOP compounds, (2 characterization of labile DOP remineralization rates and (3 examination of temperature sensitivities of labile DOP remineralization for varying bacterial populations. Results reinforce previous findings of monoester and polyphosphate lability and the relative recalcitrance of a model phosphonate: 2-aminoethylphosphonate. High resolution time-series of P monoester remineralization indicates decay constants on the order of 0.67-7.04 d-1 for bacterial populations isolated from coastal and open ocean surface waters. The variability of these rates is predictably related to incubation temperature and initial concentrations of heterotrophic bacteria. Additional controls on DOP hydrolysis included seasonal shifts in bacterial populations and the physiological state of bacteria at the initiation of DOP addition experiments. Composite results indicate that bacterial hydrolysis of P-monoesters exceeds bacterial P demand and thus DOP remineralization efficiency may control P availability to autotrophs.

  7. Effects of bacterial contamination of media on the diagnosis of Tritrichomonas foetus by culture and real-time PCR.

    Science.gov (United States)

    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 (Pmedia interfere with T. foetus identification by culture and PCR and adversely affect diagnostic sensitivity for this fastidious pathogen. Copyright © 2015 Elsevier B.V. All rights

  8. Bacterial meningitis in solid organ transplant recipients: a population-based prospective study

    NARCIS (Netherlands)

    van Veen, K. E. B.; Brouwer, M. C.; van der Ende, A.; van de Beek, D.

    2016-01-01

    Solid organ transplant (SOT) recipients are at risk of infections of the central nervous system. However, the incidence and clinical course of bacterial meningitis in SOT recipients are unclear. We studied occurrence, disease course, and prognosis of bacterial meningitis in SOT recipients in the

  9. Biodegradation potential of pure and mixed bacterial cultures for removal of 4-nitroaniline from textile dye wastewater.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2015-06-29

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P 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.

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

    KAUST Repository

    Bargiela, Rafael

    2015-06-29

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

  12. 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

    Science.gov (United States)

    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 (coral disease resembling WP may result from

  13. [Cultural structures that determine suffering among various populations].

    Science.gov (United States)

    Pagés Larraya, F

    1986-09-01

    The cross-cultural consideration of our Psychiatric Epidemiology Program outlined the profile of the madman and his discourse as both mirror and enigma of his cultural community. This enigma occurs as a result of the suffering, the violence and the slyness inherent to creativity, in the sense that his own accomplishments are inexorably questionable because of the ubiquitous presence of the tragic and das Unheimliche. The madman "malgré soi" becomes a perfect interpreter of the cultural crisis and is a real key to his deepest structural interpretation. Therefore, we uphold a "tragic erasmism" and from then on discuss the hermeneutics of Nietzsche, Freud and Heidegger.

  14. Diagnosis of bacterial vaginosis in a rural setup: Comparison of clinical algorithm, smear scoring and culture by semiquantitative technique

    Directory of Open Access Journals (Sweden)

    Rao P

    2004-01-01

    Full Text Available This study was undertaken to estimate the prevalence of bacterial vaginosis (BV and other sexually transmitted infections (STIs in a rural set up and compare the smear scoring system to that of culture by semiquantitative technique. A total of 505 married women, who were in sexually active age group of 15-44 years, were selected from three different villages. High vaginal swabs, endocervical swabs, vaginal discharge and blood were collected and processed in the laboratory. Overall prevalence of 29% reproductive tract infection was detected. Endogenous infection was commonly observed (27.92%, and very low prevalence of STIs (Trichomonas 1.18%, Syphilis 0%, Gonorrhea 0% was detected. Diagnosis of BV was possible in 104 (20.5% women by smear alone and 88 (17.42% women by semiquantitative culture.

  15. Cultural competency: providing quality care to diverse populations.

    Science.gov (United States)

    Betancourt, Joseph R

    2006-12-01

    The goal of this paper is to define cultural competence and present a practical framework to address crosscultural challenges that emerge in the clinical encounter, with a particular focus on the issue of nonadherence. English-language literature, both primary and reports from various agencies, and the author's personal experiences in clinical practice. Relevant literature on patient-centered care and cultural competence. There is a growing literature that delineates the impact of sociocultural factors, race, ethnicity, and limited-English proficiency on health and clinical care. The field of cultural competence focuses on addressing these issues. Health care providers need a practical set of tools and skills that will enable them to provide quality care to patients during a brief encounter, whatever differences in background that may exist. Cultural competence has evolved from the gathering of information and making of assumptions about patients on the basis of their sociocultural background to the development of skills to implement the principles of patient-centered care. This patient-based approach to cross-cultural care consists of first, assessing core cross-cultural issues; second, exploring the meaning of the illness to the patient; third, determining the social context in which the patient lives; and fourth, engaging in negotiation with the patient to encourage adherence. Addressing adherence is a particularly challenging issue, the determinants of which are multifactorial, and the ESFT (explanatory/social/fears/treatment) model--derived from the patient-based approach--is a tool that identifies barriers to adherence and provides strategies to address them. It obviously is impossible to learn everything about every culture and that should not be expected. Instead, we should learn about the communities we care for. More important, we should have a framework that allows us to provide appropriate care for any patient--one that deals with issues of adherence

  16. The role of silicon in enhancing resistance to bacterial blight of hydroponic- and soil-cultured rice

    Science.gov (United States)

    Song, Alin; Xue, Gaofeng; Cui, Peiyuan; Fan, Fenliang; Liu, Hongfang; Yin, Chang; Sun, Wanchun; Liang, Yongchao

    2016-01-01

    Here we report for the first time that bacterial blight of rice can be alleviated by silicon (Si) added. In both inoculated and uninoculated plants, shoot dry weight was significantly higher in the +Si plants than in the −Si plants. A soil-cultured trial showed that disease severity was 24.3% lower in the Si-amended plants than in the non-Si-amended plants. Plants that were switched from −Si to +Si nutrient solution and simultaneously inoculated with Xoo also exhibited the same high resistance to bacterial blight as the plants that were treated continuously with Si, with control efficiencies of 52.8 and 62.9%, respectively. Moreover, total concentrations of soluble phenolics and lignin in rice leaves were significantly higher in the +Si plants than in the −Si plants. Polyphenoloxidase (PPO) and phenylalanine ammonia-lyase (PAL) activities in rice leaves were observed to be higher in the +Si plants than in the −Si plants. The expression levels of Os03g0109600, Prla, Rcht2 and Lox2osPil, were also higher in +Si plants than in −Si plants post-inoculation during the experimental time. Addition of Si resulted in increased Pal transcription, and inhibited CatA and Os03g0126000 expression in the earlier and later stages of bacterial inoculation, respectively. PMID:27091552

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Verdejo-Lucas, S; Pinochet, J

    1992-03-01

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

  19. Time to antibiotic therapy and outcome in bacterial meningitis: a Danish population-based cohort study.

    Science.gov (United States)

    Bodilsen, Jacob; Dalager-Pedersen, Michael; Schønheyder, Henrik Carl; Nielsen, Henrik

    2016-08-09

    Community-acquired bacterial meningitis (CABM) is a life-threatening disease and timing of antibiotic therapy remains crucial. We aimed to analyse the impact of antibiotic timing on the outcome of CABM in a contemporary cohort. We conducted a population-based cohort study based on chart reviews of all adult cases (>16 years of age) of CABM in North Denmark from 1998 to 2014 excluding patients given pre-hospital parenteral antibiotics. We used modified Poisson regression analyses to compute the adjusted risk ratio (adj. RR) with 95 % confidence intervals (CIs) for in-hospital mortality and unfavourable outcome at discharge by time after arrival to hospital to adequate antibiotic therapy. We identified 195 adults with CABM of whom 173 patients were eligible for further analyses. The median door-to-antibiotic time was 2.0 h (interquartile range (IQR) 1.0-5.5). We observed increased adjusted risk ratios for in-hospital mortality of 1.6 (95 % CI 0.8-3.2) and an unfavourable outcome at discharge of 1.5 (95 % CI 1.0-2.2, p = 0.03) when treatment delays exceeded 6 h versus treatment within 2 h of admission. These findings corresponded to adjusted risk ratios of in-hospital mortality of 1.1 per hour of delay (95 % CI 0.8-1.5) and an unfavourable outcome at discharge of 1.1 per hour of delay (95 % CI 1.0-1.3) within the first 6 h of admission. Some patients (31 %) were diagnosed after admission and had more delays in antibiotic therapy and correspondingly increased in-hospital mortality (30 vs 14 %, p = 0.01) and unfavourable outcome (62 vs 37 %, p = 0.002). Delay in antibiotic therapy was associated with unfavourable outcome at discharge.

  20. Polymerase Chain Reaction–Electrospray–Time-of-Flight Mass Spectrometry Versus Culture for Bacterial Detection in Septic Arthritis and Osteoarthritis

    Science.gov (United States)

    Palmer, Michael P.; Melton-Kreft, Rachael; Nistico, Laura; Hiller, N. Louisa; Kim, Leon H.J.; Altman, Gregory T.; Altman, Daniel T.; Sotereanos, Nicholas G.; Hu, Fen Z.

    2016-01-01

    Background: Preliminary studies have identified known bacterial pathogens in the knees of patients with osteoarthritis (OA) before arthroplasty. Aims: The current study was designed to determine the incidence and types of bacteria present in the synovial fluid of native knee joints from adult patients with diagnoses of septic arthritis and OA. Patients and Methods: Patients were enrolled between October 2010 and January 2013. Synovial fluid samples from the affected knee were collected and evaluated with both traditional microbial culture and polymerase chain reaction–electrospray ionization–time-of-flight mass spectrometry (molecular diagnostics [MDx]) to prospectively characterize the microbial content. Patients were grouped by diagnosis into one of two cohorts, those with clinical suspicion of septic arthritis (n = 44) and those undergoing primary arthroplasty of the knee for OA (n = 21). In all cases where discrepant culture and MDx results were obtained, we performed species-specific 16S rRNA fluorescence in situ hybridization (FISH) as a confirmatory test. Results: MDx testing identified bacteria in 50% of the suspected septic arthritis cases and 29% of the arthroplasty cases, whereas culture detected bacteria in only 16% of the former and 0% of the latter group. The overall difference in detection rates for culture and MDx was very highly significant, p-value = 2.384 × 10−7. All of the culture-positive cases were typed as Staphylococcus aureus. Two of the septic arthritis cases were polymicrobial as was one of the OA cases by MDx. FISH testing of the specimens with discordant results supported the MDx findings in 91% (19/21) of the cases, including one case where culture detected S. aureus and MDx detected Streptococcus agalactiae. Conclusions: MDx were more sensitive than culture, as confirmed by FISH. FISH only identifies bacteria that are embedded or infiltrated within the tissue and is thus not susceptible to contamination. Not all

  1. Polymerase Chain Reaction-Electrospray-Time-of-Flight Mass Spectrometry Versus Culture for Bacterial Detection in Septic Arthritis and Osteoarthritis.

    Science.gov (United States)

    Palmer, Michael P; Melton-Kreft, Rachael; Nistico, Laura; Hiller, N Louisa; Kim, Leon H J; Altman, Gregory T; Altman, Daniel T; Sotereanos, Nicholas G; Hu, Fen Z; De Meo, Patrick J; Ehrlich, Garth D

    2016-12-01

    Preliminary studies have identified known bacterial pathogens in the knees of patients with osteoarthritis (OA) before arthroplasty. The current study was designed to determine the incidence and types of bacteria present in the synovial fluid of native knee joints from adult patients with diagnoses of septic arthritis and OA. Patients were enrolled between October 2010 and January 2013. Synovial fluid samples from the affected knee were collected and evaluated with both traditional microbial culture and polymerase chain reaction-electrospray ionization-time-of-flight mass spectrometry (molecular diagnostics [MDx]) to prospectively characterize the microbial content. Patients were grouped by diagnosis into one of two cohorts, those with clinical suspicion of septic arthritis (n = 44) and those undergoing primary arthroplasty of the knee for OA (n = 21). In all cases where discrepant culture and MDx results were obtained, we performed species-specific 16S rRNA fluorescence in situ hybridization (FISH) as a confirmatory test. MDx testing identified bacteria in 50% of the suspected septic arthritis cases and 29% of the arthroplasty cases, whereas culture detected bacteria in only 16% of the former and 0% of the latter group. The overall difference in detection rates for culture and MDx was very highly significant, p-value = 2.384 × 10 -7 . All of the culture-positive cases were typed as Staphylococcus aureus. Two of the septic arthritis cases were polymicrobial as was one of the OA cases by MDx. FISH testing of the specimens with discordant results supported the MDx findings in 91% (19/21) of the cases, including one case where culture detected S. aureus and MDx detected Streptococcus agalactiae. MDx were more sensitive than culture, as confirmed by FISH. FISH only identifies bacteria that are embedded or infiltrated within the tissue and is thus not susceptible to contamination. Not all suspected cases of septic arthritis contain bacteria, but a

  2. Aerococcus christensenii native aortic valve subacute bacterial endocarditis (SBE) presenting as culture negative endocarditis (CNE) mimicking marantic endocarditis.

    Science.gov (United States)

    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. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Enhanced green fluorescent protein in optofluidic Fabry-Perot microcavity to detect laser induced temperature changes in a bacterial culture

    Science.gov (United States)

    Lahoz, F.; Martín, I. R.; Walo, D.; Freire, R.; Gil-Rostra, J.; Yubero, F.; Gonzalez-Elipe, A. R.

    2017-09-01

    Thermal therapy using laser sources can be used in combination with other cancer therapies to eliminate tumors. However, high precision temperature control is required to avoid damage in healthy surrounding tissues. Therefore, in order to detect laser induced temperature changes, we have used the fluorescence signal of the enhanced Green Fluorescent Protein (eGFP) over-expressed in an E. coli bacterial culture. For that purpose, the bacteria expressing eGFP are injected in a Fabry-Perot (FP) optofluidic planar microcavity. In order to locally heat the bacterial culture, external infrared or ultraviolet lasers were used. Shifts in the wavelengths of the resonant FP modes are used to determine the temperature increase as a function of the heating laser pump power. Laser induced local temperature increments up to 6-7 °C were measured. These results show a relatively easy way to measure laser induced local temperature changes using a FP microcavity and using eGFP as a molecular probe instead of external nanoparticles, which could damage/alter the cell. Therefore, we believe that this approach can be of interest for the study of thermal effects in laser induced thermal therapies.

  4. Peptidoglycan Compositional Analysis of Enterococcus faecalis Biofilm by Stable Isotope Labeling by Amino Acids in a Bacterial Culture.

    Science.gov (United States)

    Chang, James D; Wallace, Ashley G; Foster, Erin E; Kim, Sung Joon

    2018-02-20

    Peptidoglycan (PG) is a major component of the cell wall in Enterococcus faecalis. Accurate analysis of PG composition provides crucial insights into the bacterium's cellular functions and responses to external stimuli, but this analysis remains challenging because of various chemical modifications to PG-repeat subunits. We characterized changes to the PG composition of E. faecalis grown as planktonic bacteria and biofilm by developing "stable isotope labeling by amino acids in bacterial culture" (SILAB), optimized for bacterial cultures with incomplete amino acid labeling. This comparative analysis by mass spectrometry was performed by labeling E. faecalis in biofilm with heavy Lys (l-[ 13 C 6 , 2 D 9 , 15 N 2 ]Lys) and planktonic bacteria with natural abundance l-Lys, then mixing equal amounts of bacteria from each condition, and performing cell wall isolation and mutanolysin digestion necessary for liquid chromatography and mass spectrometry. An analytical method was developed to determine muropeptide abundances using correction factors to compensate for incomplete heavy Lys isotopic enrichment (98.33 ± 0.05%) and incorporation (83.23 ± 1.16%). Forty-seven pairs of PG fragment ions from isolated cell walls of planktonic and biofilm samples were selected for SILAB analysis. We found that the PG in biofilm showed an increased level of PG cross-linking, an increased level of N-deacetylation of GlcNAc, a decreased level of O-acetylation of MurNAc, and an increased number of stem modifications by d,d- and l,d-carboxypeptidases.

  5. Culturable bacterial endophytes isolated from Mangrove tree (Rhizophora apiculata Blume) enhance seedling growth in Rice.

    Science.gov (United States)

    Deivanai, Subramanian; Bindusara, Amitraghata Santhanam; Prabhakaran, Guruswamy; Bhore, Subhash Janardhan

    2014-07-01

    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. 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. 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. 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. 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.

  6. Culture-proven bacterial meningitis in elderly patients in southern Taiwan: clinical characteristics and prognostic factors.

    Science.gov (United States)

    Chang, Chia-Chen; Lu, Chen-Hsien; Huang, Chi-Ren; Chuang, Yao-Chung; Tsai, Nai-Wen; Chen, Shu-Fang; Chang, Hsueh-Wen; Chang, Wen-Neng

    2006-06-01

    The epidemiologic landscape of causative pathogens and clinical characteristics of bacterial meningitis varies with several clinical factors including preceding/pre-existent medical and/or surgical conditions, modes of contraction, geographic distributions, status of vaccinations, the study time periods and differences among age groups. In order to delineate the epidemiology of bacterial meningitis in senior adults (ages > or =60 y/o) in southern Taiwan, we analyzed the clinical characteristics and therapeutic outcomes of 64 senior adults (42 men and 22 women, aged 60-80 years) with bacterial meningitis collected over a period of 13 years at our hospital. The prognostic factors between fatal and non-fatal groups of patients were compared. Twenty-seven of the 64 patients belonged to a nosocomial infection group, and the other 37 comprised a community-acquired infection group. Sixty percent (39/64) of the patients had a post-neurosurgical state as the most preceding event prior to infection. Liver disease (13) and diabetes mellitus (6) were the most common underlying conditions of the other 25 patients with spontaneous meningitis. Of these 64 patients, Klebsiella (K.) pneumoniae (18), Acinetobacter baumannii (5), Escherichia coli (5), and Enterobacter species (5) were the most commonly implicated Gram-negative pathogens. Staphylococcus (S.) aureus infection was increasing during the study period. The therapeutic results of this group of patients showed a mortality rate of 38% (24/64). The presence of septic shock was the most significant prognostic factor. In conclusion, for this study group, a post-neurosurgical state was the single most important preceding event for senior adults developing bacterial meningitis. Of the implicated pathogens, K. pneumoniae and S. aureus were the most common gram-negative and gram-positive pathogens, respectively. The therapeutic result of this specific group of patients showed a high mortality rate; however, the small case number and

  7. Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants

    NARCIS (Netherlands)

    Araujo, W.L.; Marcon, J.; jr. Maccheroni, W.; Elsas, van J.D.; Vuurde, van J.W.L.; Azevedo, de J.L.

    2002-01-01

    Citrus variegated chlorosis (CVC) is caused by Xylella fastidiosa, a phytopathogenic bacterium that can infect all Citrus sinensis cultivars. The endophytic bacterial communities of healthy, resistant, and CVC-affected citrus plants were studied by using cultivation as well as

  8. Microbiological studies in schirmacher oasis, Antarctica: Effect of temperature on bacterial populations

    Digital Repository Service at National Institute of Oceanography (India)

    Matondkar, S.G.P.

    and mesophiles. Pulses in the bacterial cycle were also found in the Basis as a function of daily and seasonal variations in air and soil temperature. Requirement of growth temperature of individual bacterium is the best physiological marker to workout...

  9. Effect of Single Bacterial Starter Culture on Odour Reduction During Controlled Fermentation of Cassava Tubers for Foofoo Production

    Directory of Open Access Journals (Sweden)

    Henshaw, E. E.

    2010-01-01

    Full Text Available Effects of single bacterial starter culture on odour reduction during controlled fermentation of cassava tubers for foofoo production were investigated. Pure cultures were used to ferment cassava tubers in water for 96 h. The cultures used include Bacillus subtilis, Klebsiela sp., Lactobacillus plantarum and Leuconostoc mesenteroides. L. plantarum exhibited the highest acid producing ability, decreasing the pH of the Cassava tubers from 6.2 to 3.68 with a corresponding increase in total titratable acidity (TTA from 0.082% to 0.290% during the 96 h fermentation period. The effected changes in pH and TTA by other organisms ranged respectively from 4.88 and 0.135% for Klebsiella sp., 4.68 and 0.136% for L. mesenteroides to 4.90 and 0.139% for B. subtilis with in the period. All the cultures were found to contribute in varying degree to odour reduction in fermented cassava; B. subtilis effected the highest odour reduction followed by L. plantarum.

  10. Bacterial culture and antibiotic sensitivity from the ocular conjunctiva of horses

    Directory of Open Access Journals (Sweden)

    Ana Raquel de Araújo Ferreira

    Full Text Available ABSTRACT: The aim of this study was to identify the conjunctival bacterial flora of healthy horses in Brasilia (Distrito Federal, Brazil, and to evaluate the antimicrobial susceptibility of the isolated strains. We examined 200 eyes of 100 healthy adult horses without any eye problems, belonging to the 1st Regiment of the Cavalry Guard (RCG of the Brazilian Army in Brasilia. Samples were collected from the inferior conjunctival fornix of both eyes. Drug sensitivity test was performed with the antibiotics gentamicin (10µg, tobramycin (10µg, chloramphenicol (30µg and ciprofloxacin (5µg. Of the 200 samples collected, 131 (65.5% were considered positive for bacterial growth. A total of 208 bacterial strains belonging to 19 genera were isolated, where there was prevalence of gram-positive bacteria (65%, with Staphylococcus sp. being the species of greatest incidence. It was observed that 94, 85, 81 and 68% of the isolates were sensitive to ciprofloxacin, gentamicin, chloramphenicol and tobramycin, respectively. These results can guide the empirical selection antimicrobial therapy for infections of the ocular surface of horses, pending the identification of the etiologic agent.

  11. Reorganization of the bacterial and archaeal populations associated with organic loading conditions in a thermophilic anaerobic digester.

    Science.gov (United States)

    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. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  12. Use of molecular methods to characterize the bacterial community and to monitor different native starter cultures throughout the ripening of Galician chorizo.

    Science.gov (United States)

    Fonseca, Sonia; Ivette Ouoba, Labia Irène; Franco, Inmaculada; Carballo, Javier

    2013-05-01

    The development of Lactobacillus and Staphylococcus strains used as starter cultures throughout the ripening of Galician chorizo, a traditional dry fermented sausage from the north-west of Spain, was monitored combining different molecular-based techniques. The bacterial diversity occurring in the inoculated sausages at the beginning and the end of the ripening was also studied and compared to the indigenous population in an uninoculated control batch. Real-time PCR was used to monitor the Lactobacillus and Staphylococcus community using genus and species-specific primer to quantify the occurring microbiota. The identification of isolates at genus or species level was achieved by specific PCR and 16S rRNA gene sequencing. rep-PCR using (GTG)5-PCR primer was used to characterize this bacterial community at strain level. According to the data obtained, the strains Lactobacillus sakei LS131, Staphylococcus equorum SA25 and Staphylococcus saprophyticus SB12 were dominant during the ripening process, whereas the strain Staphylococcus epidermidis SA49, that was added in order to study its behaviour with a merely scientific purpose, did not succeed in dominating ripening, since it seemed to be outcompeted by autochthonous microbiota. In conclusion, the combination of a quantitative method such as real-time PCR with the identification and typing techniques used in this study (genus and species-specific PCR, 16S rRNA gene sequencing and (GTG)5-PCR) provided accurate and complete information about the starter cultures development, assessing their growth and survival over the ripening process. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Bacterial meningitis in diabetes patients: a population-based prospective study

    Science.gov (United States)

    van Veen, Kiril E. B.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2016-01-01

    Diabetes mellitus is associated with increased infection rates. We studied clinical features and outcome of community-acquired bacterial meningitis in diabetes patients. Patients were selected from a nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 2006 to October 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were prospectively collected. A total of 183 of 1447 episodes (13%) occurred in diabetes patients. The incidence of bacterial meningitis in diabetes patients was 3.15 per 100,000 patients per year and the risk of acquiring bacterial meningitis was 2.2-fold higher for diabetes patients. S. pneumoniae was the causative organism in 139 of 183 episodes (76%) and L. monocytogenes in 11 of 183 episodes (6%). Outcome was unfavourable in 82 of 183 episodes (45%) and in 43 of 183 episodes (23%) the patient died. Diabetes was associated with death with an odds ratio of 1.63 (95% CI 1.12–2.37, P = 0.011), which remained after adjusting for known predictors of death in a multivariable analysis (OR 1.98 [95% CI 1.13–3.48], P = 0.017). In conclusion, diabetes is associated with a 2-fold higher risk of acquiring bacterial meningitis. Diabetes is a strong independent risk factor for death in community-acquired adult bacterial meningitis. PMID:27845429

  14. Bacterial meningitis in solid organ transplant recipients: a population-based prospective study.

    Science.gov (United States)

    van Veen, K E B; Brouwer, M C; van der Ende, A; van de Beek, D

    2016-10-01

    Solid organ transplant (SOT) recipients are at risk of infections of the central nervous system. However, the incidence and clinical course of bacterial meningitis in SOT recipients are unclear. We studied occurrence, disease course, and prognosis of bacterial meningitis in SOT recipients in the Netherlands. All patients with a medical history of solid organ transplantation were selected from our nationwide prospective cohort study on community-acquired bacterial meningitis in patients >16 years old, performed from March 1, 2006 to October 31, 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were collected prospectively. For transplant recipients, additional information was collected retrospectively. We identified 6 SOT recipients, all receiving renal transplants. The annual incidence of bacterial meningitis was 7-fold higher (95% confidence interval [CI] 2.94-17.02, P bacterial meningitis (fever, neck stiffness, and change in mental status). Seizures were common, occurring in 33% of patients. Streptococcus pneumoniae and Listeria monocytogenes were identified in 2 patients each, and Escherichia coli and Pseudomonas aeruginosa were both identified once. Four of 6 patients (67%) had an unfavorable functional outcome. Bacterial meningitis is a rare but devastating complication of solid organ transplantation. SOT recipients are at high risk for developing meningitis, and recognition of this condition may be difficult, owing to atypical clinical manifestation. © 2016 The Authors. Transplant Infectious Disease Published by John Wiley & Sons Ltd.

  15. Evaluating a commercial PCR assay against bacterial culture for diagnosing Streptococcus uberis and Staphylococcus aureus throughout lactation.

    Science.gov (United States)

    Steele, N M; Williamson, J H; Thresher, R; Laven, R A; Hillerton, J E

    2017-05-01

    The performance of a commercial, real-time PCR assay was compared with traditional bacterial culture for the identification of Streptococcus uberis and Staphylococcus aureus in bovine milk collected at different stages of lactation. Initial validation tests using fresh and frozen quarter milk samples identified factors that affected the success of the PCR. Therefore, the standard protocol was adjusted for samples collected at the first milking postpartum (colostrum) and from clinical mastitis cases. The adjustment involved PCR testing both undiluted and diluted (1 in 10 with sterile water) DNA extracts. The performance comparison between culture and the PCR assay used milk samples collected aseptically from individual quarters of mixed-age spring-calving dairy cows, during early, mid, and late lactation. Bacterial culture results were used to select a subset of samples for PCR testing (n = 315) that represented quarters with a current or prior Strep. uberis or Staph. aureus infection. Compared with culture, PCR had a sensitivity of 86.8% and specificity of 87.7% for detecting Strep. uberis (kappa = 0.74) and 96.4% and 99.7%, respectively, for detecting Staph. aureus (kappa = 0.96). The dilution of DNA extracts for colostrum and clinical samples increased the relative sensitivity from 79.2% to 86.8% for Strep. uberis detection and from 92.9% to 96.4% for Staph. aureus, presumably through diluting unidentified PCR inhibitors. The sensitivity for detecting Strep. uberis using PCR, relative to culture, was similar throughout lactation (85-89%), whereas relative specificity was lowest immediately postcalving (64%) but improved in mid and late lactation (98%). Specificity estimates for samples collected in early lactation can be optimized by reducing the cutoff cycle threshold (Ct) value from the recommended value of 37 to 34. Although using this value improved specificity (77%), it reduced test sensitivity (77%). The PCR assay lacked agreement with culture in early

  16. Cultural dimensions in population related issues in Nigeria ...

    African Journals Online (AJOL)

    Culture as a way of life determines to a large extent human behaviour. It is patterned, learned, shared and adaptive and transmittable from one generation to the other and has a way of influencing everything we do. It can be perpetuated and has a potential to overpower intervention programmes, social and educational ...

  17. School Violence among Culturally Diverse Populations: Sociocultural and Institutional Considerations.

    Science.gov (United States)

    Soriano, Marcel; And Others

    1994-01-01

    Notes that incidence of violence reflects disproportionate representation of ethnic and racial minorities, especially African Americans and Latinos, as both victims and victimizers. Presents model for understanding cultures in context of American society to help school psychologists develop effective violence prevention strategies. (Author/NB)

  18. Escape from the competence state in Streptococcus mutans is governed by the bacterial population density.

    Science.gov (United States)

    Dufour, D; Villemin, C; Perry, J A; Lévesque, C M

    2016-12-01

    Horizontal gene transfer through natural DNA transformation is an important evolutionary mechanism among bacteria. Transformation requires that the bacteria are physiologically competent to take and incorporate free DNA directly from the environment. Although natural genetic transformation is a remarkable feature of many naturally competent bacteria, the process is energetically expensive for the cells. Consequently, a tight control of the competence state is necessary. The objective of the present work was to help decipher the molecular mechanisms regulating the escape from the competence state in Streptococcus mutans, the principal etiological agent responsible for tooth decay in humans. Our results showed that the cessation of competence in S. mutans was abrupt, and did not involve the accumulation of a competence inhibitor nor the depletion of a competence activator in the extracellular environment. The competence state was repressed at high cell population density via concomitant repression of sigX gene encoding the master regulator of the competence regulon. Co-culture experiments performed with oral and non-oral bacteria showed that S. mutans assesses its own population density and also the microbial density of its surroundings to regulate its competence escape. Interestingly, neither the intra-species and extra-species quorum-sensing systems nor the other 13 two-component regulatory systems identified in S. mutans were involved in the cell-density-dependent escape of the competence state. Altogether, our results suggest a complex mechanism regulating the competence shut-off involving cell-density-dependent repression of sigX through an as yet undefined system, and possibly SigX protein stability. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  19. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations.

    Science.gov (United States)

    Shea, Patrick R; Beres, Stephen B; Flores, Anthony R; Ewbank, Amy L; Gonzalez-Lugo, Javier H; Martagon-Rosado, Alexandro J; Martinez-Gutierrez, Juan C; Rehman, Hina A; Serrano-Gonzalez, Monica; Fittipaldi, Nahuel; Ayers, Stephen D; Webb, Paul; Willey, Barbara M; Low, Donald E; Musser, James M

    2011-03-22

    Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is a human-adapted bacterium that causes a range of infections. Much effort has been expended to dissect the molecular basis of invasive (sterile-site) infections, but little is known about the genomes of strains causing pharyngitis (streptococcal "sore throat"). Additionally, there is essentially nothing known about the genetic relationships between populations of invasive and pharyngitis strains. In particular, it is unclear if invasive strains represent a distinct genetic subpopulation of strains that cause pharyngitis. We compared the genomes of 86 serotype M3 GAS pharyngitis strains with those of 215 invasive M3 strains from the same geographical location. The pharyngitis and invasive groups were highly related to each other and had virtually identical phylogenetic structures, indicating they belong to the same genetic pool. Despite the overall high degree of genetic similarity, we discovered that strains from different host environments (i.e., throat, normally sterile sites) have distinct patterns of diversifying selection at the nucleotide level. In particular, the pattern of polymorphisms in the hyaluronic acid capsule synthesis operon was especially different between the two strain populations. This finding was mirrored by data obtained from full-genome analysis of strains sequentially cultured from nonhuman primates. Our results answer the long-standing question of the genetic relationship between GAS pharyngitis and invasive strains. The data provide previously undescribed information about the evolutionary history of pathogenic microbes that cause disease in different anatomical sites.

  20. Lactic Acid Bacterial Starter Culture with Antioxidant and γ-Aminobutyric Acid Biosynthetic Activities Isolated from Flatfish-Sikhae Fermentation.

    Science.gov (United States)

    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.

  1. A bacterial population analysis of granular sludge from an anaerobic digester treating a maize-processing waste

    Energy Technology Data Exchange (ETDEWEB)

    Howgrave-Graham, A.R.; Wallis, F.M. (Natal Univ., Pietermaritzburg (ZA). Dept. of Microbiology and Plant Pathology); Steyn, P.L. (Pretoria Univ. (South Africa))

    1991-01-01

    Microbial population studies were conducted on a dense granular sludge, with excellent settling, thickening and nutrient removal properties, from a South African clarigester treating effluent from a factory producing glucose and other carbohydrates from maize. The bacterial population comprised a heterogeneous group including acetogens, enterobacteria, sulphate-reducers, spirochaetes, heterofermentative lactobacilli and methanogens. The presence of these bacteria and lack of propionic acid and butyric acid bacteria suggests that the microbial activity of this anaerobic digester involved acetate and lactate metabolism rather than propionate or butyrate catabolism as a source of precursors for methane production. (author).

  2. Culture-independent analysis of bacterial communities in hemolymph of American lobsters with epizootic shell disease.

    Science.gov (United States)

    Quinn, Robert A; Smolowitz, Roxanna; Chistoserdov, Andrei Y

    2013-03-26

    Epizootic shell disease (ESD) of the American lobster Homarus americanus H. Milne Edwards, 1837 is a disease of the carapace that presents grossly as large, melanized, irregularly shaped lesions, making the lobsters virtually unmarketable because of their grotesque appearance. We analyzed the bacterial communities present in the hemolymph of lobsters with and without ESD using nested-PCR of the 16S rRNA genes followed by denaturing gradient gel electrophoresis. All lobsters tested (n = 42) had bacterial communities in their hemolymph, and the community profiles were highly similar regardless of the sampling location or disease state. A number of bacteria were detected in a high proportion of samples and from numerous locations, including a Sediminibacterium sp. closely related to a symbiont of Tetraponera ants (38/42) and a Ralstonia sp. (27/42). Other bacteria commonly encountered included various Bacteroidetes, Pelomonas aquatica, and a Novosphingobium sp. One bacterium, a different Sediminibacterium sp., was detected in 20% of diseased animals (n = 29), but not in the lobsters without signs of ESD (n = 13). The bacteria in hemolymph were not the same as those known to be present in lesion communities except for the detection of a Thalassobius sp. in 1 individual. This work demonstrates that hemolymph bacteremia and the particular bacterial species present do not correlate with the incidence of ESD, providing further evidence that microbiologically, ESD is a strictly cuticular disease. Furthermore, the high incidence of the same species of bacteria in hemolymph of lobsters may indicate that they have a positive role in lobster fitness, rather than in disease, and further investigation of the role of bacteria in lobster hemolymph is required.

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

    OpenAIRE

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

    2016-01-01

    The isolation and analysis of single prokaryotic cells down to 1??m 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??m in size....

  4. Identification of bacterial cultures from archaeological wood using molecular biological techniques

    DEFF Research Database (Denmark)

    Helms, A.C.; Martiny, Adam Camillo; Hofman-Bang, H. Jacob Peider

    2004-01-01

    Anaerobic bacteria were isolated from a 1700-year-old wooden spear shaft, excavated from an archaeological site that dates from the iron age, in the southern part of Jutland, Denmark. The bacteria were cultivated in glucose- and xylose-supplemented media at 14degreesC and 20degreesC. A gene library...... affiliated to the beta-Proteobacteria. Four clones were clustered among the Geobacteriaceae, in the delta-Proteobacteria. A single clone was clustered with gram-positives. All the identified bacterial families are commonly found in soil or bog environments and many are able to utilize cellulose...

  5. Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

    Science.gov (United States)

    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

  6. Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions.

    Science.gov (United States)

    Bortolini, Cristian; Patrone, Vania; Puglisi, Edoardo; Morelli, Lorenzo

    2016-11-07

    The quality of chocolate is influenced by several parameters, one of which is bacterial diversity during fermentation and drying; a crucial factor for the generation of the optimal cocoa flavor precursors. Our understanding of the bacterial populations involved in chocolate fermentation can be improved by the use of high-throughput sequencing technologies (HTS), combined with PCR amplification of the 16S rRNA subunit. Here, we have conducted a high-throughput assessment of bacterial diversity in four processed samples of cocoa beans from different geographic origins. As part of this study, we also assessed whether different DNA extraction methods could affect the quality of our data. The dynamics of microbial populations were analyzed postharvest (fermentation and sun drying) and shipment, before entry to the industrial process. A total of 691,867 high quality sequences were obtained by Illumina MiSeq sequencing of the two bacterial 16S rRNA hypervariable regions, V3 and V4, following paired-read assembly of the raw reads. Manual curation of the 16S database allowed us to assign the correct taxonomic classifications, at species level, for 83.8% of those reads. This approach revealed a limited biodiversity and population dynamics for both the lactic acid bacteria (LAB) and acetic acid bacteria (AAB), both of which are key players during the acetification and lactic acid fermentation phases. Among the LAB, the most abundant species were Lactobacillus fermentum, Enterococcus casseliflavus, Weissella paramesenteroides, and Lactobacillus plantarum/paraplantarum. Among the AAB, Acetobacter syzygii, was most abundant, then Acetobacter senegalensis and Acetobacter pasteriuanus. Our results indicate that HTS approach has the ability to provide a comprehensive view of the cocoa bean microbiota at the species level. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.

    Science.gov (United States)

    Valenzuela-Encinas, César; Neria-González, Isabel; Alcántara-Hernández, Rocio J; Estrada-Alvarado, Isabel; Zavala-Díaz de la Serna, Francisco Javier; Dendooven, Luc; Marsch, Rodolfo

    2009-07-01

    Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m(-1) and pH 7.80 (LOW soil), with EC 56 dS m(-1) and pH 10.11 (MEDIUM soil) and with EC 159 dS m(-1) and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the alpha- and gamma-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.

  8. 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.

    Science.gov (United States)

    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.

  9. A novel approach to recycle bacterial culture waste for fermentation reuse via a microbial fuel cell-membrane bioreactor system.

    Science.gov (United States)

    Li, Jian; Zhu, Yuan; Zhuang, Liangpeng; Otsuka, Yuichiro; Nakamura, Masaya; Goodell, Barry; Sonoki, Tomonori; He, Zhen

    2015-09-01

    Biochemical production processes require water and nutrient resources for culture media preparation, but aqueous waste is generated after the target products are extracted. In this study, culture waste (including cells) produced from a lab-scale fermenter was fed into a microbial fuel cell-membrane bioreactor (MFC-MBR) system. Electrical energy was generated via the interaction between the microbial consortia and the solid electrode in the MFC. The treated wastewater was reclaimed in this process which was reused as a solvent and a nutrient source in subsequent fermentation. Polarization testing showed that the MFC produced a maximum current density of 37.53 A m(-3) with a maximum power density of 5.49 W m(-3). The MFC was able to generate 0.04 kWh of energy per cubic meter of culture waste treated. The lab-scale fermenters containing pure cultures of an engineered Pseudomonas spp. were used to generate 2-pyrone-4,6-dicarboxylic acid (PDC), a high value platform chemical. When the MFC-MBR-treated wastewater was used for the fermenter culture medium, a specific bacterial growth rate of 1.00 ± 0.05 h(-1) was obtained with a PDC production rate of 708.11 ± 64.70 mg PDC L(-1) h(-1). Comparable values for controls using pure water were 0.95 ± 0.06 h(-1) and 621.01 ± 22.09 mg PDC L(-1) h(-1) (P > 0.05), respectively. The results provide insight on a new approach for more sustainable bio-material production while at the same time generating energy, and suggest that the treated wastewater can be used as a solvent and a nutrient source for the fermentation production of high value platform chemicals.

  10. Cultural meanings of musculoskeletal diseases in Chile's Mapuche Population.

    Science.gov (United States)

    Alarcon, Ana M; Vidal, Aldo; Castro, Marcela

    2013-10-01

    Eight out of 10 Mapuche indigenous women have a musculoskeletal disorder (MSD) and do not seek early medical aid. To study both the cultural meanings and implications of MSD from the Mapuche worldview. Ethnographic study carried out from 2008 to 2011 on indigenous reserves in southern Chile. Sixty-four Mapuches participated in comprehensive interviews, which were transcribed and analyzed by the research team. Five cultural domains: (a) foro kutran/bone disease is the general denomination of MSD; (b) Re-Rume Kutran/progressive and incurable course, refers to the course of the disease; (c) Kalül fücha mawiza/body is an old tree, describes internal manifestations such as worn bones, dry body, weak blood, and spiritual weakness; (d) witrür tripai foro/deformation is the external manifestation of MSD; and (e) Reñma ka lof kutran/family and community suffering refers to the impact of MSD. The explanation of MSD is consistent with the integrated body-nature-spirit worldview of the Mapuche. To provide cultural nursing health care so that patients receive prompt diagnosis and care.

  11. Antibiotic resistance among cultured bacterial isolates from bioethanol fermentation facilities across the United States.

    Science.gov (United States)

    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.

  12. Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

    Science.gov (United States)

    González-Toril, E.; Amils, R.; Delmas, R. J.; Petit, J.-R.; Komárek, J.; Elster, J.

    2009-01-01

    Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas), in a minimal mineral (oligotrophic) media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the marine Antarctic soil the poorest (only one). Snow samples from Col du Midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone). The only microorganism identified in the Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.

  13. [The influence of solcoseryl on population and cellular parameters of HeLa and RD cultures].

    Science.gov (United States)

    Magakian, Iu A; Karalian, Z A; Karalova, E M; Abroian, L O; Akopian, L A; Gasparian, M G; Dzhagatspanian, N G; Semerdzhian, Z B; Ter-Pogosian, Z R

    2010-01-01

    Changes of population and cellular parameters of HeLa and RD cultures after introducing of solcoseryl in culture medium were studied by methods of scanning cytophotometry and cytomorphometry. Monolayer density, proliferation activity, the number of dead cells in a monolayer, the number of nucleoli in nuclei and distribution of cells in the populations by this parameter, RNA and DNA masses in nuclei and nucleoli, total volumes and surface areas of the nuclei and nucleoli were determined. It has been shown that solcoseryl differently affects the cultures both on population and on cellular levels of their organization. The results of multi-parametric analysis of the influence of solseryl on the cultures allow considering it as a biologically active compound with the features typical for cell and cell population growth regulating factors.

  14. Population characteristics and mass culture of Macrostomum orthostylum Braun 1885 (Macrostomida: Turbellaria)

    Digital Repository Service at National Institute of Oceanography (India)

    Ingole, B.S.

    to ensure survival of the population over unfavourable periods. This characteristic enables it to exploit the highly unpredictable environment that natural backwater system offers. Mass culture experiment showed that under optimal laboratory conditions 4200...

  15. Oscillating dynamics of bacterial populations and their predators in response to fresh organic matter added to soil: The simulation model 'BACWAVE-WEB'

    NARCIS (Netherlands)

    Zelenev, V.V.; Bruggen, van A.H.C.; Leffelaar, P.A.; Bloem, J.; Semenov, A.M.

    2006-01-01

    Recently, regular oscillations in bacterial populations and growth rates of bacterial feeding nematodes (BFN) were shown to occur after addition of fresh organic matter to soil. This paper presents a model developed to investigate potential mechanisms of those oscillations, and whether they were

  16. Populations of Select Cultured and Uncultured Bacteria in the Rumen of Sheep and the Effect of Diets and Ruminal Fractions

    Directory of Open Access Journals (Sweden)

    Jill Stiverson

    2011-01-01

    Full Text Available The objective of this study was to assess the importance of select cultured and uncultured bacteria in the rumen by quantifying their populations and the effect of diets and ruminal fractions. Full-length 16S rRNA gene (rrs sequences were recovered from rumen samples using specific primers designed from partial sequences recovered previously. Five uncultured bacterial operational taxonomic units (OTUs were quantified using specific quantitative PCR (qPCR in fractionated ruminal samples from sheep fed either hay alone or hay plus corn. Species Fibrobacter succinogenes, Ruminococcus albus, R. flavefaciens, Ruminobacter amylophilus, Selenomonas ruminantium, and Mitsuokella multacida and genera Butyrivibrio and Prevotella were also quantified as comparison. The full-length rrs sequence improved taxonomic assignments of partial rrs sequences. Genus Prevotella had the greatest abundance. Of the three major cultured cellulolytic species, R. flavefaciens was most abundant, followed by R. albus and F. succinogenes. The five uncultured bacterial OTUs, classified to genus Acetivibrio, genus Allobaculum, family Ruminococcaceae, order Clostridiales, or class Clostridia, had abundance comparable to that of the above species of genera except Prevotella. Corn supplementation and fractions affected distribution of the rumen bacteria, but to a limited extent. When compared to the qPCR data, sequence frequencies in the rrs clone libraries tended to overestimate the abundance of the bacteria represented. This study showed that abundance and population dynamics of uncultured bacteria can be quantified by specific qPCR, which complements the results of rrs clone libraries. This study also revealed that some uncultured bacteria might be as important as some of the well-characterized bacteria in the rumen. The approach used should be applicable to assess the abundance and potential importance of uncultured bacteria in other environments.

  17. A Study of Bacterial Cultures and their Antibiotic Sensitivities in a ...

    African Journals Online (AJOL)

    1974-06-15

    Jun 15, 1974 ... nisms, suffered from the latter infections. . 18 coagulase-positive staphylococci, 7 E. coli and 4 Sal- monella cultures, while the remaining organisms were. Pseudomonas pyocyaneus, Proteus strains, Klebsiella and. Streptococcus faecalis. Tables Il and III show the influence of nutrition on the recovery of G + ...

  18. Approach to disability in a population from the Argar Culture

    Directory of Open Access Journals (Sweden)

    Roca, María G.

    2012-06-01

    Full Text Available A new research field is being developed on disability in Archaeology and Physical Anthropology, which is investigated in this article in the context of the Argaric Culture. More than 200 skeletons, coming from sites in Granada province (Castellón Alto, Fuente Amarga, Cuesta del Negro, Terrera del Reloj and Cerro de la Encina, were studied, finding four with signs of physical impairment: one male and one female who must both have used a walking aid, and two males with shoulder dislocations. All four individuals were buried according to Argaric Culture rituals, beneath their dwellings, indicating that they were not socially rejected. Nevertheless, further insight into disability in this culture is hampered by the limited biological and archaeological data available.

    La discapacidad, entendida como la consideración de una persona con invalidez por parte de su comunidad, constituye un nuevo campo de investigación en Ar queología y Antropología Física. Aquí se investiga este concepto en el marco de la cultura de El Argar. Se han estudiado más de 200 esqueletos procedentes de yacimientos de la provincia de Granada (Castellón Alto, Fuente Amarga, Cuesta del Negro, Terrera del Reloj y Cerro de la Encina entre los cuales cuatro muestran señales de invalidez: un hombre y una mujer que debieron haber requerido ayuda para caminar y dos varones con luxaciones de hombro. Los cuatro individuos fueron enterrados según los rituales de la cultura argárica, bajo sus propias viviendas, lo que indica que no fueron rechazados socialmente. Sin embargo, no se puede profundizar sobre la concepción de la discapacidad en esta cultura puesto que los datos arqueológicos y biológicos son muy limitados.

  19. Population growth, economic security, and cultural change in wilderness counties

    Science.gov (United States)

    Paul A. Lorah

    2000-01-01

    A familiar version of the “jobs versus the environment” argument asserts that wilderness areas limit economic growth by locking up potentially productive natural resources. Analysis of the development paths of rural Western counties shows that this is unlikely: the presence of Wilderness is correlated with income, employment and population growth. Similarly, Wilderness...

  20. Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods.

    Science.gov (United States)

    Perin, Luana Martins; Savo Sardaro, Maria Luisa; Nero, Luís Augusto; Neviani, Erasmo; Gatti, Monica

    2017-08-01

    Artisanal Minas cheese is produced in Minas Gerais state, Brazil and its varieties are named according to their geographical origin (Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes). The cheese is produced with raw cow's milk and the whey from the previous cheese production ("pingo"). The high economic and cultural importance of artisanal cheese in Brazil justifies the efforts to ensure its safety, quality and provenance. This study aimed to characterize the microbial diversity composition, and geographical distribution of artisanal Minas cheese, focusing on the characterization of its autochthonous lactic acid bacteria (LAB) microbiota. Artisanal Minas cheese varieties from Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes were analyzed by culture-dependent (culturing and LAB sequencing) and -independent (repetitive extragenic palindromic-PCR (rep-PCR) and length heterogeneity-PCR, LH-PCR) methods to characterize the microbiota. The microbial counts were variable between cheese samples, and some samples presented high number of coagulase positive bacteria and coliforms that may be associated with hygienic issues. In all samples was observed a prevalence of LAB. 16S rRNA sequencing and rep-PCR of the LAB strains identified four genus (Lactobacillus, Lactococcus, Enterococcus and Weissella), ten species and more than one strain per species. Lactobacillus was the most prevalent genera in all the cheeses. LH-PCR revealed a further six genera and ten species that were not identified by culturing, highlighting the importance of combining both culture-dependent and -independent methods to fully characterize microbiota diversity. Principal component analysis of the LH-PCR data and cluster analysis of rep-PCR data revealed that the artisanal Minas cheese microbiota was influenced not only by their geographical origin but also by the cheese farm. The lack of standardization in the milking and cheese manufacturing procedures between

  1. Assessment of the bacterial diversity of human colostrum and screening of staphylococcal and enterococcal populations for potential virulence factors.

    Science.gov (United States)

    Jiménez, Esther; Delgado, Susana; Fernández, Leonides; García, Natalia; Albújar, Mar; Gómez, Adolfo; Rodríguez, Juan M

    2008-01-01

    In contrast to breast milk, little is known about the bacterial composition of human colostrum. The objective of this work was to analyze the bacterial diversity of colostrum obtained from healthy women and to characterize the dominant bacterial species for the presence of possible virulence factors. Samples of colostrum obtained from 36 healthy women were inoculated into different culture media. Several isolates from each medium were selected and identified. Staphylococcal and enterococcal isolates were submitted to genetic profiling. One representative of each profile was included in a genetic and phenotypic characterization scheme, including detection of potential virulence traits/genes and sensitivity to antibiotics. Staphylococcus epidermidis and Enterococcus faecalis were the dominant species, followed by Streptococcus mitis, Propionibacterium acnes and Staphylococcus lugdunensis. Among the 48 S. epidermidis isolates selected on the basis of their genetic profiles, the biofilm-related icaD gene and the mecA gene were detected in only 11 and six isolates, respectively. In parallel, 10 enterococcal isolates were also characterized and none of them contained the cylA, vanA, vanB, vanD, vanE and vanG genes. All of them were sensitive to vancomycin. There were no indications that the colostrum samples contained harmful bacteria.

  2. Bacterial meningitis in hematopoietic stem cell transplant recipients: a population-based prospective study

    NARCIS (Netherlands)

    van Veen, K. E. B.; Brouwer, M. C.; van der Ende, A.; van de Beek, D.

    2016-01-01

    We performed a nationwide prospective cohort study on the epidemiology and clinical features of community-acquired bacterial meningitis. Patients with a medical history of autologous or allogeneic hematopoietic stem cell transplantation (HSCT) were identified from the cohort performed from March

  3. Selection of bacterial populations in the mycosphere of Laccaria proxima : is type III secretion involved?

    NARCIS (Netherlands)

    Warmink, Jan Aaldrik; van Elsas, Jan Dirk

    The bacterial communities in the Laccaria proxima mycosphere (soil from beneath fruiting bodies) and the corresponding bulk soil were compared by cultivation-dependent and cultivation-independent methods. To assess the distribution of type III secretion systems (TTSS), a PCR-based system for the

  4. Isolation, Characterization and Application of Bacterial Population From Agricultural Soil at Sohag Province, Egypt

    Directory of Open Access Journals (Sweden)

    Bahig, A. E.

    2008-01-01

    Full Text Available Forty soil samples of agriculture soil were collected from two different sites in Sohag province, Egypt, during hot and cold seasons. Twenty samples were from soil irrigated with canal water (site A and twenty samples were from soil irrigated with wastewater (site B. This study aimed to compare the incidence of plasmids in bacteria isolated from soil and to investigate the occurrence of metal and antibiotic resistance bacteria, and consequently to select the potential application of these bacteria in bioremediation. The total bacterial count (CFU/gm in site (B was higher than that in site (A. Moreover, the CFU values in summer were higher than those values in winter at both sites. A total of 771 bacterial isolates were characterized as Bacillus, Micrococcus, Staphylococcus, Pseudomonas, Eschershia, Shigella, Xanthomonas, Acetobacter, Citrobacter, Enterobacter, Moraxella and Methylococcus. Minimum inhibitory concentrations (MICs of Pb+2, Cu+2, Zn+2, Hg+2, Co+2, Cd+2, Cr+3, Te+2, As+2 and Ni+2 for plasmid-possessed bacteria were determined and the highest MICs were 1200 µg/mL for lead, 800 µg/mL for both Cobalt and Arsenate, 1200 µg/mL for Nickel, 1000 µg/ml for Copper and less than 600 µg/mL for other metals. Bacterial isolates from both sites A and B showed multiple heavy metal resistance. A total of 337 bacterial isolates contained plasmids and the incidence of plasmids was approximately 25-50% higher in bacteria isolated from site (B than that from site (A. These isolates were resistance to different antibiotics. Approximately, 61% of the bacterial isolates were able to assimilate insecticide, carbaryl, as a sole source of carbon and energy. However, the Citrobacter AA101 showed the best growth on carbaryl.

  5. Inferring individual-level processes from population-level patterns in cultural evolution.

    Science.gov (United States)

    Kandler, Anne; Wilder, Bryan; Fortunato, Laura

    2017-09-01

    Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution.

  6. [Historical, social and cultural aspects of the deaf population].

    Science.gov (United States)

    Duarte, Soraya Bianca Reis; Chaveiro, Neuma; Freitas, Adriana Ribeiro de; Barbosa, Maria Alves; Porto, Celmo Celeno; Fleck, Marcelo Pio de Almeida

    2013-10-01

    This work redeems, contextualizes and features the social, historical and cultural aspects of the deaf community that uses the Brazilian Sign Language focusing on the social and anthropological model. The scope of this study was to conduct a bibliographical review in scientific textbooks and articles available in the Virtual Health Library, irrespective of the date of publication. 102 articles and 53 books were located, including 33 textbooks and 26 articles (four from the Lilacs database and 22 from the Medline database) that constituted the sample. Today, in contrast with the past, there are laws that guarantee the right to communication and attendance by means of the Brazilian Sign Language. The repercussion, acceptance and inclusion in health policies of the decrees enshrined in Brazilian laws is a major priority.

  7. Diagnosis of intramammary infection in samples yielding negative results or minor pathogens in conventional bacterial culturing.

    Science.gov (United States)

    Bexiga, Ricardo; Koskinen, Mikko T; Holopainen, Jani; Carneiro, Carla; Pereira, Helena; Ellis, Kathryn A; Vilela, Cristina L

    2011-02-01

    Up to half of quarter milk samples submitted for mastitis diagnosis are culture-negative results or lead to identification of coagulase-negative staphylococci or Corynebacterium bovis in conventional culturing, the so-called minor pathogens. The interpretation and usefulness of these results in terms of udder and animal health management is limited, even though the amount of resources spent is relatively high. This work aimed to test two methods of analysis of milk samples with the goal of increasing detection of intramammary pathogens. In the first study, 783 milk samples were processed in duplicate: before and after freezing at -20°C for 24 h, using standard bacteriological techniques. There was a significant difference between the two methods with samples frozen for 24 h yielding significantly fewer Gram-positive catalase-positive cocci, Gram-negative bacilli, Gram-positive bacilli and significantly more samples leading to no growth, than samples before freezing. The number of samples yielding Gram-positive catalase-negative cocci was not significantly affected by freezing. In the second study, a real-time PCR-based test was performed on milk samples with an individual quarter somatic cell count above 500,000 cells/ml that were either negative (n=51 samples) or that led to the isolation of minor pathogens in culturing: Corynebacterium bovis (n=79 samples) or non-aureus staphylococci (NAS, n=32). A mastitis pathogen, beyond the result obtained with standard bacteriology, was detected on 47% of the no-growth samples, on 35% of the samples from which C. bovis had been isolated and on 25% of the samples from which NAS had been isolated. The most commonly detected major pathogen was Escherichia coli, followed by Streptococcus uberis, Arcanobacterium pyogenes/Peptoniphilus indolicus and Streptococcus dysgalactiae. These results suggest that simply freezing milk samples for 24 h does not increase the detection of intramammary bacteria in milk samples and therefore

  8. Effects of low intensity laser in in vitro bacterial culture and in vivo infected wounds

    Directory of Open Access Journals (Sweden)

    Pâmela Rosa Pereira

    Full Text Available OBJECTIVE: to compare the effects of low intensity laser therapy on in vitro bacterial growth and in vivo in infected wounds, and to analyze the effectiveness of the AsGa Laser technology in in vivo wound infections. METHODS: in vitro: Staphylococcus aureus were incubated on blood agar plates, half of them being irradiated with 904 nm wavelength laser and dose of 3J/cm2 daily for seven days. In vivo: 32 male Wistar rats were divided into control group (uninfected and Experimental Group (Infected. Half of the animals had their wounds irradiated. RESULTS: in vitro: there was no statistically significant variation between the experimental groups as for the source plates and the derived ones (p>0.05. In vivo: there was a significant increase in the deposition of type I and III collagen in the wounds of the infected and irradiated animals when assessed on the fourth day of the experiment (p=0.034. CONCLUSION: low-intensity Laser Therapy applied with a wavelength of 904nm and dose 3J/cm2 did not alter the in vitro growth of S. aureus in experimental groups; in vivo, however, it showed significant increase in the deposition of type I and III collagen in the wound of infected and irradiated animals on the fourth day of the experiment.

  9. Biodegradation of Various Aromatic Compounds by Enriched Bacterial Cultures: Part A-Monocyclic and Polycyclic Aromatic Hydrocarbons.

    Science.gov (United States)

    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.

  10. The speciation of soluble sulphur compounds in bacterial culture fluids by X-ray absorption near edge structure spectroscopy.

    Science.gov (United States)

    Franz, Bettina; Lichtenberg, Henning; Hormes, Josef; Dahl, Christiane; Prange, Alexander

    2009-11-01

    Over the last decade X-ray absorption near edge structure (XANES) spectroscopy has been used in an increasing number of microbiological studies. In addition to other applications it has served as a valuable tool for the investigation of the sulphur globules deposited intra- or extracellularly by certain photo- and chemotrophic sulphur-oxidizing (Sox) bacteria. For XANES measurements, these deposits can easily be concentrated by filtration or sedimentation through centrifugation. However, during oxidative metabolism of reduced sulphur compounds, such as sulphide or thiosulphate, sulphur deposits are not the only intermediates formed. Soluble intermediates such as sulphite may also be produced and released into the medium. In this study, we explored the potential of XANES spectroscopy for the detection and speciation of sulphur compounds in culture supernatants of the phototrophic purple sulphur bacterium Allochromatium vinosum. More specifically, we investigated A. vinosum DeltasoxY, a strain with an in frame deletion of the soxY gene. This gene encodes an essential component of the thiosulphate-oxidizing Sox enzyme complex. Improved sample preparation techniques developed for the DeltasoxY strain allowed for the first time not only the qualitative but also the quantitative analysis of bacterial culture supernatants by XANES spectroscopy. The results thus obtained verified and supplemented conventional HPLC analysis of soluble sulphur compounds. Sulphite and also oxidized organic sulphur compounds were shown by XANES spectroscopy to be present, some of which were not seen when standard HPLC protocols were used.

  11. Bacterial meningitis in alcoholic patients: A population-based prospective study.

    Science.gov (United States)

    van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

    2017-04-01

    To study clinical features and outcome of community-acquired bacterial meningitis in alcoholic patients. Patients with a history of alcoholism were selected from our nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 2006 to October 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were prospectively collected. Of 1359 included episodes, 88 episodes (6%) occurred in 88 alcoholic patients. Seizures as presenting symptom were present in 18% alcoholic patients, and 23% presented with co-existing pneumonia. Causative organisms were Streptococcus pneumoniae in 76%, Listeria monocytogenes in 8%, and Neisseria meningitidis in 6% of patients. A high rate of systemic complications occurred with respiratory failure in 40% and endocarditis in 9% of patients. Outcome was unfavorable in 58% of alcoholic patients, and 25% died. Alcoholism was associated with unfavorable outcome in a multivariate analysis (OR 1.96; 95% CI 1.12-3.46; P = 0.019), but not with death (OR 0.76; 95% CI 0.35-1.68; P = 0.762). Alcoholic bacterial meningitis patients often have an unfavorable outcome, which appears to result from a high rate of systemic complications, mainly respiratory failure. Seizures are common in alcoholic patients and warrant caution of development of an alcohol withdrawal syndrome. Copyright © 2017. Published by Elsevier Ltd.

  12. Correlation between plasma component levels of cultured fish and resistance to bacterial infection

    Science.gov (United States)

    Maita, M.; Satoh, K.-I.; Fukuda, Y.; Lee, H.-K.; Winton, J.R.; Okamoto, N.

    1998-01-01

    Mortalities of yellowtail Seriola quinqueradiata artificially infected with Lactococcus garvieae and of rainbow trout Oncorhynchus mykiss artificially infected with Vibrio anguillarum were compared with the levels of plasma components measured prior to challenge. The levels of plasma total cholesterol, free cholesterol and phospholipid of fish surviving infection were significantly higher in both yellowtail and rainbow trout than those of fish which died during the challenge test. Mortality of yellowtail with plasma total cholesterol levels lower than 250 mg/100 ml was significantly higher than that of fish which had cholesterol levels higher than 275 mg/100 ml (p resistance in cultured fish.

  13. A new method for determining the metabolic activity of specific bacterial populations in soil using tritiated leucine and immunomagnetic separation

    DEFF Research Database (Denmark)

    Sengeløv, Gitte; Sørensen, Søren Johannes; Frette, Lone

    2000-01-01

    A new assay, using immunomagnetic separation and uptake of tritiated leucine ([3H]-Leu), was developed for measuring the in situ metabolic activity of specific bacterial populations in soil. Such assays are needed to assess the role individual species play in diverse microbial soil communities...... reduced this unspecific binding, resulting in metabolic activity of the target cells. As expected, a linear relationship...... between activity and temperature was observed, demonstrating the sensitivity of the assay. The method was applied to compare activities of the target strain in bulk soil and in the rhizosphere of barley. Contrary to what was anticipated, no significant difference in metabolic activity was observed....

  14. Weight-loss interventions for Hispanic populations: the role of culture.

    Science.gov (United States)

    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.

  15. Induction of new metabolites from the endophytic fungus Bionectria sp. through bacterial co-culture.

    Science.gov (United States)

    Kamdem, Ramsay S T; Wang, Hao; Wafo, Pascal; Ebrahim, Weaam; Özkaya, Ferhat Can; Makhloufi, Gamall; Janiak, Christoph; Sureechatchaiyan, Parichat; Kassack, Matthias U; Lin, Wenhan; Liu, Zhen; Proksch, Peter

    2018-01-01

    A new alkaloid, 1,2-dihydrophenopyrrozin (1), along with five known compounds (2-6) was isolated from an axenic culture of the endophytic fungus, Bionectria sp., obtained from seeds of the tropical plant Raphia taedigera. Co-cultivation of this fungus either with Bacillus subtilis or with Streptomyces lividans resulted in the production of two new o-aminobenzoic acid derivatives, bionectriamines A and B (7 and 8) as well as of two additional known compounds (9 and 10). None of the latter compounds (7-10) were detected in axenic cultures of the fungus or of the bacteria indicating activation of silent biogenetic gene clusters through co-cultivation with bacteria. The structures of the new compounds were unambiguously determined based on detailed NMR and MS spectroscopic analysis and by comparison with the literature. The crystal structure of agathic acid (6) is reported here for the first time. Penicolinate A (4) exhibited potent cytotoxic activity against the human ovarian cancer cell line A2780 with an IC 50 value of 4.1μM. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Study of Prevalence and Antimicrobial Susceptibility of Blood Culture Bacterial Isolates

    Directory of Open Access Journals (Sweden)

    Ayobola, E. D.

    2011-01-01

    Full Text Available Bloodstream infections are associated with significant morbidity and mortality. Definitive diagnosis is by bacteriologic culture of blood samples to identify organisms and establish antibiotic susceptibility. Between July and September 2009, 249 blood samples collected from patients at the University of Benin Teaching Hospital were processed. Positive cultures which accounted for 48(19.3% of total samples screened, were purified and identified according to standard methods. Sensitivity of bacteria to different antibiotics was determined by Kirby-Bauer disk diffusion method. Microorganisms recovered were Staphylococcus aureus (14.6%, Providencia spp., Pseudomonas aeruginosa, Enterobacter spp., Klebsiella pneumoniae and Proteus mirabilis (12.5% respectively, Escherichia coli and Staphylococcus epidermidis (8.3% respectively and Citrobacter freundii (6.3% . The highest antibiotic activities against Gram positive isolates were observed for ofloxacin (90.9%, nitrofurantoin (81.8% and gentamicin (72.7%, while in Gram negative bacteria, ofloxacin (81.1% and nalidixic acid (45.9% were most effective. The possibility of drug resistance acquisition by bacteria makes continuous surveillance of antimicrobial susceptibility patterns of bacteria essential as this will enhance efforts to identify resistance and attempt to limit its spread.

  17. Hyperspectral imaging for presumptive identification of bacterial colonies on solid chromogenic culture media

    Science.gov (United States)

    Guillemot, Mathilde; Midahuen, Rony; Archeny, Delpine; Fulchiron, Corine; Montvernay, Regis; Perrin, Guillaume; Leroux, Denis F.

    2016-04-01

    BioMérieux is automating the microbiology laboratory in order to reduce cost (less manpower and consumables), to improve performance (increased sensitivity, machine algorithms) and to gain traceability through optimization of the clinical laboratory workflow. In this study, we evaluate the potential of Hyperspectral imaging (HSI) as a substitute to human visual observation when performing the task of microbiological culture interpretation. Microbial colonies from 19 strains subcategorized in 6 chromogenic classes were analyzed after a 24h-growth on a chromogenic culture medium (chromID® CPS Elite, bioMérieux, France). The HSI analysis was performed in the VNIR region (400-900 nm) using a linescan configuration. Using algorithms relying on Linear Spectral Unmixing, and using exclusively Diffuse Reflectance Spectra (DRS) as input data, we report interclass classification accuracies of 100% using a fully automatable approach and no use of morphological information. In order to eventually simplify the instrument, the performance of degraded DRS was also evaluated using only the most discriminant 14 spectral channels (a model for a multispectral approach) or 3 channels (model of a RGB image). The overall classification performance remains unchanged for our multispectral model but is degraded for the predicted RGB model, hints that a multispectral solution might bring the answer for an improved colony recognition.

  18. Usefulness of inflammatory biomarkers in discriminating between bacterial and aseptic meningitis in hospitalized children from a population with low vaccination coverage

    Science.gov (United States)

    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 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

  19. 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.

    Science.gov (United States)

    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.

  20. 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.

    Directory of Open Access Journals (Sweden)

    Lingxiang Zhu

    Full Text Available 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.

  1. Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species

    NARCIS (Netherlands)

    Sabat, Artur J.; van Zanten, Evert; Akkerboom, Viktoria; Wisselink, Guido J; van Slochteren, Kees; de Boer, Richard F; Hendrix, Ron; Friedrich, Alexander W.; Rossen, John W. A.; Kooistra-Smid, Anna M.D. (Mirjam)

    2017-01-01

    The aim of this study was to develop an easy-to-use culture-free diagnostic method based on next generation sequencing (NGS) of PCR amplification products encompassing whole 16S-23S rRNA region to improve the resolution of bacterial species identification. To determine the resolution of the new

  2. Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain through Culture-Dependent and Independent Approaches.

    Directory of Open Access Journals (Sweden)

    Javier Pascual

    Full Text Available 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.

  3. Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches

    Science.gov (United States)

    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

  4. [Bacterial culture and drug sensitivity analysis of upper urinary tract calculi complicating with infection].

    Science.gov (United States)

    Wang, Shu; Shi, Yong-kang; Huang, Xiao-bo; Ma, Kai; Xu, Qing-quan; Xiong, Lin-lin; Li, Jian-xing; Wang, Xia-feng

    2014-10-18

    To investigate the bacteriology and drug sensitivity of upper urinary tract calculi patients, and to provide information for choosing suitable antibiotics. In the study, 21 patients who suffered from lithiasis in upper urinary tract and required an emergency drainage for acute obstruction and infection were the "acute group"; 64 patients with calculi in upper urinary tract and accompanied with no infectious symptoms were the "common group". The bacteriology and drug sensitivity of the two groups were investigated. Gram-negative bacteria infected the most common of upper urinary tract calculi patients with infection, accounting for 71.4% in the acute group and 65.7% in the common group, among which Escherichia coli were the predominant ones (35.7% in the acute group and 32.9% in the common group). No difference was found between these two groups in bacterial distribution (P>0.05). Although the average drug resistance rate of Gram-negative bacteria in the acute group was higher than that in the common group, it revealed no significant difference (P>0.05). The drug resistance rate to semisynthetic penicillin, cefuroxime and ceftriaxone were more than 50%, 60%, and 50%, respectively. Quinolones, such as ciprofloxacin and levofloxacin, got a 45% drug resistance. Aminoglycoside, carbapenema were sensitive to Gram-negative bacteria. Cefoperazone/sulbactam and piperacillin/tazobactam were more effective than ceftriaxone and piperacillin, respectively. There was no significant difference between upper urinary tract calculi patients with acute infection and common infection in bacteriology and drug sensitivity. Semisynthetic penicillin, the second generation of cephalosporin and quinolone were no longer the good choices of empirical use. Antibiotics combined with β-lactamase inhibitors would be an ideal empirical therapeutic choice.

  5. The cultural gap delivering health care services to Arab American populations in the United States.

    Science.gov (United States)

    Aboul-Enein, Basil H; Aboul-Enein, Faisal H

    2010-01-01

    The relationship between Middle Eastern patients and populations of Arab origin with western health care professionals are by no means free of cultural misunderstandings. The relationship is often strained by mutual cultural misunderstanding as well as communicative and linguistic hardship. Even though people from the Middle East do vary racially, they do have shared values and behavior. This can include the importance of family cohesion, and interactive attitudes toward ailments and health. Some issues and concerns in providing health care could vary from attaining adequate information to communicated suggested behavioral change by a patient. Culturally and linguistically appropriate guidelines are warranted to provide an understanding of the cultural distinctiveness of Arab Eastern patients by shortening the gap between the Arab cultures with the western medical culture thus improving their healthcare needs.

  6. Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

    Directory of Open Access Journals (Sweden)

    E. González-Toril

    2009-01-01

    Full Text Available Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area and the Andes (Nevado Illimani summit, Bolivia, from Antarctic aerosol (French station Dumont d'Urville and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas, in a minimal mineral (oligotrophic media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria, Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified and the marine Antarctic soil the poorest (only one. Snow samples from Col du Midi (Alps and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones. These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone. The only microorganism identified in the Antarctica soil (Brevundimonas sp. was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.

  7. Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

    Science.gov (United States)

    Kell, Douglas; Potgieter, Marnie; Pretorius, Etheresia

    2015-01-01

    For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically ‘nonculturable’ on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as ‘persisters’. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one’s bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit. PMID:26629334

  8. Regulated bioluminescence as a tool for bioremediation process monitoring and control of bacterial cultures

    Science.gov (United States)

    Burlage, Robert S.; Heitzer, Armin; Digrazia, Philip M.

    1991-01-01

    An effective on-line monitoring technique for toxic waste bioremediation using bioluminescent microorganisms has shown great potential for the description and optimization of biological processes. The lux genes of the bacterium Vibrio fischeri are used by this species to produce visible light. The lux genes can be genetically fused to the control region of a catabolic gene, with the result that bioluminescence is produced whenever the catabolic gene is induced. Thus the detection of light from a sample indicates that genetic expression from a specific gene is occurring. This technique was used to monitor biodegradation of specific contaminants from waste sites. For these studies, fusions between the lux genes and the operons for naphthalene and toluene/xylene degradation were constructed. Strains carrying one of these fusions respond sensitively and specifically to target substrates. Bioluminescence from these cultures can be rapidly measured in a nondestructive and noninvasive manner. The potential for this technique in this and other biological systems is discussed.

  9. Birthweight distribution in ART singletons resulting from embryo culture in two different culture media compared with the national population.

    Science.gov (United States)

    Lemmen, J G; Pinborg, A; Rasmussen, S; Ziebe, S

    2014-10-10

    Is there a difference in birthweight distribution in ART singletons born after IVF culture in two different culture media? There is no effect of culture media on both crude and adjusted birthweight distributions in ART singletons from nulliparous mothers. Studies on human ART singletons have reported a difference in birthweight in singletons following IVF culture in different culture media. However, other studies comparing different culture media have not shown any significant differences in birthweight. This study was a retrospective comparison of birthweights in IVF/ICSI singletons conceived after fresh embryo transfer following embryo culture in Cook or Medicult medium and in a national cohort of naturally conceived singletons in nulliparous women. The study compares four independent groups consisting of singletons in nulliparous women from Cook-d2: 2-day culture in Cook medium at Rigshospitalet (n = 974), Medicult-d2: 2-day culture in Medicult EmbryoAssist medium at Rigshospitalet (n = 147), Medicult-d3: 3-day culture in Medicult EmbryoAssist medium with and without added GM-CSF (n = 204), and DK: pregnancies from the Danish birth registry (n = 106842). The study compares the birthweights of singletons from nulliparous women in the four independent groups mentioned above; Cook-d2: Medicult-d2: Medicult-d3: and DK. In addition, distributions of large and small for gestational age infants were compared between the groups and a multiple linear regression analysis was used to determine which factors determined birthweight. We found no significant difference in the crude birthweight distributions between singletons born after culture in Cook-d2 or Medicult-groups. Singleton girls from the Cook-d2 group weighed 3302 ± 28 g, versus 3252 ± 76 in the Medicult-d2 group (difference 50 g; P = 0.547). Singleton boys from the Cook-d2 group weighed 3430 ± 27 g, versus 3354 ± 56 in the Medicult-d2 group (difference 76 g; P = 0.279). In the background population, mean

  10. Coevolution of adaptive technology, maladaptive culture and population size in a producer-scrounger game.

    Science.gov (United States)

    Lehmann, Laurent; Feldman, Marcus W

    2009-11-07

    Technology (i.e. tools, methods of cultivation and domestication, systems of construction and appropriation, machines) has increased the vital rates of humans, and is one of the defining features of the transition from Malthusian ecological stagnation to a potentially perpetual rising population growth. Maladaptations, on the other hand, encompass behaviours, customs and practices that decrease the vital rates of individuals. Technology and maladaptations are part of the total stock of culture carried by the individuals in a population. Here, we develop a quantitative model for the coevolution of cumulative adaptive technology and maladaptive culture in a 'producer-scrounger' game, which can also usefully be interpreted as an 'individual-social' learner interaction. Producers (individual learners) are assumed to invent new adaptations and maladaptations by trial-and-error learning, insight or deduction, and they pay the cost of innovation. Scroungers (social learners) are assumed to copy or imitate (cultural transmission) both the adaptations and maladaptations generated by producers. We show that the coevolutionary dynamics of producers and scroungers in the presence of cultural transmission can have a variety of effects on population carrying capacity. From stable polymorphism, where scroungers bring an advantage to the population (increase in carrying capacity), to periodic cycling, where scroungers decrease carrying capacity, we find that selection-driven cultural innovation and transmission may send a population on the path of indefinite growth or to extinction.

  11. Effects of bacterial lipopolysaccharide and X-irradiation on the production of colony-stimulating factor and the maintenance of granulopoiesis in bone marrow culture

    International Nuclear Information System (INIS)

    Izumi, H.; Miyanomae, T.; Tsurusawa, M.; Fujita, J.; Mori, K.

    1984-01-01

    Effects of bacterial lipopolysaccharide (LPS) and X-irradiation on CSF production and granulopoiesis in long-term bone marrow cultures were studied. Levels of colony-stimulating factor (CSF) increased soon after the refeeding of the culture, but the activity was undetectable at day 7. Addition of LPS induced a significant increase in CSF levels in the culture, followed by an elevated granulopoiesis. The increase in CSF levels was suppressed when culture medium that had been harvested at refeeding on day 7 was added. Although irradiation did not increase CSF production, granulopoiesis was markedly stimulated shortly after irradiation. Thus granulopoiesis in long-term bone marrow culture may also be regulated by humoral factors such as CSF, and the culture system may represent the in vivo response to haemopoietic stimuli. (author)

  12. Use of Response Surface Methodology to Optimize Culture Conditions for Hydrogen Production by an Anaerobic Bacterial Strain from Soluble Starch

    Science.gov (United States)

    Kieu, Hoa Thi Quynh; Nguyen, Yen Thi; Dang, Yen Thi; Nguyen, Binh Thanh

    2016-05-01

    Biohydrogen is a clean source of energy that produces no harmful byproducts during combustion, being a potential sustainable energy carrier for the future. Therefore, biohydrogen produced by anaerobic bacteria via dark fermentation has attracted attention worldwide as a renewable energy source. However, the hydrogen production capability of these bacteria depends on major factors such as substrate, iron-containing hydrogenase, reduction agent, pH, and temperature. In this study, the response surface methodology (RSM) with central composite design (CCD) was employed to improve the hydrogen production by an anaerobic bacterial strain isolated from animal waste in Phu Linh, Soc Son, Vietnam (PL strain). The hydrogen production process was investigated as a function of three critical factors: soluble starch concentration (8 g L-1 to 12 g L-1), ferrous iron concentration (100 mg L-1 to 200 mg L-1), and l-cysteine concentration (300 mg L-1 to 500 mg L-1). RSM analysis showed that all three factors significantly influenced hydrogen production. Among them, the ferrous iron concentration presented the greatest influence. The optimum hydrogen concentration of 1030 mL L-1 medium was obtained with 10 g L-1 soluble starch, 150 mg L-1 ferrous iron, and 400 mg L-1 l-cysteine after 48 h of anaerobic fermentation. The hydrogen concentration produced by the PL strain was doubled after using RSM. The obtained results indicate that RSM with CCD can be used as a technique to optimize culture conditions for enhancement of hydrogen production by the selected anaerobic bacterial strain. Hydrogen production from low-cost organic substrates such as soluble starch using anaerobic fermentation methods may be one of the most promising approaches.

  13. In Vitro Culture Conditions for Maintaining a Complex Population of Human Gastrointestinal Tract Microbiota

    Directory of Open Access Journals (Sweden)

    Bong-Soo Kim

    2011-01-01

    Full Text Available A stable intestinal microbiota is important in maintaining human physiology and health. Although there have been a number of studies using in vitro and in vivo approaches to determine the impact of diet and xenobiotics on intestinal microbiota, there is no consensus for the best in vitro culture conditions for growth of the human gastrointestinal microbiota. To investigate the dynamics and activities of intestinal microbiota, it is important for the culture conditions to support the growth of a wide range of intestinal bacteria and maintain a complex microbial community representative of the human gastrointestinal tract. Here, we compared the bacterial community in three culture media: brain heart infusion broth and high- and low-carbohydrate medium with different growth supplements. The bacterial community was analyzed using denaturing gradient gel electrophoresis (DGGE, pyrosequencing and real-time PCR. Based on the molecular analysis, this study indicated that the 3% fecal inoculum in low-concentration carbohydrate medium with 1% autoclaved fecal supernatant provided enhanced growth conditions to conduct in vitro studies representative of the human intestinal microbiota.

  14. Interaction between resource identity and bacterial community composition regulates bacterial respiration in aquatic ecosystems

    Directory of Open Access Journals (Sweden)

    A. P. F. Pires

    Full Text Available Abstract Resource identity and composition structure bacterial community, which in turn determines the magnitude of bacterial processes and ecological services. However, the complex interaction between resource identity and bacterial community composition (BCC has been poorly understood so far. Using aquatic microcosms, we tested whether and how resource identity interacts with BCC in regulating bacterial respiration and bacterial functional diversity. Different aquatic macrophyte leachates were used as different carbon resources while BCC was manipulated through successional changes of bacterial populations in batch cultures. We observed that the same BCC treatment respired differently on each carbon resource; these resources also supported different amounts of bacterial functional diversity. There was no clear linear pattern of bacterial respiration in relation to time succession of bacterial communities in all leachates, i.e. differences on bacterial respiration between different BCC were rather idiosyncratic. Resource identity regulated the magnitude of respiration of each BCC, e.g. Ultricularia foliosa leachate sustained the greatest bacterial functional diversity and lowest rates of bacterial respiration in all BCC. We conclude that both resource identity and the BCC interact affecting the pattern and the magnitude of bacterial respiration in aquatic ecosystems.

  15. Population heterogeneity and dynamics in starter culture and lag phase adaptation of the spoilage yeast Zygosaccharomyces bailii to weak acid preservatives.

    Science.gov (United States)

    Stratford, Malcolm; Steels, Hazel; Nebe-von-Caron, Gerhard; Avery, Simon V; Novodvorska, Michaela; Archer, David B

    2014-07-02

    The food spoilage yeast Zygosaccharomyces bailii shows great resistance to weak-acid preservatives, including sorbic acid (2, 4-hexadienoic acid). That extreme resistance was shown to be due to population heterogeneity, with a small sub-population of cells resistant to a variety of weak acids, probably caused by a lower internal pH reducing the uptake of all weak acids. In the present paper, it was found that resistant cells were extremely rare in exponential cultures, but increased by up to 8000-fold in stationary phase. Inoculation of media containing sorbic acid with a population of Z. bailii cells gave rise to what appeared to be a prolonged lag phase, suggesting adaptation to the conditions before the cells entered the period of exponential growth. However, the apparent lag phase caused by sorbic acid was largely due to the time required for the resistant sub-population to grow to detectable levels. The slow growth rate of the sub-population was identical to that of the final total population. The non-resistant bulk population remained viable for 3 days but had lost viability by 6 days and, during that time, there was no indication of any development of resistance in the bulk population. The sub-population growing in sorbic acid showed very high population diversity in colony size and internal pH. After removal of sorbic acid, the population rapidly reverted back to the normal, largely non-resistant, population distribution. The data presented suggest that a reevaluation of the lag phase in microbial batch culture is required, at least for the resistance of Z. bailii to sorbic acid. Furthermore, the significance of phenotypic diversity and heterogeneity in microbial populations is discussed more broadly with potential relevance to bacterial "persisters", natural selection and evolution. Copyright © 2014. Published by Elsevier B.V.

  16. Quantitative analysis of ruminal bacterial populations involved in lipid metabolism in dairy cows fed different vegetable oils

    DEFF Research Database (Denmark)

    Vargas-Bello-Pérez, E.; Cancino-Padilla, N.; Romero, J.

    2016-01-01

    Vegetable oils are used to increase energy density of dairy cow diets, although they can provoke changes in rumen bacteria populations and have repercussions on the biohydrogenation process. The aim of this study was to evaluate the effect of two sources of dietary lipids: soybean oil (SO......, an unsaturated source) and hydrogenated palm oil (HPO, a saturated source) on bacterial populations and the fatty acid profile of ruminal digesta. Three non-lactating Holstein cows fitted with ruminal cannulae were used in a 3×3 Latin square design with three periods consisting of 21 days. Dietary treatments...... parameters, whereas HPO can increase load of ruminal P. bryantii. Also, results observed in our targeted bacteria may have depended on the saturation degree of dietary oils....

  17. Monitoring the bacterial population dynamics during the ripening of Galician chorizo, a traditional dry fermented Spanish sausage.

    Science.gov (United States)

    Fonseca, Sonia; Cachaldora, Aida; Gómez, María; Franco, Inmaculada; Carballo, Javier

    2013-02-01

    The dynamics of the bacterial population throughout the ripening of Galician chorizo, a traditional dry fermented sausage produced in the north-west of Spain, were investigated by using classical and molecular approaches. Fermented sausages are certainly complex matrices with PCR inhibitors and background microbiota. Therefore, two different DNA preparation methods were performed to elaborate each standard curve and no significant differences were found, showing a very good correlation between both methods (R(2)>0.994). The combination of the results obtained from microbial counts, species and genus-specific PCR as well as real-time quantitative PCR (qPCR) allowed the identification for the dominant bacterial species and the study of the variation in the community composition over the ripening period. According to the data obtained both by identification of plate isolates and by real-time PCR, the dominant species among staphylococci and lactobacilli were Staphylococcus equorum and Lactobacillus sakei, respectively. However, only real-time PCR assay showed enough sensitivity to detect and quantify staphylococci in meat batter before stuffing, showing values of 5.28logCFU/g when quantifying Staphylococcus spp. and 2.87logCFU/g when quantifying S. equorum. In conclusion, real-time PCR was shown to be an efficient tool for the study of the complex associations developed in meat fermentations and for the characterization of dominant populations. Copyright © 2012. Published by Elsevier Ltd.

  18. Effects of triclosan on bacterial community composition and 'Vibrio' populations in natural seawater microcosms

    Directory of Open Access Journals (Sweden)

    Keri Ann Lydon

    2017-05-01

    Full Text Available Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, 'Vibrio', a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm can induce a significant 'Vibrio' growth response (68–1,700 fold increases in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary, Doctors Arm Canal (Big Pine Key, FL, and Clam Bank Landing (North Inlet Estuary, Georgetown, SC. Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of 'Vibrio'naceae (17-fold, Pseudoalteromonadaceae (65-fold, Alteromonadaceae (108-fold, Colwelliaceae (430-fold, and Oceanospirillaceae (1,494-fold. While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to use triclosan as a carbon source. The results further suggest the potential for selection of 'Vibrio' in coastal environments, especially sediments, where triclosan may accumulate at high levels.

  19. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    Directory of Open Access Journals (Sweden)

    Jordan Lee Harris

    Full Text Available 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.

  20. Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

    Science.gov (United States)

    Asem, Dhaneshwaree; Leo, Vincent Vineeth; Passari, Ajit Kumar; Tonsing, Mary Vanlalhruaii; Joshi, J Beslin; Uthandi, Sivakumar; Hashem, Abeer; Abd Allah, Elsayed Fathi; Singh, Bhim Pratap

    2017-01-01

    The gastrointestinal (GI) habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk) and a domesticated goat (Black Bengal) were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF) of D2 (alkaline pretreated pulpy biomass) using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL) and FPase (0.5 U/mL) activities (55°C, pH 8). The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

  1. Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

    Directory of Open Access Journals (Sweden)

    Dhaneshwaree Asem

    Full Text Available The gastrointestinal (GI habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk and a domesticated goat (Black Bengal were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF of D2 (alkaline pretreated pulpy biomass using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL and FPase (0.5 U/mL activities (55°C, pH 8. The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

  2. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    Science.gov (United States)

    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.

  3. Population dynamics of Tisbe holothuriae (Copepoda; Harpacticoida) in exploited mass cultures

    Science.gov (United States)

    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.

  4. Accuracy of cerebrospinal leucocyte count, protein and culture for the diagnosis of acute bacterial meningitis: a comparative study using Bayesian latent class analysis.

    Science.gov (United States)

    Manning, Laurens; Laman, Moses; Mare, Trevor; Hwaiwhanje, Ilomo; Siba, Peter; Davis, Timothy M E

    2014-12-01

    To examine the utility of laboratory methods other than bacterial culture in diagnosing acute bacterial meningitis (ABM). Bayesian latent class analysis was used to estimate diagnostic precision of cerebrospinal fluid (CSF) culture, leucocyte counts and protein concentrations for ABM in Melanesian children. With a cut-off of ≥20 leucocytes/mm(3) , the area under the receiver operating characteristic curve (AUC ROC) was >97.5% for leucocyte counts. A lower (93%) AUC ROC was observed for CSF protein concentrations ≥1 g/l. CSF culture had poor sensitivity and high specificity. Leucocyte counts provide sufficient diagnostic precision to aid clinical decision-making in ABM. © 2014 John Wiley & Sons Ltd.

  5. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    Science.gov (United States)

    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…

  6. RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel

    Science.gov (United States)

    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

  7. Culturable bacterial diversity from the chestnut (Castanea sativa Mill. phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases

    Directory of Open Access Journals (Sweden)

    Angel Valverde

    2017-05-01

    Full Text Available The phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill. is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.

  8. Survey of childhood empyema in Asia: Implications for detecting the unmeasured burden of culture-negative bacterial disease

    Directory of Open Access Journals (Sweden)

    Shen Xuzhuang

    2008-07-01

    Full Text Available Abstract Background Parapneumonic empyema continues to be a disease of significant morbidity and mortality among children despite recent advances in medical management. To date, only a limited number of studies have assessed the burden of empyema in Asia. Methods We surveyed medical records of four representative large pediatric hospitals in China, Korea, Taiwan and Vietnam using ICD-10 diagnostic codes to identify children Results During the study period, we identified 1,379 children diagnosed with empyema or pleural effusion (China, n = 461; Korea, n = 134; Taiwan, n = 119; Vietnam, n = 665. Diagnoses of pleural effusion (n = 1,074 were 3.5 times more common than of empyema (n = 305, although the relative proportions of empyema and pleural effusion noted in hospital records varied widely between the four sites, most likely because of marked differences in coding practices. Although pleural effusions were reported more often than empyema, children with empyema were more likely to have a cultured pathogen. In addition, we found that median age and gender distribution of children with these conditions were similar across the four countries. Among 1,379 empyema and pleural effusion specimens, 401 (29% were culture positive. Staphylococcus aureus (n = 126 was the most common organism isolated, followed by Streptococcus pneumoniae (n = 83, Pseudomonas aeruginosa (n = 37 and Klebsiella (n = 35 and Acinetobacter species (n = 34. Conclusion The age and gender distribution of empyema and pleural effusion in children in these countries are similar to the US and Western Europe. S. pneumoniae was the second leading bacterial cause of empyema and pleural effusion among Asian children. The high proportion of culture-negative specimens among patients with pleural effusion or empyema suggests that culture may not be a sufficiently sensitive diagnostic method to determine etiology in the majority of cases. Future prospective studies in different countries would

  9. Fast Filtration of Bacterial or Mammalian Suspension Cell Cultures for Optimal Metabolomics Results.

    Directory of Open Access Journals (Sweden)

    Natalie Bordag

    Full Text Available The metabolome offers real time detection of the adaptive, multi-parametric response of the organisms to environmental changes, pathophysiological stimuli or genetic modifications and thus rationalizes the optimization of cell cultures in bioprocessing. In bioprocessing the measurement of physiological intracellular metabolite levels is imperative for successful applications. However, a sampling method applicable to all cell types with little to no validation effort which simultaneously offers high recovery rates, high metabolite coverage and sufficient removal of extracellular contaminations is still missing. Here, quenching, centrifugation and fast filtration were compared and fast filtration in combination with a stabilizing washing solution was identified as the most promising sampling method. Different influencing factors such as filter type, vacuum pressure, washing solutions were comprehensively tested. The improved fast filtration method (MxP® FastQuench followed by routine lipid/polar extraction delivers a broad metabolite coverage and recovery reflecting well physiological intracellular metabolite levels for different cell types, such as bacteria (Escherichia coli as well as mammalian cells chinese hamster ovary (CHO and mouse myeloma cells (NS0.The proposed MxP® FastQuench allows sampling, i.e. separation of cells from medium with washing and quenching, in less than 30 seconds and is robustly designed to be applicable to all cell types. The washing solution contains the carbon source respectively the 13C-labeled carbon source to avoid nutritional stress during sampling. This method is also compatible with automation which would further reduce sampling times and the variability of metabolite profiling data.

  10. Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing.

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    Francesca De Filippis

    Full Text Available Microbial growth on meat to unacceptable levels contributes significantly to change meat structure, color and flavor and to cause meat spoilage. The types of microorganisms initially present in meat depend on several factors and multiple sources of contamination can be identified. The aims of this study were to evaluate the microbial diversity in beefsteaks before and after aerobic storage at 4°C and to investigate the sources of microbial contamination by examining the microbiota of carcasses wherefrom the steaks originated and of the processing environment where the beef was handled. Carcass, environmental (processing plant and meat samples were analyzed by culture-independent high-throughput sequencing of 16S rRNA gene amplicons. The microbiota of carcass swabs was very complex, including more than 600 operational taxonomic units (OTUs belonging to 15 different phyla. A significant association was found between beef microbiota and specific beef cuts (P<0.01 indicating that different cuts of the same carcass can influence the microbial contamination of beef. Despite the initially high complexity of the carcass microbiota, the steaks after aerobic storage at 4°C showed a dramatic decrease in microbial complexity. Pseudomonas sp. and Brochothrix thermosphacta were the main contaminants, and Acinetobacter, Psychrobacter and Enterobacteriaceae were also found. Comparing the relative abundance of OTUs in the different samples it was shown that abundant OTUs in beefsteaks after storage occurred in the corresponding carcass. However, the abundance of these same OTUs clearly increased in environmental samples taken in the processing plant suggesting that spoilage-associated microbial species originate from carcasses, they are carried to the processing environment where the meat is handled and there they become a resident microbiota. Such microbiota is then further spread on meat when it is handled and it represents the starting microbial association

  11. Survey on Heterotrophic Bacterial Contamination in Bottled Mineral Water by Culture Method

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    Essmaeel Ghorbanalinezhad

    2014-12-01

    Full Text Available Background and Aim: This project focuses on the level of heterotrophic baceria in bottled mineral water which could be a health concern for the elderly, infants, pregnant women and immuno-compromised patients. Materials and Methods: Different brands of bottled water samples were selected randomly and evaluated for their bacteriological quality, using different specific culture media and biochemical tests. Water samples were analyzed within 24 hours of their purchase/collection. Samples were filtered with 0.45 micron and filters were plated in different media. Then media were incubated at 37˚C for 24-48 hours. Results: Morphological study and biochemical tests revealed a number of bacteria in different   brands of  bottled water. Heterotrophic bacteria(Gram positive cocci, Spore forming gram positive bacilli, non spore forming gram positive bacilli, gram negative bacilli, and gram negative coccobacilli; Pseudomonas and Stenotrophomonas counted in 70% of bottled water samples. There were no cases of fecal contamination or the presence of E.coli. Conclusions: Bottled water is not sterile and contains trace amounts of bacteria naturally present or introduced during processing. Testing drinking water for all possible pathogens is complex, time-consuming, and expensive. If only total coliform bacteria are detected in drinking water, the source is probably environmental. Since the significance of non-pathogenic heterotrophic bacteria in relation to health and diseases is not understood, there is an urgent need to establish a maximum limit for the heterotrophic count in the bottled mineral water. Growth conditions play a critical role in the recovery of heterotrophic bacteria in bottled drinking water.

  12. Culture-based and denaturing gradient gel electrophoresis analysis of the bacterial community from Chungkookjang, a traditional Korean fermented soybean food.

    Science.gov (United States)

    Hong, Sung Wook; Choi, Jae Young; Chung, Kun Sub

    2012-10-01

    The bacterial community of Chungkookjang and raw rice-straw collected from various areas in South Korea was investigated using both culture-dependent and culture-independent methods. Pure cultures were isolated from Chungkookjang and raw rice-straw on tryptic soy agar plates with 72 to 121 colonies and identified by 16S rDNA gene sequence analysis, respectively. The traditional culture-based method and denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rDNA confirmed that Pantoea agglomerans and B. subtilis were identified as predominant in the raw rice-straw and Chungkookjang, respectively, from Iljuk district of Gyeonggi province, P. ananatis and B. licheniformis were identified as predominant in the raw rice-straw and Chungkookjang from Wonju district of Gangwon province, and Microbacterium sp. and B. licheniformis were identified as predominant in the raw rice-straw and Chungkookjang from Sunchang district of Jeolla province. Other strains, such as Bacillus, Enterococcus, Pseudomonas, Rhodococcus, and uncultured bacteria were also present in raw rice-straw and Chungkookjang. A comprehensive analysis of these microorganisms would provide a more detailed understanding of the biologically active components of Chungkookjang and help improve its quality. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis can be successfully applied to a fermented food to detect unculturable or more species than the culture-dependent method. This technique is an effective and convenient culture-independent method for studying the bacterial community in Chungkookjang. In this study, the bacterial community of Chungkookjang collected from various areas in South Korea was investigated using both culture-dependent and culture-independent methods. © 2012 Institute of Food Technologists®

  13. Population size and cultural evolution in nonindustrial food-producing societies.

    Science.gov (United States)

    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.

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

    DEFF Research Database (Denmark)

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang

    2016-01-01

    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......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...

  15. The weak shall inherit: bacteriocin-mediated interactions in bacterial populations.

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    Hadeel Majeed

    Full Text Available 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.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.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 promoting coexistence, allowing migration and evolution, and

  16. An obligatory bacterial mutualism in a multi-drug environment exhibits strong oscillatory population dynamics

    Science.gov (United States)

    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.

  17. Isolation and identification of bacterial populations of zoonotic importance from captive non-venomous snakes in Malaysia.

    Science.gov (United States)

    Abba, Yusuf; Ilyasu, Yusuf Maina; Noordin, Mustapha Mohamed

    2017-07-01

    Captivity of non-venomous snakes such as python and boa are common in zoos, aquariums and as pets in households. Poor captivity conditions expose these reptiles to numerous pathogens which may result in disease conditions. The purpose of this study was to investigate the common bacteria isolated from necropsied captive snakes in Malaysia over a five year period. A total of 27 snake carcasses presented for necropsy at the Universiti Putra Malaysia (UPM) were used in this survey. Samples were aseptically obtained at necropsy from different organs/tissues (lung, liver, heart, kindey, oesophagus, lymph node, stomach, spinal cord, spleen, intestine) and cultured onto 5% blood and McConkey agar, respectively. Gram staining, morphological evaluation and biochemical test such as oxidase, catalase and coagulase were used to tentatively identify the presumptive bacterial isolates. Pythons had the highest number of cases (81.3%) followed by anaconda (14.8%) and boa (3.7%). Mixed infection accounted for 81.5% in all snakes and was highest in pythons (63%). However, single infection was only observed in pythons (18.5%). A total of 82.7%, 95.4% and 100% of the bacterial isolates from python, anaconda and boa, respectively were gram negative. Aeromonas spp was the most frequently isolated bacteria in pythons and anaconda with incidences of 25 (18%) and 8 (36.6%) with no difference (p > 0.05) in incidence, respectively, while Salmonella spp was the most frequently isolated in boa and significantly higher (p < 0.05) than in python and anaconda. Bacteria species were most frequently isolated from the kidney of pythons 35 (25.2%), intestines of anacondas 11 (50%) and stomach of boa 3 (30%). This study showed that captive pythons harbored more bacterial species than anaconda or boa. Most of the bacterial species isolated from these snakes have public health importance and have been incriminated in human infections worldwide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Use of active consortia of constructed ternary bacterial cultures via mixture design for azo-dye decolorization enhancement.

    Science.gov (United States)

    Chen, Bor-Yann; Wang, Mei-Yun; Lu, Wei-Bin; Chang, Jo-Shu

    2007-07-16

    This first-attempt study used constructed bacterial consortia containing Escherichia coli DH5alpha (a weak decolorizer) and its UV-irradiated mutants (E. coli UVT1 and UV68; strong decolorizers) via equilateral triangle diagram and mixture experimental design to assess color removal during species evolution. The results showed that although strain DH5alpha was not an effective decolorizer, its presence might still played a significant role in affecting optimal color removal capabilities of mixed consortia (e.g., E. coli DH5alpha, UVT1 and UV68) for two model azo dyes; namely, reactive red 22 (RR22) and reactive black 5 (RB5). Contour analysis of ternary systems also clearly showed that decolorization of RR22 and RB5 by DH5alpha-containing active mixed consortia was more effective than mono-cultures of the stronger decolorizer alone (e.g., UVT1). The optimal composition of the mixed consortium (UV68, UVT1, DH5alpha) achieving the highest specific decolorization rate was (13%:58%:29%) and (0%:74%:26%) for decolorization of RR22 and RB5, respectively, with initial total cell density fixed at OD(600)=3.5+/-0.28.

  19. Response of single bacterial cells to stress gives rise to complex history dependence at the population level

    Science.gov (United States)

    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

  20. Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example.

    Science.gov (United States)

    He, Xiaoqing; Jin, Yi; Ye, Meixia; Chen, Nan; Zhu, Jing; Wang, Jingqi; Jiang, Libo; Wu, Rongling

    2017-01-01

    How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. We identified a large number of SNPs and indels across the genomes (35.69 G clean data of E. coli and 50.41 G of S. aureus ). We reported 66 and 111 SNPs that were associated with interaction in E. coli and S. aureus , respectively. 23 out of 66 polymorphic changes resulted in amino acid alterations.12 significant genes, such as murE, treA, argS , and relA , which were also identified in previous evolutionary studies. In S. aureus , 111 SNPs detected in coding sequences could be divided into 35 non-synonymous and 76 synonymous SNPs. Our study illustrated the potential of genome-wide association methods for studying rapidly evolving traits in bacteria. Genetic association study methods will facilitate the identification of genetic elements likely to cause phenotypes of interest and provide targets for further laboratory investigation.

  1. Of the Phrensy: an update on the epidemiology and pathogenesis of bacterial meningitis in the pediatric population [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Andrew Janowski

    2017-01-01

    Full Text Available In the past century, advances in antibiotics and vaccination have dramatically altered the incidence and clinical outcomes of bacterial meningitis. We review the shifting epidemiology of meningitis in children, including after the implementation of vaccines that target common meningitic pathogens and the introduction of intrapartum antibiotic prophylaxis offered to mothers colonized with Streptococcus agalactiae. We also discuss what is currently known about the pathogenesis of meningitis. Recent studies of the human microbiome have illustrated dynamic relationships of bacterial and viral populations with the host, which may potentiate the risk of bacterial meningitis.

  2. Quantitative molecular and culture analyses of bacterial elimination in oval-shaped root canals by a single-file instrumentation technique.

    Science.gov (United States)

    Alves, F R F; Rôças, I N; Almeida, B M; Neves, M A S; Zoffoli, J; Siqueira, J F

    2012-09-01

    Bacterial reduction in oval-shaped root canals by a single-instrument technique was compared ex vivo with a conventional nickel-titanium rotary technique. Data obtained from two quantification methods, quantitative real-time polymerase chain reaction (qPCR) and culture, were also compared. Oval-shaped canals of extracted teeth contaminated with Enterococcus faecalis were instrumented using either a single Reciproc instrument or the BioRaCe instrument series. Bacteriological samples were taken before (S1) and after instrumentation (S2). Bacterial quantification was performed using qPCR and culture. Intragroup analysis showed that both protocols promoted a highly significant bacterial reduction (P 0.05). As for the quantification methods, qPCR revealed significantly higher counts of E. faecalis in S1 than culture (P 0.05). The single-file technique was comparable with the conventional technique in oval-shaped canals provided the width of apical preparation, volume of irrigants and duration of irrigation are kept similar. No significant difference was observed for qPCR and culture in post-instrumentation samples, indicating that both methods can be reliably used for studies of antibacterial effectiveness. © 2012 International Endodontic Journal.

  3. Shaping bacterial population behavior through computer-interfaced control of individual cells.

    Science.gov (United States)

    Chait, Remy; Ruess, Jakob; Bergmiller, Tobias; Tkačik, Gašper; Guet, Călin C

    2017-11-16

    Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.

  4. Comparison among the Quantification of Bacterial Pathogens by qPCR, dPCR, and Cultural Methods

    Directory of Open Access Journals (Sweden)

    Matteo Ricchi

    2017-06-01

    Full Text Available The demand for rapid methods for the quantification of pathogens is increasing. Among these methods, those based on nucleic acids amplification (quantitative PCRs are the most widespread worldwide. Together with the qPCR, a new approach named digital PCR (dPCR, has rapidly gained importance. The aim of our study was to compare the results obtained using two different dPCR systems and one qPCR in the quantification of three different bacterial pathogens: Listeria monocytogenes, Francisella tularensis, and Mycobacterium avium subsp. paratuberculosis. For this purpose, three pre-existing qPCRs were used, while the same primers and probes, as well as PCR conditions, were transferred to two different dPCR systems: the QX200 (Bio-Rad and the Quant Studio 3D (Applied Biosystems. The limits of detection and limits of quantification for all pathogens, and all PCR approaches applied, were determined using genomic pure DNAs. The quantification of unknown decimal suspensions of the three bacteria obtained by the three different PCR approaches was compared through the Linear Regression and Bland and Altman analyses. Our results suggest that, both dPCRs are able to quantify the same amount of bacteria, while the comparison among dPCRs and qPCRs, showed both over and under-estimation of the bacteria present in the unknown suspensions. Our results showed qPCR over-estimated the amount of M. avium subsp. paratuberculosis and F. tularensis cells. On the contrary, qPCR, compared to QX200 dPCR, under-estimated the amount of L. monocytogenes cells. However, the maximum difference among PCRs approaches was <0.5 Log10, while cultural methods underestimated the number of bacteria by one to two Log10 for Francisella tularensis and Mycobacterium avium subsp. paratuberculosis. On the other hand, cultural and PCRs methods quantified the same amount of bacteria for L. monocytogenes, suggesting for this last pathogen, PCRs approaches can be considered as a valid alternative

  5. Analysis of single hyphal growth and fragmentation in submerged cultures using a population model

    DEFF Research Database (Denmark)

    Krabben, Preben; Nielsen, Søren; Michelsen, Michael Locht

    1997-01-01

    Descriptions of population dynamics in submerged cultures are important when studying the mechanisms of growth and fragmentation of filamentous microorganisms. Population models are traditionally formulated as population balance equations. Population models of filamentous morphology are difficult...... to solve because of random fragmentation, which introduces an integral term into the population balance equations. Balances for the systemic properties, e.g. concentration of hyphal elements, substrate concentration, average total hyphal length, and average number of growing tips, are set up. Based...... on these balances one can solve the inverse problem, i.e. determination of kinetic parameters directly from measurements of the hyphal morphology. Both a Monte Carlo method and a discretization method have been used to calculate the steady-state population distribution. The two methods are compared and the Monte...

  6. Effects of gamma-irradiation before and after cooking on bacterial population and sensory quality of Dakgalbi

    International Nuclear Information System (INIS)

    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

    2012-01-01

    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. - Highlights: ► We compared the microbial safety and sensory property of Dakgalbi irradiated before and after cooking. ► Dakgalbi irradiated after cooking can be more effective processing method on microbial safety. ► Sensory property decreased on both Dakgalbis by irradiation-induced off-flavor. ► Dakgalbi irradiated after cooking showed a better tendency on the sensory evaluation.

  7. Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacterial in compost biofilter enrichments.

    Science.gov (United States)

    Bruns, M A; Hanson, J R; Mefford, J; Scow, K M

    2001-03-01

    The gasoline additive MTBE, methyl tert-butyl ether, is a widespread and persistent groundwater contaminant. MTBE undergoes rapid mineralization as the sole carbon and energy source of bacterial strain PM1, isolated from an enrichment culture of compost biofilter material. In this report, we describe the results of microbial community DNA profiling to assess the relative dominance of isolate PM1 and other bacterial strains cultured from the compost enrichment. Three polymerase chain reaction (PCR)-based profiling approaches were evaluated: denaturing gradient gel electrophoresis (DGGE) analysis of 230 bp 16S rDNA fragments; thermal gradient gel electrophoresis (TGGE) analysis of 575 bp 16S rDNA fragments; and non-denaturing polyacrylamide gel electrophoresis of 300-1,500 bp fragments containing 16S/23S ribosomal intergenic transcribed spacer (ITS) regions. Whereas all three DNA profiling approaches indicated that PM1-like bands predominated in mixtures from MTBE-grown enrichments, ITS profiling provided the most abundant and specific sequence data to confirm strain PM1's presence in the enrichment. Moreover, ITS profiling did not produce non-specific PCR products that were observed with T/DGGE. A further advantage of ITS community profiling over other methods requiring restriction digestion (e.g. terminal restriction fragment length polymorphisms) was that it did not require an additional digestion step or the use of automated sequencing equipment. ITS bands, excised from similar locations in profiles of the enrichment and PM1 pure culture, were 99.9% identical across 750 16S rDNA positions and 100% identical across 691 spacer positions. BLAST comparisons of nearly full-length 16S rDNA sequences showed 96% similarity between isolate PM1 and representatives of at least four different genera in the Leptothrix subgroup of the beta-Proteobacteria (Aquabacterium, Leptothrix, Rubrivivax and Ideonella). Maximum likelihood and parsimony analyses of 1,249 nucleotide

  8. An individual-based approach to explain plasmid invasion in bacterial populations

    DEFF Research Database (Denmark)

    Seoane, Jose Miguel; Yankelevich, Tatiana; Dechesne, Arnaud

    2011-01-01

    , together with contact mechanics arising from cellular growth and division, are the two main processes determining the emergent inability of the pWW0 TOL plasmid to fully invade spatially structured Pseudomonas putida populations. We have also shown that pWW0 conjugation occurs mainly at advanced stages...... observe, however, that transient periods of elevated plasmid transfer in newly formed transconjugant cells are offset by unfavorable cell-to-cell contact mechanics, which ultimately precludes the pWWO TOL plasmid from fully invading tightly packed multicellular P. putida populations such as microcolonies...

  9. Bacterial meningitis

    NARCIS (Netherlands)

    Heckenberg, Sebastiaan G. B.; Brouwer, Matthijs C.; van de Beek, Diederik

    2014-01-01

    Bacterial meningitis is a neurologic emergency. Vaccination against common pathogens has decreased the burden of disease. Early diagnosis and rapid initiation of empiric antimicrobial and adjunctive therapy are vital. Therapy should be initiated as soon as blood cultures have been obtained,

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

    Science.gov (United States)

    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 genes encoding sulfonamide resistance (sul1 and sul2) were increased (P resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  11. Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations?

    Science.gov (United States)

    Muniesa, Maite; Colomer-Lluch, Marta; Jofre, Juan

    2013-07-01

    Environments without any contact with anthropogenic antibiotics show a great abundance of antibiotic resistance genes that use to be chromosomal and are part of the core genes of the species that harbor them. Some of these genes are shared with human pathogens where they appear in mobile genetic elements. Diversity of antibiotic resistance genes in non-contaminated environments is much greater than in human and animal pathogens, and in environments contaminated with antibiotic from anthropogenic activities. This suggests the existence of some bottleneck effect for the mobilization of antibiotic resistance genes among different biomes. Bacteriophages have characteristics that make them suitable vectors between different biomes, and as well for transferring genes from biome to biome. Recent metagenomic studies and detection of bacterial genes by genomic techniques in the bacteriophage fraction of different microbiota provide indirect evidences that the mobilization of genes mediated by phages, including antibiotic resistance genes, is far more relevant than previously thought. Our hypothesis is that bacteriophages might be of critical importance for evading one of the bottlenecks, the lack of ecological connectivity that modulates the pass of antibiotic resistance genes from natural environments such as waters and soils, to animal and human microbiomes. This commentary concentrates on the potential importance of bacteriophages in transferring resistance genes from the environment to human and animal body microbiomes, but there is no doubt that transduction occurs also in body microbiomes.

  12. Uncovering potential 'herbal probiotics' in Juzen-taiho-to through the study of associated bacterial populations.

    Science.gov (United States)

    Montenegro, Diego; Kalpana, Kriti; Chrissian, Christine; Sharma, Ashutosh; Takaoka, Anna; Iacovidou, Maria; Soll, Clifford E; Aminova, Olga; Heguy, Adriana; Cohen, Lisa; Shen, Steven; Kawamura, Akira

    2015-02-01

    Juzen-taiho-to (JTT) is an immune-boosting formulation of ten medicinal herbs. It is used clinically in East Asia to boost the human immune functions. The active factors in JTT have not been clarified. But, existing evidence suggests that lipopolysaccharide (LPS)-like factors contribute to the activity. To examine this possibility, JTT was subjected to a series of analyses, including high resolution mass spectrometry, which suggested the presence of structural variants of LPS. This finding opened a possibility that JTT contains immune-boosting bacteria. As the first step to characterize the bacteria in JTT, 16S ribosomal RNA sequencing was carried out for Angelica sinensis (dried root), one of the most potent immunostimulatory herbs in JTT. The sequencing revealed a total of 519 bacteria genera in A. sinensis. The most abundant genus was Rahnella, which is widely distributed in water and plants. The abundance of Rahnella appeared to correlate with the immunostimulatory activity of A. sinensis. In conclusion, the current study provided new pieces of evidence supporting the emerging theory of bacterial contribution in immune-boosting herbs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

    Science.gov (United States)

    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.

  14. Improvement of the Bacterial Pure Culture 3A by Gamma Irradiation for Increasing Efficiency in Degrading Pesticides

    International Nuclear Information System (INIS)

    Tongpim, Saowanit; Piadaeng, Nattaya

    2006-09-01

    This research work had an objective to improve bacterial activity in degrading a herbicide: 2,4-dichlorophenoxyacetic acid (2,4-D). The bacterial isolate 3 A , kept in the culture collection of Khon Kaen University that could degrade 2,4-D, was employed in this experiment. Cell suspension of isolate 3 A was exposed to gamma irradiation at various doses (1-5 kGy). The isolated survivors were screened on the basis of forming larger colonies than the parent strain 3 A when grown on mineral salts agar containing 2,4-D (MS + 2,4-D) as the sole carbon source. We obtained 70 effective isolates which 6 isolates called 3 A I2-21, 3 A I2-23, 3 A I1-51, 3 A I2-71, 3 A I1-52 and 3 A I2-73 were chosen for further studies. These 6 irradiated isolates together with the parent strain were characterized using morphological, physiological and biochemical tests. They were all identified as Pseudomonas cepacia. All isolates had optimal growth pH of 7 and grew best at 30 o C. Biodegradation experiments performed in mineral salts medium containing 200 ppm of 2,4-D showed that after 20 days of incubation 36.9%, 65.3%, 57.2%, 54.8%, 53.4%, 47.3% and 45.8% of 2,4- D was degraded by isolates 3 A , 3 A I2-21, 3 A I2-23, 3 A I1-51, 3 A I2-71, 3 A I1-52 and 3 A I2-73, respectively. Comparing the irradiated strains with parent strain 3 A revealed that the isolate 3 A I2-21 was the most effective one as it could degrade 2,4-D about 28.4% greater than the parent strain 3 A .

  15. Approach to assessing local socio-cultural impacts using projections of population growth and composition

    Energy Technology Data Exchange (ETDEWEB)

    Baldwin, T. E.; Poetsch, R.

    1977-08-01

    All assessment of future domestic development projects assumes that the problems to be examined have been properly identified and defined before the application of a projection technique. An attempt is made to codify socio-cultural problems mentioned in literature and clarify how existing demographic projection techniques can be applied to assessing the problems. The relationship between changes in local population size and composition induced by in-migration and the potential for socio-cultural incompatibilities is described heuristically. For simplification, the problems expected to emerge from differences in demographic composition are classified into three categories: (1) service needs, such as those for housing, recreation, and education; (2) types of social organizations related to capacities for, or constraints on, reaping the benefits of rapid economic development and social changes (e.g., employment and income); and (3) attitudes, values, and cultural perspectives. These areas of concern are very broad, and quantitative projections of population size and composition are more easily related to the first than to the third. Although demographic projection provides a valuable tool for estimating future social change, the knowledge about cause and effect is not sufficient to support the quantification of socio-cultural impact. Therefore, the projections are used only as relative indicators and the assessments of socio-cultural impact based on them are qualitative only. Therefore, identification and assessment of socio-cultural impacts are a means of developing plans to overcome the expected problems.

  16. Parental Opinion Concerning School Sexuality Education in a Culturally Diverse Population in the USA

    Science.gov (United States)

    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…

  17. Correlations between bacterial populations and process parameters in four full-scale anaerobic digesters treating sewage sludge.

    Science.gov (United States)

    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 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Effect of antibiotics on bacterial populations: a multi-hierachical selection process [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    José Luis Martínez

    2017-01-01

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

  19. In situ Biodegradation of Endosulfan, Imidacloprid, and Carbendazim Using Indigenous Bacterial Cultures of Agriculture Fields of Uttarakhand, India

    OpenAIRE

    Geeta Negi; Pankaj; Anjana Srivastava; Anita Sharma

    2014-01-01

    In the present study, presence of endosulfan, imidacloprid, carbendazim, in the soil /vegetables/cereals and water samples was observed in agriculture fields of Uttarakhand. In view of biodegradation of these pesticides, 9 bacterial isolates were recovered from the soil samples of the fields which tolerated endosulfan, imidacloprid, carbendazim from 100 to 200 µg/ml. Three bacterial consortia used for in vitro bioremediation experiments were consisted of 3 bacterial isolates for carbendazim, ...

  20. Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population.

    Science.gov (United States)

    Bossa-Castro, Ana M; Tekete, Cheick; Raghavan, Chitra; Delorean, Emily E; Dereeper, Alexis; Dagno, Karim; Koita, Ousmane; Mosquera, Gloria; Leung, Hei; Verdier, Valérie; Leach, Jan E

    2018-02-06

    Quantitative trait loci (QTL) that confer broad-spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and oryzae (Xoo), respectively. Controlling these diseases is particularly important in sub-Saharan Africa, where no sources of BSR are currently available in deployed varieties. The MAGIC founders and lines were genotyped by sequencing and phenotyped in the greenhouse and field by inoculation with multiple strains of Xoc and Xoo. A combination of genomewide association studies (GWAS) and interval mapping analyses revealed 11 BSR QTL, effective against both diseases, and three pathovar-specific QTL. The most promising BSR QTL (qXO-2-1, qXO-4-1 and qXO-11-2) conferred resistance to more than nine Xoc and Xoo strains. GWAS detected 369 significant SNP markers with distinguishable phenotypic effects, allowing the identification of alleles conferring disease resistance and susceptibility. The BSR and susceptibility QTL will improve our understanding of the mechanisms of both resistance and susceptibility in the long term and will be immediately useful resources for rice breeding programmes. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  1. Genetic population structure in an equatorial sparrow: roles for culture and geography.

    Science.gov (United States)

    Danner, J E; Fleischer, R C; Danner, R M; Moore, I T

    2017-06-01

    Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  2. CHROMagar COL-APSE: a selective bacterial culture medium for the isolation and differentiation of colistin-resistant Gram-negative pathogens

    DEFF Research Database (Denmark)

    Abdul Momin, Muhd Haziq F; Bean, David C; Hendriksen, Rene S.

    2017-01-01

    Purpose. A selective chromogenic culture medium for the laboratory isolation and differentiation of colistin resistant Acinetobacter, Pseudomonas, Stenotrophomonas and Enterobacteriaceae spp. (CHROMagar COL-APSE) was developed, evaluated and compared to an existing selective bacterial culture...... for the growth of COL-resistant bacterial pathogens. Due to the low limit of detection (101 c.f.u.), it may be useful as a primary isolation medium in the surveillance and recovery of COL-resistant bacteria from complex human, veterinary and environmental samples, especially those with plasmid-mediated MCR-1...... medium (SuperPolymyxin). Methodology. The medium was challenged with 84 isolates, including polymyxin B (POL B)-susceptible and -resistant type strains and colistin (COL)-resistant organisms recovered from human and animal samples. Susceptibility to COL and POL B was determined by agar dilution and broth...

  3. Comparison of bacterial culture and qPCR testing of rectal and pen floor samples as diagnostic approaches to detect enterotoxic Escherichia coli in nursery pigs

    DEFF Research Database (Denmark)

    Weber, N. R.; Nielsen, J. P.; Hjulsager, Charlotte Kristiane

    2017-01-01

    Enterotoxigenic E. coli (ETEC) are a major cause of diarrhoea in weaned pigs. The objective of this study was to evaluate the agreement at pen level among three different diagnostic approaches for the detection of ETEC in groups of nursery pigs with diarrhoea. The diagnostic approaches used were......: bacterial culturing of faecal samples from three pigs (per pen) with clinical diarrhoea and subsequent testing for virulence genes in E. coli isolates; bacterial culturing of pen floor samples and subsequent testing for virulence genes in E. coli isolates; qPCR testing of pen floor samples in order...... to determine the quantity of F18 and F4 genes. The study was carried out in three Danish pig herds and included 31 pens with a pen-level diarrhoea prevalence of > 25%, as well as samples from 93 diarrhoeic nursery pigs from these pens. All E. coli isolates were analysed by PCR and classified as ETEC when genes...

  4. Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat.

    Science.gov (United States)

    Pankratov, Timofey A; Ivanova, Anastasia O; Dedysh, Svetlana N; Liesack, Werner

    2011-07-01

    Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH. © 2011 Society for

  5. Specialized peptidoglycan hydrolases sculpt the intra-bacterial niche of predatory Bdellovibrio and increase population fitness.

    Directory of Open Access Journals (Sweden)

    Thomas R Lerner

    2012-02-01

    Full Text Available Bdellovibrio are predatory bacteria that have evolved to invade virtually all gram-negative bacteria, including many prominent pathogens. Upon invasion, prey bacteria become rounded up into an osmotically stable niche for the Bdellovibrio, preventing further superinfection and allowing Bdellovibrio to replicate inside without competition, killing the prey bacterium and degrading its contents. Historically, prey rounding was hypothesized to be associated with peptidoglycan (PG metabolism; we found two Bdellovibrio genes, bd0816 and bd3459, expressed at prey entry and encoding proteins with limited homologies to conventional dacB/PBP4 DD-endo/carboxypeptidases (responsible for peptidoglycan maintenance during growth and division. We tested possible links between Bd0816/3459 activity and predation. Bd3459, but not an active site serine mutant protein, bound β-lactam, exhibited DD-endo/carboxypeptidase activity against purified peptidoglycan and, importantly, rounded up E. coli cells upon periplasmic expression. A ΔBd0816 ΔBd3459 double mutant invaded prey more slowly than the wild type (with negligible prey cell rounding and double invasions of single prey by more than one Bdellovibrio became more frequent. We solved the crystal structure of Bd3459 to 1.45 Å and this revealed predation-associated domain differences to conventional PBP4 housekeeping enzymes (loss of the regulatory domain III, alteration of domain II and a more exposed active site. The Bd3459 active site (and by similarity the Bd0816 active site can thus accommodate and remodel the various bacterial PGs that Bdellovibrio may encounter across its diverse prey range, compared to the more closed active site that "regular" PBP4s have for self cell wall maintenance. Therefore, during evolution, Bdellovibrio peptidoglycan endopeptidases have adapted into secreted predation-specific proteins, preventing wasteful double invasion, and allowing activity upon the diverse prey peptidoglycan

  6. Bacterial communities in urban aerosols collected with wetted-wall cyclonic samplers and seasonal fluctuations of live and culturable airborne bacteria.

    Science.gov (United States)

    Ravva, Subbarao V; Hernlem, Bradley J; Sarreal, Chester Z; Mandrell, Robert E

    2012-02-01

    Airborne transmission of bacterial pathogens from point sources (e.g., ranches, dairy waste treatment facilities) to areas of food production (farms) has been suspected. Determining the incidence, transport and viability of extremely low levels of pathogens require collection of high volumes of air and characterization of live bacteria from aerosols. We monitored the numbers of culturable bacteria in urban aerosols on 21 separate days during a 9 month period using high volume cyclonic samplers at an elevation of 6 m above ground level. Culturable bacteria in aerosols fluctuated from 3 CFU to 6 million CFU/L of air per hour and correlated significantly with changes in seasonal temperatures, but not with humidity or wind speed. Concentrations of viable bacteria determined by fluorescence staining and flow cytometry correlated significantly with culturable bacteria. Members of the phylum Proteobacteria constituted 98% of the bacterial community, which was characterized using 16S rRNA gene sequencing using DNA from aerosols. Aquabacterium sp., previously characterized from aquatic environments, represented 63% of all clones and the second most common were Burkholderia sp; these are ubiquitous in nature and some are potential human pathogens. Whole genome amplification prior to sequencing resulted in a substantial decrease in species diversity compared to characterizing culturable bacteria sorted by flow cytometry based on scatter signals. Although 27 isolated colonies were characterized, we were able to culture 38% of bacteria characterized by sequencing. The whole genome amplification method amplified DNA preferentially from Phyllobacterium myrsinacearum, a minor member of the bacterial communities, whereas Variovorax paradoxus dominated the cultured organisms.

  7. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

    Science.gov (United States)

    Johnston, Eric R; Rodriguez-R, Luis M; Luo, Chengwei; Yuan, Mengting M; Wu, Liyou; He, Zhili; Schuur, Edward A G; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong; Konstantinidis, Konstantinos T

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  8. Communication and cultural interaction in health promotion strategies to migrant populations in Italy: the cross-cultural phone counselling experience.

    Science.gov (United States)

    Taglieri, Filippo Maria; Colucci, Anna; Barbina, Donatella; Fanales-Belasio, Emanuele; Luzi, Anna Maria

    2013-01-01

    In the last 10 years migration processes have progressively increased worldwide and in Italy about 5 millions of residing migrants are estimated. To meet health needs of these new residents, effective relational and communication tools, which allow a reciprocal intercultural interaction within health care structures, are therefore necessary. This article faces the main features of the relational-communication processes associated with health promotion and care in the migrant population in Italy to the aim of identifying the key and critical points within the interaction between different cultures, focusing on the role of specific professional figures, including cultural mediators and health educators. Within the activity of HIV phone counselling operated by Psycho-sociobehavioural, Communication and Training Operating Unit of National Institute of Health in Italy, an intercultural approach was successfully experienced in a project targeted to migrants (2007-2008). Specifically, the presence of cultural mediators answering in the languages of main migrants' groups allowed the increase of calls from migrant people and of the information provided.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-21

    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), andtet(W)] were reduced (P< 0.05), while those of genes encoding sulfonamide resistance (sul1andsul2) 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 ofFlavobacteriaceaespp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the familyRuminococcaceae, classBacilli, or phylumProteobacteria. 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

  10. Paths and patterns: the biology and physics of swimming bacterial populations

    Science.gov (United States)

    Kessler, J. O.; Strittmatter, R. P.; Swartz, D. L.; Wiseley, D. A.; Wojciechowski, M. F.

    1995-01-01

    The velocity distribution of swimming micro-organisms depends on directional cues supplied by the environment. Directional swimming within a bounded space results in the accumulation of organisms near one or more surfaces. Gravity, gradients of chemical concentration and illumination affect the motile behaviour of individual swimmers. Concentrated populations of organisms scatter and absorb light or consume molecules, such as oxygen. When supply is one-sided, consumption creates gradients; the presence of the population alters the intensity and the symmetry of the environmental cues. Patterns of cues interact dynamically with patterns of the consumer population. In suspensions, spatial variations in the concentration of organisms are equivalent to variations of mean mass density of the fluid. When organisms accumulate in one region whilst moving away from another region, the force of gravity causes convection that translocates both organisms and dissolved substances. The geometry of the resulting concentration-convection patterns has features that are remarkably reproducible. Of interest for biology are (1) the long-range organisation achieved by organisms that do not communicate, and (2) that the entire system, consisting of fluid, cells, directional supply of consumables, boundaries and gravity, generates a dynamic that improves the organisms' habitat by enhancing transport and mixing. Velocity distributions of the bacterium Bacillus subtilis have been measured within the milieu of the spatially and temporally varying oxygen concentration which they themselves create. These distributions of swimming speed and direction are the fundamental ingredients required for a quantitative mathematical treatment of the patterns. The quantitative measurement of swimming behaviour also contributes to our understanding of aerotaxis of individual cells.

  11. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem

    Directory of Open Access Journals (Sweden)

    Eric Robert Johnston

    2016-04-01

    Full Text Available How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 grams are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth by sequencing, and the recovery of twenty-seven high-quality, almost complete (>80% completeness population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity. Collectively

  12. Artificially constructed quorum-sensing circuits are used for subtle control of bacterial population density.

    Directory of Open Access Journals (Sweden)

    Zhaoshou Wang

    Full Text Available Vibrio fischeri is a typical quorum-sensing bacterium for which lux box, luxR, and luxI have been identified as the key elements involved in quorum sensing. To decode the quorum-sensing mechanism, an artificially constructed cell-cell communication system has been built. In brief, the system expresses several programmed cell-death BioBricks and quorum-sensing genes driven by the promoters lux pR and PlacO-1 in Escherichia coli cells. Their transformation and expression was confirmed by gel electrophoresis and sequencing. To evaluate its performance, viable cell numbers at various time periods were investigated. Our results showed that bacteria expressing killer proteins corresponding to ribosome binding site efficiency of 0.07, 0.3, 0.6, or 1.0 successfully sensed each other in a population-dependent manner and communicated with each other to subtly control their population density. This was also validated using a proposed simple mathematical model.

  13. Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

    Science.gov (United States)

    Wielgoss, Sébastien; Barrick, Jeffrey E.; Tenaillon, Olivier; Wiser, Michael J.; Dittmar, W. James; Cruveiller, Stéphane; Chane-Woon-Ming, Béatrice; Médigue, Claudine; Lenski, Richard E.; Schneider, Dominique

    2013-01-01

    Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ∼150-fold, whereas the mutY mutations reduced the rate by ∼40–60%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined. PMID:23248287

  14. Interaction between stocking density and settlement on population dynamics in suspended mussel culture

    Science.gov (United States)

    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.

  15. Quantitative analysis of ruminal bacterial populations involved in lipid metabolism in dairy cows fed different vegetable oils.

    Science.gov (United States)

    Vargas-Bello-Pérez, E; Cancino-Padilla, N; Romero, J; Garnsworthy, P C

    2016-11-01

    Vegetable oils are used to increase energy density of dairy cow diets, although they can provoke changes in rumen bacteria populations and have repercussions on the biohydrogenation process. The aim of this study was to evaluate the effect of two sources of dietary lipids: soybean oil (SO, an unsaturated source) and hydrogenated palm oil (HPO, a saturated source) on bacterial populations and the fatty acid profile of ruminal digesta. Three non-lactating Holstein cows fitted with ruminal cannulae were used in a 3×3 Latin square design with three periods consisting of 21 days. Dietary treatments consisted of a basal diet (Control, no fat supplement) and the basal diet supplemented with SO (2.7% of dry matter (DM)) or HPO (2.7% of DM). Ruminal digesta pH, NH3-N and volatile fatty acids were not affected by dietary treatments. Compared with control and HPO, total bacteria measured as copies of 16S ribosomal DNA/ml by quantitative PCR was decreased (Poils.

  16. Evaluation of the dynamics of microalgae population structure and process performance during piggery wastewater treatment in algal-bacterial photobioreactors.

    Science.gov (United States)

    García, Dimas; Posadas, Esther; Blanco, Saúl; Acién, Gabriel; García-Encina, Pedro; Bolado, Silvia; Muñoz, Raúl

    2018-01-01

    The dynamics of microalgae population during piggery wastewater (PWW) treatment in four open photobioreactors operated at 27days of hydraulic retention time, and inoculated with Chlorella sp. (R1), Acutodesmus obliquus (R2), Oscillatoria sp. (R3) and in the absence of inoculum (R4), were evaluated for 6months. In addition, the algal-bacterial biomass concentration, removal of organic matter, nutrients and heavy metals were also assessed. The results revealed a high diversity and rapid variations in the structure of microalgae populations, Chlorella sp. being dominant in R4 throughout most of the operational period. Steady state average biomass concentration ranged from 2445-2610mg/L in R1-R3 to 3265mg/L in R4. No significant differences were recorded in the removal efficiencies (REs) of total organic carbon (86-87%), inorganic carbon (62-71%), total nitrogen (82-85%) and total phosphorous (90-92%). Finally, Zn-REs accounted for 26% in R3, 37% in R2, and 49% in R1 and R4. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Understanding anti-tuberculosis drug efficacy: rethinking bacterial populations and how we model them

    Directory of Open Access Journals (Sweden)

    Dimitrios Evangelopoulos

    2015-03-01

    Full Text Available Tuberculosis still remains a global health emergency, claiming 1.5 million lives in 2013. The bacterium responsible for this disease, Mycobacterium tuberculosis (M.tb, has successfully survived within hostile host environments, adapting to immune defence mechanisms, for centuries. This has resulted in a disease that is challenging to treat, requiring lengthy chemotherapy with multi-drug regimens. One explanation for this difficulty in eliminating M.tb bacilli in vivo is the disparate action of antimicrobials on heterogeneous populations of M.tb, where mycobacterial physiological state may influence drug efficacy. In order to develop improved drug combinations that effectively target diverse mycobacterial phenotypes, it is important to understand how such subpopulations of M.tb are formed during human infection. We review here the in vitro and in vivo systems used to model M.tb subpopulations that may persist during drug therapy, and offer aspirations for future research in this field.

  18. Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks

    Directory of Open Access Journals (Sweden)

    Kirsty Dougal

    2017-08-01

    Full Text Available Twelve mature (aged 5–16 years horses and ponies of mixed breed and type were fed restricted (1.25% BM Dry matter quantities of one of two fiber based diets formulated to be iso-caloric. Diet 1 comprised of 0.8% body mass (BM of chaff based complete feed plus 0.45% BM low energy grass hay (the same hay used for both diets. Diet 2 comprised 0.1% BM of a nutrient balancer plus 1.15% BM grass hay. Fecal samples were collected at week 10 and week 16. DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the bacterial microbiome of the horse. The two most abundant phyla found in both diets and sampling periods were the Firmicutes and Bacteroidetes. There was a clear reduction in Bacteroidetes with a concordant increase in Firmicutes over time. There was a limited degree of stability within the bacterial community of the hindgut of horses, with 65% of bacteria retained, over a 6 week period whilst on a uniform diet. The presence of a core community defined by being present in all samples (each animal/diet combination included in the study and being present at 0.1% relative abundance (or greater was identified. In total 65 operational taxonomic units (OTUs were identified that fit the definition of core making up 21–28% of the total sequences recovered. As with total population the most abundant phyla were the Bacteroidetes followed by the Firmicutes, however there was no obvious shift in phyla due to period. Indeed, when the relative abundance of OTUs was examined across diets and periods there was no significant effect of diet or period alone or in combination on the relative abundance of the core OTUs.

  19. Discovering and differentiating new and emerging clonal populations of Chlamydia trachomatis with a novel shotgun cell culture harvest assay.

    Science.gov (United States)

    Somboonna, Naraporn; Mead, Sally; Liu, Jessica; Dean, Deborah

    2008-03-01

    Chlamydia trachomatis is the leading cause of preventable blindness and bacterial sexually transmitted diseases worldwide. Plaque assays have been used to clonally segregate laboratory-adapted C. trachomatis strains from mixed infections, but no assays have been reported to segregate clones from recent clinical samples. We developed a novel shotgun cell culture harvest assay for this purpose because we found that recent clinical samples do not form plaques. Clones were strain-typed by using outer membrane protein A and 16S rRNA sequences. Surprisingly, ocular trachoma reference strain A/SA-1 contained clones of Chlamydophila abortus. C. abortus primarily infects ruminants and pigs and has never been identified in populations where trachoma is endemic. Three clonal variants of reference strain Ba/Apache-2 were also identified. Our findings reflect the importance of clonal isolation in identifying constituents of mixed infections containing new or emerging strains and of viable clones for research to more fully understand the dynamics of in vivo strain-mixing, evolution, and disease pathogenesis.

  20. Genetic diversity, population structure, and traditional culture ofCamellia reticulata.

    Science.gov (United States)

    Xin, Tong; Huang, Weijuan; De Riek, Jan; Zhang, Shuang; Ahmed, Selena; Van Huylenbroeck, Johan; Long, Chunlin

    2017-11-01

    Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material ( n  = 190 individuals) from five populations at study sites using single-dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species ( H sp  = 0.3397, I sp  = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop  = 0.2937, I pop  = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio-economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

  1. Quantitation of DNA repair in brain cell cultures: implications for autoradiographic analysis of mixed cell populations

    International Nuclear Information System (INIS)

    Dambergs, R.; Kidson, C.

    1979-01-01

    Quantitation of DNA repair in the mixed cell population of mouse embryo brain cultures has been assessed by autoradiographic analysis of unscheduled DNA synthesis following UV-irradiation. The proportion of labelled neurons and the grain density over neuronal nuclei were both less than the corresponding values for glial cells. The nuclear geometries of these two classes of cell are very different. Partial correction for the different geometries by relating grain density to nuclear area brought estimates of neuronal and glial DNA repair synthesis more closely in line. These findings have general implications for autoradiographic measurement of DNA repair in mixed cell populations and in differentiated versus dividing cells. (author)

  2. Selection of microbial populations degrading recalcitrant hydrocarbons of gasoline by monitoring of culture-headspace composition.

    Science.gov (United States)

    Solano-Serena, F; Marchal, R; Lebeault, J M; Vandecasteele, J P

    2000-01-01

    A methodology was devised and was found useful for the selection of populations degrading recalcitrant hydrocarbons. The work was part of a programme aiming at developing knowledge of the intrinsic capacities of autochtonous microflorae of the environment for gasoline biodegradation. The methodology involved monitoring the progress of degradation in enrichment liquid cultures on the selected hydrocarbon by gas chromatographic analysis of CO2 production and O2 consumption. Populations degrading in particular o-xylene, 1,2,4-trimethylbenzene, cyclohexane were obtained. Concerning 2,2,4-trimethylpentane (isooctane), one microflora (and a pure strain derived from it) growing on this hydrocarbon were obtained from gasoline-polluted water.

  3. Interactions Between QTL SAP6 and SU91 on Resistance to Common Bacterial Blight in Red Kidney Bean and Pinto Bean Populations

    Science.gov (United States)

    Resistance to common bacterial blight in common bean is a complex trait that is quantitatively inherited. We examined the interaction between two independent QTL, SAP6 and SU91, which condition resistance to CBB.The QTL were studied in a pinto bean F2 population a cross between Othello (sap6 sap6 //...

  4. Invasive Candidiasis in Various Patient Populations: Incorporating Non-Culture Diagnostic Tests into Rational Management Strategies

    Science.gov (United States)

    Clancy, Cornelius J.; Shields, Ryan K.; Nguyen, M. Hong

    2016-01-01

    Mortality rates due to invasive candidiasis remain unacceptably high, in part because the poor sensitivity and slow turn-around time of cultures delay the initiation of antifungal treatment. β-d-glucan (Fungitell) and polymerase chain reaction (PCR)-based (T2Candida) assays are FDA-approved adjuncts to cultures for diagnosing invasive candidiasis, but their clinical roles are unclear. We propose a Bayesian framework for interpreting non-culture test results and developing rational patient management strategies, which considers test performance and types of invasive candidiasis that are most common in various patient populations. β-d-glucan sensitivity/specificity for candidemia and intra-abdominal candidiasis is ~80%/80% and ~60%/75%, respectively. In settings with 1%–10% likelihood of candidemia, anticipated β-d-glucan positive and negative predictive values are ~4%–31% and ≥97%, respectively. Corresponding values in settings with 3%–30% likelihood of intra-abdominal candidiasis are ~7%–51% and ~78%–98%. β-d-glucan is predicted to be useful in guiding antifungal treatment for wide ranges of populations at-risk for candidemia (incidence ~5%–40%) or intra-abdominal candidiasis (~7%–20%). Validated PCR-based assays should broaden windows to include populations at lower-risk for candidemia (incidence ≥~2%) and higher-risk for intra-abdominal candidiasis (up to ~40%). In the management of individual patients, non-culture tests may also have value outside of these windows. The proposals we put forth are not definitive treatment guidelines, but rather represent starting points for clinical trial design and debate by the infectious diseases community. The principles presented here will be applicable to other assays as they enter the clinic, and to existing assays as more data become available from different populations. PMID:29376927

  5. Role of Mobile Health in the Care of Culturally and Linguistically Diverse US Populations

    OpenAIRE

    Tirado, Miguel

    2011-01-01

    Emerging trends in the health-related use of cell phones include the proliferation of mobile health applications for the care and monitoring of patients with chronic diseases and the rise in cell phone usage by Latinos and African Americans in the United States. This article reviews public policy in four areas with the goal of improving the care of patients belonging to culturally and linguistically diverse populations: 1) mobile health service access and the physician's duty of care, 2) affo...

  6. Invasive Candidiasis in Various Patient Populations: Incorporating Non-Culture Diagnostic Tests into Rational Management Strategies

    Directory of Open Access Journals (Sweden)

    Cornelius J. Clancy

    2016-02-01

    Full Text Available Mortality rates due to invasive candidiasis remain unacceptably high, in part because the poor sensitivity and slow turn-around time of cultures delay the initiation of antifungal treatment. β-d-glucan (Fungitell and polymerase chain reaction (PCR-based (T2Candida assays are FDA-approved adjuncts to cultures for diagnosing invasive candidiasis, but their clinical roles are unclear. We propose a Bayesian framework for interpreting non-culture test results and developing rational patient management strategies, which considers test performance and types of invasive candidiasis that are most common in various patient populations. β-d-glucan sensitivity/specificity for candidemia and intra-abdominal candidiasis is ~80%/80% and ~60%/75%, respectively. In settings with 1%–10% likelihood of candidemia, anticipated β-d-glucan positive and negative predictive values are ~4%–31% and ≥97%, respectively. Corresponding values in settings with 3%–30% likelihood of intra-abdominal candidiasis are ~7%–51% and ~78%–98%. β-d-glucan is predicted to be useful in guiding antifungal treatment for wide ranges of populations at-risk for candidemia (incidence ~5%–40% or intra-abdominal candidiasis (~7%–20%. Validated PCR-based assays should broaden windows to include populations at lower-risk for candidemia (incidence ≥~2% and higher-risk for intra-abdominal candidiasis (up to ~40%. In the management of individual patients, non-culture tests may also have value outside of these windows. The proposals we put forth are not definitive treatment guidelines, but rather represent starting points for clinical trial design and debate by the infectious diseases community. The principles presented here will be applicable to other assays as they enter the clinic, and to existing assays as more data become available from different populations.

  7. Ages and stages questionnaires: adaptation to an Arabic speaking population and cultural sensitivity.

    Science.gov (United States)

    Charafeddine, Lama; Sinno, Durriyah; Ammous, Farah; Yassin, Walid; Al-Shaar, Laila; Mikati, Mohamad A

    2013-09-01

    Early detection of developmental delay is essential to initiate early intervention. The Ages and Stages Questionnaires (ASQ) correlate well with physician's assessment and have high predictive value. No such tool exists in Arabic. Translate and test the applicability and reliability of Arabic translated Ages and Stages Questionnaires (A-ASQ) in an Arabic speaking population. 733 healthy children were assessed. ASQ-II for 10 age groups (4-60 months) were translated to Arabic, back translations and cultural adaptation were performed. Test-retest reliability and internal consistency were evaluated using Pearson Correlation Coefficient (CC) and Cronbach's alpha (Cα). Mean scores per domain were compared to US normative scores using t-test. A-ASQ, after culturally relevant adaptations, was easily administered for 4-36 months age groups but not for 4-5 year old due to numerous cultural differences in the later. For the 4-36 month age groups Pearson CC ranged from 0.345 to 0.833. The internal consistency coefficients Cα scores ranged from 0.111 to 0.816. Significant differences were found in the mean domain scores of all age groups between Lebanese and US normative sample (p-value age groups. It proved to be culturally sensitive, which should be taken into consideration when adapting such tool to non-western populations. Copyright © 2013 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.

  8. No Evidence for a Culturable Bacterial Tetrodotoxin Producer in Pleurobranchaea maculata (Gastropoda: Pleurobranchidae) and Stylochoplana sp. (Platyhelminthes: Polycladida)

    OpenAIRE

    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. (Plat...

  9. Hot topic: Bovine milk samples yielding negative or nonspecific results in bacterial culturing--the possible role of PCR-single strand conformation polymorphism in mastitis diagnosis.

    Science.gov (United States)

    Schwaiger, K; Wimmer, M; Huber-Schlenstedt, R; Fehlings, K; Hölzel, C S; Bauer, J

    2012-01-01

    A large proportion of mastitis milk samples yield negative or nonspecific results (i.e., no mastitis pathogen can be identified) in bacterial culturing. Therefore, the culture-independent PCR-single strand conformation polymorphism method was applied to the investigation of bovine mastitis milk samples. In addition to the known mastitis pathogens, the method was suitable for the detection of fastidious bacteria such as Mycoplasma spp., which are often missed by conventional culturing methods. The detection of Helcococcus ovis in 4 samples might indicate an involvement of this species in pathogenesis of bovine mastitis. In conclusion, PCR-single-strand conformation polymorphism is a promising tool for gaining new insights into the bacteriological etiology of mastitis. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  10. Decolorization and degradation of azo dye--Reactive Violet 5R by an acclimatized indigenous bacterial mixed cultures-SB4 isolated from anthropogenic dye contaminated soil.

    Science.gov (United States)

    Jain, Kunal; Shah, Varun; Chapla, Digantkumar; Madamwar, Datta

    2012-04-30

    Azo dyes an important group of synthetic compounds are recalcitrant xenobiotics. Conventional technologies are unsuccessful to efficiently remove these compounds from contaminated environment. However, consorted metabolic functioning of innate microbial communities is a promising approach for bioremediation of polluted environment. Bacterial mixed cultures SB4 proficient in complete decolorization of azo dye - Reactive Violet 5R was developed through culture enrichment technique. Bacterial community composition based on 16S rRNA gene analysis revealed that mixed cultures SB4 composed of six bacterial strains namely Bacillus sp. V1DMK, Lysinibacillus sp. V3DMK, Bacillus sp. V5DMK, Bacillus sp. V7DMK, Ochrobacterium sp. V10DMK, Bacillus sp. V12DMK. SB4 grew well in minimal medium containing low amount of glucose and yeast extract (YE) (1 g/L) and decolorized 200mg/L of RV5 within 18 h under static condition. Mixed cultures SB4 decolorized wide range of azo dyes and maximum rate of decolorization was observed at 37 °C and pH 7.0. Decolorization efficiency was found to be unaltered under high RV5 and salt concentration where 1500 mg/L of RV5 was decolorized in presence of 20 g/L NaCl. We propose the asymmetric cleavage of RV5 and Fourier transformed infrared (FTIR), NMR and gas chromatography-mass spectrometry (GC-MS) confirmed the formation of four intermediatory compounds 1-diazo-2-naphthol, 4-hydroxybenzenesulphonic acid, 2-naphthol and benzenesulphonic acid. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. The bacterial gut microbiota of wood- and humus-feeding termites: Diazotrophic populations and compartment-specific response of bacterial communities to environmental factors

    OpenAIRE

    Wang, Wanyang; Brune, Andreas (Prof. Dr.)

    2018-01-01

    The subject of this thesis is the influence of the microenvironment on the symbiosis between higher termites and their intestinal bacteria. The gut environmental factors pH, hydrogen partial pressure, redox potential and nitrogen pool size were measured. Bacterial gut community structure from each highly compartmentalized gut section was investigated. Furthermore, one specific function, nitrogen fixation, was comparatively analyzed in lower termites, higher termites and cockroaches. Hydrogen...

  12. A comparative study on the effects of tylosin on select bacteria during continuous flow culture of mixed populations of gut microflora derived from a feral and a domestic pig.

    Science.gov (United States)

    Ramlachan, Nicole; Anderson, Robin C; Andrews, Kathleen; Harvey, Roger B; Nisbet, David J

    2008-02-01

    Continuous flow cultures of feral (culture FC) and domesticated (culture RPCF) pig gut microflora were established in steady state. Cultures were continuously infused with 25 or 100 microg tylosin/mL and sampled at intervals to assess effects on total culturable anaerobes, Bacteroides and Enterococcus via plating to agar supplemented without or with 100 microg tylosin/mL, the latter to assess bacterial sensitivity to tylosin. Endogenous tylosin-insensitive anaerobes within the cultures, while similar prior to tylosin administration, responded differently during tylosin administration, with concentrations in RPCF cultures becoming enriched more than in FC cultures. Tylosin-insensitive anaerobes in RPCF cultures persisted at increased concentrations after cessation of tylosin administration whereas concentrations in FC cultures decreased slightly. Concentrations of Bacteroides and endogenous Enterococcus recovered on medium without tylosin decreased to near or below detectable levels in FC cultures administered 25 or 100 microg tylosin/mL. Tylosin-insensitive Bacteroides were enriched to >5 log10 CFU/mL in RPCF cultures after 25 microg tylosin/mL but not at 100 microg tylosin/mL. Populations of endogenous tylosin-insensitive Enterococcus were enriched in RPCF but not FC cultures administered 25 or 100 microg tylosin/mL. In cultures administered 100 microg tylosin/mL, an exogenous-sourced E. faecium possessing tylosin resistance maintained itself only in the presence of tylosin. These results indicate that under the conditions of these tests, antibiotic exposure may enrich for antibiotic-insensitive bacteria populations of endogenous or exogenous origin but that the ability of an exogenous tylosin-resistant E. faecium to persist is reduced in the absence of the antibiotic, likely due to exclusion by native flora.

  13. Cultural interventions to treat addictions in Indigenous populations: findings from a scoping study

    Science.gov (United States)

    2014-01-01

    Background Cultural interventions offer the hope and promise of healing from addictions for Indigenous people.a However, there are few published studies specifically examining the type and impact of these interventions. Positioned within the Honouring Our Strengths: Culture as Intervention project, a scoping study was conducted to describe what is known about the characteristics of culture-based programs and to examine the outcomes collected and effects of these interventions on wellness. Methods This review followed established methods for scoping studies, including a final stage of consultation with stakeholders. The data search and extraction were also guided by the “PICO” (Patient/population, Intervention, Comparison, and Outcome) method, for which we defined each element, but did not require direct comparisons between treatment and control groups. Twelve databases from the scientific literature and 13 databases from the grey literature were searched up to October 26, 2012. Results The search strategy yielded 4,518 articles. Nineteen studies were included from the United States (58%) and Canada (42%), that involved residential programs (58%), and all (100%) integrated Western and culture-based treatment services. Seventeen types of cultural interventions were found, with sweat lodge ceremonies the most commonly (68%) enacted. Study samples ranged from 11 to 2,685 clients. Just over half of studies involved quasi-experimental designs (53%). Most articles (90%) measured physical wellness, with fewer (37%) examining spiritual health. Results show benefits in all areas of wellness, particularly by reducing or eliminating substance use problems in 74% of studies. Conclusions Evidence from this scoping study suggests that the culture-based interventions used in addictions treatment for Indigenous people are beneficial to help improve client functioning in all areas of wellness. There is a need for well-designed studies to address the question of best relational

  14. Xylo-Oligosaccharides and Inulin Affect Genotoxicity and Bacterial Populations Differently in a Human Colonic Simulator Challenged with Soy Protein

    Directory of Open Access Journals (Sweden)

    Michael A. Conlon

    2013-09-01

    Full Text Available High dietary intakes of some protein sources, including soy protein, can increase colonic DNA damage in animals, whereas some carbohydrates attenuate this. We investigated whether inulin and xylo-oligosaccharides (XOS could be protective against DNA strand breaks by adding them to a human colonic simulator consisting of a proximal vessel (PV (pH 5.5 and a distal vessel (DV (pH 6.8 inoculated with human faeces and media containing soy protein. Genotoxicity of the liquid phase and microbial population changes in the vessels were measured. Soy protein (3% was fermented with 1% low amylose cornstarch for 10 day followed by soy protein with 1% XOS or 1% inulin for 10 day. Inulin did not alter genotoxicity but XOS significantly reduced PV genotoxicity and increased DV genotoxicity. Inulin and XOS significantly increased butyrate concentration in the DV but not PV. Numbers of the key butyrate-producing bacterium Faecalibacterium prausnitzii were significantly increased in the PV and DV by inulin but significantly decreased by XOS in both vessels. Other bacteria examined were also significantly impacted by the carbohydrate treatments or by the vessel (i.e., pH. There was a significant overall inverse correlation between levels of damage induced by the ferments and levels of sulphate-reducing bacteria, Bacteroides fragilis, and acetate. In conclusion, dietary XOS can potentially modulate the genotoxicity of the colonic environment and specific bacterial groups and short chain fatty acids may mediate this.

  15. Xylo-Oligosaccharides and Inulin Affect Genotoxicity and Bacterial Populations Differently in a Human Colonic Simulator Challenged with Soy Protein

    Science.gov (United States)

    Christophersen, Claus T.; Petersen, Anne; Licht, Tine R.; Conlon, Michael A.

    2013-01-01

    High dietary intakes of some protein sources, including soy protein, can increase colonic DNA damage in animals, whereas some carbohydrates attenuate this. We investigated whether inulin and xylo-oligosaccharides (XOS) could be protective against DNA strand breaks by adding them to a human colonic simulator consisting of a proximal vessel (PV) (pH 5.5) and a distal vessel (DV) (pH 6.8) inoculated with human faeces and media containing soy protein. Genotoxicity of the liquid phase and microbial population changes in the vessels were measured. Soy protein (3%) was fermented with 1% low amylose cornstarch for 10 day followed by soy protein with 1% XOS or 1% inulin for 10 day. Inulin did not alter genotoxicity but XOS significantly reduced PV genotoxicity and increased DV genotoxicity. Inulin and XOS significantly increased butyrate concentration in the DV but not PV. Numbers of the key butyrate-producing bacterium Faecalibacterium prausnitzii were significantly increased in the PV and DV by inulin but significantly decreased by XOS in both vessels. Other bacteria examined were also significantly impacted by the carbohydrate treatments or by the vessel (i.e., pH). There was a significant overall inverse correlation between levels of damage induced by the ferments and levels of sulphate-reducing bacteria, Bacteroides fragilis, and acetate. In conclusion, dietary XOS can potentially modulate the genotoxicity of the colonic environment and specific bacterial groups and short chain fatty acids may mediate this. PMID:24064573

  16. A screening method for cytochrome P-450 organic peroxidase activity and application to hydrocarbon-degrading bacterial populations

    Energy Technology Data Exchange (ETDEWEB)

    Wyndham, R.C. (Univ. of Toronto, ON (Canada))

    1987-01-01

    A method to detect the expression of hemoproteins with organic hydroperoxide reducing activity was developed to screen bacterial populations isolated from heavy oils and oil sands. The method is based on the activity of cytochrome P-450 as catalyst in the reduction of cumene hydroperoxide by artificial electron donors. There was no cross-reactivity with true catalyst in the reduction of cumene hydroperoxide by artificial electron donors. There was no cross-reactivity with true peroxidases involved in the reduction of hydrogen peroxide. Cross-reactivity with catalase could be eliminated with appropriate inhibitors but did not normally interfere with the detection method. A preliminary screen resulted in the isolation of Acinetobactor calcoaceticus and a range of Gram-positive bacteria with organic peroxidase activity. Carbon monoxide difference spectra of cell-free extracts of the isolates revealed the presence of a hydrocarbon-inducible cytochrome P-450 in Acinetobacter calcoaceticus and in coryneform and actinomycete bacteria. A CO-binding cytochrome of unknown type with a Soret absorption maximum at 424 nm and cumene hydroperoxidase activity was also detected in some strains. 34 refs., 1 fig., 3 tabs.

  17. Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations.

    Science.gov (United States)

    Marchi, Nina; Hegay, Tatyana; Mennecier, Philippe; Georges, Myriam; Laurent, Romain; Whitten, Mark; Endicott, Philipp; Aldashev, Almaz; Dorzhu, Choduraa; Nasyrova, Firuza; Chichlo, Boris; Ségurel, Laure; Heyer, Evelyne

    2017-04-01

    Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups. We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups. Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis. This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure. © 2017 Wiley Periodicals, Inc.

  18. Genetics, geography, and culture: the population of S. Pietro Island (Sardinia, Italy).

    Science.gov (United States)

    Vona, G; Calò, C M; Lucia, G; Mameli, G E; Succa, V; Esteban, E; Moral, P

    1996-08-01

    An interesting aspect of the island of Sardinia (Italy) is the wide range of genetic variability within the island itself. The variability is widened by the presence of some populations of different ethnic origin who speak a language other than Sardinian. This work deals with the study of the genetic structure of the Carloforte population which inhabits the tiny island of S. Pietro 4 km off the southwest coast of Sardinia. S. Pietro was first populated in 1738 by emigrants coming from the island of Tabarka (Tunisia) who spoke an archaic form of the Ligurian dialect. Data on genetic polymorphisms in the Carloforte population are presented and discussed in relation to some Sardinian and Italian populations. Data on demographic and matrimonial structure are also presented. The genetic analyses show the Carloforte population as being clearly separated from both Sardinians and continental Italians. The isolation of Carloforte, highlighted by language diversity, endogamy, and consanguinity levels and marriage area, supports the idea of genetic diversity linked to cultural peculiarity.

  19. A comparison of bacterial populations in enhanced biological phosphorus removal processes using membrane filtration or gravity sedimentation for solids-liquid separation.

    Science.gov (United States)

    Hall, Eric R; Monti, Alessandro; Mohn, William W

    2010-05-01

    In an earlier phase of this study, we compared the performances of pilot scale treatment systems operated in either a conventional enhanced biological phosphorus removal (CEBPR) mode, or a membrane enhanced biological phosphorus removal (MEBPR) mode. In the present investigation, we characterized the bacterial community populations in these processes during parallel operation with the same municipal wastewater feed. The objectives of the study were (1) to assess the similarity of the bacterial communities supported in the two systems over time, (2) to determine if distinct bacterial populations are associated with the MEBPR and CEBPR processes, and (3) to relate the dynamics of the community composition to changes in treatment process configuration and to treatment process performance. The characteristics of the bacterial populations were first investigated with ribosomal intergenic spacer analysis, or RISA. To further understand the bacterial population dynamics, important RISA phylotypes were isolated and identified through 16S RNA gene sequencing. The parallel MEBPR and CEBPR systems developed bacterial communities that were distinct. The CEBPR community appeared to exhibit greater diversity, and this may have been the primary reason why the CEBPR treatment train demonstrated superior functional stability relative to the MEBPR counterpart. Moreover, the more diverse bacterial population apparent in the CEBPR system was observed to be more dynamic than that of the MEBPR process. Several RISA bands were found to be characteristic of either the membrane or conventional biological system. In particular, the MEBPR configuration appeared to be selective for the slow-growing organism Magnospira bakii and for the foam-associated Microthrix parvicella and Gordonia sp., while gravity separation led to the washout of M. parvicella. In both pilot trains, sequence analysis confirmed the presence of EBPR-related organisms such as Accumulibacter phosphatis. The survey of the

  20. Cross-cultural adaptation of the Social and Emotional Questionnaire on Dementia for the Brazilian population.

    Science.gov (United States)

    Belfort, Tatiana; Bramham, Jessica; Simões Neto, José Pedro; Sousa, Maria Fernanda Barroso de; Santos, Raquel Luiza dos; Nogueira, Marcela Moreira Lima; Torres, Bianca; Rosa, Rachel Dias Lopes da; Dourado, Marcia Cristina Nascimento

    2015-01-01

    Impairments in social and emotional functioning may affect the communication skills and interpersonal relationships of people with dementia and their caregivers. This study had the aim of presenting the steps involved in the cross-cultural adaptation of the Social and Emotional Questionnaire (SEQ) for the Brazilian population. Cross-cultural adaptation study, conducted at the Center for Alzheimer's Disease and Related Disorders in a public university. The process adopted in this study required six consecutive steps: initial translation, translation synthesis, back translation, committee of judges, pretesting of final version and submission to the original author. In general, the items had semantic, idiomatic, conceptual and experiential equivalence. During the first pretest, people with dementia and their caregivers had difficulties in understanding some items relating to social skills, which were interpreted ambiguously. New changes were made to allow better adjustment to the target population and, following this, a new pretest was performed. This pre-test showed that the changes were relevant and gave rise to the final version of the instrument. There was no correlation between education level and performance in the questionnaire, among people with dementia (P = 0.951). The Brazilian Portuguese version of the Social and Emotional Questionnaire was well understood and, despite the cultural and linguistic differences, the constructs of the original version were maintained.

  1. An imbalance in progenitor cell populations reflects tumour progression in breast cancer primary culture models

    LENUS (Irish Health Repository)

    Donatello, Simona

    2011-04-26

    Abstract Background Many factors influence breast cancer progression, including the ability of progenitor cells to sustain or increase net tumour cell numbers. Our aim was to define whether alterations in putative progenitor populations could predict clinicopathological factors of prognostic importance for cancer progression. Methods Primary cultures were established from human breast tumour and adjacent non-tumour tissue. Putative progenitor cell populations were isolated based on co-expression or concomitant absence of the epithelial and myoepithelial markers EPCAM and CALLA respectively. Results Significant reductions in cellular senescence were observed in tumour versus non-tumour cultures, accompanied by a stepwise increase in proliferation:senescence ratios. A novel correlation between tumour aggressiveness and an imbalance of putative progenitor subpopulations was also observed. Specifically, an increased double-negative (DN) to double-positive (DP) ratio distinguished aggressive tumours of high grade, estrogen receptor-negativity or HER2-positivity. The DN:DP ratio was also higher in malignant MDA-MB-231 cells relative to non-tumourogenic MCF-10A cells. Ultrastructural analysis of the DN subpopulation in an invasive tumour culture revealed enrichment in lipofuscin bodies, markers of ageing or senescent cells. Conclusions Our results suggest that an imbalance in tumour progenitor subpopulations imbalances the functional relationship between proliferation and senescence, creating a microenvironment favouring tumour progression.

  2. Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and and pyrosequencing for the characterisation of the caries-associated microbiome

    Directory of Open Access Journals (Sweden)

    Kathrin eSchulze-Schweifing

    2014-11-01

    Full Text Available Culture-independent analyses have greatly expanded knowledge regarding the composition of complex bacterial communities including those associated with oral diseases. A consistent finding from such studies, however, has been the under-reporting of members of the phylum Actinobacteria. In this study, five pairs of broad range primers targeting 16S rRNA genes were used in clonal analysis of 6 samples collected from tooth lesions involving dentine in subjects with active caries. Samples were also subjected to cultural analysis and pyrosequencing by means of the 454 platform. A diverse bacterial community of 229 species-level taxa was revealed by culture and clonal analysis, dominated by representatives of the genera Prevotella, Lactobacillus, Selenomonas and Streptococcus. The five most abundant species were: Lactobacillus gasseri, Prevotella denticola, Alloprevotella tannerae, S. mutans and Streptococcus sp. HOT 070, which together made up 31.6 % of the sequences. Two samples were dominated by lactobacilli, while the remaining samples had low numbers of lactobacilli but significantly higher numbers of Prevotella species. The different primer pairs produced broadly similar data but proportions of the phylum Bacteroidetes were significantly higher when primer 1387R was used. All of the primer sets underestimated the proportion of Actinobacteria compared to culture. Pyrosequencing analysis of the samples was performed to a depth of sequencing of 4293 sequences per sample which were identified to 264 species-level taxa, and resulted in significantly higher coverage estimates than the clonal analysis. Pyrosequencing, however, also underestimated the relative abundance of Actinobacteria compared to culture.

  3. A Place to Call Home: An Analysis of the Bacterial Communities in Two Tethya rubra Samaai and Gibbons 2005 Populations in Algoa Bay, South Africa.

    Science.gov (United States)

    Waterworth, Samantha C; Jiwaji, Meesbah; Kalinski, Jarmo-Charles J; Parker-Nance, Shirley; Dorrington, Rosemary A

    2017-03-25

    Sponges are important sources of bioactive secondary metabolites. These compounds are frequently synthesized by bacterial symbionts, which may be recruited from the surrounding seawater or transferred to the sponge progeny by the parent. In this study, we investigated the bacterial communities associated with the sponge Tethya rubra Samaai and Gibbons 2005. Sponge specimens were collected from Evans Peak and RIY Banks reefs in Algoa Bay, South Africa and taxonomically identified by spicule analysis and molecular barcoding. Crude chemical extracts generated from individual sponges were profiled by ultraviolet high performance liquid chromatography (UV-HPLC) and subjected to bioactivity assays in mammalian cells. Next-generation sequencing analysis of 16S rRNA gene sequences was used to characterize sponge-associated bacterial communities. T. rubra sponges collected from the two locations were morphologically and genetically indistinguishable. C hemical extracts from sponges collected at RIY banks showed mild inhibition of the metabolic activity of mammalian cells and their UV-HPLC profiles were distinct from those of sponges collected at Evans Peak. Similarly, the bacterial communities associated with sponges from the two locations were distinct with evidence of vertical transmission of symbionts from the sponge parent to its embryos. We conclude that these distinct bacterial communities may be responsible for the differences observed in the chemical profiles of the two Algoa Bay T. rubra Samaai and Gibbons 2005 populations.

  4. Distribution, antibiotic susceptibility and tolerance of bacterial isolates in culture-positive cases of endocarditis in The Netherlands

    NARCIS (Netherlands)

    van der Meer, J. T.; van Vianen, W.; Hu, E.; van Leeuwen, W. B.; Valkenburg, H. A.; Thompson, J.; Michel, M. F.

    1991-01-01

    During a two-year period data were collected nationwide in The Netherlands on 438 episodes of bacterial endocarditis (BE) in 432 patients. Of the strains isolated in these patients 419 were available for analysis. Of these, 326 were isolated in native valve endocarditis (NVE) and 93 in prosthetic

  5. Simultaneous determination of gene expression and bacterial identity in single cells in defined mixtures of pure cultures

    DEFF Research Database (Denmark)

    Poulsen, Lars K.; Dalton, Helen M.; Angels, Mark

    1997-01-01

    A protocol was developed to achieve the simultaneous determination of gene expression and bacterial identity at the level of single cells: a chromogenic beta-galactosidase activity assay was combined with in situ hybridization of Fluorescently labelled oligonucleotide probes to rRNA. The method...... allows monitoring of gene expression and quantification of beta-galactosidase activity in single cells....

  6. Process for inhibiting the growth of a culture of lactic acid bacteria, and optionally lysing the bacterial cells, and uses of the resulting lysed culture

    NARCIS (Netherlands)

    Nauta, Arjen; Venema, Gerard; Kok, Jan; Ledeboer, Aat M.

    1995-01-01

    The invention provides a process for inhibiting the growth of a culture of lactic acid bacteria, or a product containing such culture e.g. a cheese product, in which in the cells of the lactic acid bacteria a holin obtainable from bacteriophages of Gram-positive bacteria, esp. from bacteriophages of

  7. Effect of partially replacing a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows.

    Science.gov (United States)

    Castillo-Lopez, E; Moats, J; Aluthge, N D; Ramirez Ramirez, H A; Christensen, D A; Mutsvangwa, T; Penner, G B; Fernando, S C

    2018-01-01

    The effects of partial replacement of a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows were evaluated. Treatments fed were CONT, a normal diet that included barley silage, alfalfa hay and a barley-based concentrate that contained no flaxseed or faba beans; FLAX, inclusion of a nonextruded flaxseed-based product containing 55·0% flaxseed, 37·8% field peas and 6·9% alfalfa; EXT, similar to FLAX, but the product was extruded and EXTT, similar to FLAX, but product was extruded and field peas were replaced by high-tannin faba beans. The rumen bacterial population was evaluated by utilizing 16S rRNA gene sequencing. Most abundant phyla, families and genera were unaffected. However, some taxa were affected; for example, unsaturated fatty acid content was negatively correlated with Clostridiaceae, and tannin content was negatively correlated with BS11 and Paraprevotellaceae. Predominant rumen bacterial taxa were not affected, but the abundance of some taxa found in lower proportions shifted, possibly due to sensitivity to unsaturated fatty acids or tannins. Flaxseed-based products were effective for partially replacing barley-based concentrate in rations of lactating dairy cows. No negative effects of these products were observed on the abundance of predominant rumen bacterial taxa, with only minor shifts in less abundant bacteria. © 2017 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

  8. Features for culturally appropriate avatars for behavior-change promotion in at-risk populations

    Directory of Open Access Journals (Sweden)

    Lisetti C

    2009-09-01

    Full Text Available We explore how avatars can be used as social orthotics defined as therapeutic computer-based social companions aimed at promoting healthy behaviors. We review some of the health interventions deployed in helping at-risk populations along with some of the unique advantages that computer-based interventions can add to face-to-face interventions. We posit that artificial intelligence has rendered possible the creation of culturally appropriate dialog-agents for interventions and we identify specific features for social avatars that are important - if not necessary - when applied to the domain of social orthotic systems for health promotion.

  9. Persistence of Only a Minute Viable Population in Chlorotic Microcystis aeruginosa PCC 7806 Cultures Obtained by Nutrient Limitation.

    Science.gov (United States)

    Meireles, Diogo de Abreu; Schripsema, Jan; Arnholdt, Andrea Cristina Vetö; Dagnino, Denise

    2015-01-01

    Cultures from the cyanobacterial strain Microcystis aeruginosa PCC 7806 submitted to nutrient limitation become chlorotic. When returned to nutrient rich conditions these cultures regain their green colour. The aim of this study was to verify whether the cells in these cultures could be considered resting stages allowing the survival of periods of nutrient starvation as has been reported for Synechococcus PCC 7942. The experiments with Microcystis were carried out in parallel with Synechococcus cultures to rule out the possibility that any results obtained with Microcystis were due to our particular experimental conditions. The results of the experiments with Synechococcus PCC 7942 cultures were comparable to the reported in the literature. For Microcystis PCC 7806 a different response was observed. Analysis of chlorotic Microcystis cultures by flow cytometry showed that the phenotype of the cells in the population was not homogenous: the amount of nucleic acids was about the same in all cells but only around one percent of the population emitted red autofluorescence indicating the presence of chlorophyll. Monitoring of the reversion of chlorosis by flow cytometry showed that the re-greening was most likely the result of the division of the small population of red autofluorescent cells originally present in the chlorotic cultures. This assumption was confirmed by analysing the integrity of the DNA and the membrane permeability of the cells of chlorotic cultures. Most of the DNA of these cultures was degraded and only the autofluorescent population of the chlorotic cultures showed membrane integrity. Thus, contrary to what has been reported for other cyanobacterial genera, most of the cells in chlorotic Microcystis cultures are not resting stages but dead. It is interesting to note that the red autofluorescent cells of green and chlorotic cultures obtained in double strength ASM-1 medium differ with respect to metabolism: levels of emission of red autofluorescence

  10. THE REACTIONS BETWEEN BACTERIA AND ANIMAL TISSUES UNDER CONDITIONS OF ARTIFICIAL CULTIVATION : III. THE ACTION OF BACTERIAL VACCINES ON TISSUE CULTURES IN VITRO.

    Science.gov (United States)

    Smyth, H F

    1916-03-01

    These results seem to indicate that many bacteria may be utilized by tissue cells as food for growth or may contain a substance or substances stimulating cell growth or multiplication. This substance is stable and is not destroyed by heating to 100 degrees C. or by long standing. With Micrococcus aureus this action is often neutralized or overcome by a substance inhibitory to growth. The nature of these substances has not yet been determined, though several attempts along this line were made by endeavoring to split the typhoid bacterial substance according to the method of Vaughan See PDF for Structure and testing the poisonous and non-poisonous residues separately. However, at the time too little bacterial substance was used to obtain enough end-products to be of much use, and the products so obtained prevented the plasma from coagulating. Even in the uncoagulated plasma there appeared to be an increase of cells in the cultures with the non-poisonous residue. The author hopes to be able to repeat these tests with split products at a later time when more bacterial substance is available, with the hope of obtaining more definite results.

  11. Suggested guidelines for using systemic antimicrobials in bacterial skin infections: part 1—diagnosis based on clinical presentation, cytology and culture

    Science.gov (United States)

    Beco, L.; Guaguère, E.; Méndez, C. Lorente; Noli, C.; Nuttall, T.; Vroom, M.

    2013-01-01

    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. Part 2 will discuss therapy, including choice of drug and treatment regimens. PMID:23292951

  12. Bacterial community structure associated with white band disease in the elkhorn coral Acropora palmata determined using culture-independent 16S rRNA techniques.

    Science.gov (United States)

    Pantos, Olga; Bythell, John C

    2006-03-23

    Culture-independent molecular (16S ribosomal RNA) techniques showed distinct differences in bacterial communities associated with white band disease (WBD) Type I and healthy elkhorn coral Acropora palmata. Differences were apparent at all levels, with a greater diversity present in tissues of diseased colonies. The bacterial community associated with remote, non-diseased coral was distinct from the apparently healthy tissues of infected corals several cm from the disease lesion. This demonstrates a whole-organism effect from what appears to be a localised disease lesion, an effect that has also been recently demonstrated in white plague-like disease in star coral Montastraea annularis. The pattern of bacterial community structure changes was similar to that recently demonstrated for white plague-like disease and black band disease. Some of the changes are likely to be explained by the colonisation of dead and degrading tissues by a micro-heterotroph community adapted to the decomposition of coral tissues. However, specific ribosomal types that are absent from healthy tissues appear consistently in all samples of each of the diseases. These ribotypes are closely related members of a group of alpha-proteobacteria that cause disease, notably juvenile oyster disease, in other marine organisms. It is clearly important that members of this group are isolated for challenge experiments to determine their role in the diseases.

  13. Effect of feeding tannin degrading bacterial culture (Streptococcus gallolyticus strain TDGB 406) on nutrient utilization, urinary purine derivatives and growth performance of goats fed on Quercus semicarpifolia leaves.

    Science.gov (United States)

    Kumar, K; Chaudhary, L C; Agarwal, N; Kamra, D N

    2014-10-01

    To study the effect of supplementation of tannin degrading bacterial culture (Streptococcus gallolyticus strain TDGB 406) on growth performance, nutrient utilization and urinary purine derivatives of goats fed on oak (Quercus semicarpifolia) leaves. For growth study, eighteen billy goats (4 month old, average body weight 9.50 ± 1.50 kg) were distributed into three groups of six animals each. The animals of group 1 served as control while animals of groups 2 (T1) and 3 (T2) were given (@ 5 ml/kg live weight) autoclaved and live culture of isolate TDGB 406 (10(6) cells/ml) respectively. The animals were fed measured quantity of dry oak leaves as the main roughage source and ad libitum maize hay along with fixed quantity of concentrate mixture. The feeding of live culture of isolate TDGB 406 (probiotic) did not affect dry matter intake and digestibility of nutrients except that of dry matter and crude protein, which was higher in T2 group as compared to control. All the animals were in positive nitrogen balance. There was no significant effect of feeding isolate TDGB 406 on urinary purine derivatives (microbial protein production) in goats. The body weight gain and average live weight gain was significantly higher (p = 0.071) in T2 group as compared to control. Feed conversion efficiency was also better in the goats fed on live culture of TDGB 406 (T2). The feeding of tannin degrading bacterial isolate TDGB 406 as probiotic resulted in improved growth performance and feed conversion ratio in goats fed on oak leaves as one of the main roughage source. Journal of Animal Physiology and Animal Nutrition © 2013 Blackwell Verlag GmbH.

  14. Using in situ dynamic cultures to rapidly biofabricate fabric-reinforced composites of chitosan/bacterial nanocellulose for antibacterial wound dressings

    Directory of Open Access Journals (Sweden)

    Peng eZhang

    2016-03-01

    Full Text Available Bacterial nano-cellulose (BNC is considered to possess incredible potential in biomedical applications due to its innate unrivalled nano-fibrillar structure and versatile properties. However its use is largely restricted by inefficient production and by insufficient strength when it is in a highly swollen state. In this study, a fabric skeleton reinforced chitosan (CS/BNC hydrogel with high mechanical reliability and antibacterial activity was fabricated by using an efficient dynamic culture that could reserve the nano-fibrillar structure. By adding CS in culture media to 0.25-0.75% (w/v during bacterial cultivation, the CS/BNC composite hydrogel was biosynthesized in situ on a rotating drum composed of fabrics. With the proposed method, BNC biosynthesis became less sensitive to the adverse antibacterial effects of CS and the production time of the composite hydrogel with desirable thickness could be halved from 10 days to 5 days as compared to the conventional static cultures. Although its concentration was low in the medium, CS accounted for more than 38% of the CS/BNC dry weight. FE-SEM observation confirmed conservation of the nano-fibrillar networks and covering of CS on BNC. ATR-FTIR showed a decrease in the degree of intra-molecular hydrogen bonding and water absorption capacity was improved after compositing with CS. The fabric-reinforced CS/BNC composite exhibited bacteriostatic properties against Escherichia coli and Staphylococcus aureus and significantly improved mechanical properties as compared to the BNC sheets from static culture. In summary, the fabric-reinforced CS/BNC composite constitutes a desired candidate for advanced wound dressings. From another perspective, coating of BNC or CS/BNC could upgrade the conventional wound dressings made of cotton gauze to reduce pain during wound healing, especially for burn patients.

  15. Location-Related Differences in Weathering Behaviors and Populations of Culturable Rock-Weathering Bacteria Along a Hillside of a Rock Mountain.

    Science.gov (United States)

    Wang, Qi; Wang, Rongrong; He, Linyan; Sheng, Xiafang

    2017-05-01

    Bacteria play important roles in rock weathering, elemental cycling, and soil formation. However, little is known about the weathering potential and population of bacteria inhabiting surfaces of rocks. In this study, we isolated bacteria from the top, middle, and bottom rock samples along a hillside of a rock (trachyte) mountain as well as adjacent soils and characterized rock-weathering behaviors and populations of the bacteria. Per gram of rock or surface soil, 10 6 -10 7 colony forming units were obtained and total 192 bacteria were isolated. Laboratory rock dissolution experiments indicated that the proportions of the highly effective Fe (ranging from 67 to 92 %), Al (ranging from 40 to 48 %), and Cu (ranging from 54 to 81 %) solubilizers were significantly higher in the top rock and soil samples, while the proportion of the highly effective Si (56 %) solubilizers was significantly higher in the middle rock samples. Furthermore, 78, 96, and 6 % of bacteria from the top rocks, soils, and middle rocks, respectively, significantly acidified the culture medium (pH bacteria (79 %) from the rocks were different to those from the soils and most of them (species level) have not been previously reported. Furthermore, location-specific rock-weathering bacterial populations were found and Bacillus species were the most (66 %) frequently isolated rock-weathering bacteria in the rocks based on cultivation methods. Notably, the top rocks and soils had the highest and lowest diversity of rock-weathering bacterial populations, respectively. The results suggested location-related differences in element (Si, Al, Fe, and Cu) releasing effectiveness and communities of rock-weathering bacteria along the hillside of the rock mountain.

  16. Diversity in european school populations: a study in Portugal and Greece with particular attention to romany cultures

    OpenAIRE

    Stathopoulou, Charoula; Moreira, Darlinda

    2013-01-01

    The growing cultural diversity of school populations poses new challenges to schools and also to schooling equity. Schools (as well as minority and dominant group leaders) should avoid cultural closure and instead should involve recognition of different ways of knowing, in order to share cultural elements and to enable constructive interactions; these practices promote education for peace, respect for diversity and social justice. In this paper, we explore the contributions of Ethnomathematic...

  17. Simple and versatile turbidimetric monitoring of bacterial growth in liquid cultures using a customized 3D printed culture tube holder and a miniaturized spectrophotometer: application to facultative and strictly anaerobic bacteria

    Directory of Open Access Journals (Sweden)

    Margarida R. G. Maia

    2016-08-01

    Full Text Available Here we introduce a novel strategy for turbidimetric monitoring of bacterial growth in liquid culture. The instrumentation comprises a light source, a customized 3D printed culture tube holder and a miniaturized spectrophotometer, connected through optical cables. Due to its small footprint and the possibility to operate with external light, bacterial growth was directly monitored from culture tubes in a simple and versatile fashion. This new portable measurement technique was used to monitor the growth of facultative (Escherichia coli ATCC/25922, and Staphylococcus aureus ATCC/29213 and strictly (Butyrivibrio fibrisolvens JW11, Butyrivibrio proteoclasticus P18, and Propionibacterium acnes DSMZ 1897 anaerobic bacteria. For E. coli and S. aureus, the growth rates calculated from normalized optical density values were compared with those ones obtained using a benchtop spectrophotometer without significant differences (P = 0.256. For the strictly anaerobic species, a high precision (RSD < 3.5% was observed between replicates up to 48 h. Regarding its potential for customization, this manifold could accommodate further developments for customized turbidimetric monitoring, such as the use of light-emitting diodes as a light source or flow cells.

  18. Simple and Versatile Turbidimetric Monitoring of Bacterial Growth in Liquid Cultures Using a Customized 3D Printed Culture Tube Holder and a Miniaturized Spectrophotometer: Application to Facultative and Strictly Anaerobic Bacteria.

    Science.gov (United States)

    Maia, Margarida R G; Marques, Sara; Cabrita, Ana R J; Wallace, R John; Thompson, Gertrude; Fonseca, António J M; Oliveira, Hugo M

    2016-01-01

    Here we introduce a novel strategy for turbidimetric monitoring of bacterial growth in liquid culture. The instrumentation comprises a light source, a customized 3D printed culture tube holder and a miniaturized spectrophotometer, connected through optical cables. Due to its small footprint and the possibility to operate with external light, bacterial growth was directly monitored from culture tubes in a simple and versatile fashion. This new portable measurement technique was used to monitor the growth of facultative (Escherichia coli ATCC/25922, and Staphylococcus aureus ATCC/29213) and strictly (Butyrivibrio fibrisolvens JW11, Butyrivibrio proteoclasticus P18, and Propionibacterium acnes DSMZ 1897) anaerobic bacteria. For E. coli and S. aureus, the growth rates calculated from normalized optical density values were compared with those ones obtained using a benchtop spectrophotometer without significant differences (P = 0.256). For the strictly anaerobic species, a high precision (relative standard deviation < 3.5%) was observed between replicates up to 48 h. Regarding its potential for customization, this manifold could accommodate further developments for customized turbidimetric monitoring, such as the use of light-emitting diodes as a light source or flow cells.

  19. Formation of financial culture of Ukraine's population in the context of the minimization of the market asymmetry

    OpenAIRE

    V. Kornivska

    2011-01-01

    This paper presents the features of the institutionalization of the Ukrainian financial market in the context of high levels of market asymmetry due to the insufficient level of general financial culture. The author characterizes the global experience of improving the financial culture of population, and justifies the ways to overcome the market asymmetry of socio-institutional space of the Ukrainian financial market.

  20. Teaching Cultural Competence in Dental Education: A Systematic Review and Exploration of Implications for Indigenous Populations in Australia.

    Science.gov (United States)

    Forsyth, Cathryn J; Irving, Michelle J; Tennant, Marc; Short, Stephanie D; Gilroy, John A

    2017-08-01

    Indigenous and other minority populations worldwide experience higher rates of disease including poor oral health than other populations. Cultural competence of practitioners is increasingly being recognized as fundamental to health care and quality of life in addressing these disparities. The aims of this study were to conduct a systematic review of the literature about teaching cultural competence in dental education and to explore the particular relevance of that teaching for the oral health care of Indigenous populations in Australia. A systematic review employing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement was conducted of published studies that explored cultural competency interventions in dental curricula. A total of 258 studies from 2004 to 2015 were identified; after removing duplications and applying criteria for exclusion, 12 were selected for analysis, involving 1,360 participants. The principal themes identified in the qualitative analysis of these studies were curriculum content, curriculum delivery, community service-learning, reflective writing, and evaluation. Students need knowledge of health disparities and community health to better understand the perspectives of culturally diverse populations and to communicate effectively with people from various cultures. The principal strategies that improved cultural competence in the articles examined in this study were educational seminars, community service-learning, and reflective writing. These findings suggest that integration of cultural competency curricula using a combination of didactic or online training, community engagement, and reflective writing may increase the cultural knowledge and skills of dental students.

  1. Soybean cyst nematode culture collections and field populations from North Carolina and Missouri reveal high incidences of infection by viruses.

    Science.gov (United States)

    Ruark, Casey L; Koenning, Stephen R; Davis, Eric L; Opperman, Charles H; Lommel, Steven A; Mitchum, Melissa G; Sit, Tim L

    2017-01-01

    Five viruses were previously discovered infecting soybean cyst nematodes (SCN; Heterodera glycines) from greenhouse cultures maintained in Illinois. In this study, the five viruses [ScNV, ScPV, ScRV, ScTV, and SbCNV-5] were detected within SCN greenhouse and field populations from North Carolina (NC) and Missouri (MO). The prevalence and titers of viruses in SCN from 43 greenhouse cultures and 25 field populations were analyzed using qRT-PCR. Viral titers within SCN greenhouse cultures were similar throughout juvenile development, and the presence of viral anti-genomic RNAs within egg, second-stage juvenile (J2), and pooled J3 and J4 stages suggests active viral replication within the nematode. Viruses were found at similar or lower levels within field populations of SCN compared with greenhouse cultures of North Carolina populations. Five greenhouse cultures harbored all five known viruses whereas in most populations a mixture of fewer viruses was detected. In contrast, three greenhouse cultures of similar descent to one another did not possess any detectable viruses and primarily differed in location of the cultures (NC versus MO). Several of these SCN viruses were also detected in Heterodera trifolii (clover cyst) and Heterodera schachtii (beet cyst), but not the other cyst, root-knot, or reniform nematode species tested. Viruses were not detected within soybean host plant tissue. If nematode infection with viruses is truly more common than first considered, the potential influence on nematode biology, pathogenicity, ecology, and control warrants continued investigation.

  2. Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers.

    Science.gov (United States)

    Trujillo, César A; Arias-Rojas, Nathalia; Poulin, Lucie; Medina, César A; Tapiero, Anibal; Restrepo, Silvia; Koebnik, Ralf; Bernal, Adriana J

    2014-06-19

    Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time. Aiming to examine the current state of pathogen populations located in the Colombian Eastern Plains, we also used AFLP markers and we evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new molecular markers for the study of Xam populations. The population analyses showed that AFLP and VNTR provide a detailed and congruent description of Xam populations from the Colombian Eastern Plains. These two typing strategies clearly separated strains from the Colombian Eastern Plains into distinct populations probably because of geographical distance. Although the majority of analyses were congruent between typing markers, fewer VNTRs were needed to detect a higher number of genetic populations of the pathogen as well as a higher genetic flow among sampled locations than those detected by AFLPs. This study shows the advantages of VNTRs over AFLPs in the surveillance of pathogen populations and suggests the implementation of VNTRs in studies that involve large numbers of Xam isolates in order to obtain a more detailed overview of the pathogen to improve the strategies for disease control.

  3. Point-Counterpoint: A Nucleic Acid Amplification Test for Streptococcus pyogenes Should Replace Antigen Detection and Culture for Detection of Bacterial Pharyngitis.

    Science.gov (United States)

    Pritt, Bobbi S; Patel, Robin; Kirn, Thomas J; Thomson, Richard B

    2016-10-01

    Nucleic acid amplification tests (NAATs) have frequently been the standard diagnostic approach when specific infectious agents are sought in a clinic specimen. They can be applied for specific agents such as S. pyogenes, or commercial multiplex NAATs for detection of a variety of pathogens in gastrointestinal, bloodstream, and respiratory infections may be used. NAATs are both rapid and sensitive. For many years, S. pyogenes testing algorithms used a rapid and specific group A streptococcal antigen test to screen throat specimens, followed, in some clinical settings, by a throat culture for S. pyogenes to increase the sensitivity of its detection. Now S. pyogenes NAATs are being used with increasing frequency. Given their accuracy, rapidity, and ease of use, should they replace antigen detection and culture for the detection of bacterial pharyngitis? Bobbi Pritt and Robin Patel of the Mayo Clinic, where S. pyogenes NAATs have been used for well over a decade with great success, will explain the advantages of this approach, while Richard (Tom) Thomson and Tom Kirn of the NorthShore University HealthSystem will discuss their concerns about this approach to diagnosing bacterial pharyngitis. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  4. Culturally Competent Strategies for Recruitment and Retention of African American Populations into Clinical Trials.

    Science.gov (United States)

    Otado, Jane; Kwagyan, John; Edwards, Diana; Ukaegbu, Alice; Rockcliffe, Faun; Osafo, Nana

    2015-10-01

    To identify successful recruitment strategies, challenges and best practices for researchers to engage African American communities in clinical studies taken into consideration target participants' culture and context. We reviewed 50 studies conducted from 2001 to 2012 at an inner-city research center to determine the type, duration, anticipated enrollments and actual enrollments. Survey was sent to study coordinators to obtain data on recruitment and retention strategies, challenges and dropout rates. We also interviewed 25 study coordinators on challenges and strategies. Of the 50 studies, 24 had completed recruitment at the time of this report. The completed studies achieved a median recruitment rate of 88% (range: 50-110). Successful recruitment and retention strategies included: field-based strategy and snowballing. Major barriers were: distrust, compensation, education disadvantage, lack of interest, and inability to have study partner. Strategies to reduce barriers included providing informational sessions, disseminating newsletters about study outcomes. Best practices include being culturally sensitive including demonstrating a caring attitude and being responsive to participants needs. Cultural competence is critical in order to design and implement successful recruitment strategies in this population. Research teams should consist of multiethnic staff, involve the community, demonstrate trust and deliver concise education of the research endeavor. © 2015 Wiley Periodicals, Inc.

  5. Role of mobile health in the care of culturally and linguistically diverse US populations.

    Science.gov (United States)

    Tirado, Miguel

    2011-01-01

    Emerging trends in the health-related use of cell phones include the proliferation of mobile health applications for the care and monitoring of patients with chronic diseases and the rise in cell phone usage by Latinos and African Americans in the United States. This article reviews public policy in four areas with the goal of improving the care of patients belonging to culturally and linguistically diverse populations: 1) mobile health service access and the physician's duty of care, 2) affordability of and reimbursement for health related services via mobile phone, 3) protocols for mobile health enabled patient health data collection and distribution, and 4) cultural and linguistic appropriateness of health related messages delivered via cell phone. The review demonstrates the need for policy changes that would allow for reimbursement of both synchronous and asynchronous patient-provider communication, subsidize broadband access for lower-income patients, introduce standards for confidentiality of health data transmitted via cell phone as well as amplify existing cultural and linguistic standards to encompass mobile communication, and consider widespread public accessibility when certifying new technologies as "medical devices." Federal and state governments must take prompt action to ensure that the benefits of mobile health are accessible to all Americans.

  6. Bacterial diversity associated with wild caught anopheles mosquitoes from Dak Nong Province, Vietnam using culture and DNA fingerprint

    OpenAIRE

    Ngo, C. T.; Aujoulat, F.; Veas, Francisco; Jumas-Bilak, E.; 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 o...

  7. Influence of milk processing temperature on growth performance, nitrogen retention, and hindgut's inflammatory status and bacterial populations in a calf model.

    Science.gov (United States)

    Bach, Alex; Aris, Anna; Vidal, Maria; Fàbregas, Francesc; Terré, Marta

    2017-08-01

    This research communication describes a study aimed at evaluating the effects of heat treatment of milk on growth performance, N retention, and hindgut's inflammatory status and bacterial populations using young dairy calves as a model. Twenty-one Holstein calves were randomly allocated to one of three treatments: raw milk (RM), pasteurised milk (PAST), or UHT milk (UHT). Calves were submitted to a N balance study, and a biopsy from the distal colon and a faecal sample were obtained from 5 animals per treatment to determine expression of several genes and potential changes in the hindgut's bacterial population. Milk furosine content was 33-fold greater in UHT than in RM and PAST milks. Calves receiving RM grew more than those fed UHT, and urinary N excretion was greatest in calves fed UHT. Quantification of Lactobacillus was lower in calves consuming PAST or UHT, and Gram negative bacteria were greater in UHT than in PAST calves. The expression of IL-8 in the hindgut's mucosa was lowest and that of IL-10 tended to be lowest in RM calves, and expression of claudin-4 tended to be greatest in UHT calves. In conclusion, the nutritional value of UHT-treated milk may be hampered because it compromises growth and increases N excretion in young calves and may have deleterious effects on the gut's bacterial population and inflammation status.

  8. Soybean oil-degrading bacterial cultures as a potential for control of green peach aphids (Myzus persicae).

    Science.gov (United States)

    Kim, Seul Ki; Kim, Seo Ri; Choi, Min Seok; Park, Chang Eon; Kim, Young Cheol; Kim, Kil Yong; Whang, Kyung Sook; Oh, Kyung-Taek; Kim, In Seon

    2007-10-01

    Microorganisms capable of degrading crude oil were isolated and grown in soybean oil as a sole carbon source. The microbial cultures were used to control green peach aphids in vitro. Approximately 60% mortality of aphids was observed when the cultures were applied alone onto aphids. To examine the cultures as a pesticide formulation mixture, the cultures were combined with a low dose of the insecticide imidacloprid (one-fourth dose of recommended field-application rate) and applied onto aphids. The cultures enhanced significantly the insecticidal effectiveness of imidacloprid, which was higher than imidacloprid alone applied at the low dose. The isolated microorganisms exhibited high emulsifying index values and decreased surface tension values after being grown in soybean oil media. GC/MS analyses showed that microorganisms degraded soybean oil to fatty acids. The cultures were suggested to play the roles of wetting, spreading, and sticking agents to improve the effectiveness of imidacloprid. This is the first report on the control of aphids by using oil-degrading microbial cultures.

  9. Is non-union of tibial shaft fractures due to nonculturable bacterial pathogens? A clinical investigation using PCR and culture techniques

    Directory of Open Access Journals (Sweden)

    Gille Justus

    2012-05-01

    Full Text Available Abstract Background Non-union continues to be one of the orthopedist’s greatest challenges. Despite effective culture methods, the detection of low-grade infection in patients with non-union following tibial fracture still presents a challenge. We investigated whether “aseptic” tibial non-union can be the result of an unrecognized infection. Methods A total of 23 patients with non-union following tibial shaft fractures without clinical signs of infection were investigated. Intraoperative biopsy samples obtained from the non-union site were examined by means of routine culture methods and by polymerase chain reaction (PCR for the detection of 16 S ribosomal RNA (rRNA. Control subjects included 12 patients with tibial shaft fractures. Results 23 patients (8 women and 15 men; mean age: 47.4 years were included into this study. Preoperative C-reactive protein levels (mean: 20.8 mg/l and WBC counts (mean: 8,359/μl in the study group were not significantly higher than in the control group. None of the samples of non-union routine cultures yielded microorganism growth. Bacterial isolates were found by conventional culturing methods in only 1 case of an open fracture from the control group. In this case, PCR yielded negative results. 16 S rRNA was detected in tissue specimens from 2 patients (8.7% with non-union. The analysis of these variable species-specific sequences enabled the identification of specific microorganisms (1x Methylobacterium species, 1x Staphylococcus species. Both PCR-positive patients were culture-negative. Conclusions The combination of microbiological culture and broad-range PCR seems to substantially add to the number of microbiological diagnoses obtained and may improve the clinican’s ability to tailor therapy to the individual patient’s needs.

  10. Bacterial Loads Measured by the Xpert MTB/RIF Assay as Markers of Culture Conversion and Bacteriological Cure in Pulmonary TB.

    Directory of Open Access Journals (Sweden)

    Shubhada Shenai

    Full Text Available Biomarkers are needed to monitor tuberculosis (TB treatment and predict treatment outcomes. We evaluated the Xpert MTB/RIF (Xpert assay as a biomarker for TB treatment during and at the end of the 24 weeks therapy.Sputum from 108 HIV-negative, culture-positive pulmonary TB patients was analyzed using Xpert at time points before and during anti-TB therapy. Results were compared against culture. Direct Xpert cycle-threshold (Ct, a change in the Ct (delta Ct, or a novel "percent closing of baseline Ct deficit" (percent closing were evaluated as classifiers of same-day and end-of-treatment culture and therapeutic outcomes.Xpert was positive in 29/95 (30.5% of subjects at week 24; and positive one year after treatment in 8/64 (12.5% successfully-treated patients who remained free of tuberculosis. We identified a relationship between initial bacterial load measured by baseline Xpert Ct and time to culture conversion (hazard ratio 1.06, p = 0.0023, and to the likelihood of being among the 8 treatment failures at week 24 (AUC = 72.8%. Xpert Ct was even more strongly associated with culture conversion on the day the test was performed with AUCs 96.7%, 99.2%, 86.0% and 90.2%, at Day 7, Week 4, 8 and 24, respectively. Compared to baseline Ct measures alone, a combined measure of baseline Ct plus either Delta Ct or percent closing improved the classification of treatment failure status to a 75% sensitivity and 88.9% specificity.Genome loads measured by Xpert provide a potentially-useful biomarker for classifying same day culture status and predicting response to therapy.

  11. CHROMagar COL-APSE: a selective bacterial culture medium for the isolation and differentiation of colistin-resistant Gram-negative pathogens.

    Science.gov (United States)

    Abdul Momin, Muhd Haziq F; Bean, David C; Hendriksen, Rene S; Haenni, Marisa; Phee, Lynette M; Wareham, David W

    2017-11-01

    A selective chromogenic culture medium for the laboratory isolation and differentiation of colistin resistant Acinetobacter, Pseudomonas, Stenotrophomonas and Enterobacteriaceae spp. (CHROMagar COL-APSE) was developed, evaluated and compared to an existing selective bacterial culture medium (SuperPolymyxin). The medium was challenged with 84 isolates, including polymyxin B (POL B)-susceptible and -resistant type strains and colistin (COL)-resistant organisms recovered from human and animal samples. Susceptibility to COL and POL B was determined by agar dilution and broth microtitre dilution. The lower limit for the detection of COL-resistant organisms was also calculated for both CHROMagar COL-APSE and SuperPolymyxin media. The ability to isolate and correctly differentiate COL-resistant organisms within mixed cultures was also assessed and compared using both media. Using CHROMagar COL-APSE, Gram-negative pathogens (n=71) with intrinsic (n=8) or acquired COL (n=63) resistance were recovered with 100 % specificity down to the lower limit of detection of 10 1 colony-forming units (c.f.u.). The growth on SuperPolymyxin was similar, but notably weaker for COL-resistant non-fermentative bacteria (Acinetobacter, Pseudomonas and Stenotrophomonas). CHROMagar COL-APSE was also more sensitive in supporting the growth of Enterobacteriaceae with COL resistance associated with the carriage of mcr-1. CHROMagar COL-APSE is a sensitive and specific medium for the growth of COL-resistant bacterial pathogens. Due to the low limit of detection (10 1  c.f.u.), it may be useful as a primary isolation medium in the surveillance and recovery of COL-resistant bacteria from complex human, veterinary and environmental samples, especially those with plasmid-mediated MCR-1 or novel mechanisms of polymyxin resistance.

  12. PRELIMINARY STUDY ON POPULATION DYNAMIC OF HARPACTICOID COPEPOD Euterpina acutifrons IN CULTURE CONDITION

    Directory of Open Access Journals (Sweden)

    Philip Teguh Imanto

    2007-12-01

    Full Text Available The most important factor to high mortality rate in larval rearing is feeding success in early larval stage related to kind and size of natural live food. Copepod basically is the main source of natural food in the open ocean having some advantages such as smaller size of nauplii, attractive movement and high nutritional value. Observation on population dynamic of harpacticoid copepod Euterpina acutifrons was carried out using 5-L plastic bucket with initial density 100 ind./L. Green algae Nannochloropsis sp. was added to culture media at density of 50,000 cells/mL as a basic feed and additional feeds given were wheat flour (group A and chicken liver (group B at a rate of 50 mg/bucket. The result showed that there was no difference on population pattern in both groups where the incubation time took eight days to hatch, from nauplii to the copepodite stage was three days and from copepodite to adult copepod took five-to-six days. The differences came up from population number: in group (A the highest number of copepod-bearing-egg was only 133 ind., nauplii production up to 62,833 ind. and number of copepodites was 22,333 ind. lower compared to group (B with the highest copepod-egg was 308 ind., nauplii was 113,333 ind. and copepodite was 51,167 ind. The conclusion pointed out that the kind of food did not influence population pattern (quality but gave effect to population growth.

  13. Studies on salinization in Haryana soils on free-living nitrogen-fixing bacterial populations and their activity.

    Science.gov (United States)

    Kayasth, Monika; Gera, Rajesh; Dudeja, Surjit Singh; Sharma, Parveen Kumar; Kumar, Varun

    2014-03-01

    A total of 26 soil samples from saline soils of Haryana were collected. Based on their electrical conductivity (EC) values, which varied from 1.04 to 21.00 dS m(-1), the soils were categorized into non-saline soils (EC 0-2 dS m(-1)), weakly saline soils (EC 2-4 dS m(-1)), saline soils (EC 4-8 dS m(-1)), strongly saline soils (EC 8-16 dS m(-1)), and very strongly saline soils (EC >16 dS m(-1)). The pH values of these soil samples ranged from 6.03 to 8.62, while organic C, total N, and available P were in the range of 0.06-0.94%, 0.07-0.15%, and 0.11-0.29 μg g(-1) soil, respectively. As a measure of the impact of salinity on free-living N(2) fixers and their activity, the total bacterial populations on four media (Jensen's nitrogen-free medium, malate medium, Burk's medium, and soil extract agar medium) decreased from 6.12 to 3.70 log CFU g(-1) soil with increasing salinity level. PCR amplification of the nifH region of the DNA from 234 selected morphotypes from all the media showed the presence of nifH in 71 isolates. Out of these, 37% of the isolates were obtained using Jensen's medium; 35, 28, and 21% of the isolates were obtained using soil extract medium, Burk's medium, and malate medium, respectively. The majority of the free-living N(2) fixers (67%) were Gram negative. Apart from the acetylene reduction assay (ARA) activity in these isolates, other beneficial traits like ammonia excretion and indole acetic acid (IAA) production were also present. A decreasing trend in the activities was observed with increasing salinity levels. Isolates JN6, BP8, and MJ4 showed the highest ARA activity, ammonia excretion, and IAA production. The performance of isolates like BNC2 with good ARA activity, ammonia excretion, and IAA production and isolated from a very strongly saline soil should be further evaluated under high-saline conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Measuring culture: a critical review of acculturation and health in Asian immigrant populations.

    Science.gov (United States)

    Salant, Talya; Lauderdale, Diane S

    2003-07-01

    The number of studies examining how acculturation affects the health of Asian immigrants has increased in recent years. The proliferation of studies reflects the growing size and heterogeneity of Asian immigrant populations in the United States, Canada, Australia, New Zealand, and the United Kingdom. This paper compares various approaches to acculturation within the health literature on Asian immigrants by reviewing the literature in three-health domains (1) mental health (2) physical health and (3) health services use. The review critically examines the conceptualizations and measures of acculturation in these three domains and presents major findings. We observe that measurement difficulties posed by the experiences of heterogeneous Asian groups compound theoretical and disciplinary disparities between acculturation instruments. The extent to which conceptual and methodological critiques of acculturation studies in Hispanic populations apply to studies of Asian populations is also discussed. The critical review thus provides insights into the diverse ways that the relationship between culture and health is measured in this complicated and growing literature.

  15. Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico.

    Science.gov (United States)

    Liu, Jiqing; Bacosa, Hernando P; Liu, Zhanfei

    2016-01-01

    Understanding bacterial community dynamics as a result of an oil spill is important for predicting the fate of oil released to the environment and developing bioremediation strategies in the Gulf of Mexico. In this study, we aimed to elucidate the roles of temperature, water chemistry (nutrients), and initial bacterial community in selecting oil degraders through a series of incubation experiments. Surface (2 m) and bottom (1537 m) waters, collected near the Deepwater Horizon site, were amended with 200 ppm light Louisiana sweet crude oil and bacterial inoculums from surface or bottom water, and incubated at 4 or 24°C for 50 days. Bacterial community and residual oil were analyzed by pyrosequencing and gas chromatography-mass spectrometry (GC-MS), respectively. The results showed that temperature played a key role in selecting oil-degrading bacteria. Incubation at 4°C favored the development of Cycloclasticus, Pseudoalteromonas , Sulfitobacter , and Reinekea , while 24°C incubations enhanced Oleibacter, Thalassobius, Phaeobacter, and Roseobacter. Water chemistry and the initial community also had potential roles in the development of hydrocarbon-degrading bacterial communities. Pseudoalteromonas , Oleibacter , and Winogradskyella developed well in the nutrient-enriched bottom water, while Reinekea and Thalassobius were favored by low-nutrient surface water. We revealed that the combination of 4°C, crude oil and bottom inoculum was a key factor for the growth of Cycloclasticus , while the combination of surface inoculum and bottom water chemistry was important for the growth of Pseudoalteromonas . Moreover, regardless of the source of inoculum, bottom water at 24°C was a favorable condition for Oleibacter. Redundancy analysis further showed that temperature and initial community explained 57 and 19% of the variation observed, while oil and water chemistry contributed 14 and 10%, respectively. Overall, this study revealed the relative roles of temperature, water

  16. Bacterial Meningitis in Infants

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-04-01

    Full Text Available A retrospective study of 80 infantile patients (ages 30-365 days; 47 male, 33 female with culture-proven bacterial meningitis seen over a 16 year period (1986-2001 is reported from Taiwan.

  17. Neuroethics, confidentiality, and a cultural imperative in early onset Alzheimer disease: a case study with a First Nation population.

    Science.gov (United States)

    Stevenson, Shaun; Beattie, B Lynn; Vedan, Richard; Dwosh, Emily; Bruce, Lindsey; Illes, Judy

    2013-10-16

    The meaningful consideration of cultural practices, values and beliefs is a necessary component in the effective translation of advancements in neuroscience to clinical practice and public discourse. Society's immense investment in biomedical science and technology, in conjunction with an increasingly diverse socio-cultural landscape, necessitates the study of how potential discoveries in neurodegenerative diseases such as Alzheimer disease are perceived and utilized across cultures. Building on the work of neuroscientists, ethicists and philosophers, we argue that the growing field of neuroethics provides a pragmatic and constructive pathway to guide advancements in neuroscience in a manner that is culturally nuanced and relevant. Here we review a case study of one issue in culturally oriented neuroscience research where it is evident that traditional research ethics must be broadened and the values and needs of diverse populations considered for meaningful and relevant research practices. A global approach to neuroethics has the potential to furnish critical engagement with cultural considerations of advancements in neuroscience.

  18. Modified tissue culture medium for corneal storage I. Investigation of the effect of antibiotics on bacterial contamination.

    Science.gov (United States)

    Liesegang, T J; Robinson, N; Jones, D B

    1984-04-01

    A series of experiments were performed to determine the effect of modified tissue culture medium (MTCM), temperature, time, and antibiotics on the replication of Staphylococcus epidermidis and Pseudomonas aeruginosa. A known inoculum of the organisms (usually 10(6)/mL) was introduced, and the recovery of viable organisms was compared by different methods of culturing, including techniques of diluting, inactivating, or removing the antibiotic from the system. The invalidity of techniques that failed to remove the antibiotic from the system was substantiated. The newly developed antibiotic removal device was superior to all other culturing techniques. Penicillin G potassium was ineffective in the MTCM system, and gentamicin reagent solution was not uniformly effective against a gentamicin-sensitive strain of P aeruginosa. Placement of the MTCM at room temperature for two hours enhanced the antibacterial activity of gentamicin, although organisms may still be recovered in small numbers.

  19. The effects of culture independent diagnostic testing on the diagnosis and reporting of enteric bacterial pathogens in Queensland, 2010 to 2014.

    Science.gov (United States)

    May, Fiona J; Stafford, Russell J; Carroll, Heidi; Robson, Jennifer Mb; Vohra, Renu; Nimmo, Graeme R; Bates, John; Kirk, Martyn D; Fearnley, Emily J; Polkinghorne, Benjamin G

    2017-09-01

    Changes in diagnostic laboratory testing procedures can impact on the number of cases notified and the public health surveillance of enteric pathogens. Culture independent diagnostic testing using a multiplex polymerase chain reaction (PCR) test was introduced for the rapid detection of bacterial enteric pathogens in pathology laboratories in Queensland, Australia, from late 2013 onwards. We conducted a retrospective descriptive study using laboratory data to assess the impact of the introduction of PCR testing on four common enteric pathogens, Salmonella, Campylobacter, Shigella and Yersinia, in Queensland between 2010 and 2014. The number of stool specimens tested and the proportion positive for each of the four pathogens increased in 2014 after the introduction of culture independent diagnostic testing. Among the specimens tested by both PCR and culture, 12% of Salmonella positive stools, 36% of Campylobacter positive stools, 74% of Shigella / enteroinvasive Escherichia coli positive stools and 65% of Yersinia positive stools were PCR positive only. Including those where culture was not performed, 19% of Salmonella positive stools, 44% of Campylobacter positive stools, 83% of Shigella positive stools and 79% of Yersinia positive stools had no cultured isolate available for further characterisation. The detection and tracking of foodborne and non-foodborne gastrointestinal outbreaks will become more difficult as culture independent diagnostic testing becomes more widespread. Until new techniques for characterisation of pathogens directly from clinical specimens have been developed, we recommend laboratories continue to culture specimens concurrently or reflexively with culture independent diagnostic tests. This work is copyright. You may download, display, print and reproduce the whole or part of this work in unaltered form for your own personal use or, if you are part of an organisation, for internal use within your organisation, but only if you or your

  20. Cross-culturally modified University of Pennsylvania Smell Identification Test for a Turkish population.

    Science.gov (United States)

    Altundag, Aytug; Tekeli, Hakan; Salihoglu, Murat; Cayonu, Melih; Yasar, Halit; Kendirli, Mustafa T; Saglam, Omer

    2015-01-01

    The University of Pennsylvania Smell Identification Test (UPSIT) is a well-developed and popular olfactory test, which has been validated in various populations. However, there was only one study in a Turkish population, and this study indicated that the North American version of the UPSIT was not enough to evaluate the olfactory functions of Turkish population. So, we developed a cross-cultural adaptation of the UPSIT, the UPSIT-Turkish (UPSIT-T). Thus, the goal of this study was to investigate the applicability of the UPSIT-T in healthy Turkish subjects. The study included 51 healthy individuals who reported having normal olfactory function. The participants were administered the North American version of the UPSIT firstly, and then, after a day UPSIT-T was applied to the participants. The results of two smell tests were compared, and the applicability of UPSIT-T was evaluated. The mean (standard deviation) value for correctly identified odors was 27.2 ± 5.7 (range, 14-38) with the UPSIT application, whereas the mean (standard deviation) value for correctly identified odors was 35.9 ± 3.1 for UPSIT-T. There was a statistically significant increase in the scores of the participants when UPSIT-T was performed (p < 0.001). The identification rates of 10 test odorants were <80% for our study group, and 2 of 10 were <70% for the UPSIT-T. The UPSIT-T modification is an adequate olfactory test for clinical use in a Turkish population.

  1. A population balance equation model of aggregation dynamics in Taxus suspension cell cultures.

    Science.gov (United States)

    Kolewe, Martin E; Roberts, Susan C; Henson, Michael A

    2012-02-01

    The nature of plant cells to grow as multicellular aggregates in suspension culture has profound effects on bioprocess performance. Recent advances in the measurement of plant cell aggregate size allow for routine process monitoring of this property. We have exploited this capability to develop a conceptual model to describe changes in the aggregate size distribution that are observed over the course of a Taxus cell suspension batch culture. We utilized the population balance equation framework to describe plant cell aggregates as a particulate system, accounting for the relevant phenomenological processes underlying aggregation, such as growth and breakage. We compared model predictions to experimental data to select appropriate kernel functions, and found that larger aggregates had a higher breakage rate, biomass was partitioned asymmetrically following a breakage event, and aggregates grew exponentially. Our model was then validated against several datasets with different initial aggregate size distributions and was able to quantitatively predict changes in total biomass and mean aggregate size, as well as actual size distributions. We proposed a breakage mechanism where a fraction of biomass was lost upon each breakage event, and demonstrated that even though smaller aggregates have been shown to produce more paclitaxel, an optimum breakage rate was predicted for maximum paclitaxel accumulation. We believe this is the first model to use a segregated, corpuscular approach to describe changes in the size distribution of plant cell aggregates, and represents an important first step in the design of rational strategies to control aggregation and optimize process performance. Copyright © 2011 Wiley Periodicals, Inc.

  2. Cell size dependent toxicity thresholds of polycyclic aromatic hydrocarbons to natural and cultured phytoplankton populations

    Energy Technology Data Exchange (ETDEWEB)

    Echeveste, Pedro, E-mail: pedro.echeveste@uib.e [Department of Global Change Research, IMEDEA (CSIC-UIB) Instituto Mediterraneo de Estudios Avanzados, Miquel Marques 21, 07190 Esporles (Spain); Agusti, Susana, E-mail: sagusti@uib.e [Department of Global Change Research, IMEDEA (CSIC-UIB) Instituto Mediterraneo de Estudios Avanzados, Miquel Marques 21, 07190 Esporles (Spain); Dachs, Jordi, E-mail: jdmqam@cid.csic.e [Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona Salgado 18, 08034 Barcelona (Spain)

    2010-01-15

    The toxicity of pyrene and phenanthrene to phytoplankton was studied by analyzing the effect on the growth, abundance and cell viability of cultured species and natural communities of the Atlantic Ocean and the Mediterranean Sea. A decrease in cell abundance, and growth rate was observed as concentration of PAHs increased, with catastrophic cell mortality induced at the highest PAH concentration tested. A strong positive linear relationship was observed between the LC50 (the PAH concentration at which cell population will decline by a half), and the species cell volume, for both phenanthrene and pyrene. Natural communities were however significantly more sensitive to PAHs than cultured phytoplankton, as indicated by the lower slope (e.g. 0.23 and 0.65, respectively, for pyrene) of the relationship LC50 vs. cell volume. The results highlight the importance of cell size in determining the phytoplankton sensitivity to PAHs identifying the communities from the oligotrophic ocean to be more vulnerable. - Cell size is the major factor determining phytoplankton sensitivity to PAHs.

  3. Invasion fitness for gene-culture co-evolution in family-structured populations and an application to cumulative culture under vertical transmission.

    Science.gov (United States)

    Mullon, Charles; Lehmann, Laurent

    2017-08-01

    Human evolution depends on the co-evolution between genetically determined behaviors and socially transmitted information. Although vertical transmission of cultural information from parent to offspring is common in hominins, its effects on cumulative cultural evolution are not fully understood. Here, we investigate gene-culture co-evolution in a family-structured population by studying the invasion fitness of a mutant allele that influences a deterministic level of cultural information (e.g., amount of knowledge or skill) to which diploid carriers of the mutant are exposed in subsequent generations. We show that the selection gradient on such a mutant, and the concomitant level of cultural information it generates, can be evaluated analytically under the assumption that the cultural dynamic has a single attractor point, thereby making gene-culture co-evolution in family-structured populations with multigenerational effects mathematically tractable. We apply our result to study how genetically determined phenotypes of individual and social learning co-evolve with the level of adaptive information they generate under vertical transmission. We find that vertical transmission increases adaptive information due to kin selection effects, but when information is transmitted as efficiently between family members as between unrelated individuals, this increase is moderate in diploids. By contrast, we show that the way resource allocation into learning trades off with allocation into reproduction (the "learning-reproduction trade-off") significantly influences levels of adaptive information. We also show that vertical transmission prevents evolutionary branching and may therefore play a qualitative role in gene-culture co-evolutionary dynamics. More generally, our analysis of selection suggests that vertical transmission can significantly increase levels of adaptive information under the biologically plausible condition that information transmission between relatives is

  4. Direct common gram-negative bacterial identification from positive blood culture bottles by SELDI-TOF MS.

    Science.gov (United States)

    Xiao, Daiwen; Yang, Yongchang; Jiang, Wei; Zhang, Hangfeng; Liu, Hua; Yu, Hua; Xie, Chunbao; Zhong, Min; Chen, Liang; Huang, Wenfang

    2014-10-01

    A protein database was constructed and validated with identification rate over 90% for the 4 most common Gram-negative bacteria on agar plates. By protein masses comparison, 120 bacteria of the 4 species from blood culture bottles were identified. The concordance was high (Kappa=0.906) between our method and conventional approach. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  6. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

    Science.gov (United States)

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

    2015-10-22

    Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  7. Comprehensive Evaluation of the MBT STAR-BL Module for Simultaneous Bacterial Identification and β-Lactamase-Mediated Resistance Detection in Gram-Negative Rods from Cultured Isolates and Positive Blood Cultures.

    Science.gov (United States)

    Lee, Annie W T; Lam, Johnson K S; Lam, Ricky K W; Ng, Wan H; Lee, Ella N L; Lee, Vicky T Y; Sze, Po P; Rajwani, Rahim; Fung, Kitty S C; To, Wing K; Lee, Rodney A; Tsang, Dominic N C; Siu, Gilman K H

    2018-01-01

    Objective: This study evaluated the capability of a MALDI Biotyper system equipped with the newly introduced MBT STAR-BL module to simultaneously perform species identification and β-lactamase-mediated resistance detection in bacteremia -causing bacteria isolated from cultured isolates and patient-derived blood cultures (BCs). Methods: Two hundred retrospective cultured isolates and 153 prospective BCs containing Gram-negative rods (GNR) were collected and subjected to direct bacterial identification, followed by the measurement of β-lactamase activities against ampicillin, piperacillin, cefotaxime, ceftazidime, and meropenem using the MBT STAR-BL module. The results and turnaround times were compared with those of routine microbiological processing. All strains were also characterized by beta-lactamase PCR and sequencing. Results: Using the saponin-based extraction method, MALDI-TOF MS correctly identified bacteria in 116/134 (86.6%) monomicrobial BCs. The detection sensitivities for β-lactamase activities against ampicillin, piperacillin, third-generation cephalosporin and meropenem were 91.3, 100, 97.9, and 100% for cultured isolates, and 80.4, 100, 68.8, and 40% for monomicrobial BCs ( n = 134) respectively. The overall specificities ranged from 91.5 to 100%. Furthermore, the MBT STAR-BL and conventional drug susceptibility test results were concordant in 14/19 (73.7%) polymicrobial cultures