Science.gov

Sample records for intestinal microbial ecology

  1. [Microbial ecology of the intestines in health and in pathology].

    PubMed

    Goncharova, G I; Dorofeĭchuk, V G; Smolianskaia, A Z; Sokolova, K Ia

    1989-06-01

    Bifidoflora constitute 85--95 per cent of the large intestine microbiocenosis in children under 1 year of age. Bacteroides are not specific of children under 6 months of age. Lactobacilli, lactic acid streptococci, colon bacilli, enterococci and staphylococci (saprophytic, epidermal) constitute not more than 15 per cent. The predominating group peculiar of eubiosis in adults includes bifidobacteria and bacteroides. Changes in human autoflora are often induced by such factors as impaired ecology, stress, uncontrolled use of antibacterial drugs, radio- and chemotherapy, etc. Dysbacteriosis (first of all lower quantitative contents of bifidoflora) has an unfavourable effect on the intestine secretory function, absorption and certain indices of protein, lipid and mineral metabolism, vitamin synthesizing and fermentative functions and leads to disfunction of the gastrointestinal tract. It is a cause of persisting and relapsing infections in children and adults. High and optimal levels of bifidoflora in the intestine usually prevent the pathogenic action of pathogens. Lysozyme of digestive secretion and secretory immunity with immunoglobulin A prevalence also play an important role in the complicated mechanism of the protective barrier. The use of bacterial preparations such as bifidumbacterin, lactobacterin or bifilact for stabilization and recovery of high bifidoflora levels is indicated in all the cases with impaired microbiocenosis of the intestine.

  2. Yeast culture supplement during nursing and transport affects immunity and intestinal microbial ecology of weanling pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weaning and transport stress can have a negative impact on the piglet's immune system and intestinal microbiota. The objective of this study was to determine the influence of a yeast product on innate immunity and microbial ecology of the gastrointestinal tract following stress of weaning and trans...

  3. ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation.

    PubMed

    Hashimoto, Tatsuo; Perlot, Thomas; Rehman, Ateequr; Trichereau, Jean; Ishiguro, Hiroaki; Paolino, Magdalena; Sigl, Verena; Hanada, Toshikatsu; Hanada, Reiko; Lipinski, Simone; Wild, Birgit; Camargo, Simone M R; Singer, Dustin; Richter, Andreas; Kuba, Keiji; Fukamizu, Akiyoshi; Schreiber, Stefan; Clevers, Hans; Verrey, Francois; Rosenstiel, Philip; Penninger, Josef M

    2012-07-25

    Malnutrition affects up to one billion people in the world and is a major cause of mortality. In many cases, malnutrition is associated with diarrhoea and intestinal inflammation, further contributing to morbidity and death. The mechanisms by which unbalanced dietary nutrients affect intestinal homeostasis are largely unknown. Here we report that deficiency in murine angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 (Ace2), which encodes a key regulatory enzyme of the renin-angiotensin system (RAS), results in highly increased susceptibility to intestinal inflammation induced by epithelial damage. The RAS is known to be involved in acute lung failure, cardiovascular functions and SARS infections. Mechanistically, ACE2 has a RAS-independent function, regulating intestinal amino acid homeostasis, expression of antimicrobial peptides, and the ecology of the gut microbiome. Transplantation of the altered microbiota from Ace2 mutant mice into germ-free wild-type hosts was able to transmit the increased propensity to develop severe colitis. ACE2-dependent changes in epithelial immunity and the gut microbiota can be directly regulated by the dietary amino acid tryptophan. Our results identify ACE2 as a key regulator of dietary amino acid homeostasis, innate immunity, gut microbial ecology, and transmissible susceptibility to colitis. These results provide a molecular explanation for how amino acid malnutrition can cause intestinal inflammation and diarrhoea.

  4. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-03-19

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  5. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-05-15

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  6. Effects of feed additives and mixed eimeria species infection on intestinal microbial ecology of broilers.

    PubMed

    Hume, M E; Clemente-Hernández, S; Oviedo-Rondón, E O

    2006-12-01

    Evaluation of digestive microbial ecology is necessary to understand effects of growth-promoting feed. In the current study, the dynamics of intestinal microbial communities (MC) were examined in broilers fed diets supplemented with a combination of antibiotic (bacitracin methylene disalicylate) and ionophore (Coban 60), and diets containing 1 of 2 essential oil (EO) blends, Crina Poultry (CP) and Crina Alternate (CA). Five treatments were analyzed: 1) unmedicated uninfected control; 2) unmedicated infected control; 3) feed additives monensin (bacitracin methylene disalicylate) + monensin (Coban 60; AI); 4) EO blend CP; and 5) EO blend CA. Additives were mixed into a basal feed mixture, and EO were adjusted to 100 ppm. Chicks were infected by oral gavage at 19 d of age with Eimeria acervulina, Eimeria maxima, and Eimeria tenella. Duodenal, ileal, and cecal samples were taken from 12 birds per treatment just before and 7 d after challenge; 2 samples each were pooled to give a final number of 6 samples total; and all pooled samples were frozen until used for DNA extraction. Denaturing gradient gel electrophoresis was used to examine PCR-amplified fragments of the bacterial 16S ribosomal DNA variable region. Results are presented as percentages of similarity coefficients (SC). Dendrograms of PCR amplicon or band patterns indicated MC differences due to intestinal location, feed additives, and cocci challenge. Essential oil blends CP and CA affected MC in all gut sections. Each EO had different effects over MC, and they differed in most instances from the AI group. The cocci challenge caused drastic MC population shifts in duodenal, ileal, and cecal sections (36.7, 55.4, and 36.2% SC, respectively). Diets supplemented with CP supported higher SC between pre- and postchallenge MC (89.9, 83.3, and 76.4%) than AI (81.8., 57.4, and 60.0%). We concluded that mixed coccidia challenge caused drastic shifts in MC. These EO blends modulated MC better than AI, avoiding drastic

  7. Yeast culture supplement during nursing and transport affects immunity and intestinal microbial ecology of weanling pigs.

    PubMed

    Weedman, S M; Rostagno, M H; Patterson, J A; Yoon, I; Fitzner, G; Eicher, S D

    2011-06-01

    The objectives of this study were to determine the influence of a Saccharomyces cerevisiae fermentation product on innate immunity and intestinal microbial ecology after weaning and transport stress. In a randomized complete block design, before weaning and in a split-plot analysis of a 2 × 2 factorial arrangement of yeast culture (YY) and transport (TT) after weaning, 3-d-old pigs (n = 108) were randomly assigned within litter (block) to either a control (NY, milk only) or yeast culture diet (YY; delivered in milk to provide 0.1 g of yeast culture product/kg of BW) from d 4 to 21. At weaning (d 21), randomly, one-half of the NY and YY pigs were assigned to a 6-h transport (NY-TT and YY-TT) before being moved to nursery housing, and the other one-half were moved directly to nursery housing (NY-NT and YY-NT, where NT is no transport). The yeast treatment was a 0.2% S. cerevisiae fermentation product and the control treatment was a 0.2% grain blank in feed for 2 wk. On d 1 before transport and on d 1, 4, 7, and 14 after transport, blood was collected for leukocyte assays, and mesenteric lymph node, jejunal, and ileal tissue, and jejunal, ileal, and cecal contents were collected for Toll-like receptor expression (TLR); enumeration of Escherichia coli, total coliforms, and lactobacilli; detection of Salmonella; and microbial analysis. After weaning, a yeast × transport interaction for ADG was seen (P = 0.05). Transport affected (P = 0.09) ADFI after weaning. Yeast treatment decreased hematocrit (P = 0.04). A yeast × transport interaction was found for counts of white blood cells (P = 0.01) and neutrophils (P = 0.02) and for the neutrophil-to-lymphocyte ratio (P = 0.02). Monocyte counts revealed a transport (P = 0.01) effect. Interactions of yeast × transport (P = 0.001) and yeast × transport × day (P = 0.09) for TLR2 and yeast × transport (P = 0.08) for TLR4 expression in the mesenteric lymph node were detected. Day affected lactobacilli, total coliform, and E

  8. Effects of dietary supplementation with fermented ginkgo leaves on antioxidant capacity, intestinal morphology and microbial ecology in broiler chicks.

    PubMed

    Zhang, X H; Sun, Z Y; Cao, F L; Ahmad, H; Yang, X H; Zhao, L G; Wang, T

    2015-01-01

    1. The purpose of this study was to evaluate the effects of supplementing diets with three types of fermented Ginkgo-leaves (FGL) on growth, antioxidant capacity, intestinal morphology and microbial ecology in broiler chicks. 2. A total of 300 d-old broilers were randomly allocated to 4 dietary treatments with 6 replications of 10 birds each. Birds were fed on basal diets (Control) or basal diets supplemented with 0.5% FGL with Candida utilis (CF group), Aspergillus niger (AF group) or their combined fermentation (CAF group), respectively, for a 42 d feeding trial. 3. AF and CAF supplementation improved body weight gain (BWG) (22-42 d) and feed conversion ratio (22-42 d and 1-42 d). Concentrations of serum α-tocopherol in CAF group, as well as hepatic α-tocopherol in the three FGL groups were increased, while hepatic reactive oxygen species (ROS) levels were greatly decreased in group AF and CAF. Chickens in AF and CAF groups had decreased hepatic protein carbonyls and malondialdehyde (MDA), as well as jejunal and ileal protein carbonyls. The total superoxide dismutase (T-SOD) activities and glutathione (GSH) of both jejunum and ileum of the CAF group were higher than the other groups. 4. Duodenal and jejunal villous height of birds fed on the AF and CAF diets were increased, while jejunal crypt depth (CD) was decreased. Furthermore, birds fed on AF and CAF supplemented diets had increased ileal lactobacilli populations. Decreased ileal and caecal Escherichia coli and Salmonellas populations was found for the birds fed on CAF supplemented diets. 5. The present study may indicate that the improved feed efficiency and intestinal functions in the group supplemented with AF and CAF are directly connected with the improved antioxidant capacity and intestinal microbial ecology.

  9. Intestinal microbial ecology of broilers vaccinated and challenged with mixed Eimeria species, and supplemented with essential oil blends.

    PubMed

    Oviedo-Rondón, E O; Hume, M E; Hernández, C; Clemente-Hernández, S

    2006-05-01

    Intestinal microbiota is an important component in the development of defense mechanisms in the gut mucosa. This project determined the dynamics of intestinal microbial communities (MC) of broilers vaccinated at first day of age with live oocysts of Eimeria species and fed diets supplemented with 2 specific essential oil (EO) blends, Crina Poultry (CP) and Crina Alternate (CA). Five treatments were analyzed: 1) unmedicated-uninfected (UU) control; 2) unmedicated-infected (UI) control; 3) vaccinated with Advent cocci-vaccine and without feed additive (COV) supplements; 4) vaccinated with Advent and supplemented with CP; and 5) vaccinated with Advent and supplemented with CA. The EO blends were added at 100 ppm to the same basal diets. Chicks were gavage-infected at 19 d of age with Eimeria acervulina, Eimeria maxima, and Eimeria tenella. Duodenal, ileal, and cecal samples were taken from 12 birds per treatment just before the infection and 7 d after the challenge, pooled in 6 samples, and frozen. Denaturing gradient gel electrophoresis was used to examine PCR-amplified fragments of the bacterial 16S ribosomal DNA variable region. Results are presented as percentages of similarity coefficients (SC). Dendrograms of amplicon patterns indicated MC differences due to intestinal location, feed additives, and cocci infection. The EO blends CP and CA did affect MC in all gut sections. The cocci-infection caused drastic MC population shifts in duodenal, ileal, and cecal sections (36.7, 55.4, and 36.2% SC, respectively). The CP-supplemented birds had higher SC between pre- and postchallenge MC in duodenal and ileal (73.3, 81.8%) than COV (66.4, 66.5%). However, COV broilers had the smallest changes in cecal MC after infection (79.5% SC). We concluded that cocci-vaccination causes small changes in intestinal MC, but challenge causes drastic shifts. The EO blend supplementation modulates MC in cocci-vaccinated broilers, avoiding drastic shifts after a mixed coccidia infection

  10. Microbial Ecology: Where are we now?

    PubMed Central

    2016-01-01

    Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages. PMID:27975077

  11. The microbial ecology of permafrost.

    PubMed

    Jansson, Janet K; Taş, Neslihan

    2014-06-01

    Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.

  12. Microbial ecology of watery kimchi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The biochemistry and microbial ecology of 2 similar types of watery (mul) kimchi, containing sliced and unsliced radish and vegetables (nabak and dongchimi, respectively), were investigated. Samples from kimchi were fermented at 4, 10, and 20 °C were analyzed by plating on differential and selective...

  13. Manipulation of Biofilm Microbial Ecology

    SciTech Connect

    White, D.C.; Palmer, R.J., Jr.; Zinn, M.; Smith, C.A.; Burkhalter, R.; Macnaughton, S.J.; Whitaker, K.W.; Kirkegaard, R.D.

    1998-08-15

    The biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms be generated. The most effective monitoring of biofilm formation, succession and desaturation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  14. Manipulatiaon of Biofilm Microbial Ecology

    SciTech Connect

    Burkhalter, R.; Macnaughton, S.J.; Palmer, R.J.; Smith, C.A.; Whitaker, K.W.; White, D.C.; Zinn, M.; kirkegaard, R.

    1998-08-09

    The Biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms by generated. The most effective monitoring of biofilm formation, succession and desquamation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in the distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  15. [Soil microbial ecological process and microbial functional gene diversity].

    PubMed

    Zhang, Jing; Zhang, Huiwen; Li, Xinyu; Su, Zhencheng; Zhang, Chenggang

    2006-06-01

    Soil microbes in terrestrial ecosystem carry out a series of important ecological functions, such as geo-chemical cycling of elements, degradation of pollutants, and buffering to the acute changes of environment, etc. Soil microbial ecological function has a close relation with soil function, and the changes in the structure and composition of soil microbial populations can directly affect the realization of soil function. Through their produced enzymes, soil microbes take part in a series of metabolic activities, and the functional genes of coded enzymes are the functional markers of microbes. In recent ten years, molecular ecology focusing on the functional gene diversity has been developed rapidly, which gives us a new cut-in point to understand soil microbial ecological function from the point of functional gene. This paper reviewed the research advances in the functional gene diversity correlated to soil microbial ecological function, with the perspectives in this field discussed.

  16. Procedures For Microbial-Ecology Laboratory

    NASA Technical Reports Server (NTRS)

    Huff, Timothy L.

    1993-01-01

    Microbial Ecology Laboratory Procedures Manual provides concise and well-defined instructions on routine technical procedures to be followed in microbiological laboratory to ensure safety, analytical control, and validity of results.

  17. Effect of dietary alginic acid on juvenile tilapia (Oreochromis niloticus) intestinal microbial balance, intestinal histology and growth performance.

    PubMed

    Merrifield, Daniel L; Harper, Glenn M; Mustafa, Sanaa; Carnevali, Oliana; Picchietti, Simona; Davies, Simon J

    2011-04-01

    The aim of the present study was to assess the effect of a commercial alginic acid source (Ergosan) on tilapia Oreochromis niloticus intestinal microbial balance, intestinal morphology, and growth parameters. Fish were fed a basal control diet or the basal diet plus a source of alginic acid (5 g kg(-1) Ergosan; Schering-Plough Aquaculture, UK) for 9 weeks. At the end of the trial, light and electron microscopy demonstrated that the morphology of the intestinal tract at the gross and ultra-structural level was not affected by dietary alginic acid inclusion. Both groups of fish displayed healthy, normal morphology with no signs of disease, cell or tissue damage. Intestinal epithelial leucocyte infiltration was not affected by dietary alginic acid. Molecular bacterial profiles derived from PCR-DGGE illustrated highly similar microbial communities (both within the lumen and associated with the intestinal mucosa) in the respective treatment groups. Microbial ecological parameters (e.g. species diversity and richness) also remained unaffected. Although not significant, trends towards elevated survival and body protein content were observed in the alginic acid-fed fish. These results are suggestive that alginic acid does not adversely impact the indigenous gastrointestinal microbial balance and subsequently does not impact upon the epithelial brush border integrity. Validation of non-detrimental impacts of immunostimulatory products on gastric microbiota and epithelial integrity should be pursued in future studies as maintaining microbial balance and epithelial integrity is essential for proper gut functionality.

  18. Support for marine microbial ecology research

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-04-01

    Support for marine microbial ecology research A new research competition will provide support to innovative scientists in marine microbial ecology and related fields, the Gordon and Betty Moore Foundation announced on 30 March. The foundation's Investigators in Marine Microbiology program will select 10-15 current and emerging leaders based on their potential to conduct cutting-edge research on the principles that govern microbially mediated nutrient flow and the interactions among marine microbes in ocean ecosystems. The foundation will invest a total of $25 million in the new investigator program over the next 5 years. The competition is open to researchers around the world at varying stages of their careers who represent a variety of scientific backgrounds, including microbial ecology, biogeochemistry, evolutionary biology, and bioinformatics.

  19. Microarray Applications in Microbial Ecology Research.

    SciTech Connect

    Gentry, T.; Schadt, C.; Zhou, J.

    2006-04-06

    Microarray technology has the unparalleled potential tosimultaneously determine the dynamics and/or activities of most, if notall, of the microbial populations in complex environments such as soilsand sediments. Researchers have developed several types of arrays thatcharacterize the microbial populations in these samples based on theirphylogenetic relatedness or functional genomic content. Several recentstudies have used these microarrays to investigate ecological issues;however, most have only analyzed a limited number of samples withrelatively few experiments utilizing the full high-throughput potentialof microarray analysis. This is due in part to the unique analyticalchallenges that these samples present with regard to sensitivity,specificity, quantitation, and data analysis. This review discussesspecific applications of microarrays to microbial ecology research alongwith some of the latest studies addressing the difficulties encounteredduring analysis of complex microbial communities within environmentalsamples. With continued development, microarray technology may ultimatelyachieve its potential for comprehensive, high-throughput characterizationof microbial populations in near real-time.

  20. Microbial bebop: creating music from complex dynamics in microbial ecology.

    PubMed

    Larsen, Peter; Gilbert, Jack

    2013-01-01

    In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  1. The information science of microbial ecology.

    PubMed

    Hahn, Aria S; Konwar, Kishori M; Louca, Stilianos; Hanson, Niels W; Hallam, Steven J

    2016-06-01

    A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation.

  2. Microfluidics expanding the frontiers of microbial ecology.

    PubMed

    Rusconi, Roberto; Garren, Melissa; Stocker, Roman

    2014-01-01

    Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.

  3. Microfluidics Expanding the Frontiers of Microbial Ecology

    PubMed Central

    Rusconi, Roberto; Garren, Melissa; Stocker, Roman

    2014-01-01

    The ability afforded by microfluidics to observe the behaviors of microbes in highly controlled and confined microenvironments, across scales from a single cell to mixed communities, has significantly contributed to expand the frontiers of microbial ecology over the last decade. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. Here we review applications of microfluidics that have resulted in highly insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible, multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control phenomena such as biofilm formation and antibiotic resistance. PMID:24773019

  4. Transport phenomena of microbial flora in the small intestine with peristalsis.

    PubMed

    Ishikawa, T; Sato, T; Mohit, G; Imai, Y; Yamaguchi, T

    2011-06-21

    The gastrointestinal tract of humans is colonized by indigenous prokaryotic and eukaryotic microbial cells that form a complex ecological system called microbial flora. Although the microbial flora has diverse functions, its homeostasis inside the gastrointestinal tract is still largely unknown. Therefore, creating a model for investigating microbial flora in the gastrointestinal tract is important. In this study, we developed a novel numerical model to explore the transport phenomena of microbial flora in the small intestine. By simultaneously solving the flow field generated by peristalsis, the concentrations of oxygen and nutrient, and the densities of moderate anaerobes and aerobes, the effects of fluid mechanics on the transport phenomena of microbial flora are discussed. The results clearly illustrated that fluid mechanics have considerable influence not only on the bacterial population, but also on the concentration distributions of oxygen and nutrient. Especially, the flow field enhances the radial variation of the concentration fields. We also show scaling arguments for bacterial growth and oxygen consumption, which capture the main features of the results. Additionally, we investigated the transport phenomena of microbial flora in a long tube with 40 constrictions. The results showed a high growth rate of aerobes in the upstream side and a high growth rate of anaerobes in the downstream side, which qualitatively agrees with experimental observations of human intestines. These new findings provide the fundamental basis for a better understanding of the transport phenomena of microbial flora in the intestine.

  5. The outer mucus layer hosts a distinct intestinal microbial niche

    PubMed Central

    Li, Hai; Limenitakis, Julien P.; Fuhrer, Tobias; Geuking, Markus B.; Lawson, Melissa A.; Wyss, Madeleine; Brugiroux, Sandrine; Keller, Irene; Macpherson, Jamie A.; Rupp, Sandra; Stolp, Bettina; Stein, Jens V.; Stecher, Bärbel; Sauer, Uwe; McCoy, Kathy D.; Macpherson, Andrew J.

    2015-01-01

    The overall composition of the mammalian intestinal microbiota varies between individuals: within each individual there are differences along the length of the intestinal tract related to host nutrition, intestinal motility and secretions. Mucus is a highly regenerative protective lubricant glycoprotein sheet secreted by host intestinal goblet cells; the inner mucus layer is nearly sterile. Here we show that the outer mucus of the large intestine forms a unique microbial niche with distinct communities, including bacteria without specialized mucolytic capability. Bacterial species present in the mucus show differential proliferation and resource utilization compared with the same species in the intestinal lumen, with high recovery of bioavailable iron and consumption of epithelial-derived carbon sources according to their genome-encoded metabolic repertoire. Functional competition for existence in this intimate layer is likely to be a major determinant of microbiota composition and microbial molecular exchange with the host. PMID:26392213

  6. Microbial interactions: ecology in a molecular perspective.

    PubMed

    Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

    2016-12-01

    The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.

  7. Role of the Host Defense System and Intestinal Microbial Flora in the Pathogenesis of Necrotizing Enterocolitis

    PubMed Central

    Emami, Claudia N.; Petrosyan, Mikael; Giuliani, Stefano; Williams, Monica; Hunter, Catherine; Prasadarao, Nemani V.

    2009-01-01

    Abstract Background Necrotizing enterocolitis (NEC) is a devastating disease that affects primarily the intestine of premature infants. Despite recent advances in neonatology, NEC remains a major cause of morbidity and mortality in neonates. Neonatal mucosal defenses and adherence of bacterial pathogens may play an important role in the pathogenesis of NEC. Methods Review and synthesis of pertinent literature. Results Putative factors that have been implicated in the pathogenesis of NEC include abnormal patterns of gut colonization by bacteria, immaturity of the host immune system and mucosal defense mechanisms, intestinal ischemia, formula feeding, and loss of intestinal epithelial barrier integrity. Conclusion Host defenses and intestinal microbial ecology are believed to play important roles in the pathogenesis of NEC. Commensal bacteria and probiotic therapy may be of therapeutic utility in the maintenance of the gut epithelial barrier. PMID:19943775

  8. The microbial ecology of wine grape berries.

    PubMed

    Barata, A; Malfeito-Ferreira, M; Loureiro, V

    2012-02-15

    Grapes have a complex microbial ecology including filamentous fungi, yeasts and bacteria with different physiological characteristics and effects upon wine production. Some species are only found in grapes, such as parasitic fungi and environmental bacteria, while others have the ability to survive and grow in wines, constituting the wine microbial consortium. This consortium covers yeast species, lactic acid bacteria and acetic acid bacteria. The proportion of these microorganisms depends on the grape ripening stage and on the availability of nutrients. Grape berries are susceptible to fungal parasites until véraison after which the microbiota of truly intact berries is similar to that of plant leaves, which is dominated by basidiomycetous yeasts (e.g. Cryptococcus spp., Rhodotorula spp. Sporobolomyces spp.) and the yeast-like fungus Aureobasidium pullulans. The cuticle of visually intact berries may bear microfissures and softens with ripening, increasing nutrient availability and explaining the possible dominance by the oxidative or weakly fermentative ascomycetous populations (e.g. Candida spp., Hanseniaspora spp., Metschnikowia spp., Pichia spp.) approaching harvest time. When grape skin is clearly damaged, the availability of high sugar concentrations on the berry surface favours the increase of ascomycetes with higher fermentative activity like Pichia spp. and Zygoascus hellenicus, including dangerous wine spoilage yeasts (e.g. Zygosaccharomyces spp., Torulaspora spp.), and of acetic acid bacteria (e.g. Gluconobacter spp., Acetobacter spp.). The sugar fermenting species Saccharomyces cerevisiae is rarely found on unblemished berries, being favoured by grape damage. Lactic acid bacteria are minor partners of grape microbiota and while being the typical agent of malolactic fermentation, Oenococcus oeni has been seldom isolated from grapes in the vineyard. Environmental ubiquitous bacteria of the genus Enterobacter spp., Enterococcus spp., Bacillus spp

  9. The use of microarrays in microbial ecology

    SciTech Connect

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  10. A Microbial Feed Additive Abates Intestinal Inflammation in Atlantic Salmon

    PubMed Central

    Vasanth, Ghana; Kiron, Viswanath; Kulkarni, Amod; Dahle, Dalia; Lokesh, Jep; Kitani, Yoichiro

    2015-01-01

    The efficacy of a microbial feed additive (Bactocell®) in countering intestinal inflammation in Atlantic salmon was examined in this study. Fish were fed either the additive-coated feed (probiotic) or feed without it (control). After an initial 3-week feeding, an inflammatory condition was induced by anally intubating all the fish with oxazolone. The fish were offered the feeds for 3 more weeks. Distal intestine from the groups was obtained at 4 h, 24 h, and 3 weeks, after oxazolone treatment. Inflammatory responses were prominent in both groups at 24 h, documented by changes in intestinal micromorphology, expression of inflammation-related genes, and intestinal proteome. The control group was characterized by edema, widening of intestinal villi and lamina propria, infiltration of granulocytes and lymphocytes, and higher expression of genes related to inflammatory responses, mul1b, il1b, tnfa, ifng, compared to the probiotic group or other time points of the control group. Further, the protein expression in the probiotic group at 24 h after inducing inflammation revealed five differentially regulated proteins – Calr, Psma5, Trp1, Ctsb, and Naga. At 3 weeks after intubation, the inflammatory responses subsided in the probiotic group. The findings provide evidence that the microbial additive contributes to intestinal homeostasis in Atlantic salmon. PMID:26347738

  11. Microbial imbalance and intestinal pathologies: connections and contributions

    PubMed Central

    Yang, Ye; Jobin, Christian

    2014-01-01

    Microbiome analysis has identified a state of microbial imbalance (dysbiosis) in patients with chronic intestinal inflammation and colorectal cancer. The bacterial phylum Proteobacteria is often overrepresented in these individuals, with Escherichia coli being the most prevalent species. It is clear that a complex interplay between the host, bacteria and bacterial genes is implicated in the development of these intestinal diseases. Understanding the basic elements of these interactions could have important implications for disease detection and management. Recent studies have revealed that E. coli utilizes a complex arsenal of virulence factors to colonize and persist in the intestine. Some of these virulence factors, such as the genotoxin colibactin, were found to promote colorectal cancer in experimental models. In this Review, we summarize key features of the dysbiotic states associated with chronic intestinal inflammation and colorectal cancer, and discuss how the dysregulated interplay between host and bacteria could favor the emergence of E. coli with pathological traits implicated in these pathologies. PMID:25256712

  12. Microbial Biofilms: from Ecology to Molecular Genetics

    PubMed Central

    Davey, Mary Ellen; O'toole, George A.

    2000-01-01

    Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development. PMID:11104821

  13. Molecular musings in microbial ecology and evolution

    PubMed Central

    2011-01-01

    A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology. The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology. The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology). The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies

  14. Effect of Malathion on the Microbial Ecology of Activated Sludge

    DTIC Science & Technology

    2015-03-26

    EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, Senior Master Sergeant, USAF AFIT-ENV-MS-15-M-095 DEPARTMENT...Government and is not subject to copyright protection in the United States. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED...UNLIMITED. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, B.S. Senior Master Sergeant

  15. Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

    PubMed Central

    Toussaint, Nora C.; Buffie, Charlie G.; Rätsch, Gunnar; Pamer, Eric G.; Sander, Chris; Xavier, João B.

    2013-01-01

    The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from time-resolved metagenomics. This method extends generalized Lotka–Volterra dynamics to account for external perturbations. Data from recent experiments on antibiotic-mediated Clostridium difficile infection is analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Stability analysis reveals that the microbiota is intrinsically stable, explaining how antibiotic perturbations and C. difficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, the analysis suggests a subnetwork of bacterial groups implicated in protection against C. difficile. Due to its generality, our method can be applied to any high-resolution ecological time-series data to infer community structure and response to external stimuli. PMID:24348232

  16. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond

    PubMed Central

    Hiraoka, Satoshi; Yang, Ching-chia; Iwasaki, Wataru

    2016-01-01

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives. PMID:27383682

  17. Diversity, ecology and intestinal function of bifidobacteria

    PubMed Central

    2014-01-01

    The human gastrointestinal tract represents an environment which is a densely populated home for a microbiota that has evolved to positively contribute to host health. At birth the essentially sterile gastrointestinal tract (GIT) is rapidly colonized by microorganisms that originate from the mother and the surrounding environment. Within a short timeframe a microbiota establishes within the (breastfed) infant's GIT where bifidobacteria are among the dominant members, although their numerical dominance disappears following weaning. The numerous health benefits associated with bifidobacteria, and the consequent commercial relevance resulting from their incorporation into functional foods, has led to intensified research aimed at the molecular understanding of claimed probiotic attributes of this genus. In this review we provide the current status on the diversity and ecology of bifidobacteria. In addition, we will discuss the molecular mechanisms that allow this intriguing group of bacteria to colonize and persist in the GIT, so as to facilitate interaction with its host. PMID:25186128

  18. Changes in mouse gastrointestinal microbial ecology with ingestion of kale.

    PubMed

    Uyeno, Y; Katayama, S; Nakamura, S

    2014-09-01

    Kale, a cultivar of Brassica oleracea, has attracted a great deal of attention because of its health-promoting effects, which are thought to be exerted through modulation of the intestinal microbiota. The present study was performed to investigate the effects of kale ingestion on the gastrointestinal microbial ecology of mice. 21 male C57BL/6J mice were divided into three groups and housed in a specific pathogen-free facility. The animals were fed either a control diet or experimental diets supplemented with different commercial kale products for 12 weeks. Contents of the caecum and colon of the mice were processed for the determination of active bacterial populations by a bacterial rRNA-based quantification method and short-chain fatty acids by HPLC. rRNAs of Bacteroides-Prevotella, the Clostridium coccoides-Eubacterium rectale group, and Clostridium leptum subgroup constituted the major fraction of microbiota regardless of the composition of the diet. The ratio of Firmicutes to Bacteroidetes was higher in the colon samples of one of the kale diet groups than in the control. The colonic butyrate level was also higher with the kale-supplemented diet. Overall, the ingestion of kale tended to either increase or decrease the activity of specific bacterial groups in the mouse gastrointestinal tract, however, the effect might vary depending on the nutritional composition.

  19. [Microbial diversity in scorpion intestine (Buthus martensii Karsch)].

    PubMed

    Wang, Bao-Jun; Liu, Ying; Jiang, Jia-Tong; Liu, Bin; Liu, Shuang-Jiang

    2007-10-01

    Scorpion is an important officinal animal, and has a high nutritional value. In this study, the culture-independent and culture-dependent methods were used to investigate the microbial diversity in the scorpion's intestine. Results based on culture-independent method showed the bacteria to be related to alpha, beta, gamma-proteobacteria. Bacteria isolated by the culture-dependent method were high G + C, gram-positive bacteria. The genera Enterobacter, Serratia and Ochrobactrum were detected by both methods. To sum up the results from the two methods, the bacteria in scorpion intestine belong to 23 genera, which are Enterobacter, Serratia, Pseudomonas, Acinetobacter, Aeromonas, Citrobacter, Pedobacter, Delftia, Ralstonia, Ochrobactrum, Sphingomonas, Exiguobacterium, Gordonia, Nocardia, Rhodococcus, Janibacte, Kocuria, Micrococcus, Agromyces, Microbacterium, Agrococcus, Deinococcus, Ornithinimicrobium, and some uncultured species. The two methods have both advantages and shortcomings. However, when used simultaneously, they complement each other.

  20. Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

    USGS Publications Warehouse

    Hall, E.K.; Maixner, F.; Franklin, O.; Daims, H.; Richter, A.; Battin, T.

    2011-01-01

    Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

  1. Microbial DNA extraction from intestinal biopsies is improved by avoiding mechanical cell disruption

    PubMed Central

    Carbonero, Franck; Nava, Gerardo M.; Benefiel, Ann C.; Greenberg, Eugene; Gaskins, H. Rex

    2011-01-01

    Currently, standard protocols for microbial DNA extraction from intestinal tissues do not exist. We assessed the efficiency of a commercial kit with and without mechanical disruption. Better quality DNA was obtained without mechanical disruption. Thus, it appears that bead-beating is not required for efficient microbial DNA extraction from intestinal biopsies. PMID:21820015

  2. Sparse and compositionally robust inference of microbial ecological networks.

    PubMed

    Kurtz, Zachary D; Müller, Christian L; Miraldi, Emily R; Littman, Dan R; Blaser, Martin J; Bonneau, Richard A

    2015-05-01

    16S ribosomal RNA (rRNA) gene and other environmental sequencing techniques provide snapshots of microbial communities, revealing phylogeny and the abundances of microbial populations across diverse ecosystems. While changes in microbial community structure are demonstrably associated with certain environmental conditions (from metabolic and immunological health in mammals to ecological stability in soils and oceans), identification of underlying mechanisms requires new statistical tools, as these datasets present several technical challenges. First, the abundances of microbial operational taxonomic units (OTUs) from amplicon-based datasets are compositional. Counts are normalized to the total number of counts in the sample. Thus, microbial abundances are not independent, and traditional statistical metrics (e.g., correlation) for the detection of OTU-OTU relationships can lead to spurious results. Secondly, microbial sequencing-based studies typically measure hundreds of OTUs on only tens to hundreds of samples; thus, inference of OTU-OTU association networks is severely under-powered, and additional information (or assumptions) are required for accurate inference. Here, we present SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that addresses both of these issues. SPIEC-EASI combines data transformations developed for compositional data analysis with a graphical model inference framework that assumes the underlying ecological association network is sparse. To reconstruct the network, SPIEC-EASI relies on algorithms for sparse neighborhood and inverse covariance selection. To provide a synthetic benchmark in the absence of an experimentally validated gold-standard network, SPIEC-EASI is accompanied by a set of computational tools to generate OTU count data from a set of diverse underlying network topologies. SPIEC

  3. Sparse and Compositionally Robust Inference of Microbial Ecological Networks

    PubMed Central

    Kurtz, Zachary D.; Müller, Christian L.; Miraldi, Emily R.; Littman, Dan R.; Blaser, Martin J.; Bonneau, Richard A.

    2015-01-01

    16S ribosomal RNA (rRNA) gene and other environmental sequencing techniques provide snapshots of microbial communities, revealing phylogeny and the abundances of microbial populations across diverse ecosystems. While changes in microbial community structure are demonstrably associated with certain environmental conditions (from metabolic and immunological health in mammals to ecological stability in soils and oceans), identification of underlying mechanisms requires new statistical tools, as these datasets present several technical challenges. First, the abundances of microbial operational taxonomic units (OTUs) from amplicon-based datasets are compositional. Counts are normalized to the total number of counts in the sample. Thus, microbial abundances are not independent, and traditional statistical metrics (e.g., correlation) for the detection of OTU-OTU relationships can lead to spurious results. Secondly, microbial sequencing-based studies typically measure hundreds of OTUs on only tens to hundreds of samples; thus, inference of OTU-OTU association networks is severely under-powered, and additional information (or assumptions) are required for accurate inference. Here, we present SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that addresses both of these issues. SPIEC-EASI combines data transformations developed for compositional data analysis with a graphical model inference framework that assumes the underlying ecological association network is sparse. To reconstruct the network, SPIEC-EASI relies on algorithms for sparse neighborhood and inverse covariance selection. To provide a synthetic benchmark in the absence of an experimentally validated gold-standard network, SPIEC-EASI is accompanied by a set of computational tools to generate OTU count data from a set of diverse underlying network topologies. SPIEC

  4. Ecological perspectives on synthetic biology: insights from microbial population biology

    PubMed Central

    Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID

  5. Ecological perspectives on synthetic biology: insights from microbial population biology.

    PubMed

    Escalante, Ana E; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems.

  6. Dietary synbiotic application modulates Atlantic salmon (Salmo salar) intestinal microbial communities and intestinal immunity.

    PubMed

    Abid, A; Davies, S J; Waines, P; Emery, M; Castex, M; Gioacchini, G; Carnevali, O; Bickerdike, R; Romero, J; Merrifield, D L

    2013-12-01

    A feeding trial was conducted to determine the effect of dietary administration of Pediococcus acidilactici MA18/5M and short chain fructooligosaccharides (scFOS) on Atlantic salmon (Salmo salar L.) intestinal health. Salmon (initial average weight 250 g) were allocated into triplicate sea pens and were fed either a control diet (commercial diet: 45% protein, 20% lipid) or a synbiotic treatment diet (control diet + P. acidilactici at 3.5 g kg(-1) and 7 g kg(-1) scFOS) for 63 days. At the end of this period, fish were sampled for intestinal microbiology, intestinal histology and the expression of selected immune-related genes (IL1β, TNFα, IL8, TLR3 and MX-1) in the intestine. Compared to the control fish, the total bacterial levels were significantly lower in the anterior mucosa, posterior mucosa and posterior digesta of the synbiotic fed fish. qPCR revealed good recovery (log 6 bacteria g(-1)) of the probiotic in the intestinal digesta of the synbiotic fed fish and PCR-DGGE revealed that the number of OTUs, as well as the microbial community diversity and richness were significantly higher in the anterior digesta of the synbiotic fed fish than the control. Compared to the control fed fish, the mucosal fold (villi) length and the infiltration of epithelial leucocytes were significantly higher in the anterior and posterior intestine, respectively, in the synbiotic group. Real-time PCR demonstrated that all of the genes investigated were significantly up-regulated in the anterior and posterior intestine of the synbiotic fed salmon, compared to the control group. At the systemic level, serum lysozyme activity was significantly higher in the synbiotic fed fish and growth performance, feed utilisation and biometric measurements (condition factor, gutted weight and gut loss) were not affected. Together these results suggest that the synbiotic modulation of the gut microbiota has a protective action on the intestinal mucosal cells, improving morphology and stimulating

  7. The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.

    PubMed

    Kim, Hyeun Bum; Isaacson, Richard E

    2015-06-12

    The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors.

  8. [Engineering issues of microbial ecology in space agriculture].

    PubMed

    Yamashita, Masamichi; Ishikawa, Yoji; Oshima, Tairo

    2005-03-01

    Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define

  9. Ecological restoration alters microbial communities in mine tailings profiles

    PubMed Central

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-01-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings. PMID:27126064

  10. Ecological restoration alters microbial communities in mine tailings profiles.

    PubMed

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-04-29

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

  11. Ecological restoration alters microbial communities in mine tailings profiles

    NASA Astrophysics Data System (ADS)

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-04-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

  12. Microbial fuel cells and microbial ecology: applications in ruminant health and production research.

    PubMed

    Bretschger, Orianna; Osterstock, Jason B; Pinchak, William E; Ishii, Shun'ichi; Nelson, Karen E

    2010-04-01

    Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H(2)) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H(2)in the rumen. Given the crucial role that H(2) plays in ruminant digestion, it is desirable to understand the microbial relationships that control H(2) partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research.

  13. Microbial Fuel Cells and Microbial Ecology: Applications in Ruminant Health and Production Research

    PubMed Central

    Osterstock, Jason B.; Pinchak, William E.; Ishii, Shun’ichi; Nelson, Karen E.

    2009-01-01

    Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H2) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H2in the rumen. Given the crucial role that H2 plays in ruminant digestion, it is desirable to understand the microbial relationships that control H2 partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research. PMID:20024685

  14. Microbial ecology of the cryosphere: sea ice and glacial habitats.

    PubMed

    Boetius, Antje; Anesio, Alexandre M; Deming, Jody W; Mikucki, Jill A; Rapp, Josephine Z

    2015-11-01

    The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities.

  15. Energy, ecology and the distribution of microbial life

    PubMed Central

    Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

    2013-01-01

    Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

  16. Intestinal Intraepithelial Lymphocyte-Enterocyte Crosstalk Regulates Production of Bactericidal Angiogenin 4 by Paneth Cells upon Microbial Challenge

    PubMed Central

    Dalton, Jane E.; Overweg, Karin; Egan, Charlotte E.; Bongaerts, Roy J.; Newton, Darren J.; Cruickshank, Sheena M.; Andrew, Elizabeth M.; Carding, Simon R.

    2013-01-01

    Antimicrobial proteins influence intestinal microbial ecology and limit proliferation of pathogens, yet the regulation of their expression has only been partially elucidated. Here, we have identified a putative pathway involving epithelial cells and intestinal intraepithelial lymphocytes (iIELs) that leads to antimicrobial protein (AMP) production by Paneth cells. Mice lacking γδ iIELs (TCRδ-/-) express significantly reduced levels of the AMP angiogenin 4 (Ang4). These mice were also unable to up-regulate Ang4 production following oral challenge by Salmonella, leading to higher levels of mucosal invasion compared to their wild type counterparts during the first 2 hours post-challenge. The transfer of γδ iIELs from wild type (WT) mice to TCRδ-/- mice restored Ang4 production and Salmonella invasion levels were reduced to those obtained in WT mice. The ability to restore Ang4 production in TCRδ-/- mice was shown to be restricted to γδ iIELs expressing Vγ7-encoded TCRs. Using a novel intestinal crypt co-culture system we identified a putative pathway of Ang4 production initiated by exposure to Salmonella, intestinal commensals or microbial antigens that induced intestinal epithelial cells to produce cytokines including IL‑23 in a TLR-mediated manner. Exposure of TCR-Vγ7+ γδ iIELs to IL-23 promoted IL‑22 production, which triggered Paneth cells to secrete Ang4. These findings identify a novel role for γδ iIELs in mucosal defence through sensing immediate epithelial cell cytokine responses and influencing AMP production. This in turn can contribute to the maintenance of intestinal microbial homeostasis and epithelial barrier function, and limit pathogen invasion. PMID:24358364

  17. Microbial mats: an ecological niche for fungi

    PubMed Central

    Cantrell, Sharon A.; Duval-Pérez, Lisabeth

    2013-01-01

    Fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance – EPS) was explored. Fungal diversity is higher during the wet season with Acremonium, Aspergillus, Cladosporium, and Penicillium among the more common genera. Diversity is also higher in the oxic layer and in young and transient mats. Enrichments with xanthan (a model EPS) show that without antibiotics (full community) degradation is faster than enrichments with antibacterial (fungal community) and antifungal (bacterial community) agents, suggesting that degradation is performed by a consortium of organisms (bacteria and fungi). The combined evidence from all experiments indicates that bacteria carried out approximately two-third of the xanthan degradation. The pattern of degradation is similar between seasons and layers but degradation is faster in enrichments from the wet season. The research suggests that fungi thrive in these hypersaline consortia and may participate in the carbon cycle through the degradation of complex carbohydrates. PMID:23577004

  18. A Theoretical Reassessment of Microbial Maintenance and Implications for Microbial Ecology Modeling

    SciTech Connect

    Wang, Gangsheng; Post, Wilfred M

    2012-01-01

    We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a critical reassessment. We provided a rigorous proof that the true growth yield coefficient (YG) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert ( max,H) is higher than those in the other two models ( max,P and max,C), and the difference is the physiological maintenance factor (mq = a); and (3) the overall maintenance coefficient (mT) is more sensitive to mq than to the specific growth rate ( G) and YG. Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.

  19. Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities.

    PubMed

    Song, Hyun-Seob; Renslow, Ryan S; Fredrickson, Jim K; Lindemann, Stephen R

    2015-01-01

    Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community's functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities.

  20. Integrating ecological and engineering concepts of resilience in microbial communities

    DOE PAGES

    Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; ...

    2015-12-01

    We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the twomore » concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.« less

  1. Integrating ecological and engineering concepts of resilience in microbial communities

    SciTech Connect

    Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2015-12-01

    We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.

  2. Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities

    PubMed Central

    Song, Hyun-Seob; Renslow, Ryan S.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2015-01-01

    Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community's functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities. PMID:26648912

  3. Microbial ecology and genomics: A crossroads of opportunity

    SciTech Connect

    Stahl, David A.; Tiedje, James M.

    2002-08-30

    Microbes have dominated life on Earth for most of its 4.5 billionyear history. They are the foundation of the biosphere, controlling the biogeochemical cycles and affecting geology, hydrology, and local and global climates. All life is completely dependent upon them. Humans cannot survive without the rich diversity of microbes, but most microbial species can survive without humans. Extraordinary advances in molecular technology have fostered an explosion of information in microbial biology. It is now known that microbial species in culture poorly represent their natural diversity—which dwarfs conventions established for the visible world. This was revealed over the last decade using newer molecular tools to explore environmental diversity and has sparked an explosive growth in microbial ecology and technologies that may profit from the bounty of natural biochemical diversity. Several colloquia and meetings have helped formulate policy recommendations to enable sustained research programs in these areas. One such colloquium organized by the American Academy of Microbiology (“The Microbial World: Foundation of the Biosphere,” 1997) made two key recommendations: (1) develop a more complete inventory of living organisms and the interagency cooperation needed to accomplish this goal, and (2) develop strategies to harvest this remarkable biological diversity for the benefit of science, technology, and society. Complete genome sequence information was identified as an essential part of strategy development, and the recommendation was made to sequence the genome of at least one species of each of the major divisions of microbial life.

  4. Microbial ecology laboratory procedures manual NASA/MSFC

    NASA Technical Reports Server (NTRS)

    Huff, Timothy L.

    1990-01-01

    An essential part of the efficient operation of any microbiology laboratory involved in sample analysis is a standard procedures manual. The purpose of this manual is to provide concise and well defined instructions on routine technical procedures involving sample analysis and methods for monitoring and maintaining quality control within the laboratory. Of equal importance is the safe operation of the laboratory. This manual outlines detailed procedures to be followed in the microbial ecology laboratory to assure safety, analytical control, and validity of results.

  5. Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes

    PubMed Central

    Weber, Laura G.; Santoro, Alyson E.

    2016-01-01

    ABSTRACT The diverse prokaryotic communities associated with reef-building corals may provide important ecological advantages to their threatened hosts. The consistency of relationships between corals and specific prokaryotes, however, is debated, and the locations where microbially mediated processes occur in the host are not resolved. Here, we examined how the prokaryotic associates of five common Caribbean corals with different evolutionary and ecological traits differ across mucus and tissue habitats. We used physical and chemical separation of coral mucus and tissue and sequencing of partial small-subunit rRNA genes of bacteria and archaea from these samples to demonstrate that coral tissue and mucus harbor unique reservoirs of prokaryotes, with 23 to 49% and 31 to 56% of sequences exclusive to the tissue and mucus habitats, respectively. Across all coral species, we found that 46 tissue- and 22 mucus-specific microbial members consistently associated with the different habitats. Sequences classifying as “Candidatus Amoebophilus,” Bacteroidetes-affiliated intracellular symbionts of amoebae, emerged as previously unrecognized tissue associates of three coral species. This study demonstrates how coral habitat differentiation enables highly resolved examination of ecological interactions between corals and their associated microorganisms and identifies previously unrecognized tissue and mucus associates of Caribbean corals for future targeted study. IMPORTANCE This study demonstrates that coral tissue or mucus habitats structure the microbiome of corals and that separation of these habitats facilitates identification of consistent microbial associates. Using this approach, we demonstrated that sequences related to “Candidatus Amoebophilus,” recognized intracellular symbionts of amoebae, were highly associated with the tissues of Caribbean corals and possibly endosymbionts of a protistan host within corals, adding a further degree of intricacy to coral

  6. Application of multivariate statistical techniques in microbial ecology.

    PubMed

    Paliy, O; Shankar, V

    2016-03-01

    Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large-scale ecological data sets. In particular, noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amount of data, powerful statistical techniques of multivariate analysis are well suited to analyse and interpret these data sets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular data set. In this review, we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and data set structure.

  7. Application of multivariate statistical techniques in microbial ecology

    PubMed Central

    Paliy, O.; Shankar, V.

    2016-01-01

    Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large scale ecological datasets. Especially noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions, and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amounts of data, powerful statistical techniques of multivariate analysis are well suited to analyze and interpret these datasets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular dataset. In this review we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive, and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and dataset structure. PMID:26786791

  8. The biofilm ecology of microbial biofouling, biocide resistance and corrosion

    SciTech Connect

    White, D.C. |; Kirkegaard, R.D.; Palmer, R.J. Jr.; Flemming, C.A.; Chen, G.; Leung, K.T.; Phiefer, C.B.; Arrage, A.A. |

    1997-06-01

    In biotechnological or bioremediation processes it is often the aim to promote biofilm formation, and maintain active, high density biomass. In other situations, biofouling can seriously restrict effective heat transport, membrane processes, and potentate macrofouling with loss of transportation efficiency. In biotechnological or bioremediation processes it is often the aim to promote biofilm formation, and maintain active, high density biomass. In other situations, biofouling can seriously restrict effective heat transport, membrane processes, and potentate macrofouling with loss of transportation efficiency. Heterogeneous distribution of microbes and/or their metabolic activity can promote microbially influenced corrosion (MIC) which is a multibillion dollar problem. Consequently, it is important that biofilm microbial ecology be understood so it can be manipulated rationally. It is usually simple to select organisms that form biofilms by flowing a considerably dilute media over a substratum, and propagating the organisms that attach. To examine the biofilm most expeditiously, the biomass accumulation, desquamation, and metabolic activities need to be monitored on-line and non-destructively. This on-line monitoring becomes even more valuable if the activities can be locally mapped in time and space within the biofilm. Herein the authors describe quantitative measures of microbial biofouling, the ecology of pathogens in drinking water distributions systems, and localization of microbial biofilms and activities with localized MIC.

  9. Quantitative Analysis of the Human Airway Microbial Ecology Reveals a Pervasive Signature for Cystic Fibrosis

    PubMed Central

    Blainey, Paul C.; Milla, Carlos E.; Cornfield, David N.; Quake, Stephen R.

    2014-01-01

    Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the gene encoding the CF transmembrane conductance regulator. Disruption of electrolyte homeostasis at mucosal surfaces leads to severe lung, pancreatic, intestinal, hepatic, and reproductive abnormalities. Loss of lung function as a result of chronic lung disease is the primary cause of death from CF. Using high-throughput sequencing to survey microbes in the sputum of 16 CF patients and 9 control individuals, we identified diverse microbial communities in the healthy samples, contravening conventional wisdom that healthy airways are not significantly colonized. Comparing these communities with those from the CF patients revealed significant differences in microbial ecology, including differential representation of uncultivated phylotypes. Despite patient-specific differences, our analysis revealed a focal microbial profile characteristic of CF. The profile differentiated case and control groups even when classically recognized CF pathogens were excluded. As a control, lung explant tissues were also processed from a group of patients with pulmonary disease. The findings in lung tissue corroborated the presence of taxa identified in the sputum samples. Comparing the sequencing results with clinical data indicated that diminished microbial diversity is associated with severity of pulmonary inflammation within our adult CF cohort. PMID:23019655

  10. Estimating and mapping ecological processes influencing microbial community assembly

    DOE PAGES

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; ...

    2015-05-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recentlymore » developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.« less

  11. Estimating and mapping ecological processes influencing microbial community assembly

    SciTech Connect

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

    2015-05-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.

  12. Estimating and mapping ecological processes influencing microbial community assembly

    PubMed Central

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

    2015-01-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth. PMID:25983725

  13. Plasmid-mediated susceptibility to intestinal microbial antagonisms in Escherichia coli.

    PubMed

    Andremont, A; Gerbaud, G; Tancrède, C; Courvalin, P

    1985-09-01

    Self-transferable plasmid pIP1100 confers to Escherichia coli an unusually high level of resistance (1 to 2 mg/ml) to erythromycin by production of an erythromycin esterase. The effect of pIP1100 on the destiny of E. coli strains in the intestines of gnotobiotic mice was studied. In germfree mice, pIP1100 was efficiently transferred to a plasmid-free E. coli recipient. Intestinal counts of the donor, the recipient, and the transconjugants were greater than 8.5 log CFU/g of feces. When erythromycin was added to the diet of the mice, counts of the plasmid-bearing strains were only slightly lowered and partial inactivation of erythromycin was observed in the feces. Transfer of pIP1100 also occurred in human-flora-associated mice. In this model all the E. coli strains were subject to microbial antagonisms caused by the anaerobic components of the flora. However, strains harboring pIP1100 were strongly inhibited (less than 2.5 log CFU/g of feces), whereas their plasmid-free counterparts persisted at much higher population levels (greater than 5.2 log CFU/g of feces). The ecological disadvantage conferred by pIP1100 to E. coli when a complex human flora was concomitantly present in the intestine of the mice persisted during erythromycin administration. These results provide an explanation for the low incidence of isolation of highly erythromycin-resistant E. coli strains despite the extensive use of the antibiotic.

  14. Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

    SciTech Connect

    White, G.J.

    1996-08-01

    Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.

  15. Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice

    PubMed Central

    Huang, Yen-Lin; Chassard, Christophe; Hausmann, Martin; von Itzstein, Mark; Hennet, Thierry

    2015-01-01

    Rapid shifts in microbial composition frequently occur during intestinal inflammation, but the mechanisms underlying such changes remain elusive. Here we demonstrate that an increased caecal sialidase activity is critical in conferring a growth advantage for some bacteria including Escherichia coli (E. coli) during intestinal inflammation in mice. This sialidase activity originates among others from Bacteroides vulgatus, whose intestinal levels expand after dextran sulphate sodium administration. Increased sialidase activity mediates the release of sialic acid from intestinal tissue, which promotes the outgrowth of E. coli during inflammation. The outburst of E. coli likely exacerbates the inflammatory response by stimulating the production of pro-inflammatory cytokines by intestinal dendritic cells. Oral administration of a sialidase inhibitor and low levels of intestinal α2,3-linked sialic acid decrease E. coli outgrowth and the severity of colitis in mice. Regulation of sialic acid catabolism opens new perspectives for the treatment of intestinal inflammation as manifested by E. coli dysbiosis. PMID:26303108

  16. Microbial interactions and the ecology and evolution of Hawaiian Drosophilidae

    PubMed Central

    O’Connor, Timothy K.; Humphrey, Parris T.; Lapoint, Richard T.; Whiteman, Noah K.; O’Grady, Patrick M.

    2014-01-01

    Adaptive radiations are characterized by an increased rate of speciation and expanded range of habitats and ecological niches exploited by those species. The Hawaiian Drosophilidae is a classic adaptive radiation; a single ancestral species colonized Hawaii approximately 25 million years ago and gave rise to two monophyletic lineages, the Hawaiian Drosophila and the genus Scaptomyza. The Hawaiian Drosophila are largely saprophagous and rely on approximately 40 endemic plant families and their associated microbes to complete development. Scaptomyza are even more diverse in host breadth. While many species of Scaptomyza utilize decomposing plant substrates, some species have evolved to become herbivores, parasites on spider egg masses, and exploit microbes on living plant tissue. Understanding the origin of the ecological diversity encompassed by these nearly 700 described species has been a challenge. The central role of microbes in drosophilid ecology suggests bacterial and fungal associates may have played a role in the diversification of the Hawaiian Drosophilidae. Here we synthesize recent ecological and microbial community data from the Hawaiian Drosophilidae to examine the forces that may have led to this adaptive radiation. We propose that the evolutionary success of the Hawaiian Drosophilidae is due to a combination of factors, including adaptation to novel ecological niches facilitated by microbes. PMID:25566196

  17. The composition of the zebrafish intestinal microbial community varies across development

    PubMed Central

    Zac Stephens, W; Burns, Adam R; Stagaman, Keaton; Wong, Sandi; Rawls, John F; Guillemin, Karen; Bohannan, Brendan J M

    2016-01-01

    The assembly of resident microbial communities is an important event in animal development; however, the extent to which this process mirrors the developmental programs of host tissues is unknown. Here we surveyed the intestinal bacteria at key developmental time points in a sibling group of 135 individuals of a model vertebrate, the zebrafish (Danio rerio). Our survey revealed stage-specific signatures in the intestinal microbiota and extensive interindividual variation, even within the same developmental stage. Microbial community shifts were apparent during periods of constant diet and environmental conditions, as well as in concert with dietary and environmental change. Interindividual variation in the intestinal microbiota increased with age, as did the difference between the intestinal microbiota and microbes in the surrounding environment. Our results indicate that zebrafish intestinal microbiota assemble into distinct communities throughout development, and that these communities are increasingly different from the surrounding environment and from one another. PMID:26339860

  18. Sampling microbial communities in the National Ecological Observatory Network

    NASA Astrophysics Data System (ADS)

    Adams, H. E.; Parnell, J.; Powell, H.

    2012-12-01

    The National Ecological Observatory Network (NEON) is a national-scale research platform to enable the community to assess impacts of climate change, land-use change, and invasive species on ecosystem structure and function at regional and continental scales. The NEON Observatory will collect data on aquatic organisms over 30 years in 36 sites across the United States, including Alaska and Puerto Rico as well as terrestrial organisms at 60 sites including Hawaii. Included in the biological measurements are microbial measurements in terrestrial and aquatic environments, including small, wadeable streams and shallow lakes. Microbial sampling in both aquatic and terrestrial habitats is being planned to coincide with biogeochemical sampling due to similarity of time scale and influence of external drivers. Aquatic sampling is geared toward species diversity and function. Terrestrial sampling aims to collect data on diversity, function, and spatial distribution dynamics. We are in the process of prioritizing data products, so that the most dynamic processes such as enzymatic activity will be measured more frequently and more intensive measures such as metagenome sequence data will be measured on a periodic basis. Here we present our initial microbial sampling strategy and invite the community to provide comment on the design and learn about microbial data products from the Observatory.

  19. Mess management in microbial ecology: Rhetorical processes of disciplinary integration

    NASA Astrophysics Data System (ADS)

    McCracken, Christopher W.

    As interdisciplinary work becomes more common in the sciences, research into the rhetorical processes mediating disciplinary integration becomes more vital. This dissertation, which takes as its subject the integration of microbiology and ecology, combines a postplural approach to rhetoric of science research with Victor Turner's "social drama" analysis and a third-generation activity theory methodological framework to identify conceptual and practical conflicts in interdisciplinary work and describe how, through visual and verbal communication, scientists negotiate these conflicts. First, to understand the conflicting disciplinary principles that might impede integration, the author conducts a Turnerian analysis of a disciplinary conflict that took place in the 1960s and 70s, during which American ecologists and biologists debated whether they should participate in the International Biological Program (IBP). Participation in the IBP ultimately contributed to the emergence of ecology as a discipline distinct from biology, and Turnerian social drama analysis of the debate surrounding participation lays bare the conflicting principles separating biology and ecology. Second, to answer the question of how these conflicting principles are negotiated in practice, the author reports on a yearlong qualitative study of scientists working in a microbial ecology laboratory. Focusing specifically on two case studies from this fieldwork that illustrate the key concept of textually mediated disciplinary integration, the author's analysis demonstrates how scientific objects emerge in differently situated practices, and how these objects manage to cohere despite their multiplicity through textually mediated rhetorical processes of calibration and alignment.

  20. Revisiting life strategy concepts in environmental microbial ecology.

    PubMed

    Ho, Adrian; Di Lonardo, D Paolo; Bodelier, Paul L E

    2017-03-01

    Microorganisms are physiologically diverse, possessing disparate genomic features and mechanisms for adaptation (functional traits), which reflect on their associated life strategies and determine at least to some extent their prevalence and distribution in the environment. Unlike animals and plants, there is an unprecedented diversity and intractable metabolic versatility among bacteria, making classification or grouping these microorganisms based on their functional traits as has been done in animal and plant ecology challenging. Nevertheless, based on representative pure cultures, microbial traits distinguishing different life strategies had been proposed, and had been the focus of previous reviews. In the environment, however, the vast majority of naturally occurring microorganisms have yet to be isolated, restricting the association of life strategies to broad phylogenetic groups and/or physiological characteristics. Here, we reviewed the literature to determine how microbial life strategy concepts (i.e. copio- and oligotrophic strategists, and competitor-stress tolerator-ruderals framework) are applied in complex microbial communities. Because of the scarcity of direct empirical evidence elucidating the associated life strategies in complex communities, we rely heavily on observational studies determining the response of microorganisms to (a)biotic cues (e.g. resource availability) to infer microbial life strategies. Although our focus is on the life strategies of bacteria, parallels were drawn from the fungal community. Our literature search showed inconsistency in the community response of proposed copiotrophic- and oligotrophic-associated microorganisms (phyla level) to changing environmental conditions. This suggests that tracking microorganisms at finer phylogenetic and taxonomic resolution (e.g. family level or lower) may be more effective to capture changes in community response and/or that edaphic factors exert a stronger effect in community response

  1. A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.

    PubMed

    Wang, Gangsheng; Post, Wilfred M

    2012-09-01

    We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.

  2. Effects of mannan oligosaccharide and virginiamycin on the cecal microbial community and intestinal morphology of chickens raised under suboptimal conditions.

    PubMed

    Pourabedin, Mohsen; Xu, Zhengxin; Baurhoo, Bushansingh; Chevaux, Eric; Zhao, Xin

    2014-05-01

    There is an increasing movement against use of antibiotic growth promoters in animal feed. Prebiotic supplementation is a potential alternative to enhance the host's natural defense through modulation of gut microbiota. In the present study, the effect of mannan oligosaccharide (MOS) and virginiamycin (VIRG) on cecal microbial ecology and intestinal morphology of broiler chickens raised under suboptimal conditions was evaluated. MOS and VIRG induced different bacterial community structures, as revealed by denaturing gradient gel electrophoresis of 16S rDNA. The antibiotic treatment reduced cecal microbial diversity while the community equitability increased. A higher bacterial diversity was observed in the cecum of MOS-supplemented birds. Quantitative polymerase chain reaction results indicated that MOS changed the cecal microbiota in favor of the Firmicutes population but not the Bacteroidetes population. No difference was observed in total bacterial counts among treatments. MOS promoted the growth of Lactobacillus spp. and Bifidobacterium spp. in the cecum and increased villus height and goblet cell numbers in the ileum and jejunum. These results provide a deeper insight into the microbial ecological changes after supplementation of MOS prebiotic in poultry diets.

  3. The role of hyperparasitism in microbial pathogen ecology and evolution

    PubMed Central

    Parratt, Steven R; Laine, Anna-Liisa

    2016-01-01

    Many micro-organisms employ a parasitic lifestyle and, through their antagonistic interactions with host populations, have major impacts on human, agricultural and natural ecosystems. Most pathogens are likely to host parasites of their own, that is, hyperparasites, but how nested chains of parasites impact on disease dynamics is grossly neglected in the ecological and evolutionary literature. In this minireview we argue that the diversity and dynamics of micro-hyperparasites are an important component of natural host–pathogen systems. We use the current literature from a handful of key systems to show that observed patterns of pathogen virulence and disease dynamics may well be influenced by hyperparasites. Exploring these factors will shed light on many aspects of microbial ecology and disease biology, including resistance–virulence evolution, apparent competition, epidemiology and ecosystem stability. Considering the importance of hyperparasites in natural populations will have applied consequences for the field of biological control and therapeutic science, where hyperparastism is employed as a control mechanism but not necessarily ecologically understood. PMID:26784356

  4. Ecological parameters influencing microbial diversity and stability of traditional sourdough.

    PubMed

    Minervini, Fabio; De Angelis, Maria; Di Cagno, Raffaella; Gobbetti, Marco

    2014-02-03

    The quality of some leavened, sourdough baked goods is not always consistent, unless a well propagated sourdough starter culture is used for the dough fermentation. Among the different types of sourdough used, the traditional sourdough has attracted the interest of researchers, mainly because of its large microbial diversity, especially with respect to lactic acid bacteria. Variation in this diversity and the factors that cause it will impact on quality and is the subject of this review. Sourdough microbial diversity is mainly caused by the following factors: (i) sourdough is obtained through spontaneous, multi-step fermentation; (ii) it is propagated using flour, whose nutrient content may vary according to the batch and to the crop, and which is naturally contaminated by microorganisms; and (iii) it is propagated under peculiar technological parameters, which vary depending on the historical and cultural background and type of baked good. In the population dynamics leading from flour to mature sourdough, lactic acid bacteria (several species of Lactobacillus sp., Leuconostoc sp., and Weissella sp.) and yeasts (mainly Saccharomyces cerevisiae and Candida sp.) outcompete other microbial groups contaminating flour, and interact with each other at different levels. Ecological parameters qualitatively and quantitatively affecting the dominant sourdough microbiota may be classified into specific technological parameters (e.g., percentage of sourdough used as inoculum, time and temperature of fermentation) and parameters that are not fully controlled by those who manage the propagation of sourdough (e.g., chemical, enzyme and microbial composition of flour). Although some sourdoughs have been reported to harbour a persistent dominant microbiota, the stability of sourdough ecosystem during time is debated. Indeed, several factors may interfere with the persistence of species and strains associations that are typical of a given sourdough: metabolic adaptability to the

  5. Perspectives of the microbial carbon pump with special references to microbial respiration and ecological efficiency

    NASA Astrophysics Data System (ADS)

    Dang, H.; Jiao, N.

    2014-01-01

    Although respiration consumes fixed carbon and produce CO2, it provides energy for essential biological processes of an ecosystem, including the microbial carbon pump (MCP). In MCP-driving biotransformation of labile DOC to recalcitrant DOC (RDOC), microbial respiration provides the metabolic energy for environmental organic substrate sensing, cellular enzyme syntheses and catalytic processes such as uptake, secretion, modification, fixation and storage of carbon compounds. The MCP efficiency of a heterotrophic microorganism is thus related to its energy production efficiency and hence to its respiration efficiency. Anaerobically respiring microbes usually have lower energy production efficiency and lower energy-dependent carbon transformation efficiency, and consequently lower MCP efficiency at per cell level. This effect is masked by the phenomena that anoxic environments often store more organic matter. Here we point out that organic carbon preservation and RDOC production is different in mechanisms, and anaerobically respiring ecosystems could also have lower MCP ecological efficiency. Typical cases can be found in large river estuarine ecosystems. Due to strong terrigenous input of nutrients and organic matter, estuarine ecosystems usually experience intense heterotrophic respiration processes that rapidly consume dissolved oxygen, potentially producing hypoxic and anoxic zones in the water column. The lowered availability of dissolved oxygen and the excessive supply of nutrients such as nitrate from river input prompt enhanced anaerobic respiration processes. Thus, some nutrients may be consumed by anaerobically respiring heterotrophic microorganisms, instead of being utilized by phytoplankton for carbon fixation and primary production. In this situation, the ecological functioning of the estuarine ecosystem is altered and the ecological efficiency is lowered, as less carbon is fixed and less energy is produced. Ultimately this would have negatively impacts

  6. What can we learn from the microbial ecological interactions associated with polymicrobial diseases?

    PubMed

    Antiabong, J F; Boardman, W; Ball, A S

    2014-03-15

    Periodontal diseases in humans and animals are model polymicrobial diseases which are associated with a shift in the microbial community structure and function; there is therefore a need to investigate these diseases from a microbial ecological perspective. This review highlights three important areas of microbial ecological investigation of polymicrobial diseases and the lessons that could be learnt: (1) identification of disease-associated microbes and the implications for choice of anti-infective treatment; (2) the implications associated with vaccine design and development and (3) application of the dynamics of microbial interaction in the discovery of novel anti-infective agents. This review emphasises the need to invigorate microbial ecological approaches to the study of periodontal diseases and other polymicrobial diseases for greater understanding of the ecological interactions between and within the biotic and abiotic factors of the environment.

  7. Gastrointestinal microbial ecology and the safety of our food supply as related to Salmonella.

    PubMed

    Callaway, T R; Edrington, T S; Anderson, R C; Byrd, J A; Nisbet, D J

    2008-04-01

    Salmonella causes an estimated 1.3 million human foodborne illnesses and more than 500 deaths each year in the United States, representing an annual estimated cost to the economy of approximately $2.4 billion. Salmonella enterica comprises more than 2,500 serotypes. With this genetic and environmental diversity, serotypes are adapted to live in a variety of hosts, which may or may not manifest with clinical illness. Thus, Salmonella presents a multifaceted threat to food production and safety. Salmonella have been isolated from all food animals and can cause morbidity and mortality in swine, cattle, sheep, and poultry. The link between human salmonellosis and host animals is most clear in poultry. During the early part of the 20th century, a successful campaign was waged to eliminate fowl typhoid caused by Salmonella Gallinarum/Pullorum. Microbial ecology is much like macroecology; environmental niches are filled by adapted and specialized species. Elimination of S. Gallinarum cleared a niche in the on-farm and intestinal microbial ecology that was quickly exploited by Salmonella Enteritidis and other serotypes that live in other hosts, such as rodents. In the years since, human salmonellosis cases linked to poultry have increased to the point that uncooked chicken and eggs are regarded as toxic in the zeitgeist. Salmonellosis caused by poultry products have increased significantly in the past 5 yr, leading to a USDA Food Safety and Inspection Service "Salmonella Attack Plan" that aims to reduce the incidence of Salmonella in chickens below the current 19%. The prevalence of Salmonella in swine and cattle is lower, but still poses a threat to food safety and production efficiency. Thus, approaches to reducing Salmonella in animals must take into consideration that the microbial ecology of the animal is a critical factor that should be accounted for when designing intervention strategies. Use of competitive exclusion, sodium chlorate, vaccination, and bacteriophage

  8. Oral Microbial Ecology and the Role of Salivary Immunoglobulin A

    PubMed Central

    Marcotte, Harold; Lavoie, Marc C.

    1998-01-01

    In the oral cavity, indigenous bacteria are often associated with two major oral diseases, caries and periodontal diseases. These diseases seem to appear following an inbalance in the oral resident microbiota, leading to the emergence of potentially pathogenic bacteria. To define the process involved in caries and periodontal diseases, it is necessary to understand the ecology of the oral cavity and to identify the factors responsible for the transition of the oral microbiota from a commensal to a pathogenic relationship with the host. The regulatory forces influencing the oral ecosystem can be divided into three major categories: host related, microbe related, and external factors. Among host factors, secretory immunoglobulin A (SIgA) constitutes the main specific immune defense mechanism in saliva and may play an important role in the homeostasis of the oral microbiota. Naturally occurring SIgA antibodies that are reactive against a variety of indigenous bacteria are detectable in saliva. These antibodies may control the oral microbiota by reducing the adherence of bacteria to the oral mucosa and teeth. It is thought that protection against bacterial etiologic agents of caries and periodontal diseases could be conferred by the induction of SIgA antibodies via the stimulation of the mucosal immune system. However, elucidation of the role of the SIgA immune system in controlling the oral indigenous microbiota is a prerequisite for the development of effective vaccines against these diseases. The role of SIgA antibodies in the acquisition and the regulation of the indigenous microbiota is still controversial. Our review discusses the importance of SIgA among the multiple factors that control the oral microbiota. It describes the oral ecosystems, the principal factors that may control the oral microbiota, a basic knowledge of the secretory immune system, the biological functions of SIgA, and, finally, experiments related to the role of SIgA in oral microbial ecology

  9. PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp ( Marsupenaeus japonicus)

    NASA Astrophysics Data System (ADS)

    Liu, Huaide; Liu, Mei; Wang, Baojie; Jiang, Keyong; Jiang, Shan); Sun, Shujuan; Wang, Lei

    2010-07-01

    In this study, the intestinal microbiota of kuruma shrimp ( Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp. on intestinal microbial diversity. Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp. amended feed. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were then performed on DNA extracted directly from the guts. Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons, and distinct bands in the gels were sequenced. The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp. and uncultured gamma proteobacterium. Overall, the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.

  10. [The Amben correction of disorders in the intestinal microbial colonization of newborn infants with perinatal pathology].

    PubMed

    Iakushenko, M N; Tkhagapsoeva, Zh A; Bondarenko, V M

    1998-01-01

    The examination of 49 newborn infants revealed that at the early neonatal period the character of the microbial colonization of the intestine depended on the kind of perinatal pathology: in lesions of the central nervous system and conjugation jaundice the deficiency of Bifidobacterium and Escherichia was detected; in hemolytic disease opportunistic bacteria were dominant simultaneously with the deficiency of lactoflora. The study of these infants, divided into two groups differing in the administration of Amben (an inhibitor of proteolytic enzymes), showed the efficiency of Amben which stimulated the growth and development of resident microflora in the intestine, thus contributing to the maintenance of eubiosis in a given group of infants with perinatal pathology.

  11. Flagella, flexibility and flow: Physical processes in microbial ecology

    NASA Astrophysics Data System (ADS)

    Brumley, D. R.; Rusconi, R.; Son, K.; Stocker, R.

    2015-12-01

    How microorganisms interact with their environment and with their conspecifics depends strongly on their mechanical properties, on the hydrodynamic signatures they generate while swimming and on fluid flows in their environment. The rich fluid-structure interaction between flagella - the appendages microorganisms use for propulsion - and the surrounding flow, has broad reaching effects for both eukaryotic and prokaryotic microorganisms. Here, we discuss selected recent advances in our understanding of the physical ecology of microorganisms, which have hinged on the ability to directly interrogate the movement of individual cells and their swimming appendages, in precisely controlled fluid environments, and to image them at appropriately fast timescales. We review how a flagellar buckling instability can unexpectedly serve a fundamental function in the motility of bacteria, we elucidate the role of hydrodynamics and flexibility in the emergent properties of groups of eukaryotic flagella, and we show how fluid flows characteristic of microbial habitats can strongly bias the migration and spatial distribution of bacteria. The topics covered here are illustrative of the potential inherent in the adoption of experimental methods and conceptual frameworks from physics in understanding the lives of microorganisms.

  12. Microbial ecology of acid strip mine lakes in southern Indiana

    SciTech Connect

    Gyure, R.A.

    1986-01-01

    In this study, the author examined the limnology and microbial ecology of two acid strip mine lakes in the Greene-Sullivan State Forest near Dugger, Indiana. Reservoir 29 is a larger lake (225 ha) with water column pH of 2.7 and sediment pH of 3.8. Lake B, a smaller (20 ha) lake to the south of Reservoir 29, also has an acidic water column (pH 3.4) but more neutral sediments (pH 6.2). Both have very high sulfate concentrations: 20-30 mM in the water column and as high as 100 mM in the hypolimnion of Lake B. Low allochthonous carbon and nutrient input characterize these lakes as oligotrophic, although algal biomass is higher than would be expected for this trophic status. In both lakes, algal populations are not diverse, with a few species of single-celled Chlorophyta and euglenoids dominating. Algal biomass is concentrated in a thin 10 cm layer at the hypolimnion/metalimnion interface, although light intensity at this depth is low and severely limits productivity. Bacterial activity based on /sup 14/C-glucose incorporation is highest in the hypolimnion of both lakes, and sulfate-reduction is a dominant process in the sediments. Rates of sulfate-reduction compare with those in other freshwater environments, but are not as high as rates measured in high sulfate systems like saltmarsh and marine sediments.

  13. MICROBIAL ECOLOGY OF THE SUBSURFACE AT AN ABANDONED CREOSOTE WASTE SITE

    EPA Science Inventory

    The microbial ecology of pristine, slightly contaminated, and heavily contaminated subsurface materials, and four subsurface materials on the periphery of the plume at an abandoned creosote waste site was investigated. Except for the unsaturated zone of the heavily contaminated m...

  14. Deregulation of intestinal anti-microbial defense by the dietary additive, maltodextrin.

    PubMed

    Nickerson, Kourtney P; Chanin, Rachael; McDonald, Christine

    2015-01-01

    Inflammatory bowel disease (IBD) is a complex, multi-factorial disease thought to arise from an inappropriate immune response to commensal bacteria in a genetically susceptible person that results in chronic, cyclical, intestinal inflammation. Dietary and environmental factors are implicated in the initiation and perpetuation of IBD; however, a singular causative agent has not been identified. As of now, the role of environmental priming or triggers in IBD onset and pathogenesis are not well understood, but these factors appear to synergize with other disease susceptibility factors. In previous work, we determined that the polysaccharide dietary additive, maltodextrin (MDX), impairs cellular anti-bacterial responses and suppresses intestinal anti-microbial defense mechanisms. In this addendum, we review potential mechanisms for dietary deregulation of intestinal homeostasis, postulate how dietary and genetic risk factors may combine to result in disease pathogenesis, and discuss these ideas in the context of recent findings related to dietary interventions for IBD.

  15. The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins.

    PubMed

    Pinto, Elsa; Anselmo, Marisol; Calha, Manuela; Bottrill, Andrew; Duarte, Isabel; Andrew, Peter W; Faleiro, Maria L

    2017-02-01

    In this study, the intestinal microbial proteome of children with established type 1 diabetes (T1D) was compared with the proteome of healthy children (Control) with the aim to identify differences in the activity of the intestinal microbiota that not only will contribute to a deeper knowledge of the functionality of the gut in these children but also may provide new approaches to improve the control of the disease. Faecal protein extracts collected from three T1D children (aged 9.3±0.6 years) and three Control children (aged 9.3±1.5 years) were analysed using a combination of 2D gel electrophoresis and spectral counting. The results evidenced markedly differences between the intestinal proteome of T1D children and the Control. The T1D microbial intestinal proteome was enriched with proteins of clostridial cluster XVa and cluster IV and Bacteroides. In contrast, the Control proteome was enriched with bifidobacterial proteins. In both groups, proteins with moonlight function were observed. Human proteins also distinguished the two groups with T1D children depleted in exocrine pancreatic enzymes.

  16. Contrasting Ecological Processes and Functional Compositions Between Intestinal Bacterial Community in Healthy and Diseased Shrimp.

    PubMed

    Zhu, Jinyong; Dai, Wenfang; Qiu, Qiongfen; Dong, Chunming; Zhang, Jinjie; Xiong, Jinbo

    2016-11-01

    Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphaproteobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.

  17. [Effects of biochar on microbial ecology in agriculture soil: a review].

    PubMed

    Ding, Yan-Li; Liu, Jie; Wang, Ying-Ying

    2013-11-01

    Biochar, as a new type of soil amendment, has been obtained considerable attention in the research field of environmental sciences worldwide. The studies on the effects of biochar in improving soil physical and chemical properties started quite earlier, and already covered the field of soil microbial ecology. However, most of the studies considered the soil physical and chemical properties and the microbial ecology separately, with less consideration of their interactions. This paper summarized and analyzed the interrelationships between the changes of soil physical and chemical properties and of soil microbial community after the addition of biochar. Biochar can not only improve soil pH value, strengthen soil water-holding capacity, increase soil organic matter content, but also affect soil microbial community structure, and alter the abundance of soil bacteria and fungi. After the addition of biochar, the soil environment and soil microorganisms are interacted each other, and promote the improvement of soil microbial ecological system together. This review was to provide a novel perspective for the in-depth studies of the effects of biochar on soil microbial ecology, and to promote the researches on the beneficial effects of biochar to the environment from ecological aspect. The methods to improve the effectiveness of biochar application were discussed, and the potential applications of biochar in soil bioremediation were further analyzed.

  18. Functional Ecological Gene Networks to Reveal the Changes Among Microbial Interactions Under Elevated Carbon Dioxide Conditions

    SciTech Connect

    Deng, Ye; Zhou, Jizhong; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-05-17

    Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are fundamentally important for research in microbial ecology, systems microbiology, and global change.

  19. The microbial diversity, distribution, and ecology of permafrost in China: a review.

    PubMed

    Hu, Weigang; Zhang, Qi; Tian, Tian; Cheng, Guodong; An, Lizhe; Feng, Huyuan

    2015-07-01

    Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

  20. Effectiveness of ecological rescue for altered soil microbial communities and functions.

    PubMed

    Calderón, Kadiya; Spor, Aymé; Breuil, Marie-Christine; Bru, David; Bizouard, Florian; Violle, Cyrille; Barnard, Romain L; Philippot, Laurent

    2017-01-01

    Soil ecosystems worldwide are subjected to marked modifications caused by anthropogenic disturbances and global climate change, resulting in microbial diversity loss and alteration of ecosystem functions. Despite the paucity of studies, restoration ecology provides an appropriate framework for testing the potential of manipulating soil microbial communities for the recovery of ecosystem functioning. We used a reciprocal transplant design in experimentally altered microbial communities to investigate the effectiveness of introducing microbial communities in degraded soil ecosystems to restore N-cycle functioning. Microbial diversity loss resulted in alternative compositional states associated with impaired N-cycle functioning. Here, the addition of complex microbial communities to these altered communities revealed a pivotal role of deterministic community assembly processes. The diversity of some alternative compositional states was successfully increased but without significant restoration of soil N-cycle functioning. However, in the most degraded alternative state, the introduction of new microbial communities caused an overall decrease in phylogenetic diversity and richness. The successful soil colonization by newly introduced species for some compositional states indicates that priority effects could be overridden when attempting to manipulate microbial communities for soil restoration. Altogether, our result showed consistent patterns within restoration treatments with minor idiosyncratic effects. This suggests the predominance of deterministic processes and the predictability of restoration trajectories, which could be used to guide the effective management of microbial community assemblages for ecological restoration of soils.

  1. Host-microbial interactions and regulation of intestinal epithelial barrier function: From physiology to pathology

    PubMed Central

    Yu, Linda Chia-Hui; Wang, Jin-Town; Wei, Shu-Chen; Ni, Yen-Hsuan

    2012-01-01

    The gastrointestinal tract is the largest reservoir of commensal bacteria in the human body, providing nutrients and space for the survival of microbes while concurrently operating mucosal barriers to confine the microbial population. The epithelial cells linked by tight junctions not only physically separate the microbiota from the lamina propria, but also secrete proinflammatory cytokines and reactive oxygen species in response to pathogen invasion and metabolic stress and serve as a sentinel to the underlying immune cells. Accumulating evidence indicates that commensal bacteria are involved in various physiological functions in the gut and microbial imbalances (dysbiosis) may cause pathology. Commensal bacteria are involved in the regulation of intestinal epithelial cell turnover, promotion of epithelial restitution and reorganization of tight junctions, all of which are pivotal for fortifying barrier function. Recent studies indicate that aberrant bacterial lipopolysaccharide-mediated signaling in gut mucosa may be involved in the pathogenesis of chronic inflammation and carcinogenesis. Our perception of enteric commensals has now changed from one of opportunistic pathogens to active participants in maintaining intestinal homeostasis. This review attempts to explain the dynamic interaction between the intestinal epithelium and commensal bacteria in disease and health status. PMID:22368784

  2. Microbial Ecology of Thailand Tsunami and Non-Tsunami Affected Terrestrials

    PubMed Central

    Somboonna, Naraporn; Wilantho, Alisa; Jankaew, Kruawun; Assawamakin, Anunchai; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke; Tongsima, Sissades

    2014-01-01

    The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species. PMID:24710002

  3. Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.

    PubMed

    Somboonna, Naraporn; Wilantho, Alisa; Jankaew, Kruawun; Assawamakin, Anunchai; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke; Tongsima, Sissades

    2014-01-01

    The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.

  4. Methodological approaches for studying the microbial ecology of drinking water distribution systems.

    PubMed

    Douterelo, Isabel; Boxall, Joby B; Deines, Peter; Sekar, Raju; Fish, Katherine E; Biggs, Catherine A

    2014-11-15

    The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects.

  5. Acetylcholine-producing T cells in the intestine regulate antimicrobial peptide expression and microbial diversity.

    PubMed

    Dhawan, Shobhit; De Palma, Giada; Willemze, Rose A; Hilbers, Francisca W; Verseijden, Caroline; Luyer, Misha D; Nuding, Sabine; Wehkamp, Jan; Souwer, Yuri; de Jong, Esther C; Seppen, J; van den Wijngaard, René M; Wehner, Sven; Verdu, Elena; Bercik, Premek; de Jonge, Wouter J

    2016-11-01

    The cholinergic anti-inflammatory pathway reduces systemic tumor necrosis factor (TNF) via acetylcholine-producing memory T cells in the spleen. These choline acetyltransferase (ChAT)-expressing T cells are also found in the intestine, where their function is unclear. We aimed to characterize these cells in mouse and human intestine and delineate their function. We made use of the ChAT-enhanced green fluorescent protein (eGFP) reporter mice. CD4(Cre) mice were crossed to ChAT(fl/fl) mice to achieve specific deletion of ChAT in CD4(+) T cells. We observed that the majority of ChAT-expressing T cells in the human and mouse intestine have characteristics of Th17 cells and coexpress IL17A, IL22, and RORC The generation of ChAT-expressing T cells was skewed by dendritic cells after activation of their adrenergic receptor β2 To evaluate ChAT T cell function, we generated CD4-specific ChAT-deficient mice. CD4ChAT(-/-) mice showed a reduced level of epithelial antimicrobial peptides lysozyme, defensin A, and ang4, which was associated with an enhanced bacterial diversity and richness in the small intestinal lumen in CD4ChAT(-/-) mice. We conclude that ChAT-expressing T cells in the gut are stimulated by adrenergic receptor activation on dendritic cells. ChAT-expressing T cells may function to mediate the host AMP secretion, microbial growth and expansion.

  6. Microbial ecology of a crude oil contaminated aquifer

    USGS Publications Warehouse

    Bekins, B.A.; Cozzarelli, I.M.; Warren, E.; Godsy, E.M.

    2002-01-01

    Detailed microbial analyses of a glacial outwash aquifer contaminated by crude oil provide insights into the pattern of microbial succession from iron reducing to methanogenic in the anaerobic portion of the contaminant plume. We analysed sediments from this area for populations of aerobes, iron reducers, fermenters and methanogens, using the most probable number method. On the basis of the microbial data the anaerobic area can be divided into distinct physiological zones dominated by either iron-reducers or a consortium of fermenters and methanogens. Chemistry and permeability data show that methanogenic conditions develop first in areas of high hydrocarbon flux. Thus, we find methanogens both in high permeability horizons and also where separate-phase crude oil is present in either the saturated or unsaturated zone. Microbial numbers peak at the top of the separate-phase oil suggesting that growth is most rapid in locations with access to both hydrocarbons and nutrients infiltrating from the surface.

  7. Effects of alfalfa meal on the intestinal microbial diversity and immunity of growing ducks.

    PubMed

    Jiang, J F; Song, X M; Wu, J L; Jiang, Y Q

    2014-12-01

    This study was conducted to investigate the effects of alfalfa meal diets on the intestinal microbial diversity and immunity of growing egg-type ducks. A total of 128 healthy 7-week-old female egg-type Shaoxing ducks were selected and randomly assigned into four dietary treatments: 0%, 3%, 6% and 9% alfalfa meal for 8 weeks. Each treatment consisted of four replicates of eight ducks each. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to characterize the microbiota. The results showed that the DGGE fingerprints of the V6-V8 fragments of the 16S rRNA from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal had significantly higher microbiota species richness than those fed 0% alfalfa meal (p < 0.05). The Shannon-Weiner index of the microbiota from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal was significantly higher than those fed 0% alfalfa meal (p < 0.05). Molecular analysis of the caecal and faecal DNA extracts showed that the alfalfa meal diet promotes the intestinal microbial diversity, as indicated by their higher species richness and Shannon-Weiner index. However, the groups did not significantly differ in terms of average daily gain, feed intake and gain-to-feed ratio (p > 0.05), and the 3-9% alfalfa meal did not affect the growth performance of the growing egg-type ducks. The proliferation of T and B lymphocytes was significantly greater (p < 0.05) in the groups supplemented with 3%, 6% and 9% of alfalfa meal than the unsupplemented control group, and alfalfa meal promoted the lymphocytes proliferation of the growing egg-type ducks. Dietary alfalfa meal supplementation increases intestinal microbial community diversity and improves of the immune response growing egg-type ducks.

  8. Emerging role of intestinal microbiota and microbial metabolites in metabolic control.

    PubMed

    Herrema, Hilde; IJzerman, Richard G; Nieuwdorp, Max

    2017-04-01

    The role of the intestinal microbiota and microbial metabolites in the maintenance of host health and development of metabolic disease has gained significant attention over the past decade. Mechanistic insight revealing causality, however, is scarce. Work by Ussar and co-workers demonstrates that a complex interaction between microbiota, host genetics and environmental factors is involved in metabolic disease development in mice. In addition, Perry and co-workers show that the microbial metabolite acetate augments insulin resistance in rats. These studies underscore an important role of the microbiota in the development of obesity and symptoms of type 2 diabetes in rodents. If causality can be demonstrated in humans, development of novel diagnostic and therapeutic tools that target the gut microbiota will have high potential.

  9. Microbial ecology and biogeochemistry of continental Antarctic soils

    PubMed Central

    Cowan, Don A.; Makhalanyane, Thulani P.; Dennis, Paul G.; Hopkins, David W.

    2014-01-01

    The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities. PMID:24782842

  10. Diet and host-microbial crosstalk in postnatal intestinal immune homeostasis.

    PubMed

    Jain, Nitya; Walker, W Allan

    2015-01-01

    Neonates face unique challenges in the period following birth. The postnatal immune system is in the early stages of development and has a range of functional capabilities that are distinct from the mature adult immune system. Bidirectional immune-microbial interactions regulate the development of mucosal immunity and alter the composition of the microbiota, which contributes to overall host well-being. In the past few years, nutrition has been highlighted as a third element in this interaction that governs host health by modulating microbial composition and the function of the immune system. Dietary changes and imbalances can disturb the immune-microbiota homeostasis, which might alter susceptibility to several autoimmune and metabolic diseases. Major changes in cultural traditions, socioeconomic status and agriculture are affecting the nutritional status of humans worldwide, which is altering core intestinal microbial communities. This phenomenon is especially relevant to the neonatal and paediatric populations, in which the microbiota and immune system are extremely sensitive to dietary influences. In this Review, we discuss the current state of knowledge regarding early-life nutrition, its effects on the microbiota and the consequences of diet-induced perturbation of the structure of the microbial community on mucosal immunity and disease susceptibility.

  11. Microbial ecology of deep-water mid-Atlantic canyons

    USGS Publications Warehouse

    Kellogg, Christina A.

    2011-01-01

    The research described in this fact sheet will be conducted from 2012 to 2014 as part of the U.S. Geological Survey's DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) Program. This integrated, multidisciplinary effort will be investigating a variety of topics related to unique and fragile deep-sea ecosystems from the microscopic level to the ecosystem level. One goal is to improve understanding, at the microbiological scale, of the benthic communities (including corals) that reside in and around mid-Atlantic canyon habitats and their associated environments. Specific objectives include identifying and characterizing the microbial associates of deep-sea corals, characterizing the microbial biofilms on hard substrates to better determine their role in engineering the ecosystem, and adding a microbial dimension to benthic community structure and function assessments by characterizing micro-eukaryotes, bacteria, and archaea in deep-sea sediments.

  12. Technology and techniques for microbial ecology via DNA sequencing.

    PubMed

    Walters, William A; Knight, Rob

    2014-01-01

    High-throughput sequencing technology, coupled with the use of conserved marker genes, has allowed for the understanding of communities of microbes (both culturable and unculturable) as well as their phylogenetic placement. The recent explosion of sequencing data prompted the development of software that could process the vast amount of data generated and phylogenetically differentiate groups of samples. Host-associated microbial studies have revealed that microbes are highly varied between individuals and fluctuate within an individual. Large-scale studies are being undertaken that include collection of extensive environmental data to help uncover the forces that shape microbial communities.

  13. Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

    PubMed Central

    Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Yang, Yunfeng

    2011-01-01

    ABSTRACT Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO2, is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO2 enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO2 levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management. PMID:21791581

  14. Microbial Ecology of and Antimicrobial Resistance in Stored Swine Manure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Antimicrobial compounds such as tylosin have been commonly used as feed additives for domestic animals to reduce infection and promote growth. Recent reports have suggested such feeding practices may result in increased microbial resistance to antibiotics, which can have an impact on human health. ...

  15. Engineering microbial systems to explore ecological and evolutionary dynamics.

    PubMed

    Tanouchi, Yu; Smith, Robert P; You, Lingchong

    2012-10-01

    A major goal of biological research is to provide a mechanistic understanding of diverse biological processes. To this end, synthetic biology offers a powerful approach, whereby biological questions can be addressed in a well-defined framework. By constructing simple gene circuits, such studies have generated new insights into the design principles of gene regulatory networks. Recently, this strategy has been applied to analyze ecological and evolutionary questions, where population-level interactions are critical. Here, we highlight recent development of such systems and discuss how they were used to address problems in ecology and evolutionary biology. As illustrated by these examples, synthetic ecosystems provide a unique platform to study ecological and evolutionary phenomena that are challenging to study in their natural contexts.

  16. Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats.

    PubMed

    Lam, Vy; Su, Jidong; Hsu, Anna; Gross, Garrett J; Salzman, Nita H; Baker, John E

    2016-01-01

    Intestinal microbiota determine severity of myocardial infarction in rats. We determined whether low molecular weight metabolites derived from intestinal microbiota and transported to the systemic circulation are linked to severity of myocardial infarction. Plasma from rats treated for seven days with the non-absorbed antibiotic vancomycin or a mixture of streptomycin, neomycin, polymyxin B and bacitracin was analyzed using mass spectrometry-based metabolite profiling platforms. Antibiotic-induced changes in the abundance of individual groups of intestinal microbiota dramatically altered the host's metabolism. Hierarchical clustering of dissimilarities separated the levels of 284 identified metabolites from treated vs. untreated rats; 193 were altered by the antibiotic treatments with a tendency towards decreased metabolite levels. Catabolism of the aromatic amino acids phenylalanine, tryptophan and tyrosine was the most affected pathway comprising 33 affected metabolites. Both antibiotic treatments decreased the severity of an induced myocardial infarction in vivo by 27% and 29%, respectively. We then determined whether microbial metabolites of the amino acids phenylalanine, tryptophan and tyrosine were linked to decreased severity of myocardial infarction. Vancomycin-treated rats were administered amino acid metabolites prior to ischemia/reperfusion studies. Oral or intravenous pretreatment of rats with these amino acid metabolites abolished the decrease in infarct size conferred by vancomycin. Inhibition of JAK-2 (AG-490, 10 μM), Src kinase (PP1, 20 μM), Akt/PI3 kinase (Wortmannin, 100 nM), p44/42 MAPK (PD98059, 10 μM), p38 MAPK (SB203580, 10 μM), or KATP channels (glibenclamide, 3 μM) abolished cardioprotection by vancomycin, indicating microbial metabolites are interacting with cell surface receptors to transduce their signals through Src kinase, cell survival pathways and KATP channels. These inhibitors have no effect on myocardial infarct size in

  17. Effects of Fruit Toxins on Intestinal and Microbial β-Glucosidase Activities of Seed-Predating and Seed-Dispersing Rodents (Acomys spp.).

    PubMed

    Kohl, Kevin D; Samuni-Blank, Michal; Lymberakis, Petros; Kurnath, Patrice; Izhaki, Ido; Arad, Zeev; Karasov, William H; Dearing, M Denise

    2016-01-01

    Plant secondary compounds (PSCs) have profound influence on the ecological interaction between plants and their consumers. Glycosides, a class of PSC, are inert in their intact form and become toxic on activation by either plant β-glucosidase enzymes or endogenous β-glucosidases produced by the intestine of the plant-predator or its microbiota. Many insect herbivores decrease activities of endogenous β-glucosidases to limit toxin exposure. However, such an adaptation has never been investigated in nonmodel mammals. We studied three species of spiny mice (Acomys spp.) that vary in their feeding behavior of the glycoside-rich fruit of Ochradenus baccatus. Two species, the common (Acomys cahirinus) and Crete (Acomys minous) spiny mice, behaviorally avoid activating glycosides, while the golden spiny mouse (Acomys russatus) regularly consumes activated glycosides. We fed each species a nontoxic diet of inert glycosides or a toxic diet of activated fruit toxins and investigated the responses of intestinal and microbial β-glucosidase activities. We found that individuals feeding on activated toxins had lower intestinal β-glucosidase activity and that the species that behaviorally avoid activating glycosides also had lower intestinal β-glucosidase activity regardless of treatment. The microbiota represented a larger source of toxin liberation, and the toxin-adapted species (golden spiny mouse) exhibited almost a fivefold increase in microbial β-glucosidase when fed activated toxins, while other species showed slight decreases. These results are contrary to those in insects, where glycoside-adapted species have lower β-glucosidase activity. The glycoside-adapted golden spiny mouse may have evolved tolerance mechanisms such as enhanced detoxification rather than avoidance mechanisms.

  18. Intestine.

    PubMed

    Smith, J M; Skeans, M A; Horslen, S P; Edwards, E B; Harper, A M; Snyder, J J; Israni, A K; Kasiske, B L

    2016-01-01

    Intestine and intestine-liver transplant plays an important role in the treatment of intestinal failure, despite decreased morbidity associated with parenteral nutrition. In 2014, 210 new patients were added to the intestine transplant waiting list. Among prevalent patients on the list at the end of 2014, 65% were waiting for an intestine transplant and 35% were waiting for an intestine-liver transplant. The pretransplant mortality rate decreased dramatically over time for all age groups. Pretransplant mortality was highest for adult candidates, at 22.1 per 100 waitlist years compared with less than 3 per 100 waitlist years for pediatric candidates, and notably higher for candidates for intestine-liver transplant than for candidates for intestine transplant without a liver. Numbers of intestine transplants without a liver increased from a low of 51 in 2013 to 67 in 2014. Intestine-liver transplants increased from a low of 44 in 2012 to 72 in 2014. Short-gut syndrome (congenital and other) was the main cause of disease leading to both intestine and intestine-liver transplant. Graft survival improved over the past decade. Patient survival was lowest for adult intestine-liver recipients and highest for pediatric intestine recipients.

  19. An Open-Ended Investigative Microbial Ecology Laboratory for Introductory Biology

    ERIC Educational Resources Information Center

    Jones-Held, Susan; Paoletti, Robert; Glick, David; Held, Michael E.

    2010-01-01

    In this article we describe a multi-week investigative laboratory in microbial ecology/diversity and nitrogen cycling that we have used in our introductory biology course. This module encourages active student involvement in experimental design, using the scientific literature and quantitative analysis of large data sets. Students analyze soil…

  20. Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

    SciTech Connect

    Bruhn, D F; Thompson, D N; Noah, K S

    1999-06-01

    Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, Leptospirillum, Ferromicrobium, and Acidiphilium. Two temperatures (30C and 45C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. After acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to the low pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.

  1. Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

    PubMed

    von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

    2013-10-01

    The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

  2. Microbial ecology summer research program, June 20-August 26, 1983

    SciTech Connect

    Not Available

    1983-01-01

    The personnel, lecture topics, and summaries of research reports generated are presented. Research topics include: mutants of Escherichia coli affected in inducer exclusion; anaerobic chitin degradation; feeding relationships of harpacticoid copepods and microbial flora; degradation of ortho phenyl phenol by streptomycetes; biodegradation of dieldrin and aromatic compounds; the effect of neurotoxins on chemotaxis is Spirochaeta aurantia; chemotaxis and algal attachment of caulobacter; pigment formation in Lyngbya aestuari; diel movements of bacteria in a salt marsh; chemotaxis in S. Aurantia; isolation of marine toluate-oxidizing bacteria; growth inhibition of enteric bacteria by methyl-..cap alpha..-D-glucoside; studies of magnetic bacteria in brackish waters; and mechanisms of interaction between two microbial populations in activated sludge. (ACR)

  3. Groundwater Chemistry and Microbial Ecology Effects on Explosives Biodegradation

    DTIC Science & Technology

    2008-09-01

    biodegradation systems (1, 16, 24). A recent ecotoxicology study utilized DGGE to analyze the microbial community in soil in response to exposure to RDX...as a gene probe to analyze and compare polychlorinated biphenyl (PCB)-contaminated soils and an uncontaminated garden soil (43). The study indicated...uncontaminated soil . In another set of early experiments, a mercury-contaminated pond was studied by hybridizing mercury-resistance genes to community DNA and

  4. Next-generation approaches to the microbial ecology of food fermentations.

    PubMed

    Bokulich, Nicholas A; Mills, David A

    2012-07-01

    Food fermentations have enhanced human health since the dawn of time and remain a prevalent means of food processing and preservation. Due to their cultural and nutritional importance, many of these foods have been studied in detail using molecular tools, leading to enhancements in quality and safety. Furthermore, recent advances in high-throughput sequencing technology are revolutionizing the study of food microbial ecology, deepening insight into complex fermentation systems. This review provides insight into novel applications of select molecular techniques, particularly next-generation sequencing technology, for analysis of microbial communities in fermented foods. We present a guideline for integrated molecular analysis of food microbial ecology and a starting point for implementing next-generation analysis of food systems.

  5. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology.

    PubMed

    Gibson, Molly K; Forsberg, Kevin J; Dantas, Gautam

    2015-01-01

    Antibiotic resistance is a dire clinical problem with important ecological dimensions. While antibiotic resistance in human pathogens continues to rise at alarming rates, the impact of environmental resistance on human health is still unclear. To investigate the relationship between human-associated and environmental resistomes, we analyzed functional metagenomic selections for resistance against 18 clinically relevant antibiotics from soil and human gut microbiota as well as a set of multidrug-resistant cultured soil isolates. These analyses were enabled by Resfams, a new curated database of protein families and associated highly precise and accurate profile hidden Markov models, confirmed for antibiotic resistance function and organized by ontology. We demonstrate that the antibiotic resistance functions that give rise to the resistance profiles observed in environmental and human-associated microbial communities significantly differ between ecologies. Antibiotic resistance functions that most discriminate between ecologies provide resistance to β-lactams and tetracyclines, two of the most widely used classes of antibiotics in the clinic and agriculture. We also analyzed the antibiotic resistance gene composition of over 6000 sequenced microbial genomes, revealing significant enrichment of resistance functions by both ecology and phylogeny. Together, our results indicate that environmental and human-associated microbial communities harbor distinct resistance genes, suggesting that antibiotic resistance functions are largely constrained by ecology.

  6. Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

    PubMed Central

    Liang, Yuting; Zhao, Huihui; Deng, Ye; Zhou, Jizhong; Li, Guanghe; Sun, Bo

    2016-01-01

    With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential “keystone” genes, defined as either “hubs” or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions. PMID:26870020

  7. Urban microbial ecology of a freshwater estuary of Lake Michigan

    PubMed Central

    Fisher, Jenny C.; Newton, Ryan J.; Dila, Deborah K.

    2015-01-01

    Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an “urban microbial signature,” and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with

  8. Microbial ecology meets electrochemistry: electricity-driven and driving communities.

    PubMed

    Rabaey, Korneel; Rodríguez, Jorge; Blackall, Linda L; Keller, Jurg; Gross, Pamela; Batstone, Damien; Verstraete, Willy; Nealson, Kenneth H

    2007-05-01

    Bio-electrochemical systems (BESs) have recently emerged as an exciting technology. In a BES, bacteria interact with electrodes using electrons, which are either removed or supplied through an electrical circuit. The most-described type of BES is microbial fuel cells (MFCs), in which useful power is generated from electron donors as, for example, present in wastewater. This form of charge transport, known as extracellular electron transfer, was previously extensively described with respect to metals such as iron and manganese. The importance of these interactions in global biogeochemical cycles is essentially undisputed. A wide variety of bacteria can participate in extracellular electron transfer, and this phenomenon is far more widespread than previously thought. The use of BESs in diverse research projects is helping elucidate the mechanism by which bacteria shuttle electrons externally. New forms of interactions between bacteria have been discovered demonstrating how multiple populations within microbial communities can co-operate to achieve energy generation. New environmental processes that were difficult to observe or study previously can now be simulated and improved via BESs. Whereas pure culture studies make up the majority of the studies performed thus far, even greater contributions of BESs are expected to occur in natural environments and with mixed microbial communities. Owing to their versatility, unmatched level of control and capacity to sustain novel processes, BESs might well serve as the foundation of a new environmental biotechnology. While highlighting some of the major breakthroughs and addressing only recently obtained data, this review points out that despite rapid progress, many questions remain unanswered.

  9. Urban microbial ecology of a freshwater estuary of Lake Michigan.

    PubMed

    Fisher, Jenny C; Newton, Ryan J; Dila, Deborah K; McLellan, Sandra L

    Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an "urban microbial signature," and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential

  10. Transcriptome profiles of chicken intestinal intraepithelial lymphocytes altered by the intake of a multi-strain direct-fed microbials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The current study was conducted to investigate the effects of the direct-fed microbials (DFM) including three Bacillus subtilis strains on the modulation of transcriptional profile in chicken intestinal intraepithelial lymphocytes (IEL). The multiple-strain DFM product modified 453 probes from 1,98...

  11. The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities

    PubMed Central

    Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

    2012-01-01

    Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu2+, was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem. PMID:22170424

  12. A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.

    PubMed

    Buttigieg, Pier Luigi; Ramette, Alban

    2014-12-01

    The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community.

  13. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

    PubMed

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2015-01-01

    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization.

  14. Groundwater Microbial Communities, Part 9: Ecological and Hydrological Interactions

    SciTech Connect

    McKinley, James P.; Fredrickson, Jim K.; Colwell, Frederick S.

    2005-12-31

    Microbial communities in aquifers consist of diverse interactive individuals that break down complex organic matter for metabolic energy. Microbes are adapted to function over a large range in environmental conditions, ranging from freezing to boiling acidic to alkaline. They can use oxygen as a reducible metabolite during organic carbon oxidation, but, since oxygen is rapidly depleted in subsurface environments, different groups of organisms may also rely on other compounds such as reducible metals, or on fermentation. Community members are interdependent, but compete for resources, and communities often have predominant groups that rely on recognizable chemical pathways, such as sulfate reduction. The predominant group varies spatially and temporally as the available nutrients change or are depleted.

  15. Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class.

    PubMed

    Tulstrup, Monica Vera-Lise; Christensen, Ellen Gerd; Carvalho, Vera; Linninge, Caroline; Ahrné, Siv; Højberg, Ole; Licht, Tine Rask; Bahl, Martin Iain

    2015-01-01

    Antibiotics are frequently administered orally to treat bacterial infections not necessarily related to the gastrointestinal system. This has adverse effects on the commensal gut microbial community, as it disrupts the intricate balance between specific bacterial groups within this ecosystem, potentially leading to dysbiosis. We hypothesized that modulation of community composition and function induced by antibiotics affects intestinal integrity depending on the antibiotic administered. To address this a total of 60 Wistar rats (housed in pairs with 6 cages per group) were dosed by oral gavage with either amoxicillin (AMX), cefotaxime (CTX), vancomycin (VAN), metronidazole (MTZ), or water (CON) daily for 10-11 days. Bacterial composition, alpha diversity and caecum short chain fatty acid levels were significantly affected by AMX, CTX and VAN, and varied among antibiotic treatments. A general decrease in diversity and an increase in the relative abundance of Proteobacteria was observed for all three antibiotics. Additionally, the relative abundance of Bifidobacteriaceae was increased in the CTX group and both Lactobacillaceae and Verrucomicrobiaceae were increased in the VAN group compared to the CON group. No changes in microbiota composition or function were observed following MTZ treatment. Intestinal permeability to 4 kDa FITC-dextran decreased after CTX and VAN treatment and increased following MTZ treatment. Plasma haptoglobin levels were increased by both AMX and CTX but no changes in expression of host tight junction genes were found in any treatment group. A strong correlation between the level of caecal succinate, the relative abundance of Clostridiaceae 1 family in the caecum, and the level of acute phase protein haptoglobin in blood plasma was observed. In conclusion, antibiotic-induced changes in microbiota may be linked to alterations in intestinal permeability, although the specific interactions remain to be elucidated as changes in permeability did

  16. Tools and perspectives for a unified approach to understanding microbial ecology in the critical zone

    NASA Astrophysics Data System (ADS)

    Gallery, R. E.; Aronson, E. L.; Fairbanks, D.; Murphy, M. A.; Rich, V. I.; Hart, S. C.

    2015-12-01

    Microbial communities that control nutrient transformation and storage in ecosystems are themselves influenced by landscape topography and vegetative cover. Globally, disturbances such as fires and insect outbreaks are increasing in frequency and severity with enormous impacts on global carbon cycling. The resiliency of soil microbial communities to these heterogeneous disturbances determines rates of nutrient transformations as well as ecosystem structure and recovery. Natural and anthropogenic disturbances are a common thread throughout Critical Zone Observatories and ecosystems in general. Using the 2013 Thompson Ridge Fire in the Jemez River Basin CZO as a case study, we examine the effect of a wildfire disturbance regime on successional changes in soil microbiota and ecosystem fluxes across a landscape with high topographic variation. We find that, layered over the topographic controls of hotspots of biogeochemical activity, fire alters organic substrate quality, microbial biomass, community structure, and activity. For example, fire increases soil pH, which is commonly found as an explanatory variable describing bacterial community structure. Soil microbes excrete exoenzymes to decompose polymers and acquire nutrients, and these activities can indicate changing microbial function or soil quality. In these mixed conifer forests, we find shifts from carbon to nitrogen-dominated exoenzyme activities in burned forests with alkaline soils, suggesting shifts of microbial taxa and function that correspond with recovering soil microbial biomass. More generally we ask - what combination of tools and perspectives is needed to fully understand soil microbial ecology and biogeochemistry of the critical zone? Results from an NSF Science Across Virtual Institutes (SAVI) CZO Network Biogeochemistry Workshop highlight the importance of incorporating a standard suite of microbial activity and community assays along with soil biogeochemical and flux measurements to enable

  17. Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats

    PubMed Central

    Lam, Vy; Su, Jidong; Hsu, Anna; Gross, Garrett J.; Salzman, Nita H.

    2016-01-01

    Intestinal microbiota determine severity of myocardial infarction in rats. We determined whether low molecular weight metabolites derived from intestinal microbiota and transported to the systemic circulation are linked to severity of myocardial infarction. Plasma from rats treated for seven days with the non-absorbed antibiotic vancomycin or a mixture of streptomycin, neomycin, polymyxin B and bacitracin was analyzed using mass spectrometry-based metabolite profiling platforms. Antibiotic-induced changes in the abundance of individual groups of intestinal microbiota dramatically altered the host’s metabolism. Hierarchical clustering of dissimilarities separated the levels of 284 identified metabolites from treated vs. untreated rats; 193 were altered by the antibiotic treatments with a tendency towards decreased metabolite levels. Catabolism of the aromatic amino acids phenylalanine, tryptophan and tyrosine was the most affected pathway comprising 33 affected metabolites. Both antibiotic treatments decreased the severity of an induced myocardial infarction in vivo by 27% and 29%, respectively. We then determined whether microbial metabolites of the amino acids phenylalanine, tryptophan and tyrosine were linked to decreased severity of myocardial infarction. Vancomycin-treated rats were administered amino acid metabolites prior to ischemia/reperfusion studies. Oral or intravenous pretreatment of rats with these amino acid metabolites abolished the decrease in infarct size conferred by vancomycin. Inhibition of JAK-2 (AG-490, 10 μM), Src kinase (PP1, 20 μM), Akt/PI3 kinase (Wortmannin, 100 nM), p44/42 MAPK (PD98059, 10 μM), p38 MAPK (SB203580, 10 μM), or KATP channels (glibenclamide, 3 μM) abolished cardioprotection by vancomycin, indicating microbial metabolites are interacting with cell surface receptors to transduce their signals through Src kinase, cell survival pathways and KATP channels. These inhibitors have no effect on myocardial infarct size in

  18. The Forminalized Rat: A Convenient Microbial Ecosystem.

    ERIC Educational Resources Information Center

    Lee, Adrian

    1984-01-01

    Presents a series of experiments built around the bacteria found in the intestinal tract of formalinized rats as a model for discussing microbial ecology. Describes methods of examination of intestinal content, student tasks, and discussion questions; also gives a challenge problem to solve.

  19. Microbial Ecology of Anaerobic Digesters: The Key Players of Anaerobiosis

    PubMed Central

    Ali Shah, Fayyaz; Mahmood, Qaisar; Maroof Shah, Mohammad; Pervez, Arshid; Ahmad Asad, Saeed

    2014-01-01

    Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO2. The conversions of complex organic compounds to CH4 and CO2 are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed. PMID:24701142

  20. Effect of disinfectants on microbial ecology in model distribution systems.

    PubMed

    Chauret, C; Volk, C; Stover, L; Dykstra, T S; Andrews, R C; Gagnon, G A

    2005-12-01

    This research was conducted to assess the impact of various disinfectants on bacterial water quality within model distribution systems (i.e. annular reactors). After colonization with non-disinfected water, annular reactors were treated with relatively low doses of chlorine (0.4 mg/l), chlorine dioxide (0.15 mg/l), or chloramines (0.9 mg/l). Under the tested conditions, bacterial inactivation varied as a function of disinfectant type (ranking by efficiency per mg of oxidant: ClO2 > Cl2 > ClNH2) and sample type (bulk water vs. biofilm). Depending on the disinfectant, the log inactivation of suspended and attached bacteria were 0.7-1.2 and 0.5-1.0, respectively. The characterization of microbial communities in drinking water can be performed using biochemical and/or molecular methods. In this study, biochemical tests were used, showing that pseudomonad and pseudomonad-like bacteria, as in other studies, were the most predominant micro-organisms (e.g. Pseudomonas fluorescens, Brevundimonas vescularis). The ratio Gram-positive to Gram-negative organisms was 1 to 3. No drastic differences were observed between the non-treated and disinfected pipes. Based on the bacteriological data presented in these experiments, chlorine dioxide represents an alternative to chlorine for certain distribution systems.

  1. The Ecology of Microbial Communities Associated with Macrocystis pyrifera

    PubMed Central

    Michelou, Vanessa K.; Caporaso, J. Gregory; Knight, Rob; Palumbi, Stephen R.

    2013-01-01

    Kelp forests are characterized by high biodiversity and productivity, and the cycling of kelp-produced carbon is a vital process in this ecosystem. Although bacteria are assumed to play a major role in kelp forest carbon cycling, knowledge of the composition and diversity of these bacterial communities is lacking. Bacterial communities on the surface of Macrocystis pyrifera and adjacent seawater were sampled at the Hopkins Marine Station in Monterey Bay, CA, and further studied using 454-tag pyrosequencing of 16S RNA genes. Our results suggest that M. pyrifera-dominated kelp forests harbor distinct microbial communities that vary temporally. The distribution of sequence tags assigned to Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the surface of the kelp and the surrounding water. Several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed considerable temporal variation, often with similar trends in the seawater and the surface of the kelp. Bacterial community structure and membership correlated with the kelp surface serving as host, and varied over time. Several kelp-specific taxa were highly similar to other bacteria known to either prevent the colonization of eukaryotic larvae or exhibit antibacterial activities. Some of these kelp-specific bacterial associations might play an important role for M. pyrifera. This study provides the first assessment of the diversity and phylogenetic profile of the bacterial communities associated with M. pyrifera. PMID:23840715

  2. Dietary inclusion of feathers affects intestinal microbiota and microbial metabolites in growing Leghorn-type chickens.

    PubMed

    Meyer, B; Bessei, W; Bessei, A W; Vahjen, W; Zentek, J; Harlander-Matauschek, A

    2012-07-01

    Feather pecking in laying hens is a serious behavioral problem that is often associated with feather eating. The intake of feathers may influence the gut microbiota and its metabolism. The aim of this study was to determine the effect of 2 different diets, with or without 5% ground feathers, on the gut microbiota and the resulting microbial fermentation products and to identify keratin-degrading bacteria in chicken digesta. One-day-old Lohmann-Selected Leghorn chicks were divided into 3 feeding groups: group A (control), B (5% ground feathers in the diet), and C, in which the control diet was fed until wk 12 and then switched to the 5% feather diet to study the effect of time of first feather ingestion. The gut microbiota was analyzed by cultivation and denaturing gradient gel electrophoresis of ileum and cecum digesta. Short-chain fatty acids, ammonia, and lactate concentrations were measured as microbial metabolites. The concentration of keratinolytic bacteria increased after feather ingestion in the ileum (P < 0.001) and cecum (P = 0.033). Bacterial species that hydrolyzed keratin were identified as Enterococcus faecium, Lactobacillus crispatus, Lactobacillus reuteri-like species (97% sequence homology), and Lactobacillus salivarius-like species (97% sequence homology). Molecular analysis of cecal DNA extracts showed that the feather diet lowered the bacterial diversity indicated by a reduced richness (P < 0.001) and shannon (P = 0.012) index. The pattern of microbial metabolites indicated some changes, especially in the cecum. This study showed that feather intake induced an adaptation of the intestinal microbiota in chickens. It remains unclear to what extent the changed metabolism of the microbiota reflects the feather intake and could have an effect on the behavior of the hens.

  3. Defining DNA-based operational taxonomic units for microbial-eukaryote ecology.

    PubMed

    Caron, David A; Countway, Peter D; Savai, Pratik; Gast, Rebecca J; Schnetzer, Astrid; Moorthi, Stefanie D; Dennett, Mark R; Moran, Dawn M; Jones, Adriane C

    2009-09-01

    DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.

  4. Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

    SciTech Connect

    Bruhn, Debby Fox; Thompson, David Neal; Noah, Karl Scott

    1999-06-01

    Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, “Leptospirillum”, “Ferromicrobium”, and Acidiphilium. Two temperatures (30°C and 45°C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. After acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to low the pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.

  5. Radiation: microbial evolution, ecology, and relevance to mars missions

    NASA Technical Reports Server (NTRS)

    Rothschild, L. J.; Cockell, C. S.

    1999-01-01

    Ultraviolet (UV) radiation has been an important environmental parameter during the evolution of life on Earth, both in its role as a mutagen and as a selective agent. This was probably especially true during the time from 3.8 to 2.5 billion years ago, when atmospheric ozone levels were less than 1% of present levels. Early Mars may not have had an "ozone shield" either, and it never developed a significant one. Even though Mars is farther away from the Sun than the Earth, a substantial surficial UV flux is present on Mars today. But organisms respond to dose rate, and on Mars, like on Earth, organisms would be exposed to diurnal variations in UV flux. Here we present data on the effect of diurnal patterns of UV flux on microbial ecosystems in nature, with an emphasis on photosynthesis and DNA synthesis effects. These results indicate that diurnal patterns of metabolism occur in nature with a dip in photosynthesis and DNA synthesis in the afternoon, in part regulated by UV flux. Thus, diurnal patterns must be studied in order to understand the effect of UV radiation in nature. The results of this work are significant to the success of human missions to Mars for several reasons. For example, human missions must include photosynthetic organisms for food production and likely oxygen production. An evolutionary approach suggests which organisms might be best suited for high UV fluxes. The diurnal aspect of these studies is critical. Terraforming is a potential goal of Mars exploration, and it will require studies of the effect of Martian UV fluxes, including their diurnal changes, on terrestrial organisms. Such studies may suggest that diurnal changes in UV only require mitigation at some times of day or year.

  6. Radiation: microbial evolution, ecology, and relevance to mars missions.

    PubMed

    Rothschild, L J; Cockell, C S

    1999-12-06

    Ultraviolet (UV) radiation has been an important environmental parameter during the evolution of life on Earth, both in its role as a mutagen and as a selective agent. This was probably especially true during the time from 3.8 to 2.5 billion years ago, when atmospheric ozone levels were less than 1% of present levels. Early Mars may not have had an "ozone shield" either, and it never developed a significant one. Even though Mars is farther away from the Sun than the Earth, a substantial surficial UV flux is present on Mars today. But organisms respond to dose rate, and on Mars, like on Earth, organisms would be exposed to diurnal variations in UV flux. Here we present data on the effect of diurnal patterns of UV flux on microbial ecosystems in nature, with an emphasis on photosynthesis and DNA synthesis effects. These results indicate that diurnal patterns of metabolism occur in nature with a dip in photosynthesis and DNA synthesis in the afternoon, in part regulated by UV flux. Thus, diurnal patterns must be studied in order to understand the effect of UV radiation in nature. The results of this work are significant to the success of human missions to Mars for several reasons. For example, human missions must include photosynthetic organisms for food production and likely oxygen production. An evolutionary approach suggests which organisms might be best suited for high UV fluxes. The diurnal aspect of these studies is critical. Terraforming is a potential goal of Mars exploration, and it will require studies of the effect of Martian UV fluxes, including their diurnal changes, on terrestrial organisms. Such studies may suggest that diurnal changes in UV only require mitigation at some times of day or year.

  7. Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology.

    PubMed

    Khoruts, Alexander; Weingarden, Alexa R

    2014-12-01

    In the recent years fecal microbiota transplantation (FMT) has emerged as an effective therapeutic option for patients with refractory Clostridium difficile infection that is not responding to antibiotic therapy. It results in implantation of donor microbiota into recipients and restoration of normal distal gut microbial community structure. We anticipate that this form of therapy represents merely the first entry into a new class of therapeutics. There is great interest in application of FMT or defined microbial consortia to treatment of many diseases associated with dysbiosis. However, many challenges remain in development as our understanding of microbial ecology within the human body and microbiota-host interactions remain limited. Future advances in this field will be critically depending on detailed mechanistic understanding.

  8. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution.

    PubMed

    Ishii, Satoshi; Sadowsky, Michael J

    2009-04-01

    A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.

  9. Linking geochemistry to microbial ecology in hot springs: examples from southeastern Asia (Invited)

    NASA Astrophysics Data System (ADS)

    Dong, H.; Jiang, H.; Hou, W.; Wang, S.; Huang, Q.; Briggs, B. R.; Huang, L.; Hust, W.; Hedlund, B. P.; Zhang, C.; Hartnett, H. E.; Dijkstra, P.; Hungate, B. A.

    2013-12-01

    Despite recent advances in our understanding of microbial ecology in high temperature environments, important questions remain as to how geochemical conditions shape microbial ecology in hot springs. In the past three years, we have surveyed a large number of hot springs in three regions of southeastern Asia: Tengchong of Yunnan Province, China; Tibet in China; and the Philippines. These springs possess large gradients in pH (2.5-9.4), temperature (22.1-93.6oC), and water and sediment geochemistry. Within each region, these geochemical conditions are important in shaping microbial community structure and diversity. For example, in the Rehai geothermal field of Tengchong, dominant taxa within the dominant bacterial phylum Aquificae and archaeal phylum Crenarchaeota depended on pH (2.5-9.4), temperature (55.1-93.6), Na-Cl-HCO3 water type and silicate rock lithology. In the Ruidian geothermal region, springs with circum-neutral pH (6.71-7.29), moderate temperature (50-82oC), Na-HCO3 water type, and carbonate-dominated lithology, Hydrogenobacter of Aquificae dominated spring water, but the microbial community in sediments was diverse with abundant novel groups. In Tibet springs with low-moderate temperature (22-75oC) and circum-neutral pH (7.2-8.1), temperature appeared to be the most important factor in determining diversity and community structure. In acidic hot springs of the Philippines (Temperature: 60-92°C, pH 3.72-6.58), microbial communities were predominated by those related to sulfur metabolism, which are different from those in acidic springs of Tengchong. When these three regions are considered together, environmental conditions play a major role in controlling microbial community structure, but geographical location appears to be an important factor as well.

  10. Coupled Spatiotemporal Dynamics of Microbial Community Ecology, Biogeochemistry, and Hydrologic Mixing

    NASA Astrophysics Data System (ADS)

    Stegen, J.; Johnson, T. C.; Fredrickson, J.; Wilkins, M.; Konopka, A.; Nelson, W.; Arntzen, E.; Chrisler, W.; Chu, R. K.; Fansler, S.; Kennedy, D.; Resch, T.; Tfaily, M. M.

    2015-12-01

    The hyporheic zone (HZ) is a critical ecosystem component that links terrestrial, surface water, and groundwater ecosystems. A dominant feature of the HZ is groundwater-surface water mixing and the input of terrestrially—as well as aquatically—derived organic carbon. In many systems the HZ has a relatively small spatial extent, but in larger riverine systems groundwater-surface water mixing can occur 100s of meters beyond the surface water shoreline; we consider these more distal locations to be within the 'subsurface interaction zone' (SIZ) as they are beyond the traditional HZ. Microbial communities in the HZ and SIZ drive biogeochemical processes in these system components, yet relatively little is known about the ecological processes that drive HZ and SIZ microbial communities. Here, we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected through space (400m spatial extent) and time (7 month temporal extent) within the Hanford Site 300 Area. These data streams were integrated to evaluate how the influence of groundwater-surface water mixing on microbial communities changes when moving from the HZ to the broader SIZ. Our results indicate that groundwater-surface water mixing (i) consistently stimulated heterotrophic respiration, but only above a threshold of surface water intrusion, (ii) did not stimulate denitrification, (iii) caused deterministic shifts in HZ microbial communities due to changes in organic carbon composition, and (iv) did not cause shifts in SIZ microbial communities. These results suggest that microbial communities and the biogeochemical processes they drive are impacted by groundwater-surface water mixing primarily in the HZ and to a lesser extent in the SIZ.

  11. Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.

    PubMed

    Rashid, Mamoon; Stingl, Ulrich

    2015-12-01

    Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.

  12. Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing

    PubMed Central

    Röling, Wilfred F. M.; Kerler, Josef; Braster, Martin; Apriyantono, Anton; Stam, Hein; van Verseveld, Henk W.

    2001-01-01

    The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis,, and B. smithii) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans. PMID:11319073

  13. Agent-based model of fecal microbial transplant effect on bile acid metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection.

    PubMed

    Peer, Xavier; An, Gary

    2014-10-01

    Agent-based modeling is a computational modeling method that represents system-level behavior as arising from multiple interactions between the multiple components that make up a system. Biological systems are thus readily described using agent-based models (ABMs), as multi-cellular organisms can be viewed as populations of interacting cells, and microbial systems manifest as colonies of individual microbes. Intersections between these two domains underlie an increasing number of pathophysiological processes, and the intestinal tract represents one of the most significant locations for these inter-domain interactions, so much so that it can be considered an internal ecology of varying robustness and function. Intestinal infections represent significant disturbances of this internal ecology, and one of the most clinically relevant intestinal infections is Clostridium difficile infection (CDI). CDI is precipitated by the use of broad-spectrum antibiotics, involves the depletion of commensal microbiota, and alterations in bile acid composition in the intestinal lumen. We present an example ABM of CDI (the C. difficile Infection ABM, or CDIABM) to examine fundamental dynamics of the pathogenesis of CDI and its response to treatment with anti-CDI antibiotics and a newer treatment therapy, fecal microbial transplant. The CDIABM focuses on one specific mechanism of potential CDI suppression: commensal modulation of bile acid composition. Even given its abstraction, the CDIABM reproduces essential dynamics of CDI and its response to therapy, and identifies a paradoxical zone of behavior that provides insight into the role of intestinal nutritional status and the efficacy of anti-CDI therapies. It is hoped that this use case example of the CDIABM can demonstrate the usefulness of both agent-based modeling and the application of abstract functional representation as the biomedical community seeks to address the challenges of increasingly complex diseases with the goal of

  14. Performance and microbial ecology of air-cathode microbial fuel cells with layered electrode assemblies.

    PubMed

    Butler, Caitlyn S; Nerenberg, Robert

    2010-05-01

    Microbial fuel cells (MFCs) can be built with layered electrode assemblies, where the anode, proton exchange membrane (PEM), and cathode are pressed into a single unit. We studied the performance and microbial community structure of MFCs with layered assemblies, addressing the effect of materials and oxygen crossover on the community structure. Four MFCs with layered assemblies were constructed using Nafion or Ultrex PEMs and a plain carbon cloth electrode or a cathode with an oxygen-resistant polytetrafluoroethylene diffusion layer. The MFC with Nafion PEM and cathode diffusion layer achieved the highest power density, 381 mW/m(2) (20 W/m(3)). The rates of oxygen diffusion from cathode to anode were three times higher in the MFCs with plain cathodes compared to those with diffusion-layer cathodes. Microsensor studies revealed little accumulation of oxygen within the anode cloth. However, the abundance of bacteria known to use oxygen as an electron acceptor, but not known to have exoelectrogenic activity, was greater in MFCs with plain cathodes. The MFCs with diffusion-layer cathodes had high abundance of exoelectrogenic bacteria within the genus Geobacter. This work suggests that cathode materials can significantly influence oxygen crossover and the relative abundance of exoelectrogenic bacteria on the anode, while PEM materials have little influence on anode community structure. Our results show that oxygen crossover can significantly decrease the performance of air-cathode MFCs with layered assemblies, and therefore limiting crossover may be of particular importance for these types of MFCs.

  15. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum.

    PubMed

    Chiodini, Rodrick J; Dowd, Scot E; Chamberlin, William M; Galandiuk, Susan; Davis, Brian; Glassing, Angela

    2015-01-01

    Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well

  16. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum

    PubMed Central

    Chiodini, Rodrick J.; Dowd, Scot E.; Chamberlin, William M.; Galandiuk, Susan; Davis, Brian; Glassing, Angela

    2015-01-01

    Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well

  17. Effects of direct-fed microbial supplementation on broiler performance, intestinal nutrient transport and integrity under experimental conditions with increased microbial challenge.

    PubMed

    Murugesan, G R; Gabler, N K; Persia, M E

    2014-02-01

    1. The effects of Aspergillus oryzae- and Bacillus subtilis-based direct-fed microbials (DFM) were investigated on the performance, ileal nutrient transport and intestinal integrity of broiler chickens, raised under experimental conditions, with increased intestinal microbial challenge. 2. The first study was a 3 × 2 factorial experiment, with 3 dietary treatments (control (CON), CON + DFM and CON + antibiotic growth promoter) with and without challenge. Chicks were fed experimental diets from 1 to 28 d, while the challenge was provided by vaccinating with 10 times the normal dose of commercial coccidial vaccine on d 9. In a second experiment, two groups of 1 d-old broilers, housed on built-up litter (uncleaned from two previous flocks), were fed the same CON and CON + DFM diets from 1 to 21 d. 3. The challenge in the first experiment reduced performance, but no differences were observed among dietary treatments from 8 to 28 d. The challenge reduced the ileal epithelial flux for D-glucose, L-lysine, DL-methionine and phosphorus on d 21. Epithelial flux for D-glucose, L-lysine and DL-methionine were increased by DFM. Ileal trans-epithelial electrical resistance (TER) was increased in challenged broilers fed DFM, although this was not observed in unchallenged birds as indicated by a significant interaction. 4. Ileal mucin mRNA expression and colon TER were increased, and colon endotoxin permeability was reduced by DFM on d 21 in the second experiment. 5. It was concluded that the addition of DFM in the diet improved the intestinal integrity of broiler chickens raised under experimental conditions designed to provide increased intestinal microbial challenge.

  18. Planetary Biology and Microbial Ecology: Molecular Ecology and the Global Nitrogen cycle

    NASA Technical Reports Server (NTRS)

    Nealson, Molly Stone (Editor); Nealson, Kenneth H. (Editor)

    1993-01-01

    This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

  19. Arabinoxylan‐oligosaccharides (AXOS) affect the protein/carbohydrate fermentation balance and microbial population dynamics of the Simulator of Human Intestinal Microbial Ecosystem

    PubMed Central

    Sanchez, J. I.; Marzorati, M.; Grootaert, C.; Baran, M.; Van Craeyveld, V.; Courtin, C. M.; Broekaert, W. F.; Delcour, J. A.; Verstraete, W.; Van de Wiele, T.

    2009-01-01

    Summary Arabinoxylan‐oligosaccharides (AXOS) are a recently newly discovered class of candidate prebiotics as – depending on their structure – they are fermented in different regions of gastrointestinal tract. This can have an impact on the protein/carbohydrate fermentation balance in the large intestine and, thus, affect the generation of potentially toxic metabolites in the colon originating from proteolytic activity. In this study, we screened different AXOS preparations for their impact on the in vitro intestinal fermentation activity and microbial community structure. Short‐term fermentation experiments with AXOS with an average degree of polymerization (avDP) of 29 allowed part of the oligosaccharides to reach the distal colon, and decreased the concentration of proteolytic markers, whereas AXOS with lower avDP were primarily fermented in the proximal colon. Additionally, prolonged supplementation of AXOS with avDP 29 to the Simulator of Human Intestinal Microbial Ecosystem (SHIME) reactor decreased levels of the toxic proteolytic markers phenol and p‐cresol in the two distal colon compartments and increased concentrations of beneficial short‐chain fatty acids (SCFA) in all colon vessels (25–48%). Denaturant gradient gel electrophoresis (DGGE) analysis indicated that AXOS supplementation only slightly modified the total microbial community, implying that the observed effects on fermentation markers are mainly caused by changes in fermentation activity. Finally, specific quantitative PCR (qPCR) analysis showed that AXOS supplementation significantly increased the amount of health‐promoting lactobacilli as well as of Bacteroides–Prevotella and Clostridium coccoides–Eubacterium rectale groups. These data allow concluding that AXOS are promising candidates to modulate the microbial metabolism in the distal colon. PMID:21261885

  20. Expression of the aryl hydrocarbon receptor contributes to the establishment of intestinal microbial community structure in mice

    PubMed Central

    Murray, Iain A.; Nichols, Robert G.; Zhang, Limin; Patterson, Andrew D.; Perdew, Gary H.

    2016-01-01

    Environmental and genetic factors represent key components in the establishment/maintenance of the intestinal microbiota. The aryl hydrocarbon receptor (AHR) is emerging as a pleiotropic factor, modulating pathways beyond its established role as a xenobiotic sensor. The AHR is known to regulate immune surveillance within the intestine through retention of intraepithelial lymphocytes, functional redistribution of Th17/Treg balance. Consequently, environmental/genetic manipulation of AHR activity likely influences host-microbe homeostasis. Utilizing C57BL6/J Ahr−/+ and Ahr−/− co-housed littermates followed by 18 days of genotypic segregation, we examined the influence of AHR expression upon intestinal microbe composition/functionality and host physiology. 16S sequencing/quantitative PCR (qPCR) revealed significant changes in phyla abundance, particularly Verrucomicrobia together with segmented filamentous bacteria, and an increase in species diversity in Ahr−/− mice following genotypic segregation. Metagenomics/metabolomics indicate microbial composition is associated with functional shifts in bacterial metabolism. Analysis identified Ahr−/−-dependent increases in ileal gene expression, indicating increased inflammatory tone. Transfer of Ahr−/− microbiota to wild-type germ-free mice recapitulated the increase Verrucomicrobia and inflammatory tone, indicating Ahr−/−-microbial dependence. These data suggest a role for the AHR in influencing the community structure of the intestinal microbiota. PMID:27659481

  1. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    USGS Publications Warehouse

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

  2. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    SciTech Connect

    Muller, R; Denef, Vincent; Kalnejals, Linda; Suttle, K Blake; Thomas, Brian; Wilmes, P; Smith, Richard L.; Nordstrom, D Kirk; McCleskey, R Blaine; Shah, Manesh B; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems.We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism s metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ

  3. Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

    PubMed Central

    Parfrey, Laura Wegener; Walters, William A.; Knight, Rob

    2011-01-01

    High throughput sequencing technology has opened a window into the vast communities of bacteria that live on and in humans, demonstrating tremendous variability, and that they play a large role in health and disease. The eukaryotic component of the human gut microbiome remains relatively unexplored with these methods, but turning these tools toward microbial eukaryotes in the gut will likely yield myriad insights into disease as well as the ecological and evolutionary principles that govern the gut microbiota. Microbial eukaryotes are common inhabitants of the human gut worldwide and parasitic taxa are a major source of morbidity and mortality, especially in developing countries, though there are also taxa that cause no harm or are beneficial. While the role microbial eukaryotes play in healthy individuals is much less clear, there are likely many complex interactions between the bacterial, archaeal, and eukaryotic microbiota that influence human health. Integrating eukaryotic microbes into a broad view of microbiome function requires an integrated ecological approach rather than one focused on specific, disease-causing taxa. Moving forward, we expect broad surveys of the eukaryotic microbiota and associated bacteria from geographically and socioeconomically diverse populations to paint a more complete picture of the human gut microbiome in health and disease. PMID:21808637

  4. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    PubMed

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism.

  5. The Influence of Ecological Isolation on the Structural and Functional Stability of Complex Microbial Communities

    NASA Technical Reports Server (NTRS)

    Franklin, R. B.; Garland, J. L.; Mills, A. L.

    2005-01-01

    To help understand how the behavior of microorganisms and microbial communities in insular space habitats may differ from the behavior of these groups on Earth, long-term incubations (100+ days) were conducting using wastewater bioreactors (batch fed) designed to mimic "closed" and "open" ecological systems. The issue of immigration was considered, and the goal of the research was to determine whether the stability of microbial communities in space is reduced due to their prolonged isolation. Bioreactors were established by inoculating flasks of sterile synthetic wastewater with the microbial community obtained from a local treatment facility; each day, one-third of the medium in the flask was replaced with an equal volume of sterile artificial wastewater. Flasks were divided into two treatments: "closed" and "open" to recruitment of additional microorganisms. "Closed" flasks were maintained as described above, while the medium used to feed the "open" flasks was supplemented daily with a small amount of raw sewage (which provided a continuous source of new potential community members). Significant differences in microbial community structure and function developed in the two sets of communities, and the results suggest that the open community was more stable and better able to adjust to changing environmental conditions. Each community's resistance to environmental (temperature fluctuations) and biological stresses (starvation and invasion by an opportunistic pathogen Pseudomonas aeruginosa) was monitored. Experiments were also conducted to determine whether the effect of isolation changes depending on the microbial communities' initial diversity or composition; communities with a low(er) initial diversity were less stable. Overall, the results indicate that isolation will be an important factor influencing the activity of microbial communities on board spacecraft. A possible way of mitigating these effects would be to include communities with high initial

  6. Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

    PubMed Central

    Speth, Daan R.; in 't Zandt, Michiel H.; Guerrero-Cruz, Simon; Dutilh, Bas E.; Jetten, Mike S. M.

    2016-01-01

    Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date. PMID:27029554

  7. Formation of higher plant component microbial community in closed ecological system.

    PubMed

    Tirranen, L S

    2001-07-01

    Closed ecological systems (CES) place at the disposal of a researcher unique possibilities to study the role of microbial communities in individual components and of the entire system. The microbial community of the higher plant component has been found to form depending on specific conditions of the closed ecosystem: length of time the solution is reused, introduction of intrasystem waste water into the nutrient medium, effect of other component of the system, and system closure in terms of gas exchange. The higher plant component formed its own microbial complex different from that formed prior to closure. The microbial complex of vegetable polyculture is more diverse and stable than the monoculture of wheat. The composition of the components' microflora changed, species diversity decreased, individual species of bacteria and fungi whose numbers were not so great before the closure prevailed. Special attention should be paid to phytopathogenic and conditionally pathogenic species of microorganisms potentially hazardous to man or plants and the least controlled in CES. This situation can endanger creation of CES and make conjectural existence of preplanned components, man, specifically, and consequently, of CES as it is.

  8. Formation of higher plant component microbial community in closed ecological system

    NASA Astrophysics Data System (ADS)

    Tirranen, L. S.

    2001-07-01

    Closed ecological systems (CES) place at the disposal of a researcher unique possibilities to study the role of microbial communities in individual components and of the entire system. The microbial community of the higher plant component has been found to form depending on specific conditions of the closed ecosystem: length of time the solution is reused, introduction of intrasystem waste water into the nutrient medium, effect of other component of the system, and system closure in terms of gas exchange. The higher plant component formed its own microbial complex different from that formed prior to closure. The microbial complex of vegetable polyculture is more diverse and stable than the monoculture of wheat. The composition of the components' microflora changed, species diversity decreased, individual species of bacteria and fungi whose numbers were not so great before the closure prevailed. Special attention should be paid to phytopathogenic and conditionally pathogenic species of microorganisms potentially hazardous to man or plants and the least controlled in CES. This situation can endanger creation of CES and make conjectural existence of preplanned components, man, specifically, and consequently, of CES as it is.

  9. PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

    USGS Publications Warehouse

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

    2012-01-01

    Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

  10. Using Intact Iron Microbial Mats to Gain Insights Into Mat Ecology and Geochemical Niche at the Microbial Scale

    NASA Astrophysics Data System (ADS)

    Glazer, B. T.; Chan, C. S. Y.; Mcallister, S.; Leavitt, A.; Emerson, D.

    2015-12-01

    Microbial mats are formed by microorganisms working in coordinated symbiosis, often benefitting the community by controlling the local geochemical or physical environment. Thus, the ecology of the mat depends on the individual roles of microbes organized into niches within a larger architecture. Chemolithotrophic Fe-oxidizing bacteria (FeOB) form distinctive Fe oxyhydroxide biominerals which constitute the building blocks of the mat. However, the majority of our progress has been in understanding the overall community structure. Understanding the physical mat structure on the microbial scale is important to unraveling FeOB evolution, the biogeochemistry and ecology of Fe-rich habitats, and ultimately interpreting FeOB biosignatures in the rock record. Mats in freshwater and marine environments contain strikingly similar biomineral morphologies, yet they are formed by phylogenetically distinct microorganisms. This suggests that the overall architecture and underlying genetics of freshwater and marine mats has evolved to serve particular roles specific to Fe oxidation. Thus, we conducted a comparative study of Fe seep freshwater mats and marine hydrothermal mats. We have developed a new approach to sampling Fe mats in order to preserve the delicate structure for analysis by confocal and scanning electron microscopy. Our analyses of these intact mats show that freshwater and marine mats are similarly initiated by a single type of structure-former. These ecosystem engineers form either a hollow sheath or a twisted stalk biomineral during mat formation, with a highly directional structure. These microbes appear to be the vanguard organisms that anchor the community within oxygen/Fe(II) gradients, further allowing for community succession in the mat interior as evidenced by other mineralized morphologies. Patterns in biomineral thickness and directionality were indicative of redox gradients and temporal changes in the geochemical environment. These observations show that

  11. Challenges in microbial ecology: building predictive understanding of community function and dynamics.

    PubMed

    Widder, Stefanie; Allen, Rosalind J; Pfeiffer, Thomas; Curtis, Thomas P; Wiuf, Carsten; Sloan, William T; Cordero, Otto X; Brown, Sam P; Momeni, Babak; Shou, Wenying; Kettle, Helen; Flint, Harry J; Haas, Andreas F; Laroche, Béatrice; Kreft, Jan-Ulrich; Rainey, Paul B; Freilich, Shiri; Schuster, Stefan; Milferstedt, Kim; van der Meer, Jan R; Groβkopf, Tobias; Huisman, Jef; Free, Andrew; Picioreanu, Cristian; Quince, Christopher; Klapper, Isaac; Labarthe, Simon; Smets, Barth F; Wang, Harris; Soyer, Orkun S

    2016-11-01

    The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model-experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.

  12. Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions

    PubMed Central

    Wong, Hon Lun; Ahmed-Cox, Aria; Burns, Brendan Paul

    2016-01-01

    Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S’Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems. PMID:27681900

  13. Challenges in microbial ecology: building predictive understanding of community function and dynamics

    PubMed Central

    Widder, Stefanie; Allen, Rosalind J; Pfeiffer, Thomas; Curtis, Thomas P; Wiuf, Carsten; Sloan, William T; Cordero, Otto X; Brown, Sam P; Momeni, Babak; Shou, Wenying; Kettle, Helen; Flint, Harry J; Haas, Andreas F; Laroche, Béatrice; Kreft, Jan-Ulrich; Rainey, Paul B; Freilich, Shiri; Schuster, Stefan; Milferstedt, Kim; van der Meer, Jan R; Groβkopf, Tobias; Huisman, Jef; Free, Andrew; Picioreanu, Cristian; Quince, Christopher; Klapper, Isaac; Labarthe, Simon; Smets, Barth F; Wang, Harris; Soyer, Orkun S

    2016-01-01

    The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved. PMID:27022995

  14. [The effect of thermal power plant on microbial ecology and environmental quality].

    PubMed

    Yang, S S; Yang, C K; Chang, E H; Wei, C B

    1999-12-01

    To investigate the effect of thermal power plant on the microbial ecology and the environmental quality, the Hsieh-Ho Thermal Power Plant was chosen and the populations of microbes including bacteria, actinomycetes, fungi, and cellulolytic, phosphate-solubilizing and nitrogen-fixing microbes were selected as the parameters of microbial ecology. The pH values of the soil sample collected from inside and outside of the plant were 5.2-6.2 and 4.0-5.3, respectively. Moisture content in plant area was lower than that in the surrounding area. Microbial populations of the topsoils were higher than those of the subsoils. Each gram of soil contained 3.64 x 10(4)-5.16 x 10(7) colonies of bacteria, 1.75 x 10(3)-1.10 x 10(6) colonies of actinomycetes and 6.72 x 10(3)-8.78 x 10(6) colonies of fungi in the plant area; while they were 5.52 x 10(4)-2.14 x 10(7), 8.26 x 10(3)-7.25 x 10(5) and 3.49 x 10(3)-2.74 x 10(6) colonies of bacteria, actinomycetes and fungi, respectively, in the surrounding area. The effect of seasonal change on microbial populations was not significant. The ratio of cellulolytic, phosphate-solubilizing and nitrogen-fixing microbes to the total count in the plant area was also higher than that in the surrounding area, and some of them had significant differences. From the statistical analysis, the effect of thermal power generator on the population and distribution of microbes was significantly different.

  15. Microbial ecology-based methods to characterize the bacterial communities of non-model insects.

    PubMed

    Prosdocimi, Erica M; Mapelli, Francesca; Gonella, Elena; Borin, Sara; Crotti, Elena

    2015-12-01

    Among the animals of the Kingdom Animalia, insects are unparalleled for their widespread diffusion, diversity and number of occupied ecological niches. In recent years they have raised researcher interest not only because of their importance as human and agricultural pests, disease vectors and as useful breeding species (e.g. honeybee and silkworm), but also because of their suitability as animal models. It is now fully recognized that microorganisms form symbiotic relationships with insects, influencing their survival, fitness, development, mating habits and the immune system and other aspects of the biology and ecology of the insect host. Thus, any research aimed at deepening the knowledge of any given insect species (perhaps species of applied interest or species emerging as novel pests or vectors) must consider the characterization of the associated microbiome. The present review critically examines the microbiology and molecular ecology techniques that can be applied to the taxonomical and functional analysis of the microbiome of non-model insects. Our goal is to provide an overview of current approaches and methods addressing the ecology and functions of microorganisms and microbiomes associated with insects. Our focus is on operational details, aiming to provide a concise guide to currently available advanced techniques, in an effort to extend insect microbiome research beyond simple descriptions of microbial communities.

  16. Genome-resolved metagenomics reveals that sulfur metabolism dominates the microbial ecology of rising hydrothermal plumes

    NASA Astrophysics Data System (ADS)

    Anantharaman, K.; Breier, J. A., Jr.; Jain, S.; Reed, D. C.; Dick, G.

    2015-12-01

    Deep-sea hydrothermal plumes occur when hot fluids from hydrothermal vents replete with chemically reduced elements and compounds like sulfide, methane, hydrogen, ammonia, iron and manganese mix with cold, oxic seawater. Chemosynthetic microbes use these reduced chemicals to power primary production and are pervasive throughout the deep sea, even at sites far removed from hydrothermal vents. Although neutrally-buoyant hydrothermal plumes have been well-studied, rising hydrothermal plumes have received little attention even though they represent an important interface in the deep-sea where microbial metabolism and particle formation processes control the transformation of important elements and impact global biogeochemical cycles. In this study, we used genome-resolved metagenomic analyses and thermodynamic-bioenergetic modeling to study the microbial ecology of rising hydrothermal plumes at five different hydrothermal vents spanning a range of geochemical gradients at the Eastern Lau Spreading Center (ELSC) in the Western Pacific Ocean. Our analyses show that differences in the geochemistry of hydrothermal vents do not manifest in microbial diversity and community composition, both of which display only minor variance across ELSC hydrothermal plumes. Microbial metabolism is dominated by oxidation of reduced sulfur species and supports a diversity of bacteria, archaea and viruses that provide intriguing insights into metabolic plasticity and virus-mediated horizontal gene transfer in the microbial community. The manifestation of sulfur oxidation genes in hydrogen and methane oxidizing organisms hints at metabolic opportunism in deep-sea microbes that would enable them to respond to varying redox conditions in hydrothermal plumes. Finally, we infer that the abundance, diversity and metabolic versatility of microbes associated with sulfur oxidation impart functional redundancy that could allow it to persist in the dynamic settings of hydrothermal plumes.

  17. The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice

    PubMed Central

    Wisniewski, Paul J.; Noji, Michael; McGuinness, Lora R.; Lightfoot, Stanley A.

    2016-01-01

    Background The gut microbiota is now known to play an important role contributing to inflammatory-based chronic diseases. This study examined intestinal integrity/inflammation and the gut microbial communities in sedentary and exercising mice presented with a normal or high-fat diet. Methods Thirty-six, 6-week old C57BL/6NTac male mice were fed a normal or high-fat diet for 12-weeks and randomly assigned to exercise or sedentary groups. After 12 weeks animals were sacrificed and duodenum/ileum tissues were fixed for immunohistochemistry for occludin, E-cadherin, and cyclooxygenase-2 (COX-2). The bacterial communities were assayed in fecal samples using terminal restriction fragment length polymorphism (TRFLP) analysis and pyrosequencing of 16S rRNA gene amplicons. Results Lean sedentary (LS) mice presented normal histologic villi while obese sedentary (OS) mice had similar villi height with more than twice the width of the LS animals. Both lean (LX) and obese exercise (OX) mice duodenum and ileum were histologically normal. COX-2 expression was the greatest in the OS group, followed by LS, LX and OX. The TRFLP and pyrosequencing indicated that members of the Clostridiales order were predominant in all diet groups. Specific phylotypes were observed with exercise, including Faecalibacterium prausnitzi, Clostridium spp., and Allobaculum spp. Conclusion These data suggest that exercise has a strong influence on gut integrity and host microbiome which points to the necessity for more mechanistic studies of the interactions between specific bacteria in the gut and its host. PMID:26954359

  18. Culture-Dependent and -Independent Methods To Investigate the Microbial Ecology of Italian Fermented Sausages

    PubMed Central

    Rantsiou, Kalliopi; Urso, Rosalinda; Iacumin, Lucilla; Cantoni, Carlo; Cattaneo, Patrizia; Comi, Giuseppe; Cocolin, Luca

    2005-01-01

    In this study, the microbial ecology of three naturally fermented sausages produced in northeast Italy was studied by culture-dependent and -independent methods. By plating analysis, the predominance of lactic acid bacteria populations was pointed out, as well as the importance of coagulase-negative cocci. Also in the case of one fermentation, the fecal enterocci reached significant counts, highlighting their contribution to the particular transformation process. Yeast counts were higher than the detection limit (>100 CFU/g) in only one fermented sausage. Analysis of the denaturing gradient gel electrophoresis (DGGE) patterns and sequencing of the bands allowed profiling of the microbial populations present in the sausages during fermentation. The bacterial ecology was mainly characterized by the stable presence of Lactobacillus curvatus and Lactobacillus sakei, but Lactobacillus paracasei was also repeatedly detected. An important piece of evidence was the presence of Lactococcus garvieae, which clearly contributed in two fermentations. Several species of Staphylococcus were also detected. Regarding other bacterial groups, Bacillus sp., Ruminococcus sp., and Macrococcus caseolyticus were also identified at the beginning of the transformations. In addition, yeast species belonging to Debaryomyces hansenii, several Candida species, and Willopsis saturnus were observed in the DGGE gels. Finally, cluster analysis of the bacterial and yeast DGGE profiles highlighted the uniqueness of the fermentation processes studied. PMID:15812029

  19. CO2 gradient affects on deep subsurface microbial ecology during carbon sequestration

    NASA Astrophysics Data System (ADS)

    Gulliver, D.; Gregory, K.

    2011-12-01

    Geological carbon sequestration is likely to be part of a comprehensive strategy to minimize the release of greenhouse gasses into the atmosphere. Reservoir storage capacities and long-term security of these deposits will be dependent on the trapping mechanisms and mineral transformation in the deep subsurface. Therefore, a critical need exists to understand the evolution of microbial populations that may influence the biogeochemistry in the reservoirs. As the CO2 front moves through the storage aquifer, microbial communities may preside in residual brine left behind in cracks, dead flow zones, and upstream to the front; this brine will have a gradient of dissolved CO2 in which microbial interaction may behave differently, depending on the distance from the CO2 front. The evolution of microbial ecology along this CO2 gradient was investigated using fluid-slurry samples obtained from the prospective carbon sequestration site, the Arbuckle saline aquifer at the Wellington oil field, KS. The native species of these samples were investigated with a series of batch reactors under constant temperature of 40 °C, constant total pressure of 2,000 psi, and varying CO2 partial pressures of 0 psi, 20 psi, 200 psi, and 2,000 psi. After 1 day, 7 days, and 56 days of exposure in the batch reactors, fluid samples were centrifuged and the resulting pellet was biologically analyzed. Clone libraries and quantitative PCR determined that the bacterial diversity and population of the native microbial community was dependant on both the duration of exposure and the CO2 partial pressure. For example, the microbial community of 0 psi CO2 and 20 psi CO2 was predominantly related to the families halomonadaceae and marinilabiaceae while at 2,000 psi CO2 the community was predominantly in the family psychromonadaceae. The population size at 2,000 psi CO2 was also found to decrease by 3 orders of magnitude after only 7 days of CO2 exposure. Although these experiments were relatively short

  20. Early Changes in Microbial Colonization Selectively Modulate Intestinal Enzymes, but Not Inducible Heat Shock Proteins in Young Adult Swine

    PubMed Central

    Arnal, Marie-Edith; Zhang, Jing; Messori, Stefano; Bosi, Paolo; Smidt, Hauke; Lallès, Jean-Paul

    2014-01-01

    Metabolic diseases and obesity are developing worldwide in a context of plethoric intake of high energy diets. The intestine may play a pivotal role due to diet-induced alterations in microbiota composition and increased permeability to bacterial lipopolysaccharide inducing metabolic inflammation. Early programming of metabolic disorders appearing in later life is also suspected, but data on the intestine are lacking. Therefore, we hypothesized that early disturbances in microbial colonization have short- and long-lasting consequences on selected intestinal components including key digestive enzymes and protective inducible heat shock proteins (HSP). The hypothesis was tested in swine offspring born to control mothers (n = 12) or mothers treated with the antibiotic amoxicillin around parturition (n = 11), and slaughtered serially at 14, 28 and 42 days of age to assess short-term effects. To evaluate long-term consequences, young adult offspring from the same litters were offered a normal or a fat-enriched diet for 4 weeks between 140 and 169 days of age and were then slaughtered. Amoxicillin treatment transiently modified both mother and offspring microbiota. This was associated with early but transient reduction in ileal alkaline phosphatase, HSP70 (but not HSP27) and crypt depth, suggesting a milder or delayed intestinal response to bacteria in offspring born to antibiotic-treated mothers. More importantly, we disclosed long-term consequences of this treatment on jejunal alkaline phosphatase (reduced) and jejunal and ileal dipeptidylpeptidase IV (increased and decreased, respectively) of offspring born to antibiotic-treated dams. Significant interactions between early antibiotic treatment and later diet were observed for jejunal alkaline phosphatase and sucrase. By contrast, inducible HSPs were not affected. In conclusion, our data suggest that early changes in bacterial colonization not only modulate intestinal architecture and function transiently, but

  1. 'Everything is everywhere: but the environment selects': ubiquitous distribution and ecological determinism in microbial biogeography.

    PubMed

    O'Malley, Maureen A

    2008-09-01

    Recent discoveries of geographical patterns in microbial distribution are undermining microbiology's exclusively ecological explanations of biogeography and their fundamental assumption that 'everything is everywhere: but the environment selects'. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will trace the conceptual history of Beijerinck's claim that 'everything is everywhere' in relation to a more general account of its theoretical, experimental and institutional context. His principle also needs to be situated in relationship to plant and animal biogeography, which, this paper will argue, forms a continuum of thought with microbial biogeography. Finally, a brief overview of the contemporary microbiological research challenging 'everything is everywhere' reveals that philosophical issues from Beijerinck's era of microbiology still provoke intense discussion in twenty-first century investigations of microbial biogeography.

  2. A novel analysis method for paired-sample microbial ecology experiments

    DOE PAGES

    Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.; ...

    2016-05-06

    Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

  3. A novel analysis method for paired-sample microbial ecology experiments

    SciTech Connect

    Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.; Fortney, Julian L.; Bastidas-Oyanedel, Juan R.; Rodriguez, Jorge; Hazen, Terry C.; Alm, Eric J.; Humbert, Jean -Francois

    2016-05-06

    Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .

  4. A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

    PubMed

    Olesen, Scott W; Vora, Suhani; Techtmann, Stephen M; Fortney, Julian L; Bastidas-Oyanedel, Juan R; Rodríguez, Jorge; Hazen, Terry C; Alm, Eric J

    2016-01-01

    Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".

  5. Ruminal fermentation and microbial ecology of buffaloes and cattle fed the same diet.

    PubMed

    Lwin, Khin-Ohnmar; Kondo, Makoto; Ban-Tokuda, Tomomi; Lapitan, Rosalina M; Del-Barrio, Arnel N; Fujihara, Tsutomu; Matsui, Hiroki

    2012-12-01

    Although buffaloes and cattle are ruminants, their digestive capabilities and rumen microbial compositions are considered to be different. The purpose of this study was to compare the rumen microbial ecology of crossbred water buffaloes and cattle that were fed the same diet. Cattle exhibited a higher fermentation rate than buffaloes. Methane production and methanogen density were lower in buffaloes. Phylogenetic analysis of Fibrobacter succinogenes-specific 16S ribosomal RNA gene clone library showed that the diversity of groups within a species was significantly different (P < 0.05) between buffalo and cattle and most of the clones were affiliated with group 2 of the species. Population densities of F.succinogenes, Ruminococcus albus and R. flavefaciens were higher until 6 h post-feeding in cattle; however, buffaloes exhibited different traits. The population of anaerobic fungi decreased at 3 h in cattle compared to buffaloes and was similar at 0 h and 6 h. The diversity profiles of bacteria and fungi were similar in the two species. The present study showed that the profiles of the fermentation process, microbial population and diversity were similar in crossbred water buffaloes and crossbred cattle.

  6. A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments

    PubMed Central

    Vora, Suhani; Techtmann, Stephen M.; Fortney, Julian L.; Bastidas-Oyanedel, Juan R.; Rodríguez, Jorge; Hazen, Terry C.; Alm, Eric J.

    2016-01-01

    Many microbial ecology experiments use sequencing data to measure a community’s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method’s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of “bottle effects”. PMID:27152415

  7. Ecological roles and biotechnological applications of marine and intertidal microbial biofilms.

    PubMed

    Mitra, Sayani; Sana, Barindra; Mukherjee, Joydeep

    2014-01-01

    This review is a retrospective of ecological effects of bioactivities produced by biofilms of surface-dwelling marine/intertidal microbes as well as of the industrial and environmental biotechnologies developed exploiting the knowledge of biofilm formation. Some examples of significant interest pertaining to the ecological aspects of biofilm-forming species belonging to the Roseobacter clade include autochthonous bacteria from turbot larvae-rearing units with potential application as a probiotic as well as production of tropodithietic acid and indigoidine. Species of the Pseudoalteromonas genus are important examples of successful surface colonizers through elaboration of the AlpP protein and antimicrobial agents possessing broad-spectrum antagonistic activity against medical and environmental isolates. Further examples of significance comprise antiprotozoan activity of Pseudoalteromonas tunicata elicited by violacein, inhibition of fungal colonization, antifouling activities, inhibition of algal spore germination, and 2-n-pentyl-4-quinolinol production. Nitrous oxide, an important greenhouse gas, emanates from surface-attached microbial activity of marine animals. Marine and intertidal biofilms have been applied in the biotechnological production of violacein, phenylnannolones, and exopolysaccharides from marine and tropical intertidal environments. More examples of importance encompass production of protease, cellulase, and xylanase, melanin, and riboflavin. Antifouling activity of Bacillus sp. and application of anammox bacterial biofilms in bioremediation are described. Marine biofilms have been used as anodes and cathodes in microbial fuel cells. Some of the reaction vessels for biofilm cultivation reviewed are roller bottle, rotating disc bioreactor, polymethylmethacrylate conico-cylindrical flask, fixed bed reactor, artificial microbial mats, packed-bed bioreactors, and the Tanaka photobioreactor.

  8. Effects of diets containing different concentrations of mannanoligosaccharide or antibiotics on growth performance, intestinal development, cecal and litter microbial populations, and carcass parameters of broilers.

    PubMed

    Baurhoo, B; Ferket, P R; Zhao, X

    2009-11-01

    The effects of 2 levels of mannanoligosaccharide (MOS) in feed were compared with antibiotic growth promoters on growth performance, intestinal morphology, cecal and litter microbial populations, and carcass parameters in broilers raised in a sanitary environment. Dietary treatments included: 1) antibiotic growth promoter-free diet (control), 2) VIRG (diet 1 + 16.5 mg/kg of virginiamycin), 3) BACT (diet 1 + 55 mg/kg of bacitracin), 4) LMOS (diet 1 + 0.2% MOS), and 5) HMOS (diet 1 + 0.5% MOS). Birds were randomly assigned to 3 replicate pens/treatment (n = 55/pen). Body weight and feed intake were recorded weekly throughout 38 d. At d 14, 24, and 34, a 1-cm segment of duodenum, jejunum, and ileum was used in morphological analysis (n = 9 birds/d per treatment). At the same bird ages, cecal contents were assayed for lactobacilli, bifidobacteria, Salmonella, Campylobacter, and Escherichia coli, whereas litter was analyzed for Salmonella, Campylobacter, and E. coli. Carcass yields (breast fillet and tenders, thigh, drumstick, and wing) were determined at d 38. Body weight, feed conversion, and carcass yields did not differ among treatments. In contrast to birds fed VIRG or BACT, LMOS and HMOS consistently increased (P < 0.05) villi height and goblet cell number per villus in all intestinal segments at d 24 and 34. Bifidobacteria concentrations were higher (P < 0.05) in LMOS- and HMOS-fed birds at all time points. Birds and litter from all treatments were free of Salmonella. At d 14 and 24, cecal E. coli and Campylobacter counts were not different among treatments. In comparison to birds fed control, at d 34, BACT, LMOS, and HMOS significantly reduced (P < 0.05) cecal E. coli concentrations, whereas Campylobacter counts were reduced (P < 0.05) by VIRG, BACT, and LMOS. Litter bacterial counts were not altered by dietary treatments. In conclusion, under conditions of this study, MOS conferred intestinal health benefits to chickens by improving its morphological

  9. The influence of ecological and conventional plant production systems on soil microbial quality under hops (Humulus lupulus).

    PubMed

    Oszust, Karolina; Frąc, Magdalena; Gryta, Agata; Bilińska, Nina

    2014-06-03

    The knowledge about microorganisms-activity and diversity under hop production is still limited. We assumed that, different systems of hop production (within the same soil and climatic conditions) significantly influence on the composition of soil microbial populations and its functional activity (metabolic potential). Therefore, we compared a set of soil microbial properties in the field experiment of two hop production systems (a) ecological based on the use of probiotic preparations and organic fertilization (b) conventional-with the use of chemical pesticides and mineral fertilizers. Soil analyses included following microbial properties: The total number microorganisms, a bunch of soil enzyme activities, the catabolic potential was also assessed following Biolog EcoPlates®. Moreover, the abundance of ammonia-oxidizing archaea (AOA) was characterized by terminal restriction fragment length polymorphism analysis (T-RFLP) of PCR ammonia monooxygenase α-subunit (amoA) gene products. Conventional and ecological systems of hop production were able to affect soil microbial state in different seasonal manner. Favorable effect on soil microbial activity met under ecological, was more probably due to livestock-based manure and fermented plant extracts application. No negative influence on conventional hopyard soil was revealed. Both type of production fulfilled fertilizing demands. Under ecological production it was due to livestock-based manure fertilizers and fermented plant extracts application.

  10. Carbohydrate-Free Peach (Prunus persica) and Plum (Prunus domestica) Juice Affects Fecal Microbial Ecology in an Obese Animal Model

    PubMed Central

    Markel, Melissa; Martino, Hercia S.; Minamoto, Yasushi; Steiner, Jörg M.; Byrne, David; Suchodolski, Jan S.; Mertens-Talcott, Susanne U.

    2014-01-01

    Background Growing evidence shows the potential of nutritional interventions to treat obesity but most investigations have utilized non-digestible carbohydrates only. Peach and plum contain high amounts of polyphenols, compounds with demonstrated anti-obesity effects. The underlying process of successfully treating obesity using polyphenols may involve an alteration of the intestinal microbiota. However, this phenomenon is not well understood. Methodology/Principal Findings Obese Zucker rats were assigned to three groups (peach, plum, and control, n = 10 each), wild-type group was named lean (n = 10). Carbohydrates in the fruit juices were eliminated using enzymatic hydrolysis. Fecal samples were obtained after 11 weeks of fruit or control juice administration. Real-time PCR and 454-pyrosequencing were used to evaluate changes in fecal microbiota. Over 1,500 different Operational Taxonomic Units at 97% similarity were detected in all rats. Several bacterial groups (e.g. Lactobacillus and members of Ruminococcacea) were found to be more abundant in the peach but especially in the plum group (plum juice contained 3 times more total polyphenolics compared to peach juice). Principal coordinate analysis based on Unifrac-based unweighted distance matrices revealed a distinct separation between the microbiota of control and treatment groups. These changes in fecal microbiota occurred simultaneously with differences in fecal short-chain acids concentrations between the control and treatment groups as well as a significant decrease in body weight in the plum group. Conclusions This study suggests that consumption of carbohydrate-free peach and plum juice has the potential to modify fecal microbial ecology in an obese animal model. The separate contribution of polyphenols and non-polyphenols compounds (vitamins and minerals) to the observed changes is unknown. PMID:25007331

  11. Microbial diversity and biogeochemistry in glacier forefields: assessment of ecological stability in high alpine environments

    NASA Astrophysics Data System (ADS)

    Meola, M.; Lazzaro, A.; Zeyer, J.

    2012-04-01

    Microbial communities inhabiting recently deglaciated, unvegetated, high alpine soils (e.g. glacier forefields) need to be adapted to fluctuating environmental conditions, such as strong daily and seasonal humidity and temperature variations. Soil-related characteristics (e.g. oligotrophy, pH, water holding capacity, nutrient concentration) may in addition determine the presence of locally adapted microbial communities. Currently little is known on the ecological stability (resistance and resilience) of such an environment. In this project, we aim at understanding ecological stability of microbial communities of alpine glacier forefields through a reciprocal soil transplantation experiment. The study consists in i) determining bacterial phylotypes that may respond to environmental changes and ii) relating biological, chemical and physical data to observed microbial responses. We selected two different glacier forefields located in the Swiss Alps (approximately at 2500 m.a.s.l.) The Griessen forefield (Canton Obwalden) is characterized by a calcareous bedrock, while the Tiefen forefield (Canton Uri) is of siliceous composition. The sites are well characterized in terms of their geography (e.g. exposure, slope) and climatic fluctuations (Lazzaro et al. 2009, Lazzaro et al. 2011). At each site, we incubated stainless steel pots with four different soil treatments (autochthonous untreated, autochthonous sterilized, allochthonous untreated and allochthonous sterilized). The setup was repeated in quadruplicate. Soil temperature and soil moisture at 10 cm depth were measured every hour by Decagon EM 50 sensors (Decagon Devices Inc.). In July (D0), August (D1) and September (D2) 2011, soil aliquots were sampled from the pots for analysis. We plan to further extend the sampling for at least three snow-free seasons (2011-2013). Chemical analysis of the soil encompassed soluble ions, pH and DOC. Bacterial community analysis included microbial biomass (DAPI cell counts), basal

  12. Earth's Earliest Ecosystems in the C: The Use of Microbial Mats to Demonstrate General Principles of Scientific Inquiry and Microbial Ecology

    NASA Technical Reports Server (NTRS)

    Bebout, Brad M.; Bucaria, Robin

    2006-01-01

    Microbial mats are living examples of the most ancient biological communities on Earth. As Earth's earliest ecosystems, they are centrally important to understanding the history of life on our planet and are useful models for the search for life elsewhere. As relatively compact (but complete) ecosystems, microbial mats are also extremely useful for educational activities. Mats may be used to demonstrate a wide variety of concepts in general and microbial ecology, including the biogeochemical cycling of elements, photosynthesis and respiration, and the origin of the Earth's present oxygen containing atmosphere. Microbial mats can be found in a number of common environments accessible to teachers, and laboratory microbial mats can be constructed using materials purchased from biological supply houses. With funding from NASA's Exobiology program, we have developed curriculum and web-based activities centered on the use of microbial mats as tools for demonstrating general principles in ecology, and the scientific process. Our web site (http://microbes.arc.nasa.gov) includes reference materials, lesson plans, and a "Web Lab", featuring living mats maintained in a mini-aquarium. The site also provides information as to how research on microbial mats supports NASA's goals, and various NASA missions. A photo gallery contains images of mats, microscopic views of the organisms that form them, and our own research activities. An animated educational video on the web site uses computer graphic and video microscopy to take students on a journey into a microbial mat. These activities are targeted to a middle school audience and are aligned with the National Science Standards.

  13. Host Responses to Intestinal Microbial Antigens in Gluten-Sensitive Mice

    PubMed Central

    Natividad, Jane M.; Huang, Xianxi; Slack, Emma; Jury, Jennifer; Sanz, Yolanda; David, Chella; Denou, Emmanuel; Yang, Pinchang; Murray, Joseph

    2009-01-01

    Background and Aims Excessive uptake of commensal bacterial antigens through a permeable intestinal barrier may influence host responses to specific antigen in a genetically predisposed host. The aim of this study was to investigate whether intestinal barrier dysfunction induced by indomethacin treatment affects the host response to intestinal microbiota in gluten-sensitized HLA-DQ8/HCD4 mice. Methodology/Principal Findings HLA-DQ8/HCD4 mice were sensitized with gluten, and gavaged with indomethacin plus gluten. Intestinal permeability was assessed by Ussing chamber; epithelial cell (EC) ultra-structure by electron microscopy; RNA expression of genes coding for junctional proteins by Q-real-time PCR; immune response by in-vitro antigen-specific T-cell proliferation and cytokine analysis by cytometric bead array; intestinal microbiota by fluorescence in situ hybridization and analysis of systemic antibodies against intestinal microbiota by surface staining of live bacteria with serum followed by FACS analysis. Indomethacin led to a more pronounced increase in intestinal permeability in gluten-sensitized mice. These changes were accompanied by severe EC damage, decreased E-cadherin RNA level, elevated IFN-γ in splenocyte culture supernatant, and production of significant IgM antibody against intestinal microbiota. Conclusion Indomethacin potentiates barrier dysfunction and EC injury induced by gluten, affects systemic IFN-γ production and the host response to intestinal microbiota antigens in HLA-DQ8/HCD4 mice. The results suggest that environmental factors that alter the intestinal barrier may predispose individuals to an increased susceptibility to gluten through a bystander immune activation to intestinal microbiota. PMID:19649259

  14. Metabolic and Microbial Modulation of the Large Intestine Ecosystem by Non-Absorbed Diet Phenolic Compounds: A Review.

    PubMed

    Mosele, Juana I; Macià, Alba; Motilva, Maria-José

    2015-09-18

    Phenolic compounds represent a diverse group of phytochemicals whose intake is associated with a wide spectrum of health benefits. As consequence of their low bioavailability, most of them reach the large intestine where, mediated by the action of local microbiota, a series of related microbial metabolites are accumulated. In the present review, gut microbial transformations of non-absorbed phenolic compounds are summarized. Several studies have reached a general consensus that unbalanced diets are associated with undesirable changes in gut metabolism that could be detrimental to intestinal health. In terms of explaining the possible effects of non-absorbed phenolic compounds, we have also gathered information regarded their influence on the local metabolism. For this purpose, a number of issues are discussed. Firstly, we consider the possible implications of phenolic compounds in the metabolism of colonic products, such as short chain fatty acids (SCFA), sterols (cholesterol and bile acids), and microbial products of non-absorbed proteins. Due to their being recognized as affective antioxidant and anti-inflammatory agents, the ability of phenolic compounds to counteract or suppress pro-oxidant and/or pro-inflammatory responses, triggered by bowel diseases, is also presented. The modulation of gut microbiota through dietetic maneuvers including phenolic compounds is also commented on. Although the available data seems to assume positive effects in terms of gut health protection, it is still insufficient for solid conclusions to be extracted, basically due to the lack of human trials to confirm the results obtained by the in vitro and animal studies. We consider that more emphasis should be focused on the study of phenolic compounds, particularly in their microbial metabolites, and their power to influence different aspects of gut health.

  15. Ecological succession of the microbial communities of an air-conditioning cooling coil in the tropics.

    PubMed

    Acerbi, E; Chénard, C; Miller, D; Gaultier, N E; Heinle, C E; Chang, V W-C; Uchida, A; Drautz-Moses, D I; Schuster, S C; Lauro, F M

    2017-03-01

    Air-conditioning systems harbor microorganisms, potentially spreading them to indoor environments. While air and surfaces in air-conditioning systems are periodically sampled as potential sources of indoor microbes, little is known about the dynamics of cooling coil-associated communities and their effect on the downstream airflow. Here, we conducted a 4-week time series sampling to characterize the succession of an air-conditioning duct and cooling coil after cleaning. Using an universal primer pair targeting hypervariable regions of the 16S/18S ribosomal RNA, we observed a community succession for the condensed water, with the most abundant airborne taxon Agaricomycetes fungi dominating the initial phase and Sphingomonas bacteria becoming the most prevalent taxa toward the end of the experiment. Duplicate air samples collected upstream and downstream of the coil suggest that the system does not act as ecological filter or source/sink for specific microbial taxa during the duration of the experiment.

  16. Mobilifilum chasei: morphology and ecology of a spirochete from an intertidal stratified microbial mat community

    NASA Technical Reports Server (NTRS)

    Margulis, L.; Hinkle, G.; Stolz, J.; Craft, F.; Esteve, I.; Guerrero, R.

    1990-01-01

    Spirochetes were found in the lower anoxiphototrophic layer of a stratified microbial mat (North Pond, Laguna Figueroa, Baja California, Mexico). Ultra-structural analysis of thin sections of field samples revealed spirochetes approximately 0.25 micrometer in diameter with 10 or more periplasmic flagella, leading to the interpretation that these spirochetes bear 10 flagellar insertions on each end. Morphometric study showed these free-living spirochetes greatly resemble certain symbiotic ones, i.e., Borrelia and certain termite spirochetes, the transverse sections of which are presented here. The ultrastructure of this spirochete also resembles Hollandina and Diplocalyx (spirochetes symbiotic in arthropods) more than it does Spirochaeta, the well known genus of mud-dwelling spirochetes. The new spirochete was detected in mat material collected both in 1985 and in 1987. Unique morphology (i.e., conspicuous outer coat of inner membrane, large number of periplasmic flagella) and ecology prompt us to name a new free-living spirochete.

  17. Phosphoglycerides of Trichophyton terrestre and one phenotype selected from the Apollo 16 microbial ecology evaluation device.

    PubMed

    Sawyer, R T; Deskins, D C; Volz, P A

    1975-05-01

    Total lipid extracted from wild-type Trichophyton terrestre CDC-X285 was found to be 2.0 percent of the dry cell weight. The total lipid contained the following phospholipid components identified by silicic acid-impregnated thin-layer and paper chromatography: phosphatidyl inositol, phosphatidyl choline, phosphatidyl serine, and phosphatidic acid. The total lipid extracted from the phenotype T. terrestre 7048-1 isolated from the Apollo 16 Microbial Ecology Evaluation Device (MEED) was found to vary according to the time at which the phospholipids were extracted. The Trichophyton phenotype was selected from a cuvette housed in the MEED exposed to specific space parameters including ultraviolet light of known wavelengths and energy levels in deep space. The phospholipid components, identified in the phenotype were phosphatidyl ethanolamine and cardiolipin. The major lipid fraction was composed of digalactosyl diglyceride and monogalactosyl diglyceride. An unusual lipid was detected in the phenotype, which appeared to be sterol glycoside.

  18. Effect of dam parity on litter performance, transfer of passive immunity, and progeny microbial ecology.

    PubMed

    Carney-Hinkle, E E; Tran, H; Bundy, J W; Moreno, R; Miller, P S; Burkey, T E

    2013-06-01

    (P < 0.03) Shannon's diversity index compared with P4 progeny on d 7. Litter performance, passive transfer of immunity, and progeny microbial ecology were affected by dam parity.

  19. Dietary marker effects on fecal microbial ecology, fecal VFA, nutrient digestibility coefficients, and growth performance in finishing pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate rate of passage and nutrient digestibility. Yet nothing is known relative to their potential impact on fecal microbial ecology and subsequent VFA generation. Two experiments utilizing a total o...

  20. Dietary nisin modulates the gastrointestinal microbial ecology and enhances growth performance of the broiler chickens.

    PubMed

    Józefiak, Damian; Kierończyk, Bartosz; Juśkiewicz, Jerzy; Zduńczyk, Zenon; Rawski, Mateusz; Długosz, Jakub; Sip, Anna; Højberg, Ole

    2013-01-01

    Due to antimicrobial properties, nisin is one of the most commonly used and investigated bacteriocins for food preservation. Surprisingly, nisin has had limited use in animal feed as well as there are only few reports on its influence on microbial ecology of the gastrointestinal tract (GIT). The present study therefore aimed at investigating effects of dietary nisin on broiler chicken GIT microbial ecology and performance in comparison to salinomycin, the widely used ionophore coccidiostat. In total, 720 one-day-old male Ross 308 chicks were randomly distributed to six experimental groups. The positive control (PC) diet was supplemented with salinomycin (60 mg/kg). The nisin (NI) diets were supplemented with increasing levels (100, 300, 900 and 2700 IU nisin/g, respectively) of the bacteriocin. The negative control (NC) diet contained no additives. At slaughter (35 days of age), activity of specific bacterial enzymes (α- and β-glucosidases, α-galactosidases and β-glucuronidase) in crop, ileum and caeca were significantly higher (P<0.05) in the NC group, and nisin supplementation decreased the enzyme activities to levels observed for the PC group. A similar inhibitory influence on bacterial activity was reflected in the levels of short-chain fatty acids (SCFA) and putrefactive SCFA (PSCFA) in digesta from crop and ileum; no effect was observed in caeca. Counts of Bacteroides and Enterobacteriacae in ileum digesta were significantly (P<0.001) decreased by nisin and salinomycin, but no effects were observed on the counts of Clostridium perfringens, Lactobacillus/Enterococcus and total bacteria. Like salinomycin, nisin supplementation improved broiler growth performance in a dose-dependent manner; compared to the NC group, the body weight gain of the NI₉₀₀ and NI₂₇₀₀ groups was improved by 4.7 and 8.7%, respectively. Our findings suggest that dietary nisin exerts a mode of action similar to salinomycin and could be considered as a dietary supplement

  1. From Structure to Function: the Ecology of Host-Associated Microbial Communities

    PubMed Central

    Robinson, Courtney J.; Bohannan, Brendan J. M.; Young, Vincent B.

    2010-01-01

    Summary: In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota. PMID:20805407

  2. Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques.

    PubMed

    Kowalczyk, Agnieszka; Martin, Timothy James; Price, Oliver Richard; Snape, Jason Richard; van Egmond, Roger Albert; Finnegan, Christopher James; Schäfer, Hendrik; Davenport, Russell James; Bending, Gary Douglas

    2015-01-01

    Society's reliance upon chemicals over the last few decades has led to their increased production, application and release into the environment. Determination of chemical persistence is crucial for risk assessment and management of chemicals. Current established OECD biodegradation guidelines enable testing of chemicals under laboratory conditions but with an incomplete consideration of factors that can impact on chemical persistence in the environment. The suite of OECD biodegradation tests do not characterise microbial inoculum and often provide little insight into pathways of degradation. The present review considers limitations with the current OECD biodegradation tests and highlights novel scientific approaches to chemical fate studies. We demonstrate how the incorporation of molecular microbial ecology methods (i.e., 'omics') may improve the underlying mechanistic understanding of biodegradation processes, and enable better extrapolation of data from laboratory based test systems to the relevant environment, which would potentially improve chemical risk assessment and decision making. We outline future challenges for relevant stakeholders to modernise OECD biodegradation tests and put the 'bio' back into biodegradation.

  3. The ecological perspective of microbial communities in two pairs of competitive Hawaiian native and invasive macroalgae.

    PubMed

    Wang, Xin; Liu, Xianhua; Kono, Shoko; Wang, Guangyi

    2013-02-01

    Marine macroalgae are known to harbor large populations of microbial symbionts, and yet, microbe symbiosis in invasive macroalgae remains largely unknown. In this study, we applied molecular methods to study microbial communities associated with two invasive algae Acanthophora spicifera and Gracilaria salicornia and the two native algae Gracilaria coronopifolia and Laurencia nidifica at spatial and temporal scales in Hawaiian coral reef ecosystems. Bacterial communities of both the invasive and native macroalgae displayed little spatial and temporal variations, suggesting consistent and stable bacterial associations with these macroalgae. Results of this study identified three types of bacterial populations: nonspecific (present in both algal and water samples); algae-specific (found in all algal species); and species-specific (only found in individual species). The bacterial diversity of invasive algae was lower than that of their native counterparts at phylum and species levels. Notably, the vast majority (71 %) of bacterial communities associated with the invasive algae G. salicornia were representatives of Cyanobacteria, suggesting a potential ecological significance of symbiotic Cyanobacteria.

  4. Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history.

    PubMed

    Evans, Jessica K; Buchanan, Katherine L; Griffith, Simon C; Klasing, Kirk C; Addison, BriAnne

    2017-02-01

    Bacteria have had a fundamental impact on vertebrate evolution not only by affecting the evolution of the immune system, but also generating complex interactions with behavior and physiology. Advances in molecular techniques have started to reveal the intricate ways in which bacteria and vertebrates have coevolved. Here, we focus on birds as an example system for understanding the fundamental impact bacteria have had on the evolution of avian immune defenses, behavior, physiology, reproduction and life histories. The avian egg has multiple characteristics that have evolved to enable effective defense against pathogenic attack. Microbial risk of pathogenic infection is hypothesized to vary with life stage, with early life risk being maximal at either hatching or fledging. For adult birds, microbial infection risk is also proposed to vary with habitat and life stage, with molt inducing a period of increased vulnerability. Bacteria not only play an important role in shaping the immune system as well as trade-offs with other physiological systems, but also for determining digestive efficiency and nutrient uptake. The relevance of avian microbiomes for avian ecology, physiology and behavior is highly topical and will likely impact on our understanding of avian welfare, conservation, captive breeding as well as for our understanding of the nature of host-microbe coevolution.

  5. Gas chromatographic metabolic profiling: a sensitive tool for functional microbial ecology.

    PubMed

    Coucheney, Elsa; Daniell, Tim J; Chenu, Claire; Nunan, Naoise

    2008-12-01

    Microbial metabolomics, which consists of a non-targeted analysis of the metabolites released from ('exometabolome') or existing in ('endometabolome') a cell has mostly been used to study the metabolism of particular microbes. Metabolomes also represent a picture of microbial activity and we suggest that the exometabolome may also contain pertinent information for studying microbial interaction networks. Gas chromatography coupled to mass spectrometry is the most commonly used technique in metabolomics studies. It allows a wide range of metabolites to be detected but requires the derivatisation of compounds prior to detection. This type of non-targeted analysis can introduce biases to the detection and quantification of the different metabolites, particularly at the extraction and derivatisation steps. The aims of this study, therefore, were to quantify the sources of variability and to test the sensitivity of the GC metabolic profiling approach to small environmental changes such as shifts in temperature. The temperature sensitivity of metabolic profiles was compared with that of catabolic profiles obtained using Biolog microplates. Analytical variability was compared with biological variability by incubating bacterial strains isolated from soil with fructose at 20 degrees C and by replicating each step of the protocol (incubation, extraction and derivatisation). For both the endo- and the exometabolome, more than 70% of the total variability was of biological origin and principal components analysis clearly separated the strains along the first ordination axis. The endometabolome distinguished bacterial strains at the species level only, whereas separation was evident at the species and group level with the exometabolome. Temperature had a significant but differential effect on the metabolite production of the bacterial strains whilst their catabolic profiles remained relatively unaffected. The exometabolome was more sensitive to temperature shifts than the

  6. Differences in intestinal microbial metabolites in laying hens with high and low levels of repetitive feather-pecking behavior.

    PubMed

    Meyer, Beatrice; Zentek, Jürgen; Harlander-Matauschek, Alexandra

    2013-02-17

    Feather pecking in laying hens is a serious behavioral problem and is often associated with feather eating. There is some evidence that ingested feathers affect gut function. The aim of the present study was to explore whether differences in intestinal microbial metabolites in laying hens with high and low levels of repetitive feather-pecking behavior exist. Sixty high feather-pecking birds (H) and sixty low feather-pecking birds (L) of the White Leghorn breed were used for behavioral recordings of feather pecking. Feather pecking activity was observed for 5 weeks, after which 22 H birds with the highest and 22 L birds with the lowest feather pecking activity were chosen. The number of whole feathers and feather parts in the gizzard and intestinal microbial metabolites in the ileum and ceca of these laying hens was examined. Biogenic amines, short-chain fatty acids, ammonia and lactate were measured as microbial metabolites. A higher number of feather parts and particles were found in H than in L birds. Putrescine and cadaverine concentrations were higher in the ileum of the hens with low pecking activity (P<0.001 and P=0.012). In the cecum the amounts of l-lactate, d-lactate and total lactate and SCFA were higher in H birds (P=0.007, P=0.005, P=0.006, and P<0.001). Acetate, i-butyrate, i-valeriate and n-valeriate all displayed significantly higher molar ratios in the cecal contents of L birds (P=0.001, P=0.003, P=0.001, and P<0.001). Propionate and n-butyrate showed higher molar ratios in H birds (P<0.001 and P=0.034). Ammonia was higher in the ileum and cecum of the L birds (P<0.001 and P=0.004). For the first time, this study shows that birds with high and low numbers of repetitive pecking movements to the plumage of other birds differ in their intestinal microbial metabolism. Further experiments should be conducted to investigate whether these differences alter behavior in H and L feather pecking birds. The present results, however, open new avenues of research

  7. Altered intestinal microbial flora and impaired epithelial barrier structure and function in CKD: the nature, mechanisms, consequences and potential treatment.

    PubMed

    Vaziri, Nosratola D; Zhao, Ying-Yong; Pahl, Madeleine V

    2016-05-01

    Chronic kidney disease (CKD) results in systemic inflammation and oxidative stress which play a central role in CKD progression and its adverse consequences. Although many of the causes and consequences of oxidative stress and inflammation in CKD have been extensively explored, little attention had been paid to the intestine and its microbial flora as a potential source of these problems. Our recent studies have revealed significant disruption of the colonic, ileal, jejunal and gastric epithelial tight junction in different models of CKD in rats. Moreover, the disruption of the epithelial barrier structure and function found in uremic animals was replicated in cultured human colonocytes exposed to uremic human plasma in vitro We have further found significant changes in the composition and function of colonic bacterial flora in humans and animals with advanced CKD. Together, uremia-induced impairment of the intestinal epithelial barrier structure and function and changes in composition of the gut microbiome contribute to the systemic inflammation and uremic toxicity by accommodating the translocation of endotoxin, microbial fragments and other noxious luminal products in the circulation. In addition, colonic bacteria are the main source of several well-known pro-inflammatory uremic toxins such as indoxyl sulfate, p-cresol sulfate, trimethylamine-N-oxide and many as-yet unidentified retained compounds in end-stage renal disease patients. This review is intended to provide an overview of the effects of CKD on the gut microbiome and intestinal epithelial barrier structure and their role in the pathogenesis of systemic inflammation and uremic toxicity. In addition, potential interventions aimed at mitigating these abnormalities are briefly discussed.

  8. Modulatory Effects of Vasoactive Intestinal Peptide on Intestinal Mucosal Immunity and Microbial Community of Weaned Piglets Challenged by an Enterotoxigenic Escherichia coli (K88)

    PubMed Central

    Xu, Chunlan; Wang, Youming; Sun, Rui; Qiao, Xiangjin; Shang, Xiaoya; Niu, Weining

    2014-01-01

    Toll-like receptors (TLRs) recognize microbial pathogens and trigger immune response, but their regulation by neuropeptide-vasoactive intestinal peptide (VIP) in weaned piglets infected by enterotoxigenic Escherichia coli (ETEC) K88 remains unexplored. Therefore, the study was conducted to investigate its role using a model of early weaned piglets infected by ETEC K88. Male Duroc×Landrace×Yorkshire piglets (n = 24) were randomly divided into control, ETEC K88, VIP, and ETEC K88+VIP groups. On the first three days, ETEC K88 and ETEC K88+VIP groups were orally administrated with ETEC K88, other two groups were given sterile medium. Then each piglet from VIP and ETEC K88+VIP group received 10 nmol VIP intraperitoneally (i.p.) once daily, on day four and six. On the seventh day, the piglets were sacrificed. The results indicated that administration of VIP improved the growth performance, reduced diarrhea incidence of ETEC K88 challenged pigs, and mitigated the histopathological changes of intestine. Serum levels of IL-2, IL-6, IL-12p40, IFN-γ and TNF-α in the ETEC K88+ VIP group were significantly reduced compared with those in the ETEC group. VIP significantly increased IL-4, IL-10, TGF-β and S-IgA production compared with the ETEC K88 group. Besides, VIP could inhibit the expression of TLR2, TLR4, MyD88, NF-κB p65 and the phosphorylation of IκB-α, p-ERK, p-JNK, and p-38 induced by ETEC K88. Moreover, VIP could upregulate the expression of occludin in the ileum mucosa compared with the ETEC K88 group. Colon and caecum content bacterial richness and diversity were lower for pigs in the ETEC group than the unchallenged groups. These results demonstrate that VIP is beneficial for the maturation of the intestinal mucosal immune system and elicited local immunomodulatory activities. The TLR2/4-MyD88 mediated NF-κB and MAPK signaling pathway may be critical to the mechanism underlying the modulatory effect of VIP on intestinal mucosal immune function and

  9. Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities.

    PubMed

    Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C; Bell, Thomas

    2015-05-07

    Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics.

  10. Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods

    PubMed Central

    Keisam, Santosh; Romi, Wahengbam; Ahmed, Giasuddin; Jeyaram, Kumaraswamy

    2016-01-01

    Cultivation-independent investigation of microbial ecology is biased by the DNA extraction methods used. We aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different DNA extraction methods with different cell lysis principles. Our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic DNA from the food matrices compared to the widely used chemical and mechanical lysis principles. Further analysis of the bacterial community structure by Illumina MiSeq amplicon sequencing revealed a high recovery of lactic acid bacteria by the enzymatic lysis in all food types. However, Bacillaceae, Acetobacteraceae, Clostridiaceae and Proteobacteria were more abundantly recovered when mechanical and chemical lysis principles were applied. The biases generated due to the differential recovery of operational taxonomic units (OTUs) by different DNA extraction methods including DNA and PCR amplicons mix from different methods have been quantitatively demonstrated here. The different methods shared only 29.9–52.0% of the total OTUs recovered. Although similar comparative research has been performed on other ecological niches, this is the first in-depth investigation of quantifying the biases in metagenome mining from naturally fermented foods. PMID:27669673

  11. Earth's Earliest Ecosystems in the Classroom: The Use of Microbial Mats to Teach General Principles in Microbial Ecology, and Scientific Inquiry

    NASA Technical Reports Server (NTRS)

    Beboutl, Brad M.; Bucaria, Robin

    2004-01-01

    Microbial mats are living examples of the most ancient biological communities on earth, and may also be useful models for the search for life elsewhere. They are centrally important to Astrobiology. In this lecture, we will present an introduction to microbial mats, as well as an introduction to our web-based educational module on the subject of microbial ecology, featuring living mats maintained in a mini "Web Lab" complete with remotely-operable instrumentation. We have partnered with a number of outreach specialists in order to produce an informative and educational web-based presentation, aspects of which will be exported to museum exhibits reaching a wide audience. On our web site, we will conduct regularly scheduled experimental manipulations, linking the experiments to our research activities, and demonstrating fundamental principles of scientific research.

  12. Reduced microbial diversity and high numbers of one single Escherichia coli strain in the intestine of colitic mice.

    PubMed

    Wohlgemuth, Steffen; Haller, Dirk; Blaut, Michael; Loh, Gunnar

    2009-06-01

    Commensal bacteria play a role in the aetiology of inflammatory bowel diseases (IBD). High intestinal numbers of Escherichia coli in IBD patients suggest a role of this organism in the initiation or progression of chronic gut inflammation. In addition, some E. coli genotypes are more frequently detected in IBD patients than others. We aimed to find out whether gut inflammation in an IBD mouse model is associated with a particular E. coli strain. Intestinal contents and tissue material were taken from 1-, 8-, 16- and 24-week-old interleukin 10-deficient (IL-10(-/-)) mice and the respective wild-type animals. Caecal and colonic inflammation was observed in IL-10(-/-) animals from the 8 weeks of life on accompanied by a lower intestinal microbial diversity than in the respective wild-type animals. Culture- based and molecular approaches revealed that animals with gut inflammation harboured significantly higher numbers of E. coli than healthy controls. Phylogenetic grouping according to the E. coli Reference Collection (ECOR) system and strain typing by random-amplified polymorphic DNA and pulsed-field gel electrophoresis revealed that all mice were colonized by one single E. coli strain. The strain was shown to have the O7:H7:K1 serotype and to belong to the virulence-associated phylogenetic group B2. In a co-association experiment with gnotobiotic mice, the strain outnumbered E. coli ECOR strains belonging to the phylogenetic group A and B2 respectively. A high number of virulence- and fitness-associated genes were detected in the strain's genome possibly involved in the bacterial adaptation to the murine intestine.

  13. Microbial fingerprinting detects intestinal microbiota dysbiosis in Zebrafish models with chemically-induced enterocolitis

    PubMed Central

    2013-01-01

    Background Inflammatory bowel disease (IBD) involves a breakdown in interactions between the host immune response and the resident commensal microbiota. Recent studies have suggested gut physiology and pathology relevant to human IBD can be rapidly modeled in zebrafish larvae. The aim of this study was to investigate the dysbiosis of intestinal microbiota in zebrafish models with IBD-like enterocolitis using culture-independent techniques. Results IBD-like enterocolitis was induced by exposing larval zebrafish to trinitrobenzenesulfonic acid (TNBS). Pathology was assessed by histology and immunofluorescence. Changes in intestinal microbiota were evaluated by denaturing gradient gel electrophoresis (DGGE) and the predominant bacterial composition was determined with DNA sequencing and BLAST and confirmed by real-time polymerase chain reaction. Larval zebrafish exposed to TNBS displayed intestinal-fold architecture disruption and inflammation reminiscent of human IBD. In this study, we defined a reduced biodiversity of gut bacterial community in TNBS-induced coliitis. The intestinal microbiota dysbiosis in zebrafish larvae with IBD-like colitis was characterized by an increased proportion of Proteobacteria (especially Burkholderia) and a decreased of Firmicutes(Lactobacillus group), which were significantly correlated with enterocolitis severity(Pearson correlation p < 0.01). Conclusions This is the first description of intestinal microbiota dysbiosis in zebrafish IBD-like models, and these changes correlate with TNBS-induced enterocolitis. Prevention or reversal of this dysbiosis may be a viable option for reducing the incidence and severity of human IBD. PMID:24325678

  14. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids: Part II. Effects on intestinal histology and active nutrient transport

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on intestinal morphology and active nutrient absorption in weanling pigs following deliberate Salmonella infection. Pigs (n = 88) were weaned at 19 ± 2 d of age and assigned to one...

  15. Significance of microbial communities and interactions in safeguarding reactive mine tailings by ecological engineering.

    PubMed

    Nancucheo, Ivan; Johnson, D Barrie

    2011-12-01

    Pyritic mine tailings (mineral waste generated by metal mining) pose significant risk to the environment as point sources of acidic, metal-rich effluents (acid mine drainage [AMD]). While the accelerated oxidative dissolution of pyrite and other sulfide minerals in tailings by acidophilic chemolithotrophic prokaryotes has been widely reported, other acidophiles (heterotrophic bacteria that catalyze the dissimilatory reduction of iron and sulfur) can reverse the reactions involved in AMD genesis, and these have been implicated in the "natural attenuation" of mine waters. We have investigated whether by manipulating microbial communities in tailings (inoculating with iron- and sulfur-reducing acidophilic bacteria and phototrophic acidophilic microalgae) it is possible to mitigate the impact of the acid-generating and metal-mobilizing chemolithotrophic prokaryotes that are indigenous to tailing deposits. Sixty tailings mesocosms were set up, using five different microbial inoculation variants, and analyzed at regular intervals for changes in physicochemical and microbiological parameters for up to 1 year. Differences between treatment protocols were most apparent between tailings that had been inoculated with acidophilic algae in addition to aerobic and anaerobic heterotrophic bacteria and those that had been inoculated with only pyrite-oxidizing chemolithotrophs; these differences included higher pH values, lower redox potentials, and smaller concentrations of soluble copper and zinc. The results suggest that empirical ecological engineering of tailing lagoons to promote the growth and activities of iron- and sulfate-reducing bacteria could minimize their risk of AMD production and that the heterotrophic populations could be sustained by facilitating the growth of microalgae to provide continuous inputs of organic carbon.

  16. The influence of bacterial inoculants on the microbial ecology of aerobic spoilage of barley silage.

    PubMed

    Inglis, G D; Yanke, L J; Kawchuk, L M; McAllister, T A

    1999-01-01

    The aerobic decomposition of barley silage treated with two inoculants (LacA and LacB) containing mixtures of Lactobacillus plantarum and Enterococcus faecium was investigated over a 28-day period. Initially, yeast and bacterial populations were larger in silage inoculated with LacA than in silage treated with LacB or water alone (control). Differences in the succession of yeasts in silage treated with LacA were observed relative to the other two treatments. From silage treatment with LacA, Issatchenkia orientalis was the most prevalent yeast taxon over all of the sample times, and the filamentous fungus Microascus brevicaulis was also frequently isolated at later sample dates (> or = 14 days). In contrast, Saccharomyces exiguus was the most prominent yeast recovered from silage treated with LacB and water alone on days 2 and 4, although it was supplanted by I. orientalis at later sample times. Successional trends of bacteria were similar for all three treatments. Lactobacillus spp. were initially the most prevalent bacteria isolated, followed by Bacillus spp. (primarily Bacillus pumilus). However, the onset of Bacillus spp. prominence was faster in LacA silage, and Klebsiella planticola was frequently recovered at later sample times (> or = 14 days). More filamentous fungi were recovered from LacA silage on media containing carboxylmethylcellulose, pectin, or xylan. The most commonly isolated taxa were Absidia sp., Aspergillus flavus, Aspergillus fumigatus, Byssochlamys nivea, Monascus ruber, Penicillium brevicompactum, Pseudoallescheria boydii, and M. brevicaulis. The results of this study indicated that the two bacterial inoculants incorporated into barley at the time of ensilage affected the microbial ecology of silage decomposition following exposure to air. However, neither of the microbial inoculants effectively delayed aerobic spoilage of barley silage, and the rate of decomposition of silage treated with one of the inoculants (LacA) was actually enhanced.

  17. Microbial ecology of Vietnamese Tra fish (Pangasius hypophthalmus) fillets during processing.

    PubMed

    Tong Thi, Anh Ngoc; Noseda, Bert; Samapundo, Simbarashe; Nguyen, Binh Ly; Broekaert, Katrien; Rasschaert, Geertrui; Heyndrickx, Marc; Devlieghere, Frank

    2013-10-15

    There are numerous factors that can have an impact on the microbial ecology and quality of frozen Pangasius hypophthalmus fillets during processing in Vietnam. The presence of spoilage bacteria along the processing line can shorten the shelf-life of thawed frozen fish products. Therefore, the spoilage microbiota throughout the processing chain of two companies (BC: large scale factory, chlorine-based process, BW: large scale factory, water-based process and SC: small scale factory, chlorine-based process) was identified by culture-dependent techniques and 16S rRNA gene sequencing. The microbiological counts were observed to be insignificantly different (p>0.05) between BC and BW. Surprisingly, chlorine treated fillets from the SC line were revealed to have significantly higher microbial counts than potable water treated fillets at BW line. This was determined to be a result of temperature abuse during processing at SC, with temperatures even greater than 10 °C being recorded from skinning onwards. On the contrary, the microbiota related to spoilage for BC and BW lines was determined by 16S rRNA gene sequencing to be more diverse than that on the SC line. A total of 174 isolates, 20 genera and 38 species were identified along the processing chains. The genera Aeromonas, Acinetobacter, Lactococcus and Enterococcus were prevalent at various processing steps on all the processing lines evaluated. A diverse range of isolates belonging to the Enterobacteriaceae such as Providencia, Shigella, Klebsiella, Enterobacter and Wautersiella were isolated from fillets sampled on the SC line whereas Serratia was only observed on fillets sampled on the BC and BW lines. The results can be used to improve Good Manufacturing Practices for processed Pangasius fillets and to select effective measures to prolong the shelf-life of thawed Vietnamese Pangasius fillets products.

  18. Significance of Microbial Communities and Interactions in Safeguarding Reactive Mine Tailings by Ecological Engineering▿†

    PubMed Central

    N̆ancucheo, Ivan; Johnson, D. Barrie

    2011-01-01

    Pyritic mine tailings (mineral waste generated by metal mining) pose significant risk to the environment as point sources of acidic, metal-rich effluents (acid mine drainage [AMD]). While the accelerated oxidative dissolution of pyrite and other sulfide minerals in tailings by acidophilic chemolithotrophic prokaryotes has been widely reported, other acidophiles (heterotrophic bacteria that catalyze the dissimilatory reduction of iron and sulfur) can reverse the reactions involved in AMD genesis, and these have been implicated in the “natural attenuation” of mine waters. We have investigated whether by manipulating microbial communities in tailings (inoculating with iron- and sulfur-reducing acidophilic bacteria and phototrophic acidophilic microalgae) it is possible to mitigate the impact of the acid-generating and metal-mobilizing chemolithotrophic prokaryotes that are indigenous to tailing deposits. Sixty tailings mesocosms were set up, using five different microbial inoculation variants, and analyzed at regular intervals for changes in physicochemical and microbiological parameters for up to 1 year. Differences between treatment protocols were most apparent between tailings that had been inoculated with acidophilic algae in addition to aerobic and anaerobic heterotrophic bacteria and those that had been inoculated with only pyrite-oxidizing chemolithotrophs; these differences included higher pH values, lower redox potentials, and smaller concentrations of soluble copper and zinc. The results suggest that empirical ecological engineering of tailing lagoons to promote the growth and activities of iron- and sulfate-reducing bacteria could minimize their risk of AMD production and that the heterotrophic populations could be sustained by facilitating the growth of microalgae to provide continuous inputs of organic carbon. PMID:21965397

  19. Intestinal microbial affects of yeast products on weaned and transport stressed pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Study objectives were to determine effects of a commercially available yeast product (XPC, Diamond-V Mills) and stress of transportation on total Enterobacteriaceae, Escherichia coli, coliforms, and Lactobacilli populations in the intestine of weaning pigs. In a RCB design with a 2 x 2 factorial ar...

  20. Fermentable fiber ameliorates fermentable protein-induced changes in microbial ecology, but not the mucosal response, in the colon of piglets.

    PubMed

    Pieper, Robert; Kröger, Susan; Richter, Jan F; Wang, Jing; Martin, Lena; Bindelle, Jérôme; Htoo, John K; von Smolinski, Dorthe; Vahjen, Wilfried; Zentek, Jürgen; Van Kessel, Andrew G

    2012-04-01

    Dietary inclusion of fermentable carbohydrates (fCHO) is reported to reduce large intestinal formation of putatively toxic metabolites derived from fermentable proteins (fCP). However, the influence of diets high in fCP concentration on epithelial response and interaction with fCHO is still unclear. Thirty-two weaned piglets were fed 4 diets in a 2 × 2 factorial design with low fCP/low fCHO [14.5% crude protein (CP)/14.5% total dietary fiber (TDF)]; low fCP/high fCHO (14.8% CP/16.6% TDF); high fCP low fCHO (19.8% CP/14.5% TDF); and high fCP/high fCHO (20.1% CP/18.0% TDF) as dietary treatments. After 21-23 d, pigs were killed and colon digesta and tissue samples analyzed for indices of microbial ecology, tissue expression of genes for cell turnover, cytokines, mucus genes (MUC), and oxidative stress indices. Pig performance was unaffected by diet. fCP increased (P < 0.05) cell counts of clostridia in the Clostridium leptum group and total short and branched chain fatty acids, ammonia, putrescine, histamine, and spermidine concentrations, whereas high fCHO increased (P < 0.05) cell counts of clostridia in the C. leptum and C. coccoides groups, shifted the acetate to propionate ratio toward acetate (P < 0.05), and reduced ammonia and putrescine (P < 0.05). High dietary fCP increased (P < 0.05) expression of PCNA, IL1β, IL10, TGFβ, MUC1, MUC2, and MUC20, irrespective of fCHO concentration. The ratio of glutathione:glutathione disulfide was reduced (P < 0.05) by fCP and the expression of glutathione transferase was reduced by fCHO (P < 0.05). In conclusion, fermentable fiber ameliorates fermentable protein-induced changes in most measures of luminal microbial ecology but not the mucosal response in the large intestine of pigs.

  1. The high energy multicharged particle exposure of the microbial ecology evaluation device on board the Apollo 16 spacecraft

    NASA Technical Reports Server (NTRS)

    Benton, E. V.; Henke, R. P.

    1973-01-01

    The high energy multicharged cosmic-ray-particle exposure of the Microbial Ecology Evaluation Device package on board the Apollo 16 spacecraft was monitored using cellulose nitrate, Lexan polycarbonate, nuclear emulsion, and silver chloride crystal nuclear-track detectors. The results of the analysis of these detectors include the measured particle fluences, the linear energy transfer spectra, and the integral atomic number spectrum of stopping particle density. The linear energy transfer spectrum is used to compute the fractional cell loss in human kidney (T1) cells caused by heavy particles. Because the Microbial Ecology Evaluation Device was better shielded, the high-energy multicharged particle exposure was less than that measured on the crew passive dosimeters.

  2. Dynamic autoinoculation and the microbial ecology of a deep water hydrocarbon irruption.

    PubMed

    Valentine, David L; Mezić, Igor; Maćešić, Senka; Črnjarić-Žic, Nelida; Ivić, Stefan; Hogan, Patrick J; Fonoberov, Vladimir A; Loire, Sophie

    2012-12-11

    The irruption of gas and oil into the Gulf of Mexico during the Deepwater Horizon event fed a deep sea bacterial bloom that consumed hydrocarbons in the affected waters, formed a regional oxygen anomaly, and altered the microbiology of the region. In this work, we develop a coupled physical-metabolic model to assess the impact of mixing processes on these deep ocean bacterial communities and their capacity for hydrocarbon and oxygen use. We find that observed biodegradation patterns are well-described by exponential growth of bacteria from seed populations present at low abundance and that current oscillation and mixing processes played a critical role in distributing hydrocarbons and associated bacterial blooms within the northeast Gulf of Mexico. Mixing processes also accelerated hydrocarbon degradation through an autoinoculation effect, where water masses, in which the hydrocarbon irruption had caused blooms, later returned to the spill site with hydrocarbon-degrading bacteria persisting at elevated abundance. Interestingly, although the initial irruption of hydrocarbons fed successive blooms of different bacterial types, subsequent irruptions promoted consistency in the structure of the bacterial community. These results highlight an impact of mixing and circulation processes on biodegradation activity of bacteria during the Deepwater Horizon event and suggest an important role for mixing processes in the microbial ecology of deep ocean environments.

  3. Role of bacterial adhesion in the microbial ecology of biofilms in cooling tower systems

    PubMed Central

    Liu, Yang; Zhang, Wei; Sileika, Tadas; Warta, Richard; Cianciotto, Nicholas P.; Packman, Aaron

    2009-01-01

    The fate of the three heterotrophic biofilm forming bacteria, Pseudomonas aeruginosa, Klebsiella pneumoniae and Flavobacterium sp. in pilot scale cooling towers was evaluated both by observing the persistence of each species in the recirculating water and the formation of biofilms on steel coupons placed in each cooling tower water reservoir. Two different cooling tower experiments were performed: a short-term study (6 days) to observe the initial bacterial colonization of the cooling tower, and a long-term study (3 months) to observe the ecological dynamics with repeated introduction of the test strains. An additional set of batch experiments (6 days) was carried out to evaluate the adhesion of each strain to steel surfaces under similar conditions to those found in the cooling tower experiments. Substantial differences were observed in the microbial communities that developed in the batch systems and cooling towers. P. aeruginosa showed a low degree of adherence to steel surfaces both in batch and in the cooling towers, but grew much faster than K. pneumoniae and Flavobacterium in mixed-species biofilms and ultimately became the dominant organism in the closed batch systems. However, the low degree of adherence caused P. aeruginosa to be rapidly washed out of the open cooling tower systems, and Flavobacterium became the dominant microorganism in the cooling towers in both the short-term and long-term experiments. These results indicate that adhesion, retention and growth on solid surfaces play important roles in the bacterial community that develops in cooling tower systems. PMID:19177226

  4. Microbial ecology studies of spontaneous fermentation: starter culture selection for prickly pear wine production.

    PubMed

    Rodríguez-Lerma, G K; Gutiérrez-Moreno, K; Cárdenas-Manríquez, M; Botello-Álvarez, E; Jiménez-Islas, H; Rico-Martínez, R; Navarrete-Bolaños, J L

    2011-08-01

    A procedure for designing starter cultures for fermentation is illustrated for prickly pear wine production. The illustration includes kinetic studies on inoculated and spontaneous fermentation, microorganism identification studies based on molecular biology tools, and microbial ecology studies, which led to the selection of strains that are capable of synthesizing alcohol and desirable volatile compounds. Results show that a mixed starter inoculum containing Pichia fermentans and Saccharomyces cerevisiae leads to a fermented product that contains 8.37% alcohol (v/v). The gas chromatography and mass spectrometry (GC-MS) analysis shows the presence of 9 major volatile compounds (Isobutanol, Isopentanol, Ethyl acetate, Isoamyl acetate, Ethyl octanoate, Ethyl decanoate, Ethyl 9-decanoate, β-Phenylethyl acetate, and Phenylethyl alcohol) that have ethereal, fruity, aromatic notes that are considered to be essential for a fine wine flavor. These compounds harmonically synergize with the alcohol to produce a fermented product with a unique flavor and taste. Several assays using the mixed culture show that the process is stable, predictable, controllable, and reproducible. Moreover, the results show that a mixed culture leads to a broader range of aromatic products than that produced by a single, pure culture. Therefore, we conclude that combinations of Saccharomyces strains and non-Saccharomyces strains can be used to obtain high-quality fermented beverages from prickly pear juice.

  5. Impact of organic and conventional management on the phyllosphere microbial ecology of an apple crop.

    PubMed

    Ottesen, Andrea R; White, James Robert; Skaltsas, Demetra N; Newell, Michael J; Walsh, Christopher S

    2009-11-01

    Bacterial communities associated with the phyllosphere of apple trees (Malus domestica cv. Enterprise) grown under organic and conventional management were assessed to determine if increased biological food safety risks might be linked with the bacterial communities associated with either treatment. Libraries of 16S rRNA genes were generated from phyllosphere DNA extracted from a wash made from the surfaces of leaves and apples from replicated organic and conventional treatments. 16S rRNA gene libraries were analyzed with software designed to identify statistically significant differences between bacterial communities as well as shared and unique phylotypes. The identified diversity spanned eight bacterial phyla and 14 classes in the pooled organic and conventional libraries. Significant differences between organic and conventional communities were observed at four of six time points (P < 0.05). Despite the identification of significantly diverse microfloras associated with organic and conventional treatments, no detectable differences in the presence of potential enteric pathogens could be associated with either organic or conventional management. Neither of the bacterial genera most commonly associated with produce-related illness outbreaks (Salmonella and Escherichia) was observed in any of the libraries. The impressive bacterial diversity that was documented in this study provides a valuable contribution to our developing understanding of the total microbial ecology associated with the preharvest phyllospheres of food crops. The fact that organic and conventional phyllosphere bacterial communities were significantly different at numerous time points suggests that crop management methods may influence the bacterial consortia associated with the surfaces of fruits and vegetables.

  6. The effect of malathion on the activity, performance, and microbial ecology of activated sludge.

    PubMed

    Rauglas, Erik; Martin, Seth; Bailey, Kandace; Magnuson, Matthew; Phillips, Rebecca; Harper, Willie F

    2016-12-01

    This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities.

  7. Role of bacterial adhesion in the microbial ecology of biofilms in cooling tower systems.

    PubMed

    Liu, Yang; Zhang, Wei; Sileika, Tadas; Warta, Richard; Cianciotto, Nicholas P; Packman, Aaron

    2009-01-01

    The fate of the three heterotrophic biofilm forming bacteria, Pseudomonas aeruginosa, Klebsiella pneumoniae and Flavobacterium sp. in pilot scale cooling towers was evaluated both by observing the persistence of each species in the recirculating water and the formation of biofilms on steel coupons placed in each cooling tower water reservoir. Two different cooling tower experiments were performed: a short-term study (6 days) to observe the initial bacterial colonization of the cooling tower, and a long-term study (3 months) to observe the ecological dynamics with repeated introduction of the test strains. An additional set of batch experiments (6 days) was carried out to evaluate the adhesion of each strain to steel surfaces under similar conditions to those found in the cooling tower experiments. Substantial differences were observed in the microbial communities that developed in the batch systems and cooling towers. P. aeruginosa showed a low degree of adherence to steel surfaces both in batch and in the cooling towers, but grew much faster than K. pneumoniae and Flavobacterium in mixed-species biofilms and ultimately became the dominant organism in the closed batch systems. However, the low degree of adherence caused P. aeruginosa to be rapidly washed out of the open cooling tower systems, and Flavobacterium became the dominant microorganism in the cooling towers in both the short-term and long-term experiments. These results indicate that adhesion, retention and growth on solid surfaces play important roles in the bacterial community that develops in cooling tower systems.

  8. Intestinal microbial metabolism of phosphatidylcholine: a novel insight in the cardiovascular risk scenario

    PubMed Central

    Sorrentino, Claudia; Principi, Mariabeatrice; Giorgio, Floriana; Losurdo, Giuseppe; Di Leo, Alfredo

    2015-01-01

    Intestinal microbiota is a “dynamic organ” influencing host metabolism, nutrition, physiology and immune system. Among its several interactions, the role of a phosphatidylcholine metabolite derived by gut flora activity, i.e., trimethylamine-N-oxide (TMAO), allows perceiving a novel insight in the cardiovascular risk scenario, being a strong predictor of this condition. Based on current reports, including the paper of Tang et al., we describe here: the possible role of intestinal microbiota in cardiovascular risk as well as potential interventions to reduce gut flora TMAO production by diet, probiotics and antibiotics. Finally, we highlight the possibility of evaluating, monitoring and modulating TMAO in order to use its serum levels as a marker of cardiovascular risk in the next future, when the need of controlled studies on large series will be satisfied. PMID:26312245

  9. Metagenomic analysis of an ecological wastewater treatment plant’s microbial communities and their potential to metabolize pharmaceuticals

    PubMed Central

    Balcom, Ian N.; Driscoll, Heather; Vincent, James; Leduc, Meagan

    2016-01-01

    Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm. PMID:27610223

  10. Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears.

    PubMed

    Schwab, Clarissa; Gänzle, Michael

    2011-03-01

    The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C. perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.

  11. The Microbiology of Subsurface, Salt-Based Nuclear Waste Repositories: Using Microbial Ecology, Bioenergetics, and Projected Conditions to Help Predict Microbial Effects on Repository Performance

    SciTech Connect

    Swanson, Juliet S.; Cherkouk, Andrea; Arnold, Thuro; Meleshyn, Artur; Reed, Donald T.

    2016-11-17

    This report summarizes the potential role of microorganisms in salt-based nuclear waste repositories using available information on the microbial ecology of hypersaline environments, the bioenergetics of survival under high ionic strength conditions, and “repository microbiology” related studies. In areas where microbial activity is in question, there may be a need to shift the research focus toward feasibility studies rather than studies that generate actual input for performance assessments. In areas where activity is not necessary to affect performance (e.g., biocolloid transport), repository-relevant data should be generated. Both approaches will lend a realistic perspective to a safety case/performance scenario that will most likely underscore the conservative value of that case.

  12. Fine-scale distribution patterns of Synechococcus ecological diversity in microbial mats of Mushroom Spring, Yellowstone National Park.

    PubMed

    Becraft, Eric D; Cohan, Frederick M; Kühl, Michael; Jensen, Sheila I; Ward, David M

    2011-11-01

    Past analyses of sequence diversity in high-resolution protein-encoding genes have identified putative ecological species of unicellular cyanobacteria in the genus Synechococcus, which are specialized to 60°C but not 65°C in Mushroom Spring microbial mats. Because these studies were limited to only two habitats, we studied the distribution of Synechococcus sequence variants at 1°C intervals along the effluent flow channel and at 80-μm vertical-depth intervals throughout the upper photic layer of the microbial mat. Diversity at the psaA locus, which encodes a photosynthetic reaction center protein (PsaA), was sampled by PCR amplification, cloning, and sequencing methods at 60, 63, and 65°C sites. The evolutionary simulation programs Ecotype Simulation and AdaptML were used to identify putative ecologically distinct populations (ecotypes). Ecotype Simulation predicted a higher number of putative ecotypes in cases where habitat variation was limited, while AdaptML predicted a higher number of ecologically distinct phylogenetic clades in cases where habitat variation was high. Denaturing gradient gel electrophoresis was used to track the distribution of dominant sequence variants of ecotype populations relative to temperature variation and to O₂, pH, and spectral irradiance variation, as measured using microsensors. Different distributions along effluent channel flow and vertical gradients, where temperature, light, and O₂ concentrations are known to vary, confirmed the ecological distinctness of putative ecotypes.

  13. Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities.

    PubMed

    Liu, Jun; He, Xiao-Xin; Lin, Xue-Rui; Chen, Wen-Ce; Zhou, Qi-Xing; Shu, Wen-Sheng; Huang, Li-Nan

    2015-06-02

    The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota.

  14. Biochemistry and Ecology of Novel Cytochromes Catalyzing Fe(II) Oxidation by an Acidophilic Microbial Community

    NASA Astrophysics Data System (ADS)

    Singer, S. W.; Jeans, C. J.; Thelen, M. P.; Verberkmoes, N. C.; Hettich, R. C.; Chan, C. S.; Banfield, J. F.

    2007-12-01

    An acidophilic microbial community found in the Richmond Mine at Iron Mountain, CA forms abundant biofilms in extremely acidic (pH<1) and toxic metal conditions. In this ecosystem, biological Fe(II) oxidation is critical to the metabolic functioning of the community, and in turn this process generates acid mine drainage, causing an environmental catastrophe. Two conspicuous novel proteins isolated from these biofilms were identified as gene products of Leptospirillum group II and were characterized as cytochromes with unique properties. Sulfuric acid extraction of biofilm samples liberated one of these proteins, a 16 kDa cytochrome with an unusual alpha-band absorption at 579 (Cyt579). Genomic sequencing of multiple biofilms indicated that several variants of Cyt579 were present in Leptospirillum strains. Intact protein MS analysis identified the dominant variants in each biofilm and documented multiple N-terminal cleavage sites for Cyt579. By combining biochemical, geochemical and microbiological data, we established that the sequence variation and N-terminal processing of Cyt579 are selected by ecological conditions. In addition to the soluble Cyt579, the second cytochrome appears as a much larger protein complex of ~210 kDa predominant in the biofilm membrane fraction, and has an alpha-band absorption at 572 nm. The 60 kDa cytochrome subunit, Cyt572, resides in the outer membrane of LeptoII, and readily oxidizes Fe(II) at low pH (0.95 - 3.0). Several genes encoding Cyt572 were localized within a recombination hotspot between two strains of LeptoII, causing a large range of variation in the sequences. Genomic sequencing and MS proteomic studies established that the variants were also selected by ecological conditions. A general mechanistic model for Fe(II) oxidation has been developed from these studies. Initial Fe(II) oxidation by Cyt572 occurs at the outer membrane. Cyt572 then transfers electrons to Cyt579, perhaps representing an initial step in energy flow

  15. Ecology and metabolism of the beneficial intestinal commensal bacterium Faecalibacterium prausnitzii.

    PubMed

    Miquel, Sylvie; Martín, Rebeca; Bridonneau, Chantal; Robert, Véronique; Sokol, Harry; Bermúdez-Humarán, Luis G; Thomas, Muriel; Langella, Philippe

    2014-01-01

    Faecalibacterium prausnitzii is a major commensal bacterium, and its prevalence is often decreased in conditions of intestinal dysbiosis. The phylogenic identity of this bacterium was described only recently. It is still poorly characterized, and its specific growth requirements in the human gastrointestinal tract are not known. In this review, we consider F. prausnitzii metabolism, its ecophysiology in both humans and animals, and the effects of drugs and nutrition on its population. We list important questions about this beneficial and ubiquitous commensal bacterium that it would be valuable to answer.

  16. Dietary marker effects on fecal microbial ecology, fecal VFA, nutrient digestibility coefficients, and growth performance in finishing pigs.

    PubMed

    Kerr, B J; Weber, T E; Ziemer, C J

    2015-05-01

    Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate digesta rate of passage and nutrient digestibility. Yet, the potential impact of indigestible markers on fecal microbial ecology and subsequent VFA generation is not known. Two experiments utilizing a total of 72 individually fed finishing pigs were conducted to describe the impact of dietary markers on fecal microbial ecology, fecal ammonia and VFA concentrations, nutrient digestibility, and pig performance. All pigs were fed a common diet with no marker or with 0.5% Cr2O3, Fe2O3, or TiO2. In Exp. 1, after 33 d of feeding, fresh fecal samples were collected for evaluation of microbial ecology, fecal ammonia and VFA concentrations, and nutrient digestibility, along with measures of animal performance. No differences were noted in total microbes or bacterial counts in pig feces obtained from pigs fed the different dietary markers while Archaea counts were decreased (P = 0.07) in feces obtained from pigs fed the diet containing Fe2O 3compared to pigs fed the control diet. Feeding Cr2O3, Fe2O3, or TiO2 increased fecal bacterial richness (P = 0.03, 0.01, and 0.10; respectively) when compared to pigs fed diets containing no marker, but no dietary marker effects were noted on fecal microbial evenness or the Shannon-Wiener index. Analysis of denaturing gradient gel electrophoresis gels did not reveal band pattern alterations due to inclusion of dietary markers in pig diets. There was no effect of dietary marker on fecal DM, ammonia, or VFA concentrations. Pigs fed diets containing Cr2O3 had greater Ca, Cu, Fe, and P (P ≤ 0.02), but lower Ti ( P= 0.08) digestibility compared to pigs fed the control diet. Pigs fed diets containing Fe2O3 had greater Ca (P = 0.08) but lower Ti (P = 0.01) digestibility compared to pigs fed the control diet. Pigs fed diets containing TiO2 had greater Fe and Zn (P ≤ 0.09), but lower Ti ( P= 0.01) digestibility compared to pigs fed the

  17. [Optimization of treatment of children with acute intestinal infections by application of Russian biological microbial preparations].

    PubMed

    Feklisova, L V

    2005-01-01

    The article presents the results of long-term (several years) use of Russian bifido- and lactocontaing probiotics and data on the clinicolaboratory effectiveness of bifidumbacterin forte, probifor, bifidin, bifilis, calcidum, florin forte, acipol and acilact in children with various intestinal infections of known and unknown etiology. The presented results were obtained by studies conducted according to the requirements of The Governmental Program of L. A. Tarasevich State Institute of Standartization and Medical Biological Preparation Control, which included randomization of groups of patients receiving codified preparations or placebo according to their age, nosology, the degree of the process severity, premorbid status, and the time when the treatment was started. Each of the programs included several hundreds of children, receiving probiotics; in which of the programs the studies were multicentered. The courses of treatment with probiotics were short (1 to 2 weeks). No significant adverse effects were observed.

  18. Kinetics and microbial ecology of batch sulfidogenic bioreactors for co-treatment of municipal wastewater and acid mine drainage.

    PubMed

    Deng, Dongyang; Weidhaas, Jennifer L; Lin, Lian-Shin

    2016-03-15

    The kinetics and microbial ecology in sulfidogenic bioreactors used in a novel two-stage process for co-treatment of acid mine drainage (AMD) and municipal wastewater (MWW) were investigated. Michaelis-Menten modeling of COD oxidation by sulfate reducing bacteria (SRB) (Vmax=0.33mgL(-1)min(-1), Km=4.3mgL(-1)) suggested that the Vmax can be reasonably achieved given the typical COD values in MWW and anticipated mixing with AMD. Non-competitive inhibition modeling (Ki=6.55mgL(-1)) indicated that excessive iron level should be avoided to limit its effects on SRB. The COD oxidation rate was positively correlated to COD/sulfate ratio and SRB population, as evidenced by dsrA gene copies. Phylogenetic analysis revealed diverse microbial communities dominated by sulfate reducing delta-proteobacteria. Microbial community and relative quantities of SRB showed significant differences under different COD/sulfate ratios (0.2, 1 and 2), and the highest dsrA gene concentration and most complex microbial diversity were observed under COD/sulfate ratio 2. Major species were associated with Desulfovirga, Desulfobulbus, Desulfovibrio, and Syntrophus sp. The reported COD kinetics, SRB abundances and the phylogenetic profile provide insights into the co-treatment process and help identify the parameters of concerns for such technology development.

  19. Growth performance and gastrointestinal microbial ecology responses of piglets receiving Saccharomyces cerevisiae fermentation products after an oral challenge with Escherichia coli (K88).

    PubMed

    Kiarie, E; Bhandari, S; Scott, M; Krause, D O; Nyachoti, C M

    2011-04-01

    The effects of Saccharomyces cerevisiae fermentation products (YFP) on growth performance and gastrointestinal (GIT) microbial ecology in 90 weanling pigs orally challenged with Escherichia coli K88(+) (ETEC) were investigated. The YFP were an original YFP product (XPC) and a water-suspendable yeast fermentation prototype (WSYFP) from a commercial company. Treatments consisted of a negative control (NC, no in-feed or in-water additive), carbadox (AB, 55 mg of carbadox/kg of feed), XPC (in feed, 0.2%), and WSYFP (in water, 0.5, 1, or 2 g/pig per day), and each was allotted to 5 pens (3 pigs/pen). The diets met the 1998 NRC specifications. Pigs were acclimated to treatments for a 7-d period before an ETEC challenge. On d 8, blood was collected from pigs to determine the baseline packed cell volume (PCV) measurement, and pigs were orally challenged with ETEC. At various time points postchallenge, blood samples were taken, performance measures and fecal consistency scores were recorded, and gut digesta and tissue samples were taken to evaluate GIT morphology, microbial ecology, and metabolites. Preplanned contrasts were used for comparison. Pigs receiving YFP had greater ADFI than NC pigs on d 3 (424 vs. 378 g/d; P = 0.01) and d 7 (506 vs. 458 g/d; P = 0.03) postchallenge. This effect of YFP on ADFI was similar to that of AB on d 3, but pigs receiving AB ate more (576 vs. 506 g/d; P = 0.03) at d 7 than pigs receiving YFP. Pigs exhibited reduced (P < 0.001) PCV upon ETEC challenge; however, pigs receiving additives sustained a greater (P < 0.05) PCV at 72 h compared with the NC group. Compared with the NC pigs, pigs receiving YFP showed a smaller (P < 0.05) number of ileal mucosa adherent ETEC and prevalence of the order Enterobacteriales in the ileal digesta, which corresponded to less (5.09 vs. 6.97 mg/dL; P = 0.03) colonic ammonia on d 7 postchallenge. Most of the indices for ileal digesta bacterial richness and diversity were greater (P < 0.01) for YFP pigs compared

  20. Application of Sequence-based Methods in Human MicrobialEcology

    SciTech Connect

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-08-29

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  1. DEB modeling for nanotoxicology, microbial ecology, and environmental engineering. Comment on: ;Physics of metabolic organization; by Marko Jusup et al.

    NASA Astrophysics Data System (ADS)

    Holden, Patricia A.

    2017-03-01

    Jusup et al. [1] appeal to mathematical physicists, and to biologists, by providing the theoretical basis for dynamic energy budget (DEB) modeling of individual organisms and populations, while emphasizing model simplicity, universality, and applicability to real world problems. Comments herein regard the disciplinary tensions proposed by the authors and suggest that-in addition to important applications in eco- and specifically nano-toxicology-there are opportunities for DEB frameworks to inform relative complexity in microbial ecological process modeling. This commentary also suggests another audience for bridging DEB theory and application-engineers solving environmental problems.

  2. A resurgence in field research is essential to better understand the diversity, ecology, and evolution of microbial eukaryotes.

    PubMed

    Heger, Thierry J; Edgcomb, Virginia P; Kim, Eunsoo; Lukeš, Julius; Leander, Brian S; Yubuki, Naoji

    2014-01-01

    The discovery and characterization of protist communities from diverse environments are crucial for understanding the overall evolutionary history of life on earth. However, major questions about the diversity, ecology, and evolutionary history of protists remain unanswered, notably because data obtained from natural protist communities, especially of heterotrophic species, remain limited. In this review, we discuss the challenges associated with "field protistology", defined here as the exploration, characterization, and interpretation of microbial eukaryotic diversity within the context of natural environments or field experiments, and provide suggestions to help fill this important gap in knowledge. We also argue that increased efforts in field studies that combine molecular and microscopical methods offer the most promising path toward (1) the discovery of new lineages that expand the tree of eukaryotes; (2) the recognition of novel evolutionary patterns and processes; (3) the untangling of ecological interactions and functions, and their roles in larger ecosystem processes; and (4) the evaluation of protist adaptations to a changing climate.

  3. Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.

    PubMed

    Baron, Julianne L; Vikram, Amit; Duda, Scott; Stout, Janet E; Bibby, Kyle

    2014-01-01

    Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms.

  4. Prebiotic effect of fructooligosaccharide in the simulator of the human intestinal microbial ecosystem (SHIME® model).

    PubMed

    Sivieri, Katia; Morales, Martha L Villarreal; Saad, Susana M I; Adorno, Maria A Tallarico; Sakamoto, Isabel Kimiko; Rossi, Elizeu A

    2014-08-01

    Maintaining "gut health" is a goal for scientists throughout the world. Therefore, microbiota management models for testing probiotics, prebiotics, and synbiotics have been developed. The SHIME(®) model was used to study the effect of fructooligosaccharide (FOS) on the fermentation pattern of the colon microbiota. Initially, an inoculum prepared from human feces was introduced into the reactor vessels and stabilized over 2 weeks using a culture medium. This stabilization period was followed by a 2-week control period during which the microbiota was monitored. The microbiota was then subjected to a 4-week treatment period by adding 5 g/day-1 FOS to vessel one (the "stomach" compartment). Plate counts, Denaturing Gradient Gel Electrophoresis (DGGE), short-chain fatty acid (SCFA), and ammonium analyses were used to observe the influence of FOS treatment in simulated colon compartments. A significant increase (P<.01) in the Lactobacillus spp. and Bifidobacterium spp. populations was observed during the treatment period. The DGGE obtained showed the overall microbial community was changed in the ascending colon compartment of the SHIME reactor. FOS induced increase of the SCFA concentration (P<.05) during the treatment period, mainly due to significant increased levels of acetic and butyric acids. However, ammonium concentrations increased during the same period (P<.01). This study indicates the usefulness of in vitro methods that simulate the colon region as part of research towards the improvement of human health.

  5. The role of microbial diversity in the dynamics and stability of global methane consumption: microbial methane oxidation as a model-system for microbial ecology (ESF EuroDiversity METHECO)

    NASA Astrophysics Data System (ADS)

    Frenzel, P.; Metheco-Team

    2009-04-01

    Ecosystems collectively determine biogeochemical processes that regulate the Earth System. Loss of biodiversity is detrimental to ecosystems and therefore has been a central issue for environmental scientists. Although microorganisms form a major part of the Earth's biomass and biodiversity, and have a critical role in biogeochemistry and ecosystem functioning, they do not feature highly in ongoing debates about global biodiversity loss, global change and conservations issues. The neglect of microbial diversity in conservation issues is because microbial communities are regarded as being highly redundant, omnipresent, and therefore inextinguishable. This, however, is a misconception. Recently, the application of advanced molecular techniques has indicated that microbial communities display habitat preferences and are not universally distributed. Even the highly diverse microbial communities in soils can be affected by agricultural use, indicating that genetic erosion may potentially affect these communities as well. Moreover, many important environmental functions are catalyzed by specific groups of microbes with a very narrow ecological range. Recovery of these functional microbial communities after disturbance may take decades. Even if the species making up the community do not become extinct and eventually re-colonize an environment, the function and service to the biosphere is lost long enough to exert permanent, irreversible damage to the environment. Considering the global importance of microbes, combined with our ignorance of how the composition and functioning of these communities is affected, necessitates the assessment of the vulnerability and the resilience of microbial diversity. The latter is a pressing concern in biodiversity research and conservation policy, urgently needing attention in order to be able to anticipate environmental challenges we are facing. Our general hypothesis is: microbial diversity is linked to important ecosystem services and

  6. LIPID ANALYSIS TO DETERMINE THE EFFECT OF A SOURCE REMEDIAL TECHNOLOGY IN MICROBIAL ECOLOGY

    EPA Science Inventory

    Microbial community structures and related changes in the subsurface environment were investigated following in situ chemical oxidation (ISCO) treatment at Launch Complex 34, Cape Canaveral Air Station, Florida. The site has dense non-aqueous phase (DNAPL) concentrations of TCE ...

  7. Ecological Effect of Solithromycin on Normal Human Oropharyngeal and Intestinal Microbiota

    PubMed Central

    Rashid, Mamun-Ur; Rosenborg, Staffan; Panagiotidis, Georgios; Holm, Johan; Söderberg Löfdal, Karin; Nord, Carl Erik

    2016-01-01

    Solithromycin is a new fluoroketolide. The purpose of the present study was to investigate the effect of orally administered solithromycin on the human oropharyngeal and intestinal microbiota. Thirteen healthy volunteers (median age, 27.3 years) received oral solithromycin at 800 mg on day 1 followed by 400 mg daily on days 2 to 7. Fecal and saliva samples were collected at baseline and on days 2, 5, 7, 9, 14, and 21 for pharmacokinetic and microbiological analyses. Plasma samples were collected predose on days 2, 5, and 7 as proof of exposure, and solithromycin concentration ranges were 21.9 to 258 ng/ml, 18.0 to 386 ng/ml, and 16.9 to 417 ng/ml, respectively. The solithromycin concentrations in feces were 15.8 to 65.4 mg/kg, 24.5 to 82.7 mg/kg, 21.4 to 82.7 mg/kg, 12.1 to 72.4 mg/kg, 0.2 to 25.6 mg/kg, and 0 to 0.5 mg/kg on days 2, 5, 7, 9, 14, and 21, respectively. The numbers of enterobacteria and enterococci decreased and were normalized on day 14. The numbers of lactobacilli and bifidobacteria decreased from day 2 to day 14 and were normalized on day 21. The clostridia decreased on days 2, 7, and 14 and were normalized on day 21. No Clostridium difficile strains or toxins were detected during the study period. The number of Bacteroides strains was not significantly changed. The solithromycin concentrations in saliva were 0 to 1.2 mg/liter, 0 to 0.5 mg/liter, 0 to 0.5 mg/liter, and 0 to 0.1 mg/liter on days 2, 5, 7, and 9, respectively. The numbers of streptococci decreased on day 2 and were normalized on day 5. The numbers of lactobacilli, prevotellae, fusobacteria, and leptotrichiae decreased from day 2 and were normalized on day 21. PMID:27139483

  8. Microbial Ecology of Four Coral Atolls in the Northern Line Islands

    PubMed Central

    Smriga, Steven; Edwards, Robert A.; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A.; Thurber, Rebecca Vega; Willis, Bette L.; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

    2008-01-01

    Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (∼5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems

  9. Microbial ecology of four coral atolls in the Northern Line Islands.

    PubMed

    Dinsdale, Elizabeth A; Pantos, Olga; Smriga, Steven; Edwards, Robert A; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A; Thurber, Rebecca Vega; Willis, Bette L; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

    2008-02-27

    Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated ( approximately 5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef

  10. Use of Metabolic Inhibitors to Characterize Ecological Interactions in an Estuarine Microbial Food Web.

    PubMed

    DeLorenzo, M.E.; Lewitus, A.J.; Scott, G.I.; Ross, P.E.

    2001-10-01

    Understanding microbial food web dynamics is complicated by the multitude of competitive or interdependent trophic interactions involved in material and energy flow. Metabolic inhibitors can be used to gain information on the relative importance of trophic pathways by uncoupling selected microbial components and examining the net effect on ecosystem structure and function. A eukaryotic growth inhibitor (cycloheximide), a prokaryotic growth inhibitor (antibiotic mixture), and an inhibitor of photosynthesis (DCMU) were used to examine the trophodynamics of microbial communities from the tidal creek in North Inlet, a salt marsh estuary near Georgetown, South Carolina. Natural microbial communities were collected in the spring, summer, and fall after colonization onto polyurethane foam substrates deployed in the tidal creek. Bacterial abundance and productivity, heterotrophic ciliate and flagellate abundance, and phototrophic productivity, biomass, and biovolume were measured at five time points after inhibitor additions. The trophic responses of the estuarine microbial food web to metabolic inhibitors varied with season. In the summer, a close interdependency among phototrophs, bacteria, and protozoa was indicated, and the important influence of microzooplanktonic nutrient recycling was evident (i.e., a positive feedback loop). In the fall, phototroph and bacteria interactions were competitive rather than interdependent, and grazer nutrient regeneration did not appear to be an important regulatory factor for bacterial or phototrophic activities. The results indicate a seasonal shift in microbial food web structure and function in North Inlet, from a summer community characterized by microbial loop dynamics to a more linear trophic system in the fall. This study stresses the important role of microbial loops in driving primary and secondary production in estuaries such as North Inlet that are tidally dominated by fluctuations in nutrient supply and a summer

  11. Effect of monochloramine treatment on the microbial ecology of Legionella and associated bacterial populations in a hospital hot water system.

    PubMed

    Baron, Julianne L; Harris, J Kirk; Holinger, Eric P; Duda, Scott; Stevens, Mark J; Robertson, Charles E; Ross, Kimberly A; Pace, Norman R; Stout, Janet E

    2015-05-01

    Opportunistic pathogens, including Legionella spp. and non-tuberculous mycobacteria, can thrive in building hot water systems despite municipal and traditional on-site chlorine disinfection. Monochloramine is a relatively new approach to on-site disinfection, but the microbiological impact of on-site chloramine use has not been well studied. We hypothesized that comparison of the microbial ecology associated with monochloramine treatment versus no on-site treatment would yield highly dissimilar bacterial communities. Hot water samples were collected monthly from 7 locations for three months from two buildings in a Pennsylvania hospital complex supplied with common municipal water: (1) a hospital administrative building (no on-site treatment) and (2) an adjacent acute-care hospital treated on-site with monochloramine to control Legionella spp. Water samples were subjected to DNA extraction, rRNA PCR, and 454 pyrosequencing. Stark differences in the microbiome of the chloraminated water and the control were observed. Bacteria in the treated samples were primarily Sphingomonadales and Limnohabitans, whereas Flexibacter and Planctomycetaceae predominated in untreated control samples. Serendipitously, one sampling month coincided with dysfunction of the on-site disinfection system that resulted in a Legionella bloom detected by sequencing and culture. This study also demonstrates the potential utility of high-throughput DNA sequencing to monitor microbial ecology in water systems.

  12. Effects of soil type and farm management on soil ecological functional genes and microbial activities

    SciTech Connect

    Reeve, Jennifer; Schadt, Christopher Warren; Carpenter-Boggs, Lynne; Kang, S.; Zhou, Jizhong; Reganold, John P.

    2010-01-01

    Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.

  13. Fractal Hypothesis of the Pelagic Microbial Ecosystem-Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?

    PubMed

    Våge, Selina; Thingstad, T Frede

    2015-01-01

    Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales.

  14. Fractal Hypothesis of the Pelagic Microbial Ecosystem—Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?

    PubMed Central

    Våge, Selina; Thingstad, T. Frede

    2015-01-01

    Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales. PMID:26648929

  15. Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes.

    PubMed

    Pechal, Jennifer L; Benbow, M Eric

    2016-05-01

    Carrion decomposition is driven by complex relationships that affect necrobiome community (i.e. all organisms and their genes associated with a dead animal) interactions, such as insect species arrival time to carrion and microbial succession. Little is understood about how microbial communities interact with invertebrates at the aquatic-terrestrial habitat interface. The first objective of the study was to characterize internal microbial communities using high-throughput sequencing of 16S rRNA gene amplicons for aquatic insects (three mayfly species) in streams with salmon carcasses compared with those in streams without salmon carcasses. The second objective was to assess the epinecrotic microbial communities of decomposing salmon carcasses (Oncorhynchus keta) compared with those of terrestrial necrophagous insects (Calliphora terraenovae larvae and adults) associated with the carcasses. There was a significant difference in the internal microbiomes of mayflies collected in salmon carcass-bearing streams and in non-carcass streams, while the developmental stage of blow flies was the governing factor in structuring necrophagous insect internal microbiota. Furthermore, the necrophagous internal microbiome was influenced by the resource on which the larvae developed, and changes in the adult microbiome varied temporally. Overall, these carrion subsidy-driven networks respond to resource pulses with bottom-up effects on consumer microbial structure, as revealed by shifting communities over space and time.

  16. Microbial Ecology of the Dark Ocean above, at, and below the Seafloor†

    PubMed Central

    Orcutt, Beth N.; Sylvan, Jason B.; Knab, Nina J.; Edwards, Katrina J.

    2011-01-01

    Summary: The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats. PMID:21646433

  17. Microbial ecology of the dark ocean above, at, and below the seafloor.

    PubMed

    Orcutt, Beth N; Sylvan, Jason B; Knab, Nina J; Edwards, Katrina J

    2011-06-01

    The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

  18. Ecological Forecasting: Microbial Contamination and Atmospheric Loadings of Nutrients to Land and Water

    EPA Science Inventory

    The development of ecological forecasts, namely, methodologies to predict the chemical, biological, and physical changes in terrestrial and aquatic ecosystems is desirable so that effective strategies for reducing the adverse impacts of human activities and extreme natural events...

  19. Post-Genomics Approaches towards Monitoring Changes within the Microbial Ecology of the Gut

    NASA Astrophysics Data System (ADS)

    Tuohy, Kieran M.; Abecia, Leticia; Deaville, Eddie R.; Fava, Francesca; Klinder, Annett; Shen, Qing

    The human gut microbiota, comprising many hundreds of different microbial species, has closely co-evolved with its human host over the millennia. Diet has been a major driver of this co-evolution, in particular dietary non-digestible carbohydrates. This dietary fraction reaches the colon and becomes available for microbial fermentation, and it is in the colon that the great diversity of gut microorganisms resides. For the vast majority of our evolutionary history humans followed hunter-gatherer life-styles and consumed diets with many times more non-digestible carbohydrates, fiber and whole plant polyphenol rich foods than typical Western style diets today.

  20. Board-invited review: Rumen microbiology: Leading the way in microbial ecology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not ...

  1. Planetary biology and microbial ecology. Biochemistry of carbon and early life

    NASA Technical Reports Server (NTRS)

    Margulis, L. (Editor); Nealson, K. H. (Editor); Taylor, I. (Editor)

    1983-01-01

    Experiments made with cyanobacteria, phototrophic bacteria, and methanogenic bacteria are detailed. Significant carbon isotope fractionation data is included. Taken from well documented extant microbial communities, this data provides a basis of comparison for isotope fractionation values measured in Archean and Proterozoic (preCambrian) rocks. Media, methods, and techniques used to acquire data are also described.

  2. TURKEY FECAL MICROBIAL COMMUNITY STRUCTURE AND ECOLOGICAL FUNCTIONS REVEALED BY 16S RDNA AND METAGENOME SEQUENCES

    EPA Science Inventory

    Turkey feces are an important source of fecal waste in the United States. With the exception of isolated studies on bacterial pathogens, little is known about the type of bacteria inhabiting the turkey gut. In order to understand the microbial diversity and functional genes assoc...

  3. MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions.

    PubMed

    Wade, Matthew J; Oakley, Jordan; Harbisher, Sophie; Parker, Nicholas G; Dolfing, Jan

    2017-01-01

    Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. It does not require detailed knowledge of mathematical analytical techniques and is offered as a single graphical user interface containing all input and output options. The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. The software includes seven ecological interaction motifs and seven growth function models. Unlike other system analysis tools, MI-Sim is designed as a simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment of their dynamical and behavioural properties.

  4. MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions

    PubMed Central

    Oakley, Jordan; Harbisher, Sophie; Parker, Nicholas G.; Dolfing, Jan

    2017-01-01

    Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. It does not require detailed knowledge of mathematical analytical techniques and is offered as a single graphical user interface containing all input and output options. The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. The software includes seven ecological interaction motifs and seven growth function models. Unlike other system analysis tools, MI-Sim is designed as a simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment of their dynamical and behavioural properties. PMID:28273164

  5. Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics’era

    PubMed Central

    Cravo-Laureau, Cristiana; Duran, Robert

    2014-01-01

    Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment’s complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment’s reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying “omics” approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition

  6. Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics'era.

    PubMed

    Cravo-Laureau, Cristiana; Duran, Robert

    2014-01-01

    Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment's complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment's reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying "omics" approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we

  7. Effects of encapsulated Lactobacillus acidophilus along with pasteurized longan juice on the colon microbiota residing in a dynamic simulator of the human intestinal microbial ecosystem.

    PubMed

    Chaikham, Pittaya; Apichartsrangkoon, Arunee

    2014-01-01

    The effect of encapsulated Lactobacillus acidophilus LA5 along with pasteurized longan juice on the colon microbiota was investigated by applying a dynamic model of the human gastrointestinal tract. Encapsulated L. acidophilus LA5 in pasteurized longan juice or sole encapsulated L. acidophilus LA5 exhibited the efficiency of colonizing the colon and enabling the growth of colon lactobacilli as well as beneficial bifidobacteria but inhibited the growth of fecal coliforms and clostridia. Moreover, these treatments gave rise to a significant increase of lactic acid and short-chain fatty acids such as acetate, propionate, and butyrate. Although acetate displayed the highest quantity, it was likely that after incorporating encapsulated L. acidophilus LA5 plus pasteurized longan juice, quantity of butyrate exceed propionate, and acetate in comparison with their controls. Denaturant gradient gel electrophoresis patterns confirmed that various treatments affected the alteration of microbial community within the simulator of the human intestinal microbial ecosystem.

  8. A Gut Microbial Metabolite of Linoleic Acid, 10-Hydroxy-cis-12-octadecenoic Acid, Ameliorates Intestinal Epithelial Barrier Impairment Partially via GPR40-MEK-ERK Pathway*

    PubMed Central

    Miyamoto, Junki; Mizukure, Taichi; Park, Si-Bum; Kishino, Shigenobu; Kimura, Ikuo; Hirano, Kanako; Bergamo, Paolo; Rossi, Mauro; Suzuki, Takuya; Arita, Makoto; Ogawa, Jun; Tanabe, Soichi

    2015-01-01

    Gut microbial metabolites of polyunsaturated fatty acids have attracted much attention because of their various physiological properties. Dysfunction of tight junction (TJ) in the intestine contributes to the pathogenesis of many disorders such as inflammatory bowel disease. We evaluated the effects of five novel gut microbial metabolites on tumor necrosis factor (TNF)-α-induced barrier impairment in Caco-2 cells and dextran sulfate sodium-induced colitis in mice. 10-Hydroxy-cis-12-octadecenoic acid (HYA), a gut microbial metabolite of linoleic acid, suppressed TNF-α and dextran sulfate sodium-induced changes in the expression of TJ-related molecules, occludin, zonula occludens-1, and myosin light chain kinase. HYA also suppressed the expression of TNF receptor 2 (TNFR2) mRNA and protein expression in Caco-2 cells and colonic tissue. In addition, HYA suppressed the protein expression of TNFR2 in murine intestinal epithelial cells. Furthermore, HYA significantly up-regulated G protein-coupled receptor (GPR) 40 expression in Caco-2 cells. It also induced [Ca2+]i responses in HEK293 cells expressing human GPR40 with higher sensitivity than linoleic acid, its metabolic precursor. The barrier-recovering effects of HYA were abrogated by a GPR40 antagonist and MEK inhibitor in Caco-2 cells. Conversely, 10-hydroxyoctadacanoic acid, which is a gut microbial metabolite of oleic acid and lacks a carbon-carbon double bond at Δ12 position, did not show these TJ-restoring activities and down-regulated GPR40 expression. Therefore, HYA modulates TNFR2 expression, at least partially, via the GPR40-MEK-ERK pathway and may be useful in the treatment of TJ-related disorders such as inflammatory bowel disease. PMID:25505251

  9. Microbial Ecology of Subseafloor Communities at Deep-sea Hydrothermal Seamounts of the Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Huber, J. A.; Bolton, S.; Butterfield, D. A.; Baross, J. A.; Sogin, M. L.

    2006-12-01

    Circulation of hydrothermal fluids and seawater occurs within the upper 500 m of porous oceanic crust and provides a rich environment for microbial growth in the subseafloor. Enrichment cultures, geochemical indicators, and sequence analyses of PCR amplicons of ribosomal RNA genes demonstrate that these crustal fluids host a microbial community composed of organisms indigenous to the subseafloor and organisms from other deep-sea habitats, such as seawater. However, the subseafloor microbial communities remain undersampled and our knowledge of what microbes are present and how they are distributed in this dynamic environment over time and space is fragmentary. This work focuses on determining the microbial diversity and genomic content of the subseafloor microbial community at geographically and geochemically distinct deep- sea hydrothermal seamounts. The approach uses a combination of methods, including DNA-based, culturing, and geochemical methods applied to diffuse fluids from two locations: Axial Seamount on the Juan de Fuca Ridge in the northeast Pacific Ocean (45.92° N, 130° W) and seamounts along the Mariana Arc (14-22° N, 143-146° E) in the western Pacific. Both locations host recently eruptive seamounts located above 2000 m with diffusely venting fluids that contain high concentrations of carbon dioxide. However, their geological and chemical setting differs greatly; Axial is a mid-ocean ridge seamount with fluids dominated by high concentrations of hydrogen sulfide, and the Mariana seamounts are at a convergent plate boundary and host a variety of fluids, including those with very low pH and high concentrations of particulate sulfur. Initial studies reveal bacterial communities at both sites consist mainly of epsilon-proteobacteria, a physiologically and phylogenetically diverse group known to have a widespread distribution and dominance in many deep-sea vent habitats. However, while subseafloor archaeal communities at Axial are composed of autotrophic

  10. Nitrification inhibition by hexavalent chromium Cr(VI)--Microbial ecology, gene expression and off-gas emissions.

    PubMed

    Kim, Young Mo; Park, Hongkeun; Chandran, Kartik

    2016-04-01

    The goal of this study was to investigate the responses in the physiology, microbial ecology and gene expression of nitrifying bacteria to imposition of and recovery from Cr(VI) loading in a lab-scale nitrification bioreactor. Exposure to Cr(VI) in the reactor strongly inhibited nitrification performance resulting in a parallel decrease in nitrate production and ammonia consumption. Cr(VI) exposure also led to an overall decrease in total bacterial concentrations in the reactor. However, the fraction of ammonia oxidizing bacteria (AOB) decreased to a greater extent than the fraction of nitrite oxidizing bacteria (NOB). In terms of functional gene expression, a rapid decrease in the transcript concentrations of amoA gene coding for ammonia oxidation in AOB was observed in response to the Cr(VI) shock. In contrast, transcript concentrations of the nxrA gene coding for nitrite oxidation in NOB were relatively unchanged compared to Cr(VI) pre-exposure levels. Therefore, Cr(VI) exposure selectively and directly inhibited activity of AOB, which indirectly resulted in substrate (nitrite) limitation to NOB. Significantly, trends in amoA expression preceded performance trends both during imposition of and recovery from inhibition. During recovery from the Cr(VI) shock, the high ammonia concentrations in the bioreactor resulted in an irreversible shift towards AOB populations, which are expected to be more competitive in high ammonia environments. An inadvertent impact during recovery was increased emission of nitrous oxide (N2O) and nitric oxide (NO), consistent with recent findings linking AOB activity and the production of these gases. Therefore, Cr(VI) exposure elicited multiple responses on the microbial ecology, gene expression and both aqueous and gaseous nitrogenous conversion in a nitrification process. A complementary interrogation of these multiple responses facilitated an understanding of both direct and indirect inhibitory impacts on nitrification.

  11. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

    SciTech Connect

    Denef, Vincent; Kalnejals, Linda; Muller, R; Wilmes, P; Baker, Brett J.; Thomas, Brian; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillumgroup II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the 15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.

  12. Microbial Ecology in Anaerobic Digestion at Agitated and Non-Agitated Conditions

    PubMed Central

    Tian, Zhuoli; Cabrol, Léa; Ruiz-Filippi, Gonzalo; Pullammanappallil, Pratap

    2014-01-01

    To investigate the distribution and dynamics of microbial community in anaerobic digestion at agitated and non-agitated condition, 454 pyrosequencing of 16s rRNA was conducted. It revealed the distinct community compositions between the two digesters and their progressive shifting over time. Methanogens and syntrophic bacteria were found much less abundant in the agitated digester, which was mainly attributed to the presence of bacterial genera Acetanaerobacterium and Ruminococcus with relatively high abundance. The characterization of the microbial community corroborated the digestion performance affected at the agitated condition, where lower methane yield and delayed methane production rate were observed. This was further verified by the accumulation of propionic acid in the agitated digester. PMID:25313520

  13. Emerging concepts on microbial processes in the bathypelagic ocean - ecology, biogeochemistry, and genomics

    NASA Astrophysics Data System (ADS)

    Nagata, Toshi; Tamburini, Christian; Arístegui, Javier; Baltar, Federico; Bochdansky, Alexander B.; Fonda-Umani, Serena; Fukuda, Hideki; Gogou, Alexandra; Hansell, Dennis A.; Hansman, Roberta L.; Herndl, Gerhard J.; Panagiotopoulos, Christos; Reinthaler, Thomas; Sohrin, Rumi; Verdugo, Pedro; Yamada, Namiha; Yamashita, Youhei; Yokokawa, Taichi; Bartlett, Douglas H.

    2010-08-01

    This paper synthesizes recent findings regarding microbial distributions and processes in the bathypelagic ocean (depth >1000 m). Abundance, production and respiration of prokaryotes reflect supplies of particulate and dissolved organic matter to the bathypelagic zone. Better resolution of carbon fluxes mediated by deep microbes requires further testing on the validity of conversion factors. Archaea, especially marine Crenarchaeota Group I, are abundant in deep waters where they can fix dissolved inorganic carbon. Viruses appear to be important in the microbial loop in deep waters, displaying remarkably high virus to prokaryote abundance ratios in some oceanic regions. Sequencing of 18S rRNA genes revealed a tremendous diversity of small-sized protists in bathypelagic waters. Abundances of heterotrophic nanoflagellates (HNF) and ciliates decrease with depth more steeply than prokaryotes; nonetheless, data indicated that HNF consumed half of prokaryote production in the bathypelagic zone. Aggregates are important habitats for deep-water microbes, which produce more extracellular enzymes (on a per-cell basis) than surface communities. The theory of marine gel formation provides a framework to unravel complex interactions between microbes and organic polymers. Recent data on the effects of hydrostatic pressure on microbial activities indicate that bathypelagic microbial activity is generally higher under in situ pressure conditions than at atmospheric pressures. High-throughput sequencing of 16S rRNA genes revealed a remarkable diversity of Bacteria in the bathypelagic ocean. Metagenomics and comparative genomics of piezophiles reveal not only the high diversity of deep sea microbes but also specific functional attributes of these piezophilic microbes, interpreted as an adaptation to the deep water environment. Taken together, the data compiled on bathypelagic microbes indicate that, despite high-pressure and low-temperature conditions, microbes in the bathypelagic

  14. Ecology.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    This set of teaching aids consists of nine Audubon Nature Bulletins, providing teachers and students with informational reading on various ecological topics. The bulletins have these titles: Schoolyard Laboratories, Owls and Predators, The Forest Community, Life in Freshwater Marshes, Camouflage in the Animal World, Life in the Desert, The…

  15. Microbial ecology of the closed artificial ecosystem MELiSSA (Micro-Ecological Life Support System Alternative): reinventing and compartmentalizing the Earth's food and oxygen regeneration system for long-haul space exploration missions.

    PubMed

    Hendrickx, Larissa; De Wever, Heleen; Hermans, Veronik; Mastroleo, Felice; Morin, Nicolas; Wilmotte, Annick; Janssen, Paul; Mergeay, Max

    2006-01-01

    MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system uses the combined activity of different living organisms: microbial cultures in bioreactors, a plant compartment and a human crew. In this minireview, the development of a short-cut ecological system for the biotransformation of organic waste is discussed from a microorganism's perspective. The artificial ecological model--still in full development--that is inspired by Earth's own geomicrobiological ecosystem serves as an ideal study object on microbial ecology and will become an indispensable travel companion in manned space exploration.

  16. IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

    PubMed Central

    Lagkouvardos, Ilias; Joseph, Divya; Kapfhammer, Martin; Giritli, Sabahattin; Horn, Matthias; Haller, Dirk; Clavel, Thomas

    2016-01-01

    The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users’ own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org. PMID:27659943

  17. IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies.

    PubMed

    Lagkouvardos, Ilias; Joseph, Divya; Kapfhammer, Martin; Giritli, Sabahattin; Horn, Matthias; Haller, Dirk; Clavel, Thomas

    2016-09-23

    The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users' own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org.

  18. Physico-chemical gradients within the hydrothermal chimney Roane define sharp boundaries for microbial community ecology

    NASA Astrophysics Data System (ADS)

    Frank, K. L.; Kelley, D. S.; Girguis, P. R.

    2011-12-01

    The unique physico-chemical gradients characteristic of hydrothermal vents provide diverse niches for prokaryotic communities. To date, our knowledge of environmental constraints on microbial colonization and metabolic activity within active sulfide structures has been limited by the lack of co-registered in situ chemistry and appropriate, taxonomic and metabolic genetic markers. Here we characterize de novo endolithic microbial colonization using a sulfide microbial incubator within the hydrothermal vent Roane during a one-year deployment, with co-registered temperature, fluid chemistry and mineralogy. Taxanomic assessment of phylogenetic diversity via 16S rDNA extracted from the outer (40-70°C) and middle (150-240°C) chambers of the incubator revealed patterns of distribution comparable to previously published observations. However, quantitative and statistical analyses of 16S rDNA sequences from two chambers revealed very distinct communities, with less than 5% of the identified operational taxonomic units common to both chambers. Analyses of metagenomic data suggest an elevated potential for motility and select biosynthetic pathways in the outer chamber community. In contrast, the middle chamber community exhibits a greater potential for quorum sensing, biofilm formation and archaeal lipid biosynthesis. Striking differences in metabolic potential were also apparent. These data suggest that the distribution, abundance and physiological capacity of these communities is strongly governed by chemical and physical variability of the environment.

  19. Microbial Ecology Dynamics Reveal a Succession in the Core Microbiota Involved in the Ripening of Pasta Filata Caciocavallo Pugliese Cheese

    PubMed Central

    De Pasquale, Ilaria; Buchin, Solange; De Angelis, Maria; Gobbetti, Marco

    2014-01-01

    Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese. Plate counts revealed that cheese manufacture affected the microbial ecology. The results agreed with those from culture-independent approaches. As shown by urea-PAGE, reverse-phase high pressure liquid chromatography (RP-HPLC), and free-amino-acid (FAA) analyses, the extent of secondary proteolysis mainly increased after 30 to 45 days of ripening. VOCs and volatile free fatty acids (VFFA) were identified by a purge-and-trap method (PT) and solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS), respectively. Except for aldehydes, the levels of most of VOCs and VFFA mainly increased from 30 to 45 days onwards. As shown through pyrosequencing analysis, raw cows' milk was contaminated by Firmicutes (53%), Proteobacteria (39%), Bacteroidetes (7.8%), Actinobacteria (0.06%), and Fusobacteria (0.03%), with heterogeneity at the genus level. The primary starter Streptococcus thermophilus dominated the curd population. Other genera occurred at low incidence or sporadically. The microbial dynamics reflected on the overall physiological diversity. At 30 days, a microbial succession was clearly highlighted. The relative abundance of Streptococcus sp. and especially St. thermophilus decreased, while that of Lactobacillus casei, Lactobacillus sp., and especially Lactobacillus paracasei increased consistently. Despite the lower relative abundance compared to St. thermophilus, mesophilic lactobacilli were the only organisms positively correlated with the concentration of FAAs, area of hydrophilic peptide peaks, and several VOCs (e.g., alcohols, ketones, esters and all furans). This study showed that a core microbiota was naturally selected during middle ripening, which

  20. Microbial ecology dynamics reveal a succession in the core microbiota involved in the ripening of pasta filata caciocavallo pugliese cheese.

    PubMed

    De Pasquale, Ilaria; Di Cagno, Raffaella; Buchin, Solange; De Angelis, Maria; Gobbetti, Marco

    2014-10-01

    Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese. Plate counts revealed that cheese manufacture affected the microbial ecology. The results agreed with those from culture-independent approaches. As shown by urea-PAGE, reverse-phase high pressure liquid chromatography (RP-HPLC), and free-amino-acid (FAA) analyses, the extent of secondary proteolysis mainly increased after 30 to 45 days of ripening. VOCs and volatile free fatty acids (VFFA) were identified by a purge-and-trap method (PT) and solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS), respectively. Except for aldehydes, the levels of most of VOCs and VFFA mainly increased from 30 to 45 days onwards. As shown through pyrosequencing analysis, raw cows' milk was contaminated by Firmicutes (53%), Proteobacteria (39%), Bacteroidetes (7.8%), Actinobacteria (0.06%), and Fusobacteria (0.03%), with heterogeneity at the genus level. The primary starter Streptococcus thermophilus dominated the curd population. Other genera occurred at low incidence or sporadically. The microbial dynamics reflected on the overall physiological diversity. At 30 days, a microbial succession was clearly highlighted. The relative abundance of Streptococcus sp. and especially St. thermophilus decreased, while that of Lactobacillus casei, Lactobacillus sp., and especially Lactobacillus paracasei increased consistently. Despite the lower relative abundance compared to St. thermophilus, mesophilic lactobacilli were the only organisms positively correlated with the concentration of FAAs, area of hydrophilic peptide peaks, and several VOCs (e.g., alcohols, ketones, esters and all furans). This study showed that a core microbiota was naturally selected during middle ripening, which

  1. Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies.

    PubMed

    Mieczan, Tomasz; Tarkowska-Kukuryk, Monika

    2017-03-06

    Interactions between bacteria and protists are essential to the ecosystem ecology of fens. Until now, however, there has been almost no information on how restoration procedures in carbonate fens affect the functioning of microbial food webs. Changes in vegetation patterns resulting from restoration may take years to be observed, whereas microbial processes display effects even after short-term exposure to changes in environmental conditions caused by restoration. Therefore, microbial processes and patterns can be used as sensitive indicators of changes in environmental conditions. The present study attempts to verify the hypothesis that the species richness and abundance of microbial loop components would differ substantially before and after restoration. The effect of restoration processes on the functioning of the food web was investigated for a 10 years in a carbonate-rich fen, before and after restoration. The restoration procedure (particularly the improvement in hydrological conditions) distinctly modified the taxonomic composition and functioning of microbial food webs. This is reflected in the increased abundance and diversity of testate amoeba, i.e. top predators, within the microbial food web and in the pronounced increase in the abundance of bacteria. This study suggests potential use of microbial loop components as bio-indicators and bio-monitoring tools for hydrological status of fens and concentrations of nutrients. Better understanding of what regulates microbial populations and activity in fens and unravelling of these fundamental mechanisms are particularly critical in order to more accurately predict how fens will respond to global change or anthropogenic disturbances.

  2. Effects of Supplementation of the Synbiotic Ecologic® 825/FOS P6 on Intestinal Barrier Function in Healthy Humans: A Randomized Controlled Trial

    PubMed Central

    Wilms, E.; Gerritsen, J.; Smidt, H.; Besseling-van der Vaart, I.; Rijkers, G. T.; Garcia Fuentes, A. R.; Masclee, A. A. M.; Troost, F. J.

    2016-01-01

    Background and Aims Probiotics, prebiotics and synbiotics have been suggested as dietary strategies to improve intestinal barrier function. This study aimed to assess the effect of two weeks synbiotic supplementation on intestinal permeability under basal and stressed conditions. Secondary aims were the assessment of two weeks synbiotic supplementation on systemic immune function and gastrointestinal symptoms including defecation pattern. Design Twenty healthy adults completed a double-blind, controlled, randomized, parallel design study. Intervention Groups either received synbiotic (1.5 × 1010 CFU Ecologic® 825 + 10 g fructo-oligosaccharides (FOS P6) per day) or control supplements for two weeks. Outcomes Intestinal segment specific permeability was assessed non-invasively by oral administration of multiple sugar probes and, subsequently, assessing the excretion of these probes in urine. This test was conducted at baseline and at the end of intervention, in the absence and in the presence of an indomethacin challenge. Indomethacin was applied to induce a compromised gut state. Plasma zonulin, cytokines and chemokines were measured at baseline and at the end of intervention. Gastrointestinal symptoms and stool frequency were recorded at baseline and daily during intervention. Results Significantly more male subjects were in the synbiotic group compared to the control group (P = 0.025). Indomethacin significantly increased urinary lactulose/rhamnose ratio versus without indomethacin, both in the control group (P = 0.005) and in the synbiotic group (P = 0.017). Urinary sugar recoveries and ratios, plasma levels of zonulin, cytokines and chemokines, and gastrointestinal symptom scores were not significantly different after control or synbiotic intervention. Stool frequency within the synbiotic group was significantly increased during synbiotic intervention compared to baseline (P = 0.039) and higher compared to control intervention (P = 0.045). Conclusion Two weeks

  3. Shift in the Microbial Ecology of a Hospital Hot Water System following the Introduction of an On-Site Monochloramine Disinfection System

    PubMed Central

    Baron, Julianne L.; Vikram, Amit; Duda, Scott; Stout, Janet E.; Bibby, Kyle

    2014-01-01

    Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital’s hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms. PMID:25033448

  4. Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease

    PubMed Central

    Gong, Xiaojie; Wang, Lili; Yu, Xinjuan

    2016-01-01

    A considerable number of studies have been conducted to study the microbial profiles in inflammatory conditions. A common phenomenon in inflammatory bowel disease (IBD) is the reduction of the diversity of microbiota, which demonstrates that microbial diversity negatively correlates with disease severity in IBD. Increased microbial diversity is known to occur in disease remission. Species diversity plays an important role in maintaining the stability of the intestinal ecosystem as well as normal ecological function. A reduction in microbial diversity corresponds to a decrease in the stability of the ecosystem and can impair ecological function. Fecal microbiota transplantation (FMT), probiotics, and prebiotics, which aim to modulate the microbiota and restore its normal diversity, have been shown to be clinically efficacious. In this study, we hypothesized that a reduction in microbial diversity could play a role in the development of IBD. PMID:28074093

  5. Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission.

    PubMed

    Kohl, Kevin D; Brun, Antonio; Magallanes, Melisa; Brinkerhoff, Joshua; Laspiur, Alejandro; Acosta, Juan Carlos; Caviedes-Vidal, Enrique; Bordenstein, Seth R

    2017-02-01

    Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.

  6. Development and rheological properties of ecological emulsions formulated with a biosolvent and two microbial polysaccharides.

    PubMed

    Trujillo-Cayado, L A; Alfaro, M C; Muñoz, J; Raymundo, A; Sousa, I

    2016-05-01

    The influence of gum concentration and rhamsan/welan gum ratio on rheological properties, droplet size distribution and physical stability of eco-friendly O/W emulsions stabilized by an ecological surfactant were studied in the present work. The emulsions were prepared with 30wt% α-pinene, a terpenic solvent and an ecological alternative for current volatile organic compounds. Rheological properties of emulsions showed an important dependence on the two studied variables. Flow curves were fitted to the Cross model and no synergistic effect between rhamsan and welan gums was demonstrated. Emulsions with submicron mean diameters were obtained regardless of the gum concentration or the rhamsan/welan ratio used. Multiple light scattering illustrated that creaming was practically eliminated by the incorporation of polysaccharides. The use of rhamsan and welan gums as stabilizers lead to apparent enhancements in emulsion rheology and physical stability.

  7. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

    PubMed Central

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-01-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29–30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75–87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy–diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome. PMID:26953601

  8. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters.

    PubMed

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-09-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29-30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75-87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy-diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome.

  9. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

    PubMed Central

    van Overbeek, Leonard S.; Berg, Gabriele; Pirttilä, Anna Maria; Compant, Stéphane; Campisano, Andrea; Döring, Matthias; Sessitsch, Angela

    2015-01-01

    SUMMARY All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions. PMID:26136581

  10. Molecular Ecological and Stable Isotopic Studies of Nitrogen Fixation in Modern Microbial Mats

    NASA Technical Reports Server (NTRS)

    Bebout, B. M.; Crumbliss, L. L.; DesMarais, D. J.; Hogan, M. E.; Omoregie, E.; Turk, K. A.; Zehr, J. P.

    2003-01-01

    Nitrogen is usually the element limiting biological productivity in the marine environment. Microbial mats, laminated microbial communities analogous to some of the oldest forms of life on Earth, are often the sites of high rates of N fixation (the energetically expensive conversion of atmospheric dinitrogen into a biologically useful form). The N fixing enzyme nitrogenase is generally considered to be of ancient origin, and is widely distributed throughout the Bacterial and Archaeal domains of life, indicating an important role for this process over evolutionary time. The stable isotopic signature of N fixation is purportedly recognizable in organic matter (ancient kerogens as well as present-day microbial mats) as a delta (15)N(sub organic) near zero. We studied two microbial mats exhibiting different rates of N fixation in order to better understand the impact of N fixation on the delta (15)N (sub organic) of the mats, as well as what organisms are important in this process. Mats dominated by the cyanobacterium Microcoleus chthonoplastes grow in permanently submerged hypersaline salterns, and exhibit low rates of N fixation, whereas mats dominated by the cyanobacterium Lyngbya spp grow in an intertidal area, and exhibit rates of N fixation an order of magnitude higher. To examine successional stages in mat growth, both developing and established mats at each location were sampled. PCR and RT-PCR based approaches were used to identify, respectively, the organisms containing nifH (one of the genes that encode nitrogenase) as well as those expressing nifH in these mats. Both mats exhibited a distinct diel cycle of N fixation, with highest rates occurring at night. The delta (15)N(sub organic) of the subtidal Microcoleus mats is near zero whereas the delta (15)N(sub organic) is slightly more positive (+ 2-3%), in the intertidal Lyngbya mats, an interesting difference in view of the fact that overall rates of activity in the intertidal mats are much higher that those

  11. Pigs that are divergent in feed efficiency, differ in intestinal enzyme and nutrient transporter gene expression, nutrient digestibility and microbial activity.

    PubMed

    Vigors, S; Sweeney, T; O'Shea, C J; Kelly, A K; O'Doherty, J V

    2016-11-01

    Feed efficiency is an important trait in the future sustainability of pig production, however, the mechanisms involved are not fully elucidated. The objective of this study was to examine nutrient digestibility, organ weights, select bacterial populations, volatile fatty acids (VFA's), enzyme and intestinal nutrient transporter gene expression in a pig population divergent in feed efficiency. Male pigs (n=75; initial BW 22.4 kg SEM 2.03 kg) were fed a standard finishing diet for 43 days before slaughter to evaluate feed intake and growth for the purpose of calculating residual feed intake (RFI). Phenotypic RFI was calculated as the residuals from a regression model regressing average daily feed intake (ADFI) on average daily gain (ADG) and midtest BW0.60 (MBW). On day 115, 16 pigs (85 kg SEM 2.8 kg), designated as high RFI (HRFI) and low RFI (LRFI) were slaughtered and digesta was collected to calculate the coefficient of apparent ileal digestibility (CAID), total tract nutrient digestibility (CATTD), microbial populations and VFA's. Intestinal tissue was collected to examine intestinal nutrient transporter and enzyme gene expression. The LRFI pigs had lower ADFI (P<0.001), improved feed conversion ratio (P<0.001) and an improved RFI value relative to HRFI pigs (0.19 v. -0.14 SEM 0.08; P<0.001). The LRFI pigs had an increased CAID of gross energy (GE), and an improved CATTD of GE, nitrogen and dry matter compared to HRFI pigs (P<0.05). The LRFI pigs had higher relative gene expression levels of fatty acid binding transporter 2 (FABP2) (P<0.01), the sodium/glucose co-transporter 1 (SGLT1) (P<0.05), the glucose transporter GLUT2 (P<0.10), and the enzyme sucrase-isomaltase (SI) (P<0.05) in the jejunum. The LRFI pigs had increased populations of lactobacillus spp. in the caecum compared with HRFI pigs. In colonic digesta HRFI pigs had increased acetic acid concentrations (P<0.05). Differences in nutrient digestibility, intestinal microbial populations and gene

  12. Comparison of Yacon (Smallanthus sonchifolius) Tuber with Commercialized Fructo-oligosaccharides (FOS) in Terms of Physiology, Fermentation Products and Intestinal Microbial Communities in Rats

    PubMed Central

    UTAMI, Ni Wayan Arya; SONE, Teruo; TANAKA, Michiko; NAKATSU, Cindy H; SAITO, Akihiko; ASANO, Kozo

    2013-01-01

    The yacon (Smallanthus sonchifolius) tuber was examined with regard to its prebiotic effects compared with commercialized fructo-oligosaccharides (FOS). A feed containing 10% yacon tuber, which is equivalent to 5% commercialized FOS in terms of the amount of fructo-oligosaccharides (GF2, GF3 and GF4), was administrated to rats for 28 days. The yacon diet changed the intestinal microbial communities beginning in the first week, resulting in a twofold greater concentration of cecal short-chain fatty acids (SCFAs). The SCFA composition differed, but the cecal pH in rats fed yacon tuber was equal to that in rats fed FOS. Serum triglycerides were lower in rats fed yacon compared with rats fed FOS and the control diet. Cecal size was greater with the yacon tuber diet compared with the control diet. The abundant fermentation in the intestines created a selective environment for the intestinal microbiota, which included Lactobacillus acidophilus, Bifidobacterium pseudolongum, Bifidobacterium animalis and Barnesiella spp. according to identification with culture-independent analysis, 16S rRNA gene PCR-DGGE combined with cloning and sequencing. Barnesiella spp. and B. pseudolongum were only found in the rats fed the yacon diet, while L. acidophilus and B. animalis were found in abundance in rats fed both the yacon and FOS diets. The genus Barnesiella has not previously been reported to be associated with yacon or FOS fermentation. We concluded that the physiological and microbiological effects of the yacon tuber were different from those of FOS. Differences in cecal size, blood triglycerides and microbial community profiles including their metabolites (SCFAs) between the yacon tuber and FOS were shown to be more greatly affected by the yacon tuber rather than FOS. PMID:24936376

  13. Comparison of Yacon (Smallanthus sonchifolius) Tuber with Commercialized Fructo-oligosaccharides (FOS) in Terms of Physiology, Fermentation Products and Intestinal Microbial Communities in Rats.

    PubMed

    Utami, Ni Wayan Arya; Sone, Teruo; Tanaka, Michiko; Nakatsu, Cindy H; Saito, Akihiko; Asano, Kozo

    2013-01-01

    The yacon (Smallanthus sonchifolius) tuber was examined with regard to its prebiotic effects compared with commercialized fructo-oligosaccharides (FOS). A feed containing 10% yacon tuber, which is equivalent to 5% commercialized FOS in terms of the amount of fructo-oligosaccharides (GF2, GF3 and GF4), was administrated to rats for 28 days. The yacon diet changed the intestinal microbial communities beginning in the first week, resulting in a twofold greater concentration of cecal short-chain fatty acids (SCFAs). The SCFA composition differed, but the cecal pH in rats fed yacon tuber was equal to that in rats fed FOS. Serum triglycerides were lower in rats fed yacon compared with rats fed FOS and the control diet. Cecal size was greater with the yacon tuber diet compared with the control diet. The abundant fermentation in the intestines created a selective environment for the intestinal microbiota, which included Lactobacillus acidophilus, Bifidobacterium pseudolongum, Bifidobacterium animalis and Barnesiella spp. according to identification with culture-independent analysis, 16S rRNA gene PCR-DGGE combined with cloning and sequencing. Barnesiella spp. and B. pseudolongum were only found in the rats fed the yacon diet, while L. acidophilus and B. animalis were found in abundance in rats fed both the yacon and FOS diets. The genus Barnesiella has not previously been reported to be associated with yacon or FOS fermentation. We concluded that the physiological and microbiological effects of the yacon tuber were different from those of FOS. Differences in cecal size, blood triglycerides and microbial community profiles including their metabolites (SCFAs) between the yacon tuber and FOS were shown to be more greatly affected by the yacon tuber rather than FOS.

  14. The grounding of the Bahia Paraiso: Microbial ecology of the 1989 Antarctic oil spill.

    PubMed

    Karl, D M

    1992-07-01

    On 28 January 1989 the Bahia Paraiso ran aground and sank near Palmer Station, Antarctica. At least 6.8 × 10(5) liters of diesel fuel arctic (DFA) were released into semi-enclosed Arthur Harbor and deposited in the nearby intertidal regions. Approximately 6 weeks later, a group of scientists was deployed to evaluate the impact of the oil spill on the surrounding coastal marine ecosystem.Microbial hydrocarbon oxidation potential ((14)CO2 evolved from (14)C-labeled hexadecane) was detected throughout both the oil-impacted and control regions. Hexadecane was mineralized at extremely low rates (0.13-1.21 pmol g(-1) sediment dry weight day(-1)); microbiological turnover time exceeded 2 years. The acute effects of DFA (measured over exposure periods of 3-7 days) on the metabolic activities of sedimentary microorganisms appear to be negligible even at seawater saturation concentrations of DFA. Long-term exposure (120 days) to varying concentrations of DFA resulted in significant decreases (>90%) in total ATP, but had either no effect or a slight stimulatory effect on metabolic activity and production. In contrast to planktonic microbial communities, increasing incubation temperatures of between 0 and 30°C had a positive effect on rates of metabolism and production of sedimentary assemblages. These results may influence the overall weathering rates of hydrocarbons deposited in the intertidal and supratidal regions of Arthur Harbor and other polar regions.

  15. Microbial ecology of corals, sponges, and algae in mesophotic coral environments

    USGS Publications Warehouse

    Olson, Julie B.; Kellogg, Christina A.

    2010-01-01

    Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone.

  16. From Field to Laboratory: A New Database Approach for Linking Microbial Field Ecology with Laboratory Studies

    NASA Technical Reports Server (NTRS)

    Bebout, Leslie; Keller, R.; Miller, S.; Jahnke, L.; DeVincenzi, D. (Technical Monitor)

    2002-01-01

    The Ames Exobiology Culture Collection Database (AECC-DB) has been developed as a collaboration between microbial ecologists and information technology specialists. It allows for extensive web-based archiving of information regarding field samples to document microbial co-habitation of specific ecosystem micro-environments. Documentation and archiving continues as pure cultures are isolated, metabolic properties determined, and DNA extracted and sequenced. In this way metabolic properties and molecular sequences are clearly linked back to specific isolates and the location of those microbes in the ecosystem of origin. Use of this database system presents a significant advancement over traditional bookkeeping wherein there is generally little or no information regarding the environments from which microorganisms were isolated. Generally there is only a general ecosystem designation (i.e., hot-spring). However within each of these there are a myriad of microenvironments with very different properties and determining exactly where (which microenvironment) a given microbe comes from is critical in designing appropriate isolation media and interpreting physiological properties. We are currently using the database to aid in the isolation of a large number of cyanobacterial species and will present results by PI's and students demonstrating the utility of this new approach.

  17. An underground tale: contribution of microbial activity to plant iron acquisition via ecological processes

    PubMed Central

    Jin, Chong Wei; Ye, Yi Quan; Zheng, Shao Jian

    2014-01-01

    Background Iron (Fe) deficiency in crops is a worldwide agricultural problem. Plants have evolved several strategies to enhance Fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid Fe deficiency in Fe-limited soils. Soil micro-organisms also play a critical role in plant Fe acquisition; however, the mechanisms behind their promotion of Fe acquisition remain largely unknown. Scope This review focuses on the possible mechanisms underlying the promotion of plant Fe acquisition by soil micro-organisms. Conclusions Fe-deficiency-induced root exudates alter the microbial community in the rhizosphere by modifying the physicochemical properties of soil, and/or by their antimicrobial and/or growth-promoting effects. The altered microbial community may in turn benefit plant Fe acquisition via production of siderophores and protons, both of which improve Fe bioavailability in soil, and via hormone generation that triggers the enhancement of Fe uptake capacity in plants. In addition, symbiotic interactions between micro-organisms and host plants could also enhance plant Fe acquisition, possibly including: rhizobium nodulation enhancing plant Fe uptake capacity and mycorrhizal fungal infection enhancing root length and the nutrient acquisition area of the root system, as well as increasing the production of Fe3+ chelators and protons. PMID:24265348

  18. Mesophilic versus thermophilic anaerobic digestion of cattle manure: methane productivity and microbial ecology

    PubMed Central

    Moset, Veronica; Poulsen, Morten; Wahid, Radziah; Højberg, Ole; Møller, Henrik Bjarne

    2015-01-01

    In this study, productivity and physicochemical and microbiological (454 sequencing) parameters, as well as environmental criteria, were investigated in anaerobic reactors to contribute to the ongoing debate about the optimal temperature range for treating animal manure, and expand the general knowledge on the relation between microbiological and physicochemical process indicators. For this purpose, two reactor sizes were used (10 m3 and 16 l), in which two temperature conditions (35°C and 50°C) were tested. In addition, the effect of the hydraulic retention time was evaluated (16 versus 20 days). Thermophilic anaerobic digestion showed higher organic matter degradation (especially fiber), higher pH and higher methane (CH4) yield, as well as better percentage of ultimate CH4 yield retrieved and lower residual CH4 emission, when compared with mesophilic conditions. In addition, lower microbial diversity was found in the thermophilic reactors, especially for Bacteria, where a clear intensification towards Clostridia class members was evident. Independent of temperature, some similarities were found in digestates when comparing with animal manure, including low volatile fatty acids concentrations and a high fraction of Euryarchaeota in the total microbial community, in which members of Methanosarcinales dominated for both temperature conditions; these indicators could be considered a sign of process stability. PMID:25737010

  19. Microbial ecology of corals, sponges, and algae in mesophotic coral environments.

    PubMed

    Olson, Julie B; Kellogg, Christina A

    2010-07-01

    Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone.

  20. Immune and genetic gardening of the intestinal microbiome

    PubMed Central

    Jacobs, Jonathan P.; Braun, Jonathan

    2014-01-01

    The mucosal immune system – consisting of adaptive and innate immune cells as well as the epithelium – is profoundly influenced by its microbial environment. There is now growing evidence that the converse is also true, that the immune system shapes the composition of the intestinal microbiome. During conditions of health, this bidirectional interaction achieves a homeostasis in which inappropriate immune responses to nonpathogenic microbes are averted and immune activity suppresses blooms of potentially pathogenic microbes (pathobionts). Genetic alteration in immune/epithelial function can affect host gardening of the intestinal microbiome, contributing to the diversity of intestinal microbiota within a population and in some cases allowing for unfavorable microbial ecologies (dysbiosis) that confer disease susceptibility. PMID:24613921

  1. Microbial ecological perspectives of space-exposed microbes: A genetic approach

    NASA Astrophysics Data System (ADS)

    Venkateswaran, Kasthuri; Osman, Shariff; Spry, James A.; Mancinelli, Rocco; Rabbow, Elke; Rettberg, Petra; Horneck, Gerda

    2008-09-01

    A radiation resistant strain of Bacillus pumilus isolated from a spacecraft assembly environment is being exposed to several conditions associated with the space environment (Feb, 2008). The radiation exposures are being carried out aboard ISS using the European Technology Exposure Platform and Experiment Facility (EXPOSE) and include: (i) space vacuum, (ii) solar extraterrestrial UV radiation including vacuum-UV, (iii) simulated Martian UV radiation regime, and (iv) galactic cosmic radiation. The viability of exposed and unexposed microorganisms as well as the integrity of the cell wall or spore envelop (membrane, wall and coat layers) and damage to the DNA will be assessed when the exposed spores return to Earth. In addition to these standard methods for assessing cellular damage, the global response elicited in spores by space exposure will be probed in germinated spore survivors using transcription microarrays. During ground simulation experiments the desiccated spores survived full Martian UV (200 - 400 nm) for 5 min (30 W m-2) and were only slightly affected by Martian atmospheric conditions in the absence of UV. Although prolonged UV irradiation (>5 min to 12 hours; 30 W m-2) killed substantial portions of the spore microcosms (~5 to 6 logs reduction under Martian UV), dramatic spore survival was apparent when spores were shield by dust (~2 logs reduction). It is presumed that the mitigation of UV damage (200-400 nm) to dust covered, desiccated spores and their survival on spacecraft-grade aluminum is strain specific. The more pronounced UV resistances observed in wild-type strains, as compared to laboratory strains suggested that discussions and conclusions regarding the survival of microbes in extraterrestrial environments should not be generalized based solely on laboratory strain responses to simulated conditions. The data generated is important for the assessment of the probability and mechanisms of microbial survival, microbial contaminants of risk to

  2. Adaptive long-term monitoring of soil health in metal phytostabilization: ecological attributes and ecosystem services based on soil microbial parameters.

    PubMed

    Epelde, Lur; Becerril, José M; Alkorta, Itziar; Garbisu, Carlos

    2014-01-01

    Phytostabilization is a promising option for the remediation of metal contaminated soils which requires the implementation of long-term monitoring programs. We here propose to incorporate the paradigm of "adaptive monitoring", which enables monitoring programs to evolve iteratively as new information emerges and research questions change, to metal phytostabilization. Posing good questions that cover the chemical, toxicological and ecological concerns associated to metal contaminated soils is critical for an efficient long-term phytostabilization monitoring program. Regarding the ecological concerns, soil microbial parameters are most valuable indicators of the effectiveness of metal phytostabilization processes in terms of recovery of soil health. We suggest to group soil microbial parameters in higher-level categories such as "ecological attributes" (vigor, organization, stability) or "ecosystem services" in order to facilitate interpretation and, most importantly, to provide long-term phytostabilization monitoring programs with the required stability through time against changes in techniques, methods, interests, etc. that will inevitably occur during the monitoring program. Finally, a Phytostabilization Monitoring Card, based on both ecological attributes and ecosystem services, for soil microbial properties is provided.

  3. Microbial ecology of the skin in the era of metagenomics and molecular microbiology.

    PubMed

    Hannigan, Geoffrey D; Grice, Elizabeth A

    2013-12-01

    The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.

  4. Spreading Topsoil Encourages Ecological Restoration on Embankments: Soil Fertility, Microbial Activity and Vegetation Cover

    PubMed Central

    Rivera, Desirée; Mejías, Violeta; Jáuregui, Berta M.; López-Archilla, Ana Isabel; Peco, Begoña

    2014-01-01

    The construction of linear transport infrastructure has severe effects on ecosystem functions and properties, and the restoration of the associated roadslopes contributes to reduce its impact. This restoration is usually approached from the perspective of plant cover regeneration, ignoring plant-soil interactions and the consequences for plant growth. The addition of a 30 cm layer of topsoil is a common practice in roadslope restoration projects to increase vegetation recovery. However topsoil is a scarce resource. This study assesses the effects of topsoil spreading and its depth (10 to 30 cm) on two surrogates of microbial activity (β-glucosidase and phosphatase enzymes activity and soil respiration), and on plant cover, plant species richness and floristic composition of embankment vegetation. The study also evaluates the differences in selected physic-chemical properties related to soil fertility between topsoil and the original embankment substrate. Topsoil was found to have higher values of organic matter (11%), nitrogen (44%), assimilable phosphorous (50%) and silt content (54%) than the original embankment substrate. The topsoil spreading treatment increased microbial activity, and its application increased β-glucosidase activity (45%), phosphatase activity (57%) and soil respiration (60%). Depth seemed to affect soil respiration, β-glucosidase and phosphatase activity. Topsoil application also enhanced the species richness of restored embankments in relation to controls. Nevertheless, the depth of the spread topsoil did not significantly affect the resulting plant cover, species richness or floristic composition, suggesting that both depths could have similar effects on short-term recovery of the vegetation cover. A significant implication of these results is that it permits the application of thinner topsoil layers, with major savings in this scarce resource during the subsequent slope restoration work, but the quality of topsoil relative to the

  5. Spreading topsoil encourages ecological restoration on embankments: soil fertility, microbial activity and vegetation cover.

    PubMed

    Rivera, Desirée; Mejías, Violeta; Jáuregui, Berta M; Costa-Tenorio, Marga; López-Archilla, Ana Isabel; Peco, Begoña

    2014-01-01

    The construction of linear transport infrastructure has severe effects on ecosystem functions and properties, and the restoration of the associated roadslopes contributes to reduce its impact. This restoration is usually approached from the perspective of plant cover regeneration, ignoring plant-soil interactions and the consequences for plant growth. The addition of a 30 cm layer of topsoil is a common practice in roadslope restoration projects to increase vegetation recovery. However topsoil is a scarce resource. This study assesses the effects of topsoil spreading and its depth (10 to 30 cm) on two surrogates of microbial activity (β-glucosidase and phosphatase enzymes activity and soil respiration), and on plant cover, plant species richness and floristic composition of embankment vegetation. The study also evaluates the differences in selected physic-chemical properties related to soil fertility between topsoil and the original embankment substrate. Topsoil was found to have higher values of organic matter (11%), nitrogen (44%), assimilable phosphorous (50%) and silt content (54%) than the original embankment substrate. The topsoil spreading treatment increased microbial activity, and its application increased β-glucosidase activity (45%), phosphatase activity (57%) and soil respiration (60%). Depth seemed to affect soil respiration, β-glucosidase and phosphatase activity. Topsoil application also enhanced the species richness of restored embankments in relation to controls. Nevertheless, the depth of the spread topsoil did not significantly affect the resulting plant cover, species richness or floristic composition, suggesting that both depths could have similar effects on short-term recovery of the vegetation cover. A significant implication of these results is that it permits the application of thinner topsoil layers, with major savings in this scarce resource during the subsequent slope restoration work, but the quality of topsoil relative to the

  6. Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity.

    PubMed

    Fontana, Cecilia; Bassi, Daniela; López, Constanza; Pisacane, Vincenza; Otero, Maria Claudia; Puglisi, Edoardo; Rebecchi, Annalisa; Cocconcelli, Pier Sandro; Vignolo, Graciela

    2016-11-07

    Llama represents for the Andean regions a valid alternative to bovine and pork meat and thanks to the high proteins and low fat content; it can constitute a good product for the novel food market. In this study, culture-dependent and independent methods were applied to investigate the microbial ecology of naturally fermented llama sausages produced in Northwest Argentina. Two different production technologies of llama sausage were investigated: a pilot-plant scale (P) and an artisanal one (A). Results obtained by High-Throughput Sequencing (HTS) of 16S rRNA amplicons showed that the production technologies influenced the development of microbial communities with a different composition throughout the entire fermentation process. Both sequencing and microbiological counts demonstrated that Lactic Acid Bacteria (LAB) contributed largely to the dominant microbiota. When a total of 230 isolates were approached by RAPD-PCR, presumptive LAB strains from P production exhibited an initial variability in RAPD fingerprints switching to a single profile at the final of ripening, while A production revealed a more heterogeneous RAPD pattern during the whole fermentation process. The constant presence of Lactobacillus sakei along the fermentation in both productions was revealed by HTS and confirmed by species-specific PCR from isolated strains. The technological characterization of Lb. sakei isolates evidenced their ability to grow at 15°C, pH4.5 and 5% NaCl (95%). Most strains hydrolyzed myofibrillar and sarcoplasmic proteins. Bacteriocins encoding genes and antimicrobial resistance were found in 35% and 42.5% of the strains, respectively. An appropriate choice of a combination of autochthonous strains in a starter formulation is fundamental to improve and standardize llama sausages safety and quality.

  7. The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: evidence of a role for fibrobacters.

    PubMed

    McDonald, James E; Houghton, James N I; Rooks, David J; Allison, Heather E; McCarthy, Alan J

    2012-04-01

    Cellulose is reputedly the most abundant organic polymer in the biosphere, yet despite the fundamental role of cellulolytic microorganisms in global carbon cycling and as potential sources of novel enzymes for biotechnology, their identity and ecology is not well established. Cellulose is a major component of landfill waste and its degradation is therefore a key feature of the anaerobic microbial decomposition process. Here, we targeted a number of taxa containing known cellulolytic anaerobes (members of the bacterial genus Fibrobacter, lineages of Clostridium clusters I, III, IV and XIV, and anaerobic fungi of the Neocallimastigales) in landfill leachate and colonized cellulose 'baits' via PCR and quantitative PCR (qPCR). Fibrobacter spp. and Clostridium clusters III, IV and XIV were detected in almost all leachate samples and cluster III and XIV clostridia were the most abundant (1-6% and 1-17% of total bacterial 16S rRNA gene copies respectively). Two landfill leachate microcosms were constructed to specifically assess those microbial communities that colonize and degrade cellulose substrates in situ. Scanning electron microscopy (SEM) of colonized cotton revealed extensive cellulose degradation in one microcosm, and Fibrobacter spp. and Clostridium cluster III represented 29% and 17%, respectively, of total bacterial 16S rRNA gene copies in the biofilm. Visible cellulose degradation was not observed in the second microcosm, and this correlated with negligible relative abundances of Clostridium cluster III and Fibrobacter spp. (≤ 0.1%), providing the first evidence that the novel fibrobacters recently detected in landfill sites and other non-gut environments colonize and degrade cellulose substrates in situ.

  8. Going back to the roots: the microbial ecology of the rhizosphere.

    PubMed

    Philippot, Laurent; Raaijmakers, Jos M; Lemanceau, Philippe; van der Putten, Wim H

    2013-11-01

    The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.

  9. Microbial ecology of extreme environments: Antarctic dry valley yeasts and growth in substrate-limited habitats

    NASA Technical Reports Server (NTRS)

    Vishniac, H. S.

    1982-01-01

    The success of the Antarctic Dry Valley yeasts presumeably results from adaptations to multiple stresses, to low temperatures and substrate-limitation as well as prolonged resting periods enforced by low water availability. Previous investigations have suggested that the crucial stress is substrate limitation. Specific adaptations may be pinpointed by comparing the physiology of the Cryptococcus vishniacii complex, the yeasts of the Tyrol Valley, with their congeners from other habitats. Progress was made in methods of isolation and definition of ecological niches, in the design of experiments in competition for limited substrate, and in establishing the relationships of the Cryptococcus vishniacii complex with other yeasts. In the course of investigating relationships, a new method for 25SrRNA homology was developed. For the first time it appears that 25SrRNA homology may reflect parallel or convergent evolution.

  10. Sterol-inhibiting fungicide impacts on soil microbial ecology in Atlantic Coastal Plain soils

    NASA Astrophysics Data System (ADS)

    White, P. M.; Potter, T. L.; Strickland, T. C.

    2008-12-01

    Seventy-five percent of the peanuts (Arachus hypogaia) produced in the United States are grown in the Atlantic Coastal Plain region. Portions of this area, including Alabama and Georgia, exhibit a subtropical climate that promotes soil-borne plant fungal diseases. Most fields receive repeated fungicide applications during the growing season to suppress the disease causing organisms, such as Sclerotium rolfsii, Rhizoctonia solani, and Cylindrocladium parasiticum. Information regarding fungicide effects on the soil microbial community, with components principally responsible for transformation and fate of fungicides and other soil-applied pesticides, is limited. The objectives of the study were to assess soil microbial community response to (1) varying rates of the sterol-inhibiting fungicide tebuconazole (0, single application, season max, 2x season max), and (2) field rates of the sterol-inhibitors cyproconazole, prothioconazole, tebuconazole, and flutriafol, and thiol-competitor chlorothalonil. The sterol-inhibitors exhibited different half lives, as listed in the FOOTPRINT database, ranging from <1 day to >1300 d. Chlorothalonil was chosen because it is the most frequently applied fungicide to peanut. Shifts in the fungi, gram positive and gram negative bacteria, were monitored during the experiments using phospholipid fatty acid (PLFA) profiles. Ergosterol levels and pesticide decay rates were also monitored to evaluate the effectiveness of the fungicide and soil residence time, respectively. In the rate study, the highest rate of tebuconazole reduced the fungal biomarker 18:2ω6,9c to 2.6 nmol g-1 dry soil at 17 d, as compared to the control (4.1 nmol g-1 dry soil). However, levels of the fungal PLFA biomarker were similar regardless of rate at 0 and 32 d. The gram negative bacterial PLFA mole percent was greater at 17 d for the two highest rates of tebuconazole, but was similar at 0 and 32 d. Gram positive and fungal mole percents were not affected at any time

  11. Competitive Oxidation Kinetics and Microbial Ecology: Intermediate Sulfur Transformations in Acid Mine Drainage Environments

    NASA Astrophysics Data System (ADS)

    Druschel, G. K.; Hamers, R. J.; Banfield, J. F.

    2001-12-01

    Experimental studies have demonstrated that oxidation of pyrite proceeds through several intermediate sulfur species, notably elemental sulfur, thiosulfate, and polythionates (Schippers et al., 1996). However, detailed sampling and analysis of flowing waters and pore waters failed to detect intermediate sulfur species in the 5-way area of the Richmond metal sulfide deposit at the Iron Mountain Mine in northern California. Potential energy available from the oxidation of intermediate sulfur species is considerable, so microbial activity may explain absence of intermediate sulfur compounds at the site. However, the abundance of sulfur-oxidizing microorganisms in areas of active pyrite oxidation at the 5-way is generally low (Bond et al. 2000). Rapid inorganic oxidation rates may prevent microorganisms from utilizing these intermediate sulfur species, thus shaping the structure of microbial communities in acid mine drainage (AMD) environments. Rates and mechanisms of oxidation for tetrathionate and elemental sulfur have been experimentally determined. Batch and flow-through experiments have indicated very slow oxidation of elemental sulfur in inorganic solutions analogous to AMD environments. Results for tetrathionate indicate the importance of non-metabolic and inorganic processes, including surface catalysis and the generation of hydroxyl radicals. Surface catalysis occurs through trithionate on iron oxide surfaces. Hydroxyl radicals may be formed directly by microbes living in proximity to pyrite surfaces, or at pyrite surfaces undergoing wetting and drying cycles. Further experiments investigating the importance of organic compounds associated with iron-oxidizing microorganisms acting as electron transport shuttles and/or wetting agents and ab initio calculations of the electronic structure of potential reactants and intermediates are currently being performed. It is suggested that inorganic processes involved with seasonal wetting and drying of pyritic sediment

  12. Orally Administered Berberine Modulates Hepatic Lipid Metabolism by Altering Microbial Bile Acid Metabolism and the Intestinal FXR Signaling Pathway.

    PubMed

    Sun, Runbin; Yang, Na; Kong, Bo; Cao, Bei; Feng, Dong; Yu, Xiaoyi; Ge, Chun; Huang, Jingqiu; Shen, Jianliang; Wang, Pei; Feng, Siqi; Fei, Fei; Guo, Jiahua; He, Jun; Aa, Nan; Chen, Qiang; Pan, Yang; Schumacher, Justin D; Yang, Chung S; Guo, Grace L; Aa, Jiye; Wang, Guangji

    2017-02-01

    Previous studies suggest that the lipid-lowering effect of berberine (BBR) involves actions on the low-density lipoprotein receptor and the AMP-activated protein kinase signaling pathways. However, the implication of these mechanisms is unclear because of the low bioavailability of BBR. Because the main action site of BBR is the gut and intestinal farnesoid X receptor (FXR) plays a pivotal role in the regulation of lipid metabolism, we hypothesized that the effects of BBR on intestinal FXR signaling pathway might account for its pharmacological effectiveness. Using wild type (WT) and intestine-specific FXR knockout (FXR(int-/-)) mice, we found that BBR prevented the development of high-fat-diet-induced obesity and ameliorated triglyceride accumulation in livers of WT, but not FXR(int-/-) mice. BBR increased conjugated bile acids in serum and their excretion in feces. Furthermore, BBR inhibited bile salt hydrolase (BSH) activity in gut microbiota, and significantly increased the levels of tauro-conjugated bile acids, especially tauro-cholic acid(TCA), in the intestine. Both BBR and TCA treatment activated the intestinal FXR pathway and reduced the expression of fatty-acid translocase Cd36 in the liver. These results indicate that BBR may exert its lipid-lowering effect primarily in the gut by modulating the turnover of bile acids and subsequently the ileal FXR signaling pathway. In summary, we provide the first evidence to suggest a new mechanism of BBR action in the intestine that involves, sequentially, inhibiting BSH, elevating TCA, and activating FXR, which lead to the suppression of hepatic expression of Cd36 that results in reduced uptake of long-chain fatty acids in the liver.

  13. Exogenous lactobacilli mitigate microbial changes associated with grain fermentation in vitro

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cereal grains are often included in equine diets. Sugars and starch in grains can be digested and absorbed in the small intestine, but a high proportion of grain in the diet can allow starch to reach the hindgut, disturbing the microbial ecology. Streptococci and lactobacilli both catabolize starch ...

  14. Microbial ecology of Gorgonzola rinds and occurrence of different biotypes of Listeria monocytogenes.

    PubMed

    Cocolin, Luca; Nucera, Daniele; Alessandria, Valentina; Rantsiou, Kalliopi; Dolci, Paola; Grassi, Maria Auxilia; Lomonaco, Sara; Civera, Tiziana

    2009-07-31

    In this study we investigated the microbiota of Gorgonzola rinds and maturing shelf swabs collected in 5 different maturing cellars in the Northwest part of Italy, in association with the detection and characterization of Listeria monocytogenes. Culture-dependent and -independent methods were performed in order to profile the main microbial populations present on the rinds and in the maturing shelves and species-specific PCR and Pulsed Field Gel Electrophoresis (PFGE) were used to identify and type L. monocytogenes isolates. The microflora was predominated by lactic acid bacteria and coagulase negative cocci, while enterococci and yeasts were very variable between the samples. Arthrobacter sp., Carnobacterium sp., Staphylococcus sp. and Brevibacterium linens, as bacteria, and Debaryomyces hansenii, as yeast, were detected by Denaturing Gradient Gel Electrophoresis (DGGE). Cluster analysis of the DGGE profiles clearly highlighted a cellar-specific microflora. L. monocytogenes was isolated in 11.1% of the rinds and 29.4% of the swabs and the molecular characterization of the isolates suggests a route of contamination from the maturing shelves to the rinds. No correlation was found between DGGE profiles and presence or absence of L. monocytogenes.

  15. Occurrence and Ecological Significance of GTP in the Ocean and in Microbial Cells

    PubMed Central

    Karl, D. M.

    1978-01-01

    A comparison between the ATP concentrations based on peak height light emission values (0 to 3 s) and integrated light flux determinations (15 to 75 s) for a variety of seawater samples revealed that the integrated method of light detection consistently yielded higher ATP concentrations, ranging from 1.38 to 2.35 times larger than the corresponding peak ATP values. A significant correlation (r = 0.923) was observed for a plot of ΔADP (i.e., integrated ATP - peak ATP) versus GTP + UTP, suggesting that the analytical interference on the ATP assay was the result of the presence of non-adenine nucleotide triphosphates. Size-fractionation studies revealed an enrichment of the non-adenine nucleotide triphosphates, relative to ATP, in the smallest size fraction analyzed (<10 μm). Investigations were conducted with 20 species of unicellular marine algae to determine their intracellular nucleotide concentrations, and these determinations were compared to the levels measured in lab cultures of the marine bacterium Serratia marinorubra. These results indicated that the intracellular GTP/ATP ratios in S. marinorubra increase in direct proportion to the rate of cell growth, and that the GTP/ATP ratios in bacteria are much greater than in growing algae, presumably due to the differences in rates of cellular biosynthesis. It is concluded that quantitative determinations of GTP/ATP ratios in environmental sample extracts may be useful for measuring microbial growth. PMID:16345313

  16. Dynamics of microbial diversity profiles in waters of different qualities. Approximation to an ecological quality indicator.

    PubMed

    Garrido, L; Sánchez, O; Ferrera, I; Tomàs, N; Mas, J

    2014-01-15

    Over the past two decades, the amount of reclaimed water has increased throughout the world to face the current water shortage, and as a consequence there is an increasing interest to develop good indicators of water quality, beyond the traditional fecal indicators. In order to meet this need, in this work the microbial profiles of different wastewater treatment plant effluents, both secondary and tertiary, were studied and compared with water samples from an uncontaminated natural aquifer. Taking into account the most abundant phylogenetic groups found in these water samples, we calculated the Bacteroidetes, Gammaproteobacteria and Nitrospira/Betaproteobacteria (BGN:β) ratio and found significant differences between the mean ratios of the four water qualities. The secondary effluent ratios were never below 1.3 and the tertiary effluent and groundwater ratios were never over 0.85. Furthermore, calculation of this index with previous published data supports our results and indicates that the BGN:β ratio is a possible alternative indicator of water quality.

  17. Performance and microbial ecology of a nitritation sequencing batch reactor treating high-strength ammonia wastewater

    PubMed Central

    Chen, Wenjing; Dai, Xiaohu; Cao, Dawen; Wang, Sha; Hu, Xiaona; Liu, Wenru; Yang, Dianhai

    2016-01-01

    The partial nitrification (PN) performance and the microbial community variations were evaluated in a sequencing batch reactor (SBR) for 172 days, with the stepwise elevation of ammonium concentration. Free ammonia (FA) and low dissolved oxygen inhibition of nitrite-oxidized bacteria (NOB) were used to achieve nitritation in the SBR. During the 172 days operation, the nitrogen loading rate of the SBR was finally raised to 3.6 kg N/m3/d corresponding the influent ammonium of 1500 mg/L, with the ammonium removal efficiency and nitrite accumulation rate were 94.12% and 83.54%, respectively, indicating that the syntrophic inhibition of FA and low dissolved oxygen contributed substantially to the stable nitrite accumulation. The results of the 16S rRNA high-throughput sequencing revealed that Nitrospira, the only nitrite-oxidizing bacteria in the system, were successively inhibited and eliminated, and the SBR reactor was dominated finally by Nitrosomonas, the ammonium-oxidizing bacteria, which had a relative abundance of 83%, indicating that the Nitrosomonas played the primary roles on the establishment and maintaining of nitritation. Followed by Nitrosomonas, Anaerolineae (7.02%) and Saprospira (1.86%) were the other mainly genera in the biomass. PMID:27762325

  18. On the use of antibiotics to reduce rhizoplane microbial populations in root physiology and ecology investigations

    NASA Technical Reports Server (NTRS)

    Smart, D. R.; Ferro, A.; Ritchie, K.; Bugbee, B. G.

    1995-01-01

    No straightforward method exists for separating the proportion of ion exchange and respiration due to rhizoplane microbial organisms from that of root ion exchange and respiration. We examined several antibiotics that might be used for the temporary elimination of rhizoplane bacteria from hydroponically grown wheat roots (Triticum aestivum cv. Veery 10). Each antibiotic was tested for herbicidal activity and plate counts were used to enumerate bacteria and evaluate antibiotic kinetics. Only lactam antibiotics (penicillins and cephalosporins) did not reduce wheat growth rates. Aminoglycosides, the pyrimidine trimethoprim, colistin and rifampicin reduced growth rates substantially. Antibiotics acted slowly, with maximum reductions in rhizoplane bacteria occurring after more than 48 h of exposure. Combinations of nonphytotoxic antibiotics reduced platable rhizoplane bacteria by as much as 98%; however, this was generally a reduction from about 10(9) to 10(6) colony forming units per gram of dry root mass, so that many viable bacteria remained on root surfaces. We present evidence which suggests that insufficient bacterial biomass exists on root surfaces of nonstressed plants grown under well-aerated conditions to quantitatively interfere with root nitrogen absorption measurements.

  19. Deep Sequencing and Ecological Characterization of Gut Microbial Communities of Diverse Bumble Bee Species

    PubMed Central

    Lim, Haw Chuan; Chu, Chia-Ching; Seufferheld, Manfredo J.; Cameron, Sydney A.

    2015-01-01

    Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA) to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs) belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5%) bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera. PMID:25768110

  20. On the use of antibiotics to reduce rhizoplane microbial populations in root physiology and ecology investigations.

    PubMed

    Smart, D R; Ferro, A; Ritchie, K; Bugbee, B G

    1995-01-01

    No straightforward method exists for separating the proportion of ion exchange and respiration due to rhizoplane microbial organisms from that of root ion exchange and respiration. We examined several antibiotics that might be used for the temporary elimination of rhizoplane bacteria from hydroponically grown wheat roots (Triticum aestivum cv. Veery 10). Each antibiotic was tested for herbicidal activity and plate counts were used to enumerate bacteria and evaluate antibiotic kinetics. Only lactam antibiotics (penicillins and cephalosporins) did not reduce wheat growth rates. Aminoglycosides, the pyrimidine trimethoprim, colistin and rifampicin reduced growth rates substantially. Antibiotics acted slowly, with maximum reductions in rhizoplane bacteria occurring after more than 48 h of exposure. Combinations of nonphytotoxic antibiotics reduced platable rhizoplane bacteria by as much as 98%; however, this was generally a reduction from about 10(9) to 10(6) colony forming units per gram of dry root mass, so that many viable bacteria remained on root surfaces. We present evidence which suggests that insufficient bacterial biomass exists on root surfaces of nonstressed plants grown under well-aerated conditions to quantitatively interfere with root nitrogen absorption measurements.

  1. Hypolithic cyanobacteria, dry limit of photosynthesis, and microbial ecology in the hyperarid Atacama Desert.

    PubMed

    Warren-Rhodes, Kimberley A; Rhodes, Kevin L; Pointing, Stephen B; Ewing, Stephanie A; Lacap, Donnabella C; Gómez-Silva, Benito; Amundson, Ronald; Friedmann, E Imre; McKay, Christopher P

    2006-10-01

    The occurrence of hypolithic cyanobacteria colonizing translucent stones was quantified along the aridity gradient in the Atacama Desert in Chile, from less arid areas to the hyperarid core where photosynthetic life and thus primary production reach their limits. As mean rainfall declines from 21 to microbially depauperate bare soil. These findings suggest that photosynthetic life is extremely unlikely on the present-day surface of Mars, but may have existed in the past. If so, such microhabitats would probably be widely dispersed, difficult to detect, and millimeters away from virtually lifeless surroundings.

  2. Comparison of microbial community assays for the assessment of stream biofilm ecology.

    PubMed

    Vinten, A J A; Artz, R R E; Thomas, N; Potts, J M; Avery, L; Langan, S J; Watson, H; Cook, Y; Taylor, C; Abel, C; Reid, E; Singh, B K

    2011-06-01

    We investigated a range of microbiological community assays performed on scrapes of biofilms formed on artificial diffusing substrates deployed in 8 streams in eastern Scotland, with a view to using them to characterize ecological response to stream water quality. The assays considered were: Multiplex Terminal Restriction Fragment Length Polymorphism or M-TRFLP (a molecular method), Phospholipid Fatty Acid or PLFA analysis (a biochemical method) and MICRORESP™ (a physiological method) alongside TDI, diatom species, and chlorophyll a content. Four of the streams were classified as of excellent status (3-6μg/L Soluble Reactive Phosphorus (SRP)) with respect to soluble P content under the EU Water Framework Directive and four were of borderline good/moderate or moderate status (43-577μg/L SRP). At each site, 3 replicates of 3 solute diffusion treatments were deployed in a Latin square design. Solute diffusion treatments were: KCl (as a control solute), N and P (to investigate the effect of nutrient enrichment), or the herbicide isoproturon (as a "high impact" control, which aimed to affect biofilm growth in a way detectable by all assays). Biofilms were sampled after 4weeks deployment in a low flow period of early summer 2006. The chlorophyll a content of biofilms after 4weeks was 2.0±0.29mg/m(2) (mean±se). Dry matter content was 16.0±13.1g/m(2). The M-TRFLP was successfully used for generating community profiles of cyanobacteria, algae and bacteria and was much faster than diatom identification. The PFLA and TDI were successful after an increase in the sample size, due to low counts. The MICRORESP(™) assays were often below or near detection limit. We estimated the per-sample times for the successful assays as follows: M-TRFLP: 20min, PLFA 40min, TDI 90min. Using MANOVA on the first 5 principal co-ordinates, all the assays except MICRORESP(™) showed significant differences between sites, but none of the assays showed a significant effect of either initial

  3. Improving the quality of rice straw by urea and calcium hydroxide on rumen ecology, microbial protein synthesis in beef cattle.

    PubMed

    Polyorach, S; Wanapat, M

    2015-06-01

    Four rumen-fistulated beef cattle were randomly assigned to four treatments according to a 4 × 4 Latin square design to study the influence of urea and calcium hydroxide [Ca(OH)2 ] treatment of rice straw to improve the nutritive value of rice straw. Four dietary treatments were as follows: untreated rice straw, 50 g/kg urea-treated rice straw, 20 g/kg urea + 20 g/kg calcium hydroxide-treated rice straw and 30 g/kg urea + 20 g/kg calcium hydroxide-treated rice straw. All animals were kept in individual pens and fed with concentrate at 0.5 g/kg of BW (DM), rice straw was fed ad libitum. The experiment was conducted for four periods, and each period lasted for 21 days. During the first 14 days, DM feed intake measurements were made while during the last 7 days, all cattle were moved to metabolism crates for total faeces and urine collections. The results revealed that 20 g/kg urea + 20 g/kg calcium hydroxide-treated rice straw improved the nutritive value of rice straw, in terms of dry matter intake, digestibility, ruminal volatile fatty acids, population of bacteria and fungi, nitrogen retention and microbial protein synthesis. Based on this study, it could be concluded that using urea plus calcium hydroxide was one alternative method to improve the nutritive value of rice straw, rumen ecology and fermentation and thus a reduction of treatment cost.

  4. Biodegradation of dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHs) with plant and nutrients and their effects on the microbial ecological kinetics.

    PubMed

    Sun, Guangdong; Zhang, Xu; Hu, Qing; Zhang, Heqing; Zhang, Dayi; Li, Guanghe

    2015-02-01

    Four pilot-scale test mesocosms were conducted for the remediation of organochlorine pesticides (OCPs)-contaminated aged soil. The results indicate that the effects on degradation of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) were in the following order: nutrients/plant bioaugmentation (81.18 % for HCHs; 85.4 % for DDTs) > nutrients bioaugmentation > plant bioaugmentation > only adding water > control, and nutrients/plant bioaugmentation greatly enhanced the degradation of HCHs (81.18 %) and DDTs (85.4 %). The bacterial community structure, diversity and composition were assessed by 454-pyrosequencing of 16S recombinant RNA (rRNA), whereas the abundance of linA gene was determined by quantitative polymerase chain reaction. Distinct differences in bacterial community composition, structure, and diversity were a function of remediation procedure. Predictability of HCH/DDT degradation in soils was also investigated. A positive correlation between linA gene abundance and the removal ratio of HCHs was indicated by correlation analyses. A similar relationship was also confirmed between the degradation of HCHs/DDTs and the abundance of some assemblages (Gammaproteobacteria and Flavobacteria). Our results offer microbial ecological insight into the degradation of HCHs and DDTs in aged contaminated soil, which is helpful for the intensification of bioremediation through modifying plant-microbe patterns, and cessation of costly and time-consuming assays.

  5. Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II.

    PubMed

    Logan, Alan C; Katzman, Martin A; Balanzá-Martínez, Vicent

    2015-03-10

    Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be "dirtied up in a controlled manner." He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same.

  6. Microbial ecology and performance of ammonia oxidizing bacteria (AOB) in biological processes treating petrochemical wastewater with high strength of ammonia: effect of Na(2)CO(3) addition.

    PubMed

    Whang, L M; Yang, K H; Yang, Y F; Han, Y L; Chen, Y J; Cheng, S S

    2009-01-01

    This study evaluated nitrification performance and microbial ecology of AOB in a full-scale biological process, powder activated carbon treatment (PACT), and a pilot-scale biological process, moving bed biofilm reactor (MBBR), treating wastewater collected from a petrochemical industry park. The petrochemical influent wastewater characteristics showed a relative low carbon to nitrogen ratio around 1 with average COD and ammonia concentrations of 310 mg/L and 325 mg-N/L, respectively. The average nitrification efficiency of the full-scale PACT process was around 11% during this study. For the pilot-scale MBBR, the average nitrification efficiency was 24% during the Run I operation mode, which provided a slightly better performance in nitrification than that of the PACT process. During the Run II operation, the pH control mode was switched from addition of NaOH to Na(2)CO(3), leading to a significant improvement in nitrification efficiency of 51%. In addition to a dramatic change in nitrification performance, the microbial ecology of AOB, monitored with the terminal restriction fragment length polymorphism (T-RFLP) molecular methodology, was found to be different between Runs I and II. The amoA-based TRFLP results indicated that Nitrosomonas europaea lineage was the dominant AOB population during Run I operation, while Nitrosospira-like AOB was dominant during Run II operation. To confirm the effects of Na(2)CO(3) addition on the nitrification performance and AOB microbial ecology observed in the MBBR process, batch experiments were conducted. The results suggest that addition of Na(2)CO(3) as a pH control strategy can improve nitrification performance and also influence AOB microbial ecology as well. Although the exact mechanisms are not clear at this time, the results showing the effects of adding different buffering chemicals such as NaOH or Na(2)CO(3) on AOB populations have never been demonstrated until this study.

  7. An organotypic slice model for ex vivo study of neural, immune, and microbial interactions of mouse intestine.

    PubMed

    Schwerdtfeger, Luke A; Ryan, Elizabeth P; Tobet, Stuart A

    2016-02-15

    Organotypic tissue slices provide seminatural, three-dimensional microenvironments for use in ex vivo study of specific organs and have advanced investigative capabilities compared with isolated cell cultures. Several characteristics of the gastrointestinal tract have made in vitro models for studying the intestine challenging, such as maintaining the intricate structure of microvilli, the intrinsic enteric nervous system, Peyer's patches, the microbiome, and the active contraction of gut muscles. In the present study, an organotypic intestinal slice model was developed that allows for functional investigation across regions of the intestine. Intestinal tissue slices were maintained ex vivo for several days in a physiologically relevant environment that preserved normal enterocyte structure, intact and proliferating crypt cells, submucosal organization, and muscle wall composure. Cell death was measured by a membrane-impermeable DNA binding indicator, ethidium homodimer, and less than 5% of cells were labeled in all regions of the villi and crypt epithelia at 24 h ex vivo. This tissue slice model demonstrated intact myenteric and submucosal neuronal plexuses and functional interstitial cells of Cajal to the extent that nonstimulated, segmental contractions occurred for up to 48 h ex vivo. To detect changes in physiological responses, slices were also assessed for segmental contractions in the presence and absence of antibiotic treatment, which resulted in slices with lesser or greater amounts of commensal bacteria, respectively. Segmental contractions were significantly greater in slices without antibiotics and increased native microbiota. This model renders mechanisms of neuroimmune-microbiome interactions in a complex gut environment available to direct observation and controlled perturbation.

  8. Microbial and genetic ecology of tropical Vertisols under intensive chemical farming.

    PubMed

    Malhotra, Jaya; Aparna, K; Dua, Ankita; Sangwan, Naseer; Trimurtulu, N; Rao, D L N; Lal, Rup

    2015-01-01

    There are continued concerns on unscientific usage of chemical fertilizers and pesticides, particularly in many developing countries leading to adverse consequences for soil biological quality and agricultural sustainability. In farmers' fields in tropical Vertisols of peninsular India, "high" fertilizer and pesticide usage at about 2.3 times the recommended rates in black gram (Vigna mungo) did not have a deleterious effect on the abundance of culturable microorganisms, associative nitrogen fixers, nitrifiers, and 16S rRNA gene diversity compared to normal rates. However, "very high" application at about five times the fertilizers and 1.5 times pesticides in chilies (Capsicum annuum) adversely affected the populations of fungi, actinomycetes, and ammonifiers, along with a drastic change in the eubacterial community profile and diversity over normal rates. Actinobacteria were dominant in black gram normal (BG1) (47%), black gram high (BG2) (36%), and chili normal (CH1) (30%) and were least in chili very high (CH2) (14%). Geodermatophilus formed 20% of Actinobacteria in BG1 but disappeared in BG2, CH1, and CH2. Asticcacaulis dominated at "very high" input site (CH2). Diversity of nitrogen fixers was completely altered; Dechloromonas and Anaeromyxobacter were absent in BG1 but proliferated well in BG2. There was reduction in rhizobial nifH sequences in BG2 by 46%. Phylogenetic differences characterized by UniFrac and principal coordinate analysis showed that BG2 and CH2 clustered together depicting a common pattern of genetic shift, while BG1 and CH1 fell at different axis. Overall, there were adverse consequences of "very high" fertilizer and pesticide usage on soil microbial diversity and function in tropical Vertisols.

  9. The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism.

    PubMed

    Selma, María V; Romo-Vaquero, María; García-Villalba, Rocío; González-Sarrías, Antonio; Tomás-Barberán, Francisco A; Espín, Juan C

    2016-04-01

    We recently identified three metabotypes (0, A and B) that depend on the metabolic profile of urolithins produced from polyphenol ellagic acid (EA). The gut microbiota and Gordonibacter spp. recently were identified as species able to produce urolithins. A higher percentage of metabotype B was found in patients with metabolic syndrome or colorectal cancer in comparison with healthy individuals. The aim of the present study was to analyse differences in EA metabolism between healthy overweight-obese and normoweight individuals and evaluate the role of gut microbial composition including Gordonibacter. Although the three metabotypes were confirmed in both groups, metabotype B prevailed in overweight-obese (31%) versus normoweight (20%) individuals while metabotype A was higher in normoweight (70%) than the overweight-obese group (57%). This suggests that weight gain favours the growth of bacteria capable of producing urolithin B and/or isourolithin A with respect to urolithin A-producing bacteria. Gordonibacter spp. levels were not significantly different between normoweight and overweight-obese groups but higher Gordonibacter levels were found in metabotype A individuals than in those with metabotype B. Other bacterial species have been reported to show a much closer relationship to obesity and dysbiosis than Gordonibacter. However, Gordonibacter levels are negatively correlated with metabotype B, which prevails in metabolic syndrome and colorectal cancer. This is the first report that links overweight and obesity with an alteration in the catabolism of EA, and where the correlation of Gordonibacter to this alteration is shown. Future investigation of Gordonibacter and urolithin metabotypes as potential biomarkers or therapeutic targets of obesity-related diseases is warranted.

  10. Laxative treatment with polyethylene glycol decreases microbial primary bile salt dehydroxylation and lipid metabolism in the intestine of rats.

    PubMed

    van der Wulp, Mariëtte Y M; Derrien, Muriel; Stellaard, Frans; Wolters, Henk; Kleerebezem, Michiel; Dekker, Jan; Rings, Edmond H H M; Groen, Albert K; Verkade, Henkjan J

    2013-10-01

    Polyethylene glycol (PEG) is a frequently used osmotic laxative that accelerates gastrointestinal transit. It has remained unclear, however, whether PEG affects intestinal functions. We aimed to determine the effect of PEG treatment on intestinal sterol metabolism. Rats were treated with PEG in drinking water (7%) for 2 wk or left untreated (controls). We studied the enterohepatic circulation of the major bile salt (BS) cholate with a plasma stable isotope dilution technique and determined BS profiles and concentrations in bile, intestinal lumen contents, and feces. We determined the fecal excretion of cholesterol plus its intestinally formed metabolites. Finally, we determined the cytolytic activity of fecal water (a surrogate marker of colorectal cancer risk) and the amount and composition of fecal microbiota. Compared with control rats, PEG treatment increased the pool size (+51%; P < 0.01) and decreased the fractional turnover of cholate (-32%; P < 0.01). PEG did not affect the cholate synthesis rate, corresponding with an unaffected fecal primary BS excretion. PEG reduced fecal excretion of secondary BS and of cholesterol metabolites (each P < 0.01). PEG decreased the cytolytic activity of fecal water [54 (46-62) vs. 87 (85-92)% erythrocyte potassium release in PEG-treated and control rats, respectively; P < 0.01]. PEG treatment increased the contribution of Verrucomicrobia (P < 0.01) and decreased that of Firmicutes (P < 0.01) in fecal flora. We concluded that PEG treatment changes the intestinal bacterial composition, decreases the bacterial dehydroxylation of primary BS and the metabolism of cholesterol, and increases the pool size of the primary BS cholate in rats.

  11. Microbes and microbial Toxins: paradigms for microbial-mucosal toxins. V. Cholera: invasion of the intestinal epithelial barrier by a stably folded protein toxin.

    PubMed

    Lencer, W I

    2001-05-01

    Cholera toxin (CT) produced by Vibrio cholerae is the virulence factor responsible for the massive secretory diarrhea seen in Asiatic cholera. To cause disease, CT enters the intestinal epithelial cell as a stably folded protein by co-opting a lipid-based membrane receptor, ganglioside G(M1). G(M1) sorts the toxin into lipid rafts and a retrograde trafficking pathway to the endoplasmic reticulum, where the toxin unfolds and transfers its enzymatic subunit to the cytosol, probably by dislocation through the translocon sec61p. The molecular determinants that drive entry of CT into this pathway are encoded entirely within the structure of the protein toxin itself.

  12. The MICROBE (Microcosm Investigation of Carbonate Reef/Ocean Microbial Biogeochemistry & Ecology) Project

    NASA Astrophysics Data System (ADS)

    Hannides, A. K.; Gaidos, E. J.; Sansone, F. J.

    2003-12-01

    We present a methodology to manipulate carbonate reef sediments in order to study the geochemical and microbiological response of reef systems to perturbations. We specifically plan to study the effects of changes in the atmospheric partial pressure of CO2. Our laboratory set-up will consist of cores containing carbonate reef sediments and overlying water. These microcosms are designed to replicate the gross hydraulic and geochemical characteristics of sediments in a natural tropical reef patch. This is achieved by reproducing the advective transport of water and particulates in and out of the sediments induced by tides and surface waves. Seawater from nearby reefs is to be introduced into the cores with reversible peristaltic pumps. The pumps will vary the overlying water column and simulate the changes in hydrostatic head that accompany waves and tides. The parameters characterizing these oscillations will be set at values reflecting those at nearby natural settings. Sediment column characteristics will be determined non-destructively through openings at various depths down the sediment cores. These openings are fitted with rubber septa and shut-off valves, which allow gas-tight sampling of porewaters. An additional set of openings allows for the removal of small amounts of sediments using augers. Our porewater analyses will include dissolved O2, CO2, CH4 and alkalinity, ammonium, sulfide, and iron and manganese ions. Our solid phase analyses will include carbonate composition and framework structure, and iron and manganese abundances in the carbonate phases. We will measure microbial abundance in porewater and the sediment particles by DAPI cell counts and will assay community composition using Denaturing Gradient Gel Electrophoresis (DGGE). Our goal is to use this methodology to observe and record carbonate precipitation and dissolution by microbiota under varying carbon dioxide regimes. pCO2 concentrations will be manipulated by bubbling a N2/CO2 mixture

  13. Dietary protein concentration affects intestinal microbiota of adult cats: a study using DGGE and qPCR to evaluate differences in microbial populations in the feline gastrointestinal tract.

    PubMed

    Lubbs, D C; Vester, B M; Fastinger, N D; Swanson, K S

    2009-02-01

    The objective of this study was to identify qualitative and quantitative differences in microbial populations of adult cats fed diets containing different protein concentrations. Following a 4 week baseline period, eight healthy adult domestic short-hair queens (>1-year-old) were randomly allotted to a moderate-protein (MP; n = 4) or high-protein (HP; n = 4) diet for 8 weeks. Fresh faecal samples were collected after baseline and 8 weeks on treatment and stored at -80 degrees C. Following DNA extraction, samples were analyzed using denaturing gradient gel electrophoresis to distinguish qualitative changes between diets. Quantitative polymerase chain reaction was used to measure E. coli, Bifidobacterium, Clostridium perfringens, and Lactobacillus populations. Compared to baseline, cats fed MP had a bacterial similarity index of 66.7% as opposed to 40.6% similarity for those fed HP, exhibiting marked changes in intestinal bacteria of cats fed HP. Bifidobacterium populations were greater (p < 0.05) in cats fed MP versus HP (9.44 vs. 5.63 CFU/g). Clostridium perfringens populations were greater (p < 0.05) in cats fed HP than MP (12.39 vs. 10.83 CFU/g). In this experiment, a high-protein diet resulted in a dramatic shift in microbial populations. Decreased Bifidobacterium population in cats fed HP may justify prebiotic supplementation for such diets.

  14. Carbon mass balance and microbial ecology in a laboratory scale reactor achieving simultaneous sludge reduction and nutrient removal.

    PubMed

    Huang, Pei; Li, Liang; Kotay, Shireen Meher; Goel, Ramesh

    2014-04-15

    Solids reduction in activated sludge processes (ASP) at source using process manipulation has been researched widely over the last two-decades. However, the absence of nutrient removal component, lack of understanding on the organic carbon, and limited information on key microbial community in solids minimizing ASP preclude the widespread acceptance of sludge minimizing processes. In this manuscript, we report simultaneous solids reduction through anaerobiosis along with nitrogen and phosphorus removals. The manuscript also reports carbon mass balance using stable isotope of carbon, microbial ecology of nitrifiers and polyphosphate accumulating organisms (PAOs). Two laboratory scale reactors were operated in anaerobic-aerobic-anoxic (A(2)O) mode. One reactor was run in the standard mode (hereafter called the control-SBR) simulating conventional A(2)O type of activated sludge process and the second reactor was run in the sludge minimizing mode (called the modified-SBR). Unlike other research efforts where the sludge minimizing reactor was maintained at nearly infinite solids retention time (SRT). To sustain the efficient nutrient removal, the modified-SBR in this research was operated at a very small solids yield rather than at infinite SRT. Both reactors showed consistent NH3-N, phosphorus and COD removals over a period of 263 days. Both reactors also showed active denitrification during the anoxic phase even if there was no organic carbon source available during this phase, suggesting the presence of denitrifying PAOs (DNPAOs). The observed solids yield in the modified-SBR was 60% less than the observed solids yield in the control-SBR. Specific oxygen uptake rate (SOUR) for the modified-SBR was almost 44% more than the control-SBR under identical feeding conditions, but was nearly the same for both reactors under fasting conditions. The modified-SBR showed greater diversity of ammonia oxidizing bacteria and PAOs compared to the control-SBR. The diversity of PAOs

  15. An organotypic slice model for ex vivo study of neural, immune, and microbial interactions of mouse intestine

    PubMed Central

    Schwerdtfeger, Luke A.; Ryan, Elizabeth P.

    2015-01-01

    Organotypic tissue slices provide seminatural, three-dimensional microenvironments for use in ex vivo study of specific organs and have advanced investigative capabilities compared with isolated cell cultures. Several characteristics of the gastrointestinal tract have made in vitro models for studying the intestine challenging, such as maintaining the intricate structure of microvilli, the intrinsic enteric nervous system, Peyer's patches, the microbiome, and the active contraction of gut muscles. In the present study, an organotypic intestinal slice model was developed that allows for functional investigation across regions of the intestine. Intestinal tissue slices were maintained ex vivo for several days in a physiologically relevant environment that preserved normal enterocyte structure, intact and proliferating crypt cells, submucosal organization, and muscle wall composure. Cell death was measured by a membrane-impermeable DNA binding indicator, ethidium homodimer, and less than 5% of cells were labeled in all regions of the villi and crypt epithelia at 24 h ex vivo. This tissue slice model demonstrated intact myenteric and submucosal neuronal plexuses and functional interstitial cells of Cajal to the extent that nonstimulated, segmental contractions occurred for up to 48 h ex vivo. To detect changes in physiological responses, slices were also assessed for segmental contractions in the presence and absence of antibiotic treatment, which resulted in slices with lesser or greater amounts of commensal bacteria, respectively. Segmental contractions were significantly greater in slices without antibiotics and increased native microbiota. This model renders mechanisms of neuroimmune-microbiome interactions in a complex gut environment available to direct observation and controlled perturbation. PMID:26680736

  16. The effects of inulin, dried Jerusalem artichoke tuber and a multispecies probiotic preparation on microbiota ecology and immune status of the large intestine in young pigs.

    PubMed

    Barszcz, Marcin; Taciak, Marcin; Skomiał, Jacek

    2016-08-01

    The study aimed at determining the effect of two types of prebiotics and a multispecies probiotic on microbiota activity and composition, as well as mucosal immunity in the large intestine of young pigs. In total 48 piglets were divided into 6 groups (n = 8), which received from day 10 of life probiotic-unsupplemented (PU) or probiotic-supplemented (PS) diets. Probiotics were added at 0.5 g/kg diet and contained: Lactococcus lactis, Carnobacterium divergens, Lactobacillus casei, Lactobacillus plantarum and Saccharomyces cerevisiae. The PU and PS diets were formulated without prebiotic addition (control) or with addition of 2% of inulin from chicory root (IN) or 4% of dried Jerusalem artichoke tubers (DJA). After 40 days of feeding, digesta and tissue samples were taken from the caecum and three sections of the colon for analyses of microbiota activity and composition, secretory immunoglobulin A (sIgA) and intraepithelial lymphocytes (IEL). IN diets decreased the caecal digesta pH and β-glucosidase activity but increased propionic, valeric and total short chain fatty acid (SCFA) concentrations compared to control diets. Feeding DJA diets increased caecal valeric acid level, decreased the concentration of isoacids in the colon, reduced β-glucosidase and β-glucuronidase activity in the middle colon and increased Bifidobacterium spp. populations in the proximal and distal colon. PS diets increased the caecal acetic acid and total SCFA level, and Clostridium spp. populations in the distal colon. Neither probiotic nor prebiotics affected sIgA level or IEL number in the large intestine. In conclusion, DJA modified the microbiota ecology in the large intestine of young pigs to a greater extent than IN and the applied probiotic did not enhance effects of prebiotics.

  17. Ecological drift and local exposures drive enteric bacterial community differences within species of Galápagos iguanas.

    PubMed

    Lankau, Emily W; Hong, Pei-Ying; Mackie, Roderick I

    2012-04-01

    Diet strongly influences the intestinal microbial communities through species sorting. Alternatively, these communicates may differ because of chance variation in local microbial exposures or species losses among allopatric host populations (i.e. ecological drift). We investigated how these forces shape enteric communities of Galápagos marine and land iguanas. Geographically proximate populations shared more similar communities within a host ecotype, suggesting a role for ecological drift during host colonization of the islands. Additionally, evidence of taxa sharing between proximate heterospecific host populations suggests that contemporary local exposures also influence the gut community assembly. While selective forces such as host-bacterial interactions or dietary differences are dominant drivers of intestinal community differences among hosts, historical and contemporary processes of ecological drift may lead to differences in bacterial composition within a host species. Whether such differences in community structure translate into geographic variation in benefits derived from these intimate microbial communities remains to be explored.

  18. Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock

    PubMed Central

    Yang, Chengjian; Rooke, John A.; Cabeza, Irene; Wallace, Robert J.

    2016-01-01

    Ruminal methane production is among the main targets for greenhouse gas (GHG) mitigation for the animal agriculture industry. Many compounds have been evaluated for their efficacy to suppress enteric methane production by ruminal microorganisms. Of these, nitrate as an alternative hydrogen sink has been among the most promising, but it suffers from variability in efficacy for reasons that are not understood. The accumulation of nitrite, which is poisonous when absorbed into the animal’s circulation, is also variable and poorly understood. This review identifies large gaps in our knowledge of rumen microbial ecology that handicap the further development and safety of nitrate as a dietary additive. Three main bacterial species have been associated historically with ruminal nitrate reduction, namely Wolinella succinogenes, Veillonella parvula, and Selenomonas ruminantium, but others almost certainly exist in the largely uncultivated ruminal microbiota. Indications are strong that ciliate protozoa can reduce nitrate, but the significance of their role relative to bacteria is not known. The metabolic fate of the reduced nitrate has not been studied in detail. It is important to be sure that nitrate metabolism and efforts to enhance rates of nitrite reduction do not lead to the evolution of the much more potent GHG, nitrous oxide. The relative importance of direct inhibition of archaeal methanogenic enzymes by nitrite or the efficiency of capture of hydrogen by nitrate reduction in lowering methane production is also not known, nor are nitrite effects on other members of the microbiota. How effective would combining mitigation methods be, based on our understanding of the effects of nitrate and nitrite on the microbiome? Answering these fundamental microbiological questions is essential in assessing the potential of dietary nitrate to limit methane emissions from ruminant livestock. PMID:26904008

  19. Different Land Use Intensities in Grassland Ecosystems Drive Ecology of Microbial Communities Involved in Nitrogen Turnover in Soil

    PubMed Central

    Meyer, Annabel; Focks, Andreas; Radl, Viviane; Keil, Daniel; Welzl, Gerhard; Schöning, Ingo; Boch, Steffen; Marhan, Sven; Kandeler, Ellen; Schloter, Michael

    2013-01-01

    Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity. PMID:24039974

  20. Empirical links between trace metal cycling and marine microbial ecology during a large perturbation to Earth's carbon cycle

    NASA Astrophysics Data System (ADS)

    Owens, Jeremy D.; Reinhard, Christopher T.; Rohrssen, Megan; Love, Gordon D.; Lyons, Timothy W.

    2016-09-01

    Understanding the global redox state of the oceans and its cause-and-effect relationship with periods of widespread organic-carbon deposition is vital to interpretations of Earth's climatic and biotic feedbacks during periods of expanded oceanic oxygen deficiency. Here, we present a compilation of new and published data from an organic-rich locality within the proto-North Atlantic Ocean during the Cenomanian-Turonian boundary event that shows a dramatic drawdown of redox-sensitive trace elements. Iron geochemistry independently suggests euxinic deposition (i.e., anoxic and sulfidic bottom waters) for the entire section, thus confirming its potential as an archive of global marine metal inventories. In particular, depleted molybdenum (Mo) and vanadium (V) concentrations effectively record the global expansion of euxinic and oxygen-deficient but non-sulfidic waters, respectively. The V drawdown precedes the OAE, fingerprinting an expansion of oxygen deficiency prior to an expansion of euxinia. Molybdenum drawdown, in contrast, is delayed with respect to V and coincides with the onset of OAE2. Parallel lipid biomarker analyses provide evidence for significant and progressive reorganization of marine microbial ecology during the OAE in this region of the proto-North Atlantic, with the smallest relative eukaryotic contributions to total primary production occurring during metal-depleted intervals. This relationship may be related to decreasing supplies of enzymatically important trace elements. Similarly, box modeling suggests that oceanic drawdown of Mo may have approached levels capable of affecting marine nitrogen fixation. Predictions of possible nitrogen stress on eukaryotic production, locally and globally, are consistent with the low observed levels of Mo and a rise in 2-methylhopane index values during the peak of the OAE. At the same time, the environmental challenge presented by low dissolved oxygen and euxinia coincides with increased turnover rates of

  1. Different land use intensities in grassland ecosystems drive ecology of microbial communities involved in nitrogen turnover in soil.

    PubMed

    Meyer, Annabel; Focks, Andreas; Radl, Viviane; Keil, Daniel; Welzl, Gerhard; Schöning, Ingo; Boch, Steffen; Marhan, Sven; Kandeler, Ellen; Schloter, Michael

    2013-01-01

    Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity.

  2. Changes in soil microbial biomass and residual indices as ecological indicators of land use change in temperate permanent grassland.

    PubMed

    Murugan, Rajasekaran; Loges, Ralf; Taube, Friedhelm; Sradnick, André; Joergensen, Rainer Georg

    2014-05-01

    The relationship between microbial biomass, residues and their contribution to microbial turnover is important to understand ecosystem C storage. The effects of permanent grassland (100 % ryegrass--PG), conversion to modified grassland (mixture of grass and clover--MG) or maize monoculture (MM) on the dynamics of soil organic C (SOC), microbial biomass, fungal ergosterol and microbial residues (bacterial muramic acid and fungal glucosamine) were investigated. Cattle slurry was applied to quantify the effects of fertilisation on microbial residues and functional diversity of microbial community across land use types. Slurry application significantly increased the stocks of microbial biomass C and S and especially led to a shift in microbial residues towards bacterial tissue. The MM treatment decreased the stocks of SOC, microbial biomass C, N and S and microbial residues compared with the PG and MG treatments at 0-40 cm depth. The MM treatment led to a greater accumulation of saprotrophic fungi, as indicated by the higher ergosterol-to-microbial biomass C ratio and lower microbial biomass C/S ratio compared with the grassland treatments. The absence of a white clover population in the PG treatment caused a greater accumulation of fungal residues (presumably arbuscular mycorrhizal fungi (AMF), which do not contain ergosterol but glucosamine), as indicated by the significantly higher fungal C-to-bacterial C ratio and lower ergosterol-to-microbial biomass C ratio compared with the MG treatment. In addition to these microbial biomass and residual indices, the community level physiological profiles (CLPP) demonstrated distinct differences between the PG and MG treatments, suggesting the potential of these measurements to act as an integrative indicator of soil functioning.

  3. Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation.

    PubMed

    Yang, Gang; Xu, Zhenjiang; Tian, Xiangli; Dong, Shuanglin; Peng, Mo

    2015-02-27

    β-glucan is a prebiotic well known for its beneficial outcomes on sea cucumber health through modifying the host intestinal microbiota. High-throughput sequencing techniques provide an opportunity for the identification and characterization of microbes. In this study, we investigated the intestinal microbial community composition, interaction among species, and intestinal immune genes in sea cucumber fed with diet supplemented with or without β-glucan supplementation. The results show that the intestinal dominant classes in the control group are Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, whereas Alphaproteobacteria, Flavobacteriia, and Verrucomicrobiae are enriched in the β-glucan group. Dietary β-glucan supplementation promoted the proliferation of the family Rhodobacteraceae of the Alphaproteobacteria class and the family Verrucomicrobiaceae of the Verrucomicrobiae class and reduced the relative abundance of the family Flavobacteriaceae of Flavobacteria class. The ecological network analysis suggests that dietary β-glucan supplementation can alter the network interactions among different microbial functional groups by changing the microbial community composition and topological roles of the OTUs in the ecological network. Dietary β-glucan supplementation has a positive impact on immune responses of the intestine of sea cucumber by activating NF-κB signaling pathway, probably through modulating the balance of intestinal microbiota.

  4. Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis.

    PubMed

    Jia, Huijuan; Hanate, Manaka; Aw, Wanping; Itoh, Hideomi; Saito, Kenji; Kobayashi, Shoko; Hachimura, Satoshi; Fukuda, Shinji; Tomita, Masaru; Hasebe, Yukio; Kato, Hisanori

    2017-03-08

    Gut microbiota is an essential factor in the shaping of intestinal immune system development and driving inflammation in inflammatory bowel disease (IBD). We report the effects and microbe-host interactions underlying an intervention using fine powder of eggshell membrane (ESM) against IBD. ESM attenuated lipopolysaccharide-induced inflammatory cytokine production and promoted the Caco-2 cell proliferation by up-regulating growth factors in vitro. In a murine model of dextran sodium sulphate-induced colitis, ESM significantly suppressed the disease activity index and colon shortening. These effects were associated with significant ameliorations of gene expressions of inflammatory mediators, intestinal epithelial cell proliferation, restitution-related factors and antimicrobial peptides. Multifaceted integrated omics analyses revealed improved levels of energy metabolism-related genes, proteins and metabolites. Concomitantly, cecal metagenomic information established an essential role of ESM in improving dysbiosis characterized by increasing the diversity of bacteria and decreasing absolute numbers of pathogenic bacteria such as Enterobacteriaceae and E. coli, as well as in the regulation of the expansion of Th17 cells by suppressing the overgrowth of segmented filamentous bacteria. Such modulations have functional effects on the host; i.e., repairing the epithelium, regulating energy requirements and eventually alleviating mucosal inflammation. These findings are first insights into ESM's modulation of microbiota and IBD suppression, providing new perspectives on the prevention/treatment of IBD.

  5. Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis

    PubMed Central

    Jia, Huijuan; Hanate, Manaka; Aw, Wanping; Itoh, Hideomi; Saito, Kenji; Kobayashi, Shoko; Hachimura, Satoshi; Fukuda, Shinji; Tomita, Masaru; Hasebe, Yukio; Kato, Hisanori

    2017-01-01

    Gut microbiota is an essential factor in the shaping of intestinal immune system development and driving inflammation in inflammatory bowel disease (IBD). We report the effects and microbe-host interactions underlying an intervention using fine powder of eggshell membrane (ESM) against IBD. ESM attenuated lipopolysaccharide-induced inflammatory cytokine production and promoted the Caco-2 cell proliferation by up-regulating growth factors in vitro. In a murine model of dextran sodium sulphate-induced colitis, ESM significantly suppressed the disease activity index and colon shortening. These effects were associated with significant ameliorations of gene expressions of inflammatory mediators, intestinal epithelial cell proliferation, restitution-related factors and antimicrobial peptides. Multifaceted integrated omics analyses revealed improved levels of energy metabolism-related genes, proteins and metabolites. Concomitantly, cecal metagenomic information established an essential role of ESM in improving dysbiosis characterized by increasing the diversity of bacteria and decreasing absolute numbers of pathogenic bacteria such as Enterobacteriaceae and E. coli, as well as in the regulation of the expansion of Th17 cells by suppressing the overgrowth of segmented filamentous bacteria. Such modulations have functional effects on the host; i.e., repairing the epithelium, regulating energy requirements and eventually alleviating mucosal inflammation. These findings are first insights into ESM’s modulation of microbiota and IBD suppression, providing new perspectives on the prevention/treatment of IBD. PMID:28272447

  6. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park.

    PubMed

    Becraft, Eric D; Wood, Jason M; Rusch, Douglas B; Kühl, Michael; Jensen, Sheila I; Bryant, Donald A; Roberts, David W; Cohan, Frederick M; Ward, David M

    2015-01-01

    Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.

  7. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

    PubMed Central

    Becraft, Eric D.; Wood, Jason M.; Rusch, Douglas B.; Kühl, Michael; Jensen, Sheila I.; Bryant, Donald A.; Roberts, David W.; Cohan, Frederick M.; Ward, David M.

    2015-01-01

    Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time. PMID:26157420

  8. Microbial ecology measurement system

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The sensitivity and potential rapidity of the PIA test that was demonstrated during the feasibility study warranted continuing the effort to examine the possibility of adapting this test to an automated procedure that could be used during manned missions. The effort during this program has optimized the test conditions for two important respiratory pathogens, influenza virus and Mycoplasma pneumoniae, developed a laboratory model automated detection system, and investigated a group antigen concept for virus detection. Preliminary tests on the handling of oropharygeal clinical samples for PIA testing were performed using the adenovirus system. The results obtained indicated that the PIA signal is reduced in positive samples and is increased in negative samples. Treatment with cysteine appeared to reduce nonspecific agglutination in negative samples but did not maintain the signal in positive samples.

  9. Establishment of Intestinal Bacteriology

    PubMed Central

    MITSUOKA, Tomotari

    2014-01-01

    Research on intestinal bacteria began around the end of the 19th century. During the last 5 decades of the 20th century, research on the intestinal microbiota made rapid progress. At first, in my work, I first developed a method of comprehensive analysis of the intestinal microbiota, and then I established classification and identification methods for intestinal anaerobes. Using these methods I discovered a number of ecological rules governing the intestinal microbiota and the role of the intestinl microbiota in health and disease. Moreover, using germfree animals, it was proven that the intestinal microbiota has a role in carcinogenesis and aging in the host. Thus, a new interdisciplinary field, “intestinal bacteriology” was established. PMID:25032084

  10. Influence of dietary peas and organic acids and probiotic supplementation on performance and caecal microbial ecology of broiler chickens.

    PubMed

    Czerwiński, J; Højberg, O; Smulikowska, S; Engberg, R M; Mieczkowska, A

    2010-04-01

    1. The effect of dietary pea and addition of organic acid blend (OA) or probiotic (Pro) on performance and caecal microbial ecology of broiler chickens was studied. 2. A growth trial was conducted with 160 Ross 308 female broilers from d 1 to 35 of age. There were 8 treatment groups based on either control (S) or white pea (P). Both S and P were supplemented with OA (Galliacid - fumaric acid, calcium formate, calcium propionate and potassium sorbate coated with plant triglycerides, Vetagro) and or with Pro (LABYuc-Probio - lactic acid bacteria, Saccharomyces cerevisiae and Yucca schidigeri extract, Mifarmex GmbH). 3. Inclusion of peas in the diet increased feed intake and decreased gain:feed ratio in comparison to the control diet. Neither probiotic nor OA supplementations affected broiler performance. 4. The caecal microbiota was characterised in 37-d-old birds by fluorescent in situ hybridisation (FISH) and terminal-restriction fragment length polymorphism (T-RFLP). Total bacterial counts in caecal contents were slightly higher for birds fed the pea diets, but were not affected by OA or Pro supplements. 5. Neither pea nor Pro affected the Lactobacillus/Enterococcus and Streptococcus/Lactococcus counts in caecal contents, whereas OA supplementation slightly increased the Lactobacillus/Enterococcus counts. The composition of the Lactobacillus/Enterococcus population was altered by inclusion of peas as revealed by the T-RFLP patterns. 6. The DNA fingerprint further suggested that the caecal microbiota was dominated by the lactic acid bacterium Streptococcus alactolyticus. 7. In ileal contents, the concentration of short-chain fatty acids (SCFA) was decreased only by Pro supplementation. In caecal contents, the SCFA concentration was higher for birds fed on the pea diets, and increased significantly with Pro supplementation 8. In conclusion, the results indicate that the use of pea and probiotics in broiler feed may stimulate the caecal commensal microbiota (growth

  11. Sequence-based Methods in Human Microbial Ecology: A The 2nd HumanGenome Comes of Age

    SciTech Connect

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-06-01

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail (Handelsman 2004; Harris et al. 2004; Hugenholtz et al. 1998; Moreira and Lopez-Garcia 2002; Rappe and Giovannoni 2003). Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because these techniques now allow not only cataloging of microbial diversity, but also insight into microbial functions, it is time for clinical microbiologists to apply these tools to the microbial communities that abound on and within us, in what has been aptly called ''the second Human Genome Project'' (Relman and Falkow 2001). In this review we will discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis and treatment of known infectious diseases, and finally to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  12. Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation

    SciTech Connect

    Yang, Gang; Xu, Zhenjiang; Tian, Xiangli; Dong, Shuanglin; Peng, Mo

    2015-02-27

    β-glucan is a prebiotic well known for its beneficial outcomes on sea cucumber health through modifying the host intestinal microbiota. High-throughput sequencing techniques provide an opportunity for the identification and characterization of microbes. In this study, we investigated the intestinal microbial community composition, interaction among species, and intestinal immune genes in sea cucumber fed with diet supplemented with or without β-glucan supplementation. The results show that the intestinal dominant classes in the control group are Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, whereas Alphaproteobacteria, Flavobacteriia, and Verrucomicrobiae are enriched in the β-glucan group. Dietary β-glucan supplementation promoted the proliferation of the family Rhodobacteraceae of the Alphaproteobacteria class and the family Verrucomicrobiaceae of the Verrucomicrobiae class and reduced the relative abundance of the family Flavobacteriaceae of Flavobacteria class. The ecological network analysis suggests that dietary β-glucan supplementation can alter the network interactions among different microbial functional groups by changing the microbial community composition and topological roles of the OTUs in the ecological network. Dietary β-glucan supplementation has a positive impact on immune responses of the intestine of sea cucumber by activating NF-κB signaling pathway, probably through modulating the balance of intestinal microbiota. - Highlights: • Dietary β-glucan supplementation increases the abundance of Rhodobacteraceae and Verrucomicrobiaceae in the intestine. • Dietary β-glucan supplementation changes the topological roles of OTUs in the ecological network. • Dietary β-glucan supplementation has a positive impact on the immune response of intestine of sea cucumber.

  13. Targeting Unknowns Just Underfoot: Microbial Ecology and Community Genomics of C Cycling in Soil Informed and Enabled with DNA-SIP

    NASA Astrophysics Data System (ADS)

    Pepe-Ranney, C. P.; Campbell, A.; Buckley, D. H.

    2015-12-01

    Microorganisms drive biogeochemical cycles and because soil is a large global carbon (C) reservoir (soil contains more C than plants and the atmosphere combined), soil microorganisms are important players in the global C-cycle. Frustratingly, however, many soil microorganisms resist cultivation and soil communities are astoundingly complex. This makes soil microbiology difficult to study and without a solid understanding of soil microbial ecology, models of soil C feedbacks to climate change are under-informed. Stable isotope probing (SIP) is a useful approach for establishing identity-function connections in microbial communities but has been challenging to employ in soil due to the inadequate resolution of microbial community fingerprinting techniques. High throughput DNA sequencing improves SIP resolving power transforming it into a powerful tool for studying the soil C cycle. We conducted a DNA-SIP experiment to track flow of xylose-C, a labile component of plant biomass, and cellulose-C, the most abundant global biopolymer, through a soil microbial community. We could track 13C into microbial DNA even when added 13C amounted to less than 5% of native C and found Spartobacteria, Chloroflexi, and Planctomycetes taxa were among those that assimilated 13C cellulose. These lineages are cosmopolitan in soil but little is known of their ecophysiology. By profiling SSU rRNA genes across entire DNA-SIP density gradients, we assessed relative DNA atom % 13C per taxon in 13C treatments and found cellulose degraders exhibited signal consistent with a specialist lifestyle with respect to C preference. Further, DNA-SIP enriches DNA of targeted microorganisms (Verrucomicrobia cellulose degraders were enriched by nearly two orders of magnitude) and this enriched DNA can serve as template for community genomics. We produced draft genomes from soil cellulose degraders including microorganisms belonging to Verrucomicrobia, Chloroflexi, and Planctomycetes from SIP enriched DNA

  14. Evaluation of alternatives to antibiotics using an Escherichia coli K88+ model of piglet diarrhea: effects on gut microbial ecology.

    PubMed

    Bhandari, S K; Xu, B; Nyachoti, C M; Giesting, D W; Krause, D O

    2008-04-01

    Enterotoxigenic Escherichia coli is a major problem in the swine industry and results in scouring, increased mortality, and poor performance in the period immediately postweaning. The traditional way to control this problem is to include subtherapeutic antibiotics in the feed, but this is no longer acceptable to consumers; thus, alternatives to antibiotics are needed. One of the supplements that has been effective in reducing scouring in the absence of antibiotics is animal blood products produced from the rendering process. This is also becoming a problem because of concerns regarding the transfer of transmissible spongiform encephalopathies to humans from animals. In this research, we investigated the effects of spray-dried porcine plasma (SDPP), a Bacillus subtilis direct-fed microbial (DFM), a blend of organic acids, and sweeteners on E. coli-induced scouring. A total of 108 pigs of approximately 17 d of age were assigned to 6 treatments, with 3 pigs per pen, in 2 blocks, with each block having 3 replicates. The 2 blocks were initiated approximately 2 mo apart, because a sufficient number of pigs were not available that met our inclusion criteria in the first block. Diet 1 was a negative control containing no antibiotics (NC). Diet 2 was the positive control and included the same ingredient composition as NC except that antibiotics (110 mg/kg of chlortetracycline, 110 mg/kg of sulfamethazine, and 55 mg/kg of penicillin) were added (PC). Diet 3 was equal to the NC, but with a B. subtilis probiotic (DFM). Diet 4 was the NC to which SDPP was added. Diet 5 was the NC plus a combination of SDPP and DFM (SDPP + DFM). Diet 6 was the NC plus a combination of supplements, including SDPP and a blend of organic acids, DFM, and a sweetener (Blend). At 24 d of age, the pigs were experimentally infected with 6.3 x 10(9) cfu/mL of E. coli K88. All pigs were euthanized 7 d after infection and tissues were obtained for analysis. There were no significant differences among

  15. Adding mucins to an in vitro batch fermentation model of the large intestine induces changes in microbial population isolated from porcine feces depending on the substrate.

    PubMed

    Tran, T H T; Boudry, C; Everaert, N; Théwis, A; Portetelle, D; Daube, G; Nezer, C; Taminiau, B; Bindelle, J

    2016-02-01

    Adding mucus to in vitro fermentation models of the large intestine shows that some genera, namely lactobacilli, are dependent on host-microbiota interactions and that they rely on mucosal layers to increase their activity. This study investigated whether this dependence on mucus is substrate dependent and to what extent other genera are impacted by the presence of mucus. Inulin and cellulose were fermented in vitro by a fecal inoculum from pig in the presence or not of mucin beads in order to compare fermentation patterns and bacterial communities. Mucins increased final gas production with inulin and shifted short-chain fatty acid molar ratios (P < 0.001). Quantitative real-time PCR analyses revealed that Lactobacillus spp. and Bifidobacterium spp. decreased with mucins, but Bacteroides spp. increased when inulin was fermented. A more in-depth community analysis indicated that the mucins increased Proteobacteria (0.55 vs 0.25%, P = 0.013), Verrucomicrobia (5.25 vs 0.03%, P = 0.032), Ruminococcaceae, Bacteroidaceae and Akkermansia spp. Proteobacteria (5.67 vs 0.55%, P < 0.001) and Lachnospiraceae (33 vs 10.4%) were promoted in the mucus compared with the broth, while Ruminococcaceae decreased. The introduction of mucins affected many microbial genera and fermentation patterns, but from PCA results, the impact of mucus was independent of the fermentation substrate.

  16. Medium-chain triglyceride as an alternative of in-feed colistin sulfate to improve growth performance and intestinal microbial environment in newly weaned pigs.

    PubMed

    Yen, Hung-Che; Lai, Wei-Kang; Lin, Chuan-Shun; Chiang, Shu-Hsing

    2015-01-01

    Five hundred and twenty-eight newly weaned pigs were given four treatments, with eight replicates per treatment. Sixteen to 18 pigs were assigned per replicate and were fed diets supplemented with 0 or 3% medium-chain triglyceride (MCT) and 0 or 40 ppm colistin sulfate (CS) in a 2 × 2 factorial arrangement for 2 weeks. The results showed that dietary supplementation with MCT improved the gain-to-feed ratio during days 3-7 and in the overall period (P < 0.05). Dietary supplementation with MCT decreased coliforms counts (C) in colon and rectum content (P < 0.05). Dietary supplementation with CS decreased C and lactic acid bacteria plus C counts (L + C) in cecum (P < 0.05), and C, L + C (P < 0.01) and ratio of L and C (P < 0.05) in colon and rectum contents. The lack of interactions between MCT and CS indicates different modes of action and additive effects between the two supplementations. In conclusion, supplementation with MCT in diet with or without CS could improve the intestinal microbial environment and the feed utilization efficiency of newly weaned pigs.

  17. Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut.

    PubMed

    Yin, Jinbao; Zhang, Xu-Xiang; Wu, Bing; Xian, Qiming

    2015-12-01

    Antibiotics have been widely used for disease prevention and treatment of the human and animals, and for growth promotion in animal husbandry. Antibiotics can disturb the intestinal microbial community, which play a fundamental role in animals' health. Misuse or overuse of antibiotics can result in increase and spread of microbial antibiotic resistance, threatening human health and ecological safety. In this study, we used Illumina Hiseq sequencing, (1)H nuclear magnetic resonance spectroscopy and metagenomics approaches to investigate intestinal microbial community shift and antibiotic resistance alteration of the mice drinking the water containing tetracycline hydrochloride (TET). Two-week TET administration caused reduction of gut microbial diversity (from 194 to 89 genera), increase in Firmicutes abundance (from 24.9 to 39.8%) and decrease in Bacteroidetes abundance (from 69.8 to 51.2%). Metagenomic analysis showed that TET treatment affected the intestinal microbial functions of carbohydrate, ribosomal, cell wall/membrane/envelope and signal transduction, which is evidenced by the alteration in the metabolites of mouse serum. Meanwhile, in the mouse intestinal microbiota, TET treatment enhanced the abundance of antibiotic resistance genes (ARGs) (from 307.3 to 1492.7 ppm), plasmids (from 425.4 to 3235.1 ppm) and integrons (from 0.8 to 179.6 ppm) in mouse gut. Our results indicated that TET administration can disturb gut microbial community and physiological metabolism of mice, and increase the opportunity of ARGs and mobile genetic elements entering into the environment with feces discharge.

  18. Intestinal M cells

    PubMed Central

    Ohno, Hiroshi

    2016-01-01

    We have an enormous number of commensal bacteria in our intestine, moreover, the foods that we ingest and the water we drink is sometimes contaminated with pathogenic microorganisms. The intestinal epithelium is always exposed to such microbes, friend or foe, so to contain them our gut is equipped with specialized gut-associated lymphoid tissue (GALT), literally the largest peripheral lymphoid tissue in the body. GALT is the intestinal immune inductive site composed of lymphoid follicles such as Peyer’s patches. M cells are a subset of intestinal epithelial cells (IECs) residing in the region of the epithelium covering GALT lymphoid follicles. Although the vast majority of IEC function to absorb nutrients from the intestine, M cells are highly specialized to take up intestinal microbial antigens and deliver them to GALT for efficient mucosal as well as systemic immune responses. I will discuss recent advances in our understanding of the molecular mechanisms of M-cell differentiation and functions. PMID:26634447

  19. Study of the succession of microbial communities for sulfur cycle response to ecological factors change in sediment of sewage system.

    PubMed

    Liu, Yanchen; Dong, Qian; Wu, Chen; Zhou, Xiaohong; Shi, Hanchang

    2015-06-01

    The biological reaction process of sulfur in biofilms and sediments causes serious problems of corrosion and odor in sewage systems. This study aims to reveal the distribution and shift of microbial diversity that survives inside the sediment in response to surrounding changes in sewage systems. The successions of microbial community were compared via denaturing gradient gel electrophoresis and by constructing phylogenetic trees via maximum likelihood method. The results indicated that the shift of microbial diversity is not significant along the vertical layer inside the sediment. The influences of sediment accumulation time on the shift in microbial diversity are evident, particularly with the switch of the accumulation stage. Implementing a control strategy for oxygen injection and nitrate addition evidently inhibits and stimulates some dominant sulfate-reducing bacterial strains in the sediment. The diversity in the total bacteria is positively related with ORP, dissolved oxygen, and sulfide concentration.

  20. Microbial and geochemical investigations of dissolved organic carbon and microbial ecology of native waters from the Biscayne and Upper Floridan Aquifers

    USGS Publications Warehouse

    Lisle, John T.; Harvey, Ron W.; Aiken, George R.; Metge, David W.

    2010-01-01

    Groundwater resources in the United States are under ever-increasing demands for potable, irrigation, and recreational uses. Additionally, aquifer systems are being used or targeted for use as storage areas for treated surface waters and (or) groundwaters via injection (for example, aquifer storage and recovery). To date, the influence that the nutrients, including carbon, in the injected water have on native microbial communities and the biogeochemistry in the subsurface zones used for storage of the injectate has not been determined. In this report, we describe a series of experiments that establishes a baseline dataset for the quantity and quality of organic and inorganic carbon and nutrients in the Biscayne Aquifer (BA) and Upper Floridan Aquifer (UFA) in south Florida. The most significant differences between the BA (26 meters below surface) and UFA (366 meters below surface) are the average specific conductance (0.552 and 6.12 microsiemens per centimeter, respectively), dissolved oxygen (1.6 and 0 milligrams per liter, respectively), and oxidation-reduction potential (40.3 and -358 millivolts, respectively). The dissolved organic carbon from the BA is characterized by carbon originating from terrestrial sources and microbial activities, while the UFA has a distinctive microbial signature. Acetate and lactate are the dominant carbon constituents in both aquifers. Additionally, components of the dissolved organic carbon from the UFA have a total trihalomethane-formation potential that is approximately threefold greater than the maximum contaminat level of 80 micrograms per liter established by the U.S. Environmental Protection Agency. The average native bacterial abundances in the aquifers are similar with 4.69x10^4 cells per milliliter in the BA and 1.33x10^4 cells per milliliter in the UFA. The average bacteriophage abundances are also similar with 1.15x10^5 virus-like particles in the BA and 1.92x10^5 virus-like particles in the UFA. Interestingly, ciliated

  1. Intestinal Microbial Dysbiosis and Colonic Epithelial Cell Hyperproliferation by Dietary α-Mangostin is Independent of Mouse Strain

    PubMed Central

    Gutierrez-Orozco, Fabiola; Thomas-Ahner, Jennifer M.; Galley, Jeffrey D.; Bailey, Michael T.; Clinton, Steven K.; Lesinski, Gregory B.; Failla, Mark L.

    2015-01-01

    Beverages and supplements prepared from mangosteen fruit are claimed to support gut health and immunity, despite the absence of supporting evidence from clinical trials. We recently reported that α-mangostin (α-MG), the most abundant xanthone in mangosteen fruit, altered the intestinal microbiome, promoted dysbiosis, and exacerbated colitis in C57BL/6J mice. The objective of this study was to determine whether induction of dysbiosis by dietary α-MG is limited to the C57BL/6J strain or represents a more generic response to chronic intake of the xanthone on the gut microbiota of mice. C3H, Balb/c, Nude FoxN1nu, and C57BL/6J mice, each demonstrating unique microbiomes, were fed standard diet or diet containing 0.1% α-MG for four weeks. Dietary α-MG significantly altered the cecal and colonic microbiota in all four strains of mice, promoting a reduction in generally assumed beneficial bacterial groups while increasing the abundance of pathogenic bacteria. Consumption of α-MG was associated with reduced abundance of Firmicutes and increased abundance of Proteobacteria. The abundance of Lachnospiraceae, Ruminococcaceae, and Lactobacillaceae was reduced in α-MG-fed mice, while that of Enterobacteriaceae and Enterococcaceae was increased. Dietary α-MG also was associated with increased proliferation of colonic epithelial cells, infiltration of immune cells, infiltration of immune cells and increased fluid content in stool. These results suggest that ingestion of pharmacologic doses of xanthones in mangosteen-containing supplements may adversely alter the gut microbiota and should be used with caution. PMID:25621505

  2. Mixed culture models for predicting intestinal microbial interactions between Escherichia coli and Lactobacillus in the presence of probiotic Bacillus subtilis.

    PubMed

    Yang, J J; Niu, C C; Guo, X H

    2015-01-01

    Bacillus has been proposed as a probiotic due to its in vivo effectiveness in the gastrointestinal tract through antimicrobial activities. The present study investigates the effects of Lactobacillus alone or in the presence of Bacillus subtilis MA139 on the inhibition of pathogenic Escherichia coli K88. Mixed cultures were used to predict the possible interactions among these bacteria within the intestinal tract of animals. B. subtilis MA139 was first assayed for its inhibition against E. coli K88 both under shaking and static culture conditions. A co-culture assay was employed under static conditions to test the inhibitory effects of Lactobacillus reuteri on E. coli K88, with or without addition of B. subtilis MA139. The results showed that B. subtilis MA139 had marked inhibition against E. coli K88 under shaking conditions and weak inhibition under static conditions. Lactobacillus alone as well as in combination with B. subtilis MA139 spores exerted strong inhibition against E. coli K88 under static conditions. However, the inhibition by Lactobacillus in combination with B. subilis spores was much higher than that by Lactobacillus alone (P<0.01). B. subtilis MA139 significantly decreased the pH and oxidation-reduction potential values of the co-culture broth compared to that of Lactobacillus alone (P<0.05). The viability of Lactobacillus increased when co-cultured with B. subtilis MA139 because of significantly higher Lactobacillus counts and lower pH values in the broth (P<0.05). The role of Bacillus in the mixed culture models suggests that Bacillus may produce beneficial effects by increasing the viability of lactobacilli and subsequently inhibiting the growth of pathogenic E. coli. Therefore, the combination of Bacillus and Lactobacillus species as a probiotic is recommended.

  3. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids: Part II. Effects on intestinal histology and active nutrient transport.

    PubMed

    Walsh, M C; Rostagno, M H; Gardiner, G E; Sutton, A L; Richert, B T; Radcliffe, J S

    2012-08-01

    The objective of this study was to evaluate the effects of water-delivered, direct-fed microbials (DFM) or organic acids on intestinal morphology and active nutrient absorption in weanling pigs after deliberate Salmonella infection. Pigs (n = 88) were weaned at 19 ± 2 d of age and assigned to 1 of the following treatments, which were administered for 14 d: 1) control diet; 2) control diet + DFM (Enterococcus faecium, Bacillus subtilis, and Bacillus licheniformis) in drinking water at 10(9) cfu/L for each strain of bacteria; 3) control diet + organic acid-based blend (predominantly propionic, acetic, and benzoic acids) in drinking water at 2.58 mL/L; and 4) control diet + 55 mg/kg carbadox. Pigs were challenged with 10(10) cfu Salmonella enterica var Typhimurium 6 d after commencement of treatments. Pigs (n = 22/d) were harvested before Salmonella challenge and on d 2, 4, and 8 after challenge. Duodenal, jejunal, and ileal mucosal tissues were sampled for measurement of villus height and crypt depth. Jejunal tissue was sampled for determination of active nutrient absorption in modified Ussing chambers. Duodenal villus height was greater in pigs fed in-feed antibiotic before infection (P < 0.05). Jejunal crypts were deeper in DFM- and acid-treated pigs on d 4 after infection compared with all other treatments (P < 0.05). Salmonella infection resulted in a linear decrease in phosphorus (P < 0.001) and glucose (P < 0.05) active transport, and an increase (P < 0.001) in glutamine uptake immediately after challenge. Salmonella infection reduced basal short-circuit current (I(sc)); however, water-delivered DFM or organic acid treatments caused greater basal I(sc) on d 2 after challenge than did carbadox. Carbachol-induced chloride ion secretion was greatest in negative control pigs before infection (P < 0.01) and DFM-treated pigs (P < 0.05) after infection. In conclusion, both the DFM and acidification treatments induced increases in basal active ion movement and jejunal

  4. Effect of Scrophularia striata and Ferulago angulata, as alternatives to virginiamycin, on growth performance, intestinal microbial population, immune response, and blood constituents of broiler chickens.

    PubMed

    Rostami, Farhad; Ghasemi, Hossein A; Taherpour, Kamran

    2015-09-01

    An experiment was conducted to investigate the comparative effect of Scrophularia striata, Ferulago angulata, and virginiamycin (VM) on performance, intestinal microbial population, immune response, and blood constituents of broilers. A total of 300 Ross 308 male broiler chickens were randomly assigned to 5 treatments, with 5 replicates/treatment (10 chickens/pen). Birds were fed either a corn-soybean meal basal diet (control) or the basal diet supplemented with 200 mg/kg VM; 4 g/kg S. striata (SS1); 8 g/kg S. striata (SS2); 4 g/kg F. angulata (FA1); or 8 g/kg F. angulata (FA2). After 6 wk, the BW, ADG, and feed-to-gain ratio (F:G) of the VM, SS1, and FA1 groups were better (P<0.01) compared with the control group. At 42 d, cecal lactobacillus counts were higher (P=0.032) in SS2 and FA2 groups compared with the control and VM groups. In addition, broilers fed any of the diets exhibited lower coliform counts (P<0.05) in the ileum and ceca than those fed the control diet. Total and IgG antibody titers against SRBC for secondary responses, relative spleen weight, and lymphocyte counts were higher (P<0.05) in birds fed the SS2 or FA2 diet compared with the control group. Moreover, feeding the SS2 or FA2 diet decreased (P<0.05) the blood heterophil/lymphocyte ratio and plasma triglyceride level, whereas only the SS2 diet increased (P=0.037) the white blood cell counts compared with the control diet. All diets, except for the VM diet, decreased (P=0.009) the plasma cholesterol level compared to the control treatment. The plasma high-density lipoprotein cholesterol level was also increased (P=0.042) in the SS2 and FA2 groups. In conclusion, dietary S. striata or F. angulata at a level of 4 g/kg diet enhanced growth performance, which was comparable to that of VM used as an antibiotic growth promoter. Furthermore, a high dose of both herbs (8 g/kg diet) could beneficially affect the intestinal health and immune status of broilers.

  5. Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet

    PubMed Central

    Heinritz, Sonja N.; Weiss, Eva; Eklund, Meike; Aumiller, Tobias; Louis, Sandrine; Rings, Andreas; Messner, Sabine; Camarinha-Silva, Amélia; Seifert, Jana; Bischoff, Stephan C.; Mosenthin, Rainer

    2016-01-01

    The intestinal microbiota and its metabolites appear to be an important factor for gastrointestinal function and health. However, research is still needed to further elaborate potential relationships between nutrition, gut microbiota and host’s health by means of a suitable animal model. The present study examined the effect of two different diets on microbial composition and activity by using the pig as a model for humans. Eight pigs were equally allotted to two treatments, either fed a low-fat/high-fiber (LF), or a high-fat/low-fiber (HF) diet for 7 weeks. Feces were sampled at day 7 of every experimental week. Diet effects on fecal microbiota were assessed using quantitative real-time PCR, DNA fingerprinting and metaproteomics. Furthermore, fecal short-chain fatty acid (SCFA) profiles and ammonia concentrations were determined. Gene copy numbers of lactobacilli, bifidobacteria (P<0.001) and Faecalibacterium prausnitzii (P<0.05) were higher in the LF pigs, while Enterobacteriaceae were more abundant in the HF pigs (P<0.001). Higher numbers of proteins affiliated to Enterobacteriaceae were also present in the HF samples. Proteins for polysaccharide breakdown did almost exclusively originate from Prevotellaceae. Total and individual fecal SCFA concentrations were higher for pigs of the LF treatment (P<0.05), whereas fecal ammonia concentrations did not differ between treatments (P>0.05). Results provide evidence that beginning from the start of the experiment, the LF diet stimulated beneficial bacteria and SCFA production, especially butyrate (P<0.05), while the HF diet fostered those bacterial groups which have been associated with a negative impact on health conditions. These findings correspond to results in humans and might strengthen the hypothesis that the response of the porcine gut microbiota to a specific dietary modulation is in support of using the pig as suitable animal model for humans to assess diet-gut-microbiota interactions. Data are available

  6. Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure as influenced by three swine management systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vastly different microbial constituents in both the pig and the manure lagoons used to treat the fecal waste of the operation. While some of these changes may not be negative, it is possible th...

  7. Soil Microbial Activity Benchmarks (Provisional) for Ecological Risk Assessments at Explosives-Contaminated Sites: Promoting Range Sustainability

    DTIC Science & Technology

    2008-12-01

    identifiable phospholipid fatty acids (PLFAs) from 34 to 14 (Fuller and Manning, 2004). Actinomycetes were reported to have a substantially lower EC50... actinomycetes is unclear at the present time. Sensitive techniques routinely detected differences in generic microbial community functions at low TNT

  8. Nesting ecology and cuticular microbial loads in dampwood (Zootermopsis angusticollis) and drywood termites (Incisitermes minor, I. schwarzi, Cryptotermes cavifrons)

    PubMed Central

    Rosengaus, Rebeca B.; Moustakas, Jacqueline E.; Calleri, Daniel V.; Traniello, James F.A.

    2003-01-01

    Termites form one-piece nests in wood that can vary in their moisture content and degree of decomposition, and thus microbial richness. To estimate the microbial load of nests and the potential risk they pose for colony members, we quantified the number of microbes in the nest and on the cuticle of the dampwood termite, Zootermopsis angusticollis, and three drywood termites, Incisitermes minor, I. schwarzi, and Cryptotermes cavifrons. The number of colony forming units (CFUs) cultured from nest material samples and washes of the cuticle of larvae and nymphs were determined. CFUs recorded from nest material was low (fewer than 60 CFUs/g) in the drywood termites and comparatively high in the dampwood species, as more than 800 bacterial and fungal CFUs/g were cultured from the nest material of Z. angusticollis. Similarly, cuticular microbial loads were negligible in the drywood termites sampled, ranging from 0.5 to fewer than 16 CFUs/cm2, whereas approximately 200 CFUs/cm2 were cultured from Z. angusticollis. The nesting and feeding habits of these basal species likely influence colony microbial load and the degree of pathogen exposure, which in turn could favor adaptations to resist disease that vary with termite nesting biology. Abbreviation: CFU colony forming unit PMID:15841247

  9. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions.

    PubMed

    Schuerger, Andrew C; Lee, Pascal

    2015-06-01

    Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20°C to -1°C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle.

  10. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions

    PubMed Central

    Lee, Pascal

    2015-01-01

    Abstract Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (−20°C to −1°C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12–18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle. Key Words: Planetary protection

  11. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions

    NASA Technical Reports Server (NTRS)

    Schuerger, Andrew C.; Lee, Pascal

    2015-01-01

    Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20C to -1C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle. Key Words: Planetary protection-Contamination-Habitability-Haughton Crater-Mars. Astrobiology

  12. A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology

    PubMed Central

    Stoeck, Thorsten; Breiner, Hans-Werner; Filker, Sabine; Ostermaier, Veronika; Kammerlander, Barbara; Sonntag, Bettina

    2014-01-01

    Analyses of high-throughput environmental sequencing data have become the ‘gold-standard’ to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive ‘rare microbial biosphere’ and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes. PMID:23848238

  13. A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology.

    PubMed

    Stoeck, Thorsten; Breiner, Hans-Werner; Filker, Sabine; Ostermaier, Veronika; Kammerlander, Barbara; Sonntag, Bettina

    2014-02-01

    Analyses of high-throughput environmental sequencing data have become the 'gold-standard' to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive 'rare microbial biosphere' and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes.

  14. Estimating evolution of δ(13)CH(4) during methanization of municipal solid waste based on chemical reactions, isotope accumulation in products and microbial ecology.

    PubMed

    Vavilin, V A

    2012-01-01

    Natural isotopic composition in substrate may be used to reveal the metabolic pathways of substrate transformation by microbial community. In this paper, a change in δ(13)CH(4) during methanization of reconstituted municipal solid waste was described using a mathematical model based on stoichiometric chemical reactions, equation for the (13)C isotope accumulation in products at the low natural C(13)/C(12) ratio and microbial ecology. A set of experimental data used in the model was taken from Qu et al. (2009a). According to the model, during mesophilic municipal solid waste methanization initially hydrogenotrophic and further aceticlastic methanogenesis dominated. At the final stage hydrogenotrophic methanogenesis followed by acetate oxidation dominated again. In spite of rather high measured values of δ(13)C for CO(2) above -21‰, a sharp decrease in δ(13)CH(4) from -20‰ to -60‰ at the final stage was explained by a larger fractionation against (13)C during methanogenesis from H(2)/H(2)CO(3) due to a kinetic isotope effect when hydrogenotrophic methanogens preferentially take down light (12)C. The model also confirmed that in thermophilic conditions a comparatively stable value of δ(13)CH(4) about -60‰ measured earlier (Qu et al. 2009b) was due to a dominance of hydrogenotrophic methanogenesis during all methanization process of cardboard waste.

  15. Ecology and life history of an amoebomastigote, Paratetramitus jugosus, from a microbial mat: new evidence for multiple fission

    NASA Technical Reports Server (NTRS)

    Enzien, M.; McKhann, H. I.; Margulis, L.

    1989-01-01

    Five microbial habitats (gypsum crust, gypsum photosynthetic community, Microcoleus mat, Thiocapsa scum, and black mud) were sampled for the presence of the euryhaline, rapidly growing amoebomastigote, Paratetramitus jugosus. Field investigations of microbial mats from Baja California Norte, Mexico, and Salina Bido near Matanzas, Cuba, reveal that P. jugosus is most frequently found in the Thiocapsa layer of microbial mats. Various stages of the life history were studied using phase-contrast, differential-interference, and transmission electron microscopy. Mastigote stages were induced and studied by electron microscopy; mastigotes that actively feed on bacteria bear two or more undulipodia. A three-dimensional drawing of the kinetid ("basal apparatus") based on electron micrographs is presented. Although promitoses were occasionally observed, it is unlikely that they can account for the rapid growth of P. jugosus populations on culture media. Dense, refractile, spherical, and irregular-shaped bodies were seen at all times in all cultures along with small mononucleate (approximately 2-7 micrometers diameter) amoebae. Cytochemical studies employing two different fluorescent stains for DNA (DAPI, mithramycin) verified the presence of DNA in these small bodies. Chromatin-like material seen in electron micrographs within the cytoplasm and blebbing off nuclei were interpreted to the chromatin bodies. Our interpretation, consistent with the data but not proven, is that propagation by multiple fission of released chromatin bodies that become small amoebae may occur in Paratetramitus jugosus. These observations are consistent with descriptions of amoeba propagules in the early literature (Hogue, 1914).

  16. Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells.

    PubMed

    Cluff, Maryam A; Hartsock, Angela; MacRae, Jean D; Carter, Kimberly; Mouser, Paula J

    2014-06-03

    Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process.

  17. Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms

    NASA Technical Reports Server (NTRS)

    Nichols, P. D.; Henson, J. M.; Guckert, J. B.; Nivens, D. E.; White, D. C.

    1985-01-01

    Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

  18. Final Technical Report: DOE-Biological Ocean Margins Program. Microbial Ecology of Denitrifying Bacteria in the Coastal Ocean.

    SciTech Connect

    Lee Kerkhof

    2013-01-01

    The focus of our research was to provide a comprehensive study of the bacterioplankton populations off the coast of New Jersey near the Rutgers University marine field station using terminal restriction fragment polymorphism analysis (TRFLP) coupled to 16S rRNA genes for large data set studies. Our three revised objectives to this study became: (1) to describe bacterioplankton population dynamics in the Mid Atlantic Bight using TRFLP analysis of 16S rRNA genes. (2) to determine whether spatial and temporal factors are driving bacterioplankton community dynamics in the MAB using monthly samping along our transect line over a 2-year period. (3) to identify dominant members of a coastal bacterioplankton population by clonal library analysis of 16S rDNA genes and sequencing of PCR product corresponding to specific TRFLP peaks in the data set. Although open ocean time-series sites have been areas of microbial research for years, relatively little was known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35m (n=178). The data revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth (figure 2-next page). Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally

  19. Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms.

    PubMed

    Nichols, P D; Henson, J M; Guckert, J B; Nivens, D E; White, D C

    1985-01-01

    Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

  20. Effect of storage conditions on the microbial ecology and biochemical stability of cell wall components in brewers' spent grain.

    PubMed

    Robertson, James A; I'Anson, Kerry J A; Brocklehurst, Tim F; Faulds, Craig B; Waldron, Keith W

    2010-06-23

    The composition of brewers' spent grain (BSG) makes it susceptible to microbial attack and chemical deterioration. This can constrain its appeal as an industrial feedstock. The current study has monitored the effects of BSG storage as fresh material (20 degrees C), refrigerated and autoclaved, measured against frozen material in relation to microbial proliferation and modification to plant cell wall polysaccharides and component phenolic acids. At 20 degrees C there was a rapid colonization by microbes and an associated loss of components from BSG. Refrigeration gave a similar but lower level response. When stored frozen, BSG showed no changes in composition but autoclaving resulted in a solubilization of polysaccharides and associated phenolics. Changes were associated with the temperature profile determined during autoclaving and were also partially due to the breakdown of residual starch. Losses of highly branched arabinoxylan (AX) and the related decrease in ferulic acid cross-linking were also found. The results confirm the need for storage stabilization of BSG and demonstrate that the methods selected for stabilization can themselves lead to a substantial modification to BSG.

  1. A synthetic ecology perspective: How well does behavior of model organisms in the laboratory predict microbial activities in natural habitats?

    SciTech Connect

    Yu, Zheng; Krause, Sascha M. B.; Beck, David A. C.; Chistoserdova, Ludmila

    2016-06-15

    In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified cooccurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. Furthermore, these findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.

  2. DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.

    PubMed

    Hugerth, Luisa W; Wefer, Hugo A; Lundin, Sverker; Jakobsson, Hedvig E; Lindberg, Mathilda; Rodin, Sandra; Engstrand, Lars; Andersson, Anders F

    2014-08-01

    The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571-1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.

  3. Intestinal Cancer

    MedlinePlus

    ... connects your stomach to your large intestine. Intestinal cancer is rare, but eating a high-fat diet ... increase your risk. Possible signs of small intestine cancer include Abdominal pain Weight loss for no reason ...

  4. Intestinal leiomyoma

    MedlinePlus

    Leiomyoma - intestine ... McLaughlin P, Maher MM. The duodenum and small intestine. In: Adam A, Dixon AK, Gillard JH, Schaefer- ... Roline CE, Reardon RF. Disorders of the small intestine. In: Marx JA, Hockberger RS, Walls RM, et ...

  5. Intestinal obstruction

    MedlinePlus

    Paralytic ileus; Intestinal volvulus; Bowel obstruction; Ileus; Pseudo-obstruction - intestinal; Colonic ileus ... objects that are swallowed and block the intestines) Gallstones (rare) Hernias Impacted stool Intussusception (telescoping of 1 ...

  6. Intestinal Obstruction

    MedlinePlus

    An intestinal obstruction occurs when food or stool cannot move through the intestines. The obstruction can be complete or partial. ... abdomen Inability to pass gas Constipation A complete intestinal obstruction is a medical emergency. It often requires surgery. ...

  7. Soil Ecology

    NASA Astrophysics Data System (ADS)

    Killham, Ken

    1994-04-01

    Soil Ecology is designed to meet the increasing challenge faced by today's environmental scientists, ecologists, agriculturalists, and biotechnologists for an integrated approach to soil ecology. It emphasizes the interrelations among plants, animals, and microbes, by first establishing the fundamental physical and chemical properties of the soil habitat and then functionally characterizing the major components of the soil biota and some of their most important interactions. The fundamental principles underpinning soil ecology are established and this then enables an integrated approach to explore and understand the processes of soil nutrient (carbon, nitrogen, and phosphorus) cycling and the ecology of extreme soil conditions such as soil-water stress. Two of the most topical aspects of applied soil ecology are then selected. First, the ecology of soil pollution is examined, focusing on acid deposition and radionuclide pollution. Second, manipulation of soil ecology through biotechnology is discussed, illustrating the use of pesticides and microbial inocula in soils and pointing toward the future by considering the impact of genetically modified inocula on soil ecology.

  8. High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

    PubMed Central

    2013-01-01

    Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described. PMID:23475615

  9. TREATMENT OF LONG-EVANS RATS WITH A DEFINED MIXTURE OF DRINKING WATER DISINFECTION BY-PRODUCTS IMPACTS INTESTINAL MICROBIAL METABOLISM.

    EPA Science Inventory

    Water treatment results in the production of numerous halogenated disinfection by-products (DBPs), and has been associated with human colorectal cancer. Because the intestinal microbiota can bioactivate promutagens and procarcinogens, several studies have been done to examine the...

  10. Phototrophs in high-iron-concentration microbial mats: physiological ecology of phototrophs in an iron-depositing hot spring

    NASA Technical Reports Server (NTRS)

    Pierson, B. K.; Parenteau, M. N.; Griffin, B. M.

    1999-01-01

    At Chocolate Pots Hot Springs in Yellowstone National Park the source waters have a pH near neutral, contain high concentrations of reduced iron, and lack sulfide. An iron formation that is associated with cyanobacterial mats is actively deposited. The uptake of [(14)C]bicarbonate was used to assess the impact of ferrous iron on photosynthesis in this environment. Photoautotrophy in some of the mats was stimulated by ferrous iron (1.0 mM). Microelectrodes were used to determine the impact of photosynthetic activity on the oxygen content and the pH in the mat and sediment microenvironments. Photosynthesis increased the oxygen concentration to 200% of air saturation levels in the top millimeter of the mats. The oxygen concentration decreased with depth and in the dark. Light-dependent increases in pH were observed. The penetration of light in the mats and in the sediments was determined. Visible radiation was rapidly attenuated in the top 2 mm of the iron-rich mats. Near-infrared radiation penetrated deeper. Iron was totally oxidized in the top few millimeters, but reduced iron was detected at greater depths. By increasing the pH and the oxygen concentration in the surface sediments, the cyanobacteria could potentially increase the rate of iron oxidation in situ. This high-iron-content hot spring provides a suitable model for studying the interactions of microbial photosynthesis and iron deposition and the role of photosynthesis in microbial iron cycling. This model may help clarify the potential role of photosynthesis in the deposition of Precambrian banded iron formations.

  11. A synthetic ecology perspective: How well does behavior of model organisms in the laboratory predict microbial activities in natural habitats?

    DOE PAGES

    Yu, Zheng; Krause, Sascha M. B.; Beck, David A. C.; ...

    2016-06-15

    In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sedimentmore » for a few decades and have identified a number of species genetically equipped for this activity. We have also identified cooccurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. Furthermore, these findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.« less

  12. Molting in Salmonella Enteritidis-challenged laying hens fed alfalfa crumbles. II. Fermentation and microbial ecology response.

    PubMed

    Dunkley, K D; McReynolds, J L; Hume, M E; Dunkley, C S; Callaway, T R; Kubena, L F; Nisbet, D J; Ricke, S C

    2007-10-01

    The objective of this study was to examine microbial population shifts and short-chain fatty acid (SCFA) responses in the gastrointestinal tract of Salmonella Enteritidis-challenged molted and nonmolted hens fed different dietary regimens. Fifteen Salmonella-free Single Comb Leghorn hens (>50 wk old) were assigned to 3 treatment groups of 5 birds each based on diet in 2 trials: 100% alfalfa crumbles (ALC), full-fed (FF, nonmolted) 100% commercial layer ration, and feed withdrawal (FW). A forced molt was induced by either a 12-d alfalfa diet or FW. In all treatment groups, each hen was challenged by crop gavage orally 4 d after molt induction with a 1-mL inoculum containing 10(6) cfu of Salmonella Enteritidis. Fecal and cecal samples (d 4, 6, 8, 11, and necropsy on d 12) were collected postchallenge. Microbial population shifts were evaluated by PCR-based 16S ribosomal RNA gene amplification and denaturing gradient gel electrophoresis, and SCFA concentrations were measured. Total SCFA in fecal and cecal contents for FW molted hens were generally lower (P < or = 0.05) in the later stages of the molt period when compared to ALC and FF treatment groups. The overall trend of SCFA in cecal and fecal samples exhibited similar patterns. In trials 1 and 2, hens molted with ALC diet generally yielded more similar amplicon band patterns with the FF hens in both fecal and cecal samples by the end of the molting period than with FW hens. The results of these studies suggest that ALC molted hens supported microflora and fermentation activities, which were more comparable to FF hens than FW hens by the end of the molting period.

  13. Improvements of polymerase chain reaction and capillary electrophoresis single-strand conformation polymorphism methods in microbial ecology: toward a high-throughput method for microbial diversity studies in soil.

    PubMed

    Zinger, Lucie; Gury, Jérôme; Giraud, Frédéric; Krivobok, Serge; Gielly, Ludovic; Taberlet, Pierre; Geremia, Roberto A

    2007-08-01

    The molecular signature of bacteria from soil ecosystems is an important tool for studying microbial ecology and biogeography. However, a high-throughput technology is needed for such studies. In this article, we tested the suitability of available methods ranging from soil DNA extraction to capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) for high-throughput studies. Our results showed that the extraction method does not dramatically influence CE-SSCP profiles, and that DNA extraction of a 0.25 g soil sample is sufficient to observe overall bacterial diversity in soil matrices. The V3 region of the 16S rRNA gene was amplified by PCR, and the extension time was found to be critical. We have also found that proofreading DNA polymerases generate a better signal in CE-SSCP profiles. Experiments performed with different soil matrices revealed the repeatability, efficiency, and consistency of CE-SSCP. Studies on PCR and CE-SSCP using single-species genomic DNA as a matrix showed that several ribotypes may migrate at the same position, and also that single species can produce double peaks. Thus, the extrapolation between number of peaks and number of species remains difficult. Additionally, peak detection is limited by the analysis software. We conclude that the presented method, including CE-SSCP and the analyzing step, is a simple and effective technique to obtain the molecular signature of a given soil sample.

  14. Health relevance of intestinal protein fermentation in young pigs.

    PubMed

    Pieper, R; Villodre Tudela, C; Taciak, M; Bindelle, J; Pérez, J F; Zentek, J

    2016-12-01

    The physiological role of the gastrointestinal microbiota has become an important subject of nutrition research in pigs in the past years, and the importance of intestinal microbial activity in the etiology of disease is doubtless. This review summarizes the recent knowledge related to the microbial ecology of protein fermentation and the appearance of protein-derived metabolites along the pig intestine. The amount of fermentable protein depends on factors such as dietary protein concentration, protein digestibility due to secondary or tertiary structure, the interaction with dietary compounds or anti-nutritional factors, and the secretion of endogenous proteins into the gut lumen. High protein diets increase the luminal concentrations and epithelial exposure to putatively toxic metabolites and increase the risk for post-weaning diarrhea, but the mechanisms are not yet clarified. Although the use of fermentable carbohydrates to reduce harmful protein-derived metabolites in pigs is well-established, recent studies suggest that the inclusion of fermentable carbohydrates into diets with low protein digestibility or high dietary protein level may not ameliorate all negative effects with regard to epithelial response. Based on the current knowledge, the use of diets with low levels of high-quality protein may help to reduce the risk for intestinal disease in young pigs.

  15. Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology

    PubMed Central

    Ufarté, Lisa; Potocki-Veronese, Gabrielle; Laville, Élisabeth

    2015-01-01

    The rapid expansion of new sequencing technologies has enabled large-scale functional exploration of numerous microbial ecosystems, by establishing catalogs of functional genes and by comparing their prevalence in various microbiota. However, sequence similarity does not necessarily reflect functional conservation, since just a few modifications in a gene sequence can have a strong impact on the activity and the specificity of the corresponding enzyme or the recognition for a sensor. Similarly, some microorganisms harbor certain identified functions yet do not have the expected related genes in their genome. Finally, there are simply too many protein families whose function is not yet known, even though they are highly abundant in certain ecosystems. In this context, the discovery of new protein functions, using either sequence-based or activity-based approaches, is of crucial importance for the discovery of new enzymes and for improving the quality of annotation in public databases. This paper lists and explores the latest advances in this field, along with the challenges to be addressed, particularly where microfluidic technologies are concerned. PMID:26097471

  16. Effects of pH and ORP on microbial ecology and kinetics for hydrogen production in continuously dark fermentation.

    PubMed

    Song, Jiaxiu; An, Dong; Ren, Nanqi; Zhang, Yongming; Chen, Ying

    2011-12-01

    The microbial structure and kinetic characteristics of the hydrogen producing strains in two fermentative continuous stirred-tank reactors (CSTRs) were studied by controlling pH and oxidation and reduction potential (ORP). The fluorescence in situ hybridization (FISH) tests were conducted to investigate the fermentative performance of Clostridium histolyticum (C. histolyticum), Clostridium lituseburense (C. lituseburense) and Enterobacteriaceae. The experimental results showed that in ethanol-type reactor 1#, the relative abundance of the strains was 48%, 30% and 22%. Comparatively, the relative abundance in butyric acid-type reactor 2# was 24%, 55% and 19% with butyric acids and hydrogen as the main products. The kinetic results indicated that the hydrogen yield coefficients YP/X in both reactors were 8.357 and 5.951 l-H2/g, while the coefficients of the cellular yield were 0.0268 and 0.0350 g-Cell/g, respectively. At the same biomass, the hydrogen yield in ethanol-type reactors was more than that in butyric acid reactors. However, the cellular synthesis rate in ethanol-type reactors was low when the same carbon source was used.

  17. Effects of Physical Properties of Feed on Microbial Ecology and Survival of Salmonella enterica Serovar Typhimurium in the Pig Gastrointestinal Tract

    PubMed Central

    Mikkelsen, Lene Lind; Naughton, Patrick J.; Hedemann, Mette S.; Jensen, Bent Borg

    2004-01-01

    A two-by-two factorial experiment with pigs was conducted to study the effect of feed grinding (fine and coarse) and feed processing (pelleted and nonpelleted) on physicochemical properties, microbial populations, and survival of Salmonella enterica serovar Typhimurium DT12 in the gastrointestinal tracts of pigs. Results demonstrated a strong effect of diet on parameters measured in the stomachs of the pigs, whereas the effect was less in the other parts of the gastrointestinal tract. Pigs fed the coarse nonpelleted (C-NP) diet showed more solid gastric content with higher dry matter content than pigs fed the fine nonpelleted (F-NP), coarse pelleted (C-P), or fine pelleted (F-P) diet. Pigs fed the C-NP diet also showed significantly increased number of anaerobic bacteria (P < 0.05), increased concentrations of organic acids, and reduced pH in the stomach. In addition, pigs fed the C-NP diet showed increased in vitro death rate of S. enterica serovar Typhimurium DT12 in content from the stomach (P < 0.001). Pigs fed the C-NP diet had a significantly higher concentration of undissociated lactic acid in gastric content than pigs fed the other diets (P < 0.001). A strong correlation between the concentration of undissociated lactic acid and the death rate of S. enterica serovar Typhimurium DT12 was found. In the distal small intestine, cecum, and midcolon, significantly lower numbers of coliform bacteria were observed in pigs fed the coarse diets than in pigs fed the fine diets (P < 0.01). Pigs fed the C-NP diet showed the lowest number of coliform bacteria in these segments of the gastrointestinal tract. Pigs fed the coarse diets showed increased concentration of butyric acid in the cecum (P < 0.05) and colon (P < 0.10) compared with pigs fed the fine diets. It was concluded that feeding a coarsely ground meal feed to pigs changes the physicochemical and microbial properties of content in the stomach, which decreases the survival of Salmonella during passage through

  18. Impact of inocula and growth mode on the molecular microbial ecology of anaerobic ammonia oxidation (anammox) bioreactor communities.

    PubMed

    Park, Hongkeun; Rosenthal, Alex; Jezek, Roland; Ramalingam, Krish; Fillos, John; Chandran, Kartik

    2010-09-01

    The composition of distinctly inoculated granular anammox and biofilm-based completely autotrophic nitrogen removal over nitrite (CANON) bioreactors was investigated from start-up through continuous long-term operation via denaturing gradient gel electrophoresis (DGGE) and sequencing. The granular anammox reactor was seeded with sludge from an operational anammox reactor in Strass, Austria. The CANON reactor was seeded with activated sludge from a local wastewater treatment plant in New York City. The principal anammox bacteria (AMX) shifted from members related to Kuenenia stuttgartiensis present in the initial inoculum to members related to Candidatus Brocadia fulgida during pre-enrichment (before this study) and to members related to Candidatus Brocadia sp. 40 (during this study) in the granular reactor. AMX related to C. Brocadia sp. 40 were also enriched from activated sludge in the CANON reactor. The estimated doubling times of AMX in the granular and CANON reactors were 5.3 and 8.9 days, respectively, which are lower than the value of 11 days, reported previously. Both the granular anammox and CANON reactors also fostered significant amounts of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). The fractions of AMX and two groups of NOB were generally similar in the granular anammox and CANON reactors. However, the diversity and fractions of AOB in the two reactors was markedly different. Therefore, it is suggested that the composition of the feed and extant substrate concentrations in the reactor likely select for the microbial community composition more than the inocula and reactor configuration. Further, such selection is not equivalent for all resident communities.

  19. Changes in gut microbial populations, intestinal morphology, expression of tight junction proteins, and cytokine production between two pig breeds after challenge with Escherichia coli K88: a comparative study.

    PubMed

    Gao, Y; Han, F; Huang, X; Rong, Y; Yi, H; Wang, Y

    2013-12-01

    This study hypothesized that the gut microbial populations, intestinal morphology, and cytokine production are differentially altered in 2 different pig breeds, namely, Chinese native Jinhua pigs and European Landrace pigs, after orally challenge with enterotoxigenic Escherichia coli (ETEC) K88. A total of 12 Jinhua pigs and 12 Landrace pigs were allocated to either the nonchallenged or the challenged groups (6 pigs per group). The challenged pigs were orally administered ETEC K88, and their nonchallenged counterparts were given sterile Luria-Bertani broth. Selected gut microbial populations, intestinal morphology, mRNA expression of tight junction proteins, and the levels of ileal cytokines and secretory immunoglobulin A (sIgA) production were measured in Jinhua and Landrace pigs. The results showed that the challenged Jinhua pigs exhibited a significantly (P < 0.05) lower incidence of diarrhea compared with their Landrace counterparts. The Escherichia coli (E.coli) population and the percentage of E. coli in the total bacteria population were increased in response to ETEC K88 challenge in both Jinhua and Landrace pigs. The challenged Landrace pigs shed more E. coli (P < 0.05) and had higher percentage of E. coli in the total bacteria population in the colon (P < 0.05) compared with their Jinhua counterparts. Both pig breeds tended to exhibit greater villous atrophy and crypt depth reduction in all of the intestinal segments with challenge. The expression of tight junction proteins decreased in response to ETEC K88 challenge in both pig breeds. The levels of the proinflammatory cytokines interferon (IFN)-γ, tumor necrosis factor-α, and IL-6 and the secretion of sIgA were positively altered whereas the levels of the anti-inflammatory cytokine IL-4 and transforming growth factor (TGF)-β were negatively altered by ETEC K88 challenge in both breeds. Jinhua pigs exhibited significantly higher levels of IFN-γ and TGF-β (P < 0.05) in the challenged group. Our

  20. Functional Molecular Ecological Networks

    PubMed Central

    Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-01-01

    Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. PMID:20941329

  1. Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model

    PubMed Central

    Ribière, Céline; Peyret, Pierre; Parisot, Nicolas; Darcha, Claude; Déchelotte, Pierre J.; Barnich, Nicolas; Peyretaillade, Eric; Boucher, Delphine

    2016-01-01

    Gut microbiota dysbiosis are associated with a wide range of human diseases, including inflammatory bowel diseases. The physiopathology of these diseases has multifactorial aetiology in which environmental factors, particularly pollution could play a crucial role. Among the different pollutants listed, Polycyclic Aromatic Hydrocarbons (PAHs) are subject to increased monitoring due to their wide distribution and high toxicity on Humans. Here, we used 16S rRNA gene sequencing to investigate the impact of benzo[a]pyrene (BaP, most toxic PAH) oral exposure on the faecal and intestinal mucosa-associated bacteria in C57BL/6 mice. Intestinal inflammation was also evaluated by histological observations. BaP oral exposure significantly altered the composition and the abundance of the gut microbiota and led to moderate inflammation in ileal and colonic mucosa. More severe lesions were observed in ileal segment. Shifts in gut microbiota associated with moderate inflammatory signs in intestinal mucosa would suggest the establishment of a pro-inflammatory intestinal environment following BaP oral exposure. Therefore, under conditions of genetic susceptibility and in association with other environmental factors, exposure to this pollutant could trigger and/or accelerate the development of inflammatory pathologies. PMID:27503127

  2. Terpenes tell different tales at different scales: glimpses into the Chemical Ecology of conifer - bark beetle - microbial interactions.

    PubMed

    Raffa, Kenneth F

    2014-01-01

    , biochemical time), relationships among inducible and constitutive defenses, population dynamics, and plastic host-selection behavior (stand level, ecological time), and climate-driven range expansion of a native eruptive species into semi-naïve and potentially naïve habitats (geographical level, evolutionary time). I approach this problem by focusing primarily on one chemical group, terpenes, by emphasizing the curvilinear and threshold-structured basis of most underlying relationships, and by focusing on the system's feedback structure, which can either buffer or amplify relationships across scales.

  3. Antibiotic Resistance in Animal-waste-impacted Farm Soil: From Molecular Mechanisms to Microbial Evolution and Ecology

    NASA Astrophysics Data System (ADS)

    You, Y.; Ward, M. J.; Hilpert, M.

    2012-12-01

    Antibiotic resistance is a growing public health problem worldwide and the routine use of antibiotics in industrial animal production has sparked debate on whether this practice might constitute an environmental and public health concern. At a broiler farm, electromagnetic induction (EMI) surveying assisted soil sampling from a chicken-waste-impacted site and a marginally affected site. Consistent with the EMI survey, disparity existed between the two sites with regard to soil pH, tetracycline resistance (TcR) levels among heterotrophic culturable soil bacteria, and the incidence/prevalence of a number of tet and erm genes in the soils. No significant difference was observed in these aspects between the marginally affected site and several sites in a regional state forest that has not been in agricultural use for decades. Shortly after our sampling, the farm closed down and all the waste was removed. This unique change in situation offered us an unusual opportunity to examine the reversibility of any impact of the chicken waste on the soil microbial community. Two years after the event, several antibiotic resistance genes (ARGs) were still detected in the waste-impacted soil, and quantitative real-time PCR (qPCR) data showed that their relative abundance remained at substantial levels. A mobilizable tet(L)-carrying plasmid, pSU1, was identified in several chicken-waste-exposed soil bacteria of three different genera. Quantification of the plasmid's mobilization gene suggested that pSU1 had contributed to the prevalence and persistence of tet(L) in the waste-impacted soil. A second mobilizable tet(L)-carrying plasmid, pBSDMV9, isolated from the same soil, contained a region with 98.8% nucleotide identity to pSU1. The mosaic structure of the plasmids and the highly conserved nature of the tet(L) genes suggested that plasmid rearrangement favoring the acquisition of tet(L) may have occurred in the soil relatively recently. Additionally, in one chicken

  4. Why Microbial Communities?

    ScienceCinema

    Fredrickson, Jim (PNNL)

    2016-07-12

    The Microbial Communities Initiative is a 5-year investment by Pacific Northwest National Laboratory that integrates biological/ecological experimentation, analytical chemistry, and simulation modeling. The objective is to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities. Dr. Fredrickson introduces the symposium by defining microbial communities and describing their scientific relevance as they relate to solving problems in energy, climate, and sustainability.

  5. Altitudinal Contrasts in Drought-Driven Aeolian Microbial Inputs to Montane Soil Ecology: Impacts of a 500-Year Drought in the Sierra Nevada, California

    NASA Astrophysics Data System (ADS)

    Aronson, E. L.; Carey, C.; Riebe, C. S.; Aciego, S.; Hart, S. C.

    2014-12-01

    Mounting evidence shows that California is currently experiencing the most severe drought since 1580, and it is likely that extreme droughts will become more common as the climate changes. Any drought - particularly one of this magnitude - can elevate dust transport, from fallow croplands and bare natural ecosystems, to sometimes distant locations. The transported dust may bring nutrients and microorganisms, with unknown, but potentially transformational, impacts on the ecosystems where dust is deposited. In this project, we are measuring the mass, provenance (using isotopic chemistry), chemical makeup, and microbial composition of dust transported to the Sierra Nevada mountain range. Dust is being collected at three sites along an elevational gradient in the Southern Sierra Critical Zone Observatory (SSCZO), ranging from 400 m to 2000 m elevation. At each site, dust has been collected monthly in Summer 2014 from passive dust collectors and from filters (1 um pore size) on the eddy covariance tower active CO2 samplers. To complement dust collection, soil samples (10 cm depth) have been collected within the footprint of the towers. Dust fluxes were found to be highest at the 2000 meter-high site, with a maximum of 231 mg dust collected in July 2014. The lowest dust fluxes were found at the medium elevation site, at 1100 m, with 21 mg dust in July. The provenance of dust samples will be determined using radiogenic strontium (Sr) and neodymium (Nd) isotopic tracers. Nutrients and microbial composition of dust and soil samples will also be analyzed. This approach will allow us to identify the effects of mega-droughts on i) dust-related contributions to the geobiology and biogeochemistry of soils and ecosystems, ii) the role of local versus distant dust sources of microorganisms, including bacteria, archaea and fungi, and of nutrients to the Sierra Nevada, and iii) the role of elevation in determining the ecological effects of mega-drought-induced dust transport. In the

  6. [Intestinal microbiota].

    PubMed

    Perez, Horacio Joaquín; Menezes, Maria Elisabeth; d'Acâmpora, Armando José

    2014-01-01

    There is accumulative evidence on the multiple functions of the intestinal microflora in relation to the homeostasis of the host. At first considered as a simple mutualism, today this relationship proves to be essential to the health and to pathologic processes, particularly metabolic (eg, obesity) and gastrointestinal (eg, inflammatory bowel disease and functional disorders). The first studies were conducted on the microbiota from fecal material cultured anaerobically. With the advent of molecular biology, it has become possible to determine qualitative and quantitatively the dominant, subdominant and transients species. In recent years, there were advances in the understanding of the relationship betwen the microbiota and the host, as well as among the microorganisms in their respective niches. These advances result from translational integration of microbiology with specialities such as molecular biology, cell phisiology, immunology and ecology. There are few studies on the spatial distribution of the microflora in the gut. Unravelling the topography of the microflora in mammals is a way to validate new animal models for the study of microflora.

  7. High-fat diet modifies the PPAR-γ pathway leading to disruption of microbial and physiological ecosystem in murine small intestine

    PubMed Central

    Tomas, Julie; Mulet, Céline; Saffarian, Azadeh; Cavin, Jean-Baptiste; Ducroc, Robert; Regnault, Béatrice; Kun Tan, Chek; Duszka, Kalina; Burcelin, Rémy; Wahli, Walter; Sansonetti, Philippe J.; Pédron, Thierry

    2016-01-01

    Diet is among the most important factors contributing to intestinal homeostasis, and basic functions performed by the small intestine need to be tightly preserved to maintain health. Little is known about the direct impact of high-fat (HF) diet on small-intestinal mucosal defenses and spatial distribution of the microbiota during the early phase of its administration. We observed that only 30 d after HF diet initiation, the intervillous zone of the ileum—which is usually described as free of bacteria—became occupied by a dense microbiota. In addition to affecting its spatial distribution, HF diet also drastically affected microbiota composition with a profile characterized by the expansion of Firmicutes (appearance of Erysipelotrichi), Proteobacteria (Desulfovibrionales) and Verrucomicrobia, and decrease of Bacteroidetes (family S24-7) and Candidatus arthromitus. A decrease in antimicrobial peptide expression was predominantly observed in the ileum where bacterial density appeared highest. In addition, HF diet increased intestinal permeability and decreased cystic fibrosis transmembrane conductance regulator (Cftr) and the Na-K-2Cl cotransporter 1 (Nkcc1) gene and protein expressions, leading to a decrease in ileal secretion of chloride, likely responsible for massive alteration in mucus phenotype. This complex phenotype triggered by HF diet at the interface between the microbiota and the mucosal surface was reversed when the diet was switched back to standard composition or when mice were treated for 1 wk with rosiglitazone, a specific agonist of peroxisome proliferator-activated receptor-γ (PPAR-γ). Moreover, weaker expression of antimicrobial peptide-encoding genes and intervillous bacterial colonization were observed in Ppar-γ–deficient mice, highlighting the major role of lipids in modulation of mucosal immune defenses. PMID:27638207

  8. Intestinal Obstruction

    MedlinePlus

    ... Wall Hernias Inguinal Hernia Acute Mesenteric Ischemia Appendicitis Ileus Intestinal Obstruction Ischemic Colitis Perforation of the Digestive ... Wall Hernias Inguinal Hernia Acute Mesenteric Ischemia Appendicitis Ileus Intestinal Obstruction Ischemic Colitis Perforation of the Digestive ...

  9. Simultaneous UPLC-MS/MS analysis of native catechins and procyanidins and their microbial metabolites in intestinal contents and tissues of male Wistar Furth inbred rats.

    PubMed

    Goodrich, Katheryn M; Neilson, Andrew P

    2014-05-01

    Procyanidins have been extensively investigated for their potential health protective activities. However, the potential bioactivities of procyanidins are limited by their poor bioavailability. The majority of the ingested dose remains unabsorbed and reaches the colon where extensive microbial metabolism occurs. Most existing analytical methods measure either native compounds (catechins and procyanidins), or their microbial metabolites. The objectives of this study were to develop a high-throughput extraction and UPLC-MS/MS method for simultaneous measurement of both native procyanidins and their metabolites, facilitating high-throughput analysis of native and metabolite profiles in various regions of the colon. The present UPLC-MS/MS method facilitates simultaneous resolution and detection of authentic standards of 14 native catechin monomers and procyanidins, as well as 24 microbial metabolites. Detection and resolution of an additional 3 procyanidin dimers and 10 metabolites for which standards were not available was achieved. Elution and adequate resolution of both native compounds and metabolites were achieved within 10min. The intraday repeatability for native compounds was between 1.1 and 16.5%, and the interday repeatability for native compounds was between 2.2 and 25%. Intraday and interday repeatability for metabolites was between 0.6 and 24.1% and 1 and 23.9%, respectively. Observed lower limits of quantification for native compounds were ∼9-350fmol on-column, and for the microbial metabolites were ∼0.8-12,000fmol on-column. Observed lower limits of detection for native compounds were ∼4.5-190fmol on-column, and for metabolites were 0.304-6020fmol on-column. For native monomers and procyanidins, extraction recoveries ranged from 38 to 102%. Extraction recoveries for the 9 microbial metabolites tested ranged from 41 to 95%. Data from tissue analysis of rats gavaged with grape seed extract indicate fairly high accumulation of native compounds

  10. A new arhythmacanthid species (Acanthocephala) in the intestine of Symphurus plagiusa and Ciclopsetta chittendeni from the coast of Campeche, Mexico, with ecological and histopathological observations.

    PubMed

    Santana-Piñeros, Ana María; Cruz-Quintana, Yanis; Centeno-Chalé, Oscar Arturo; Vidal-Martínez, Victor M

    2013-10-01

    A new species of Acanthocephaloides was recovered in the intestine of Symphurus plagiusa, the blackcheek tonguefish, and Cyclopsetta chittendeni, the Mexican flounder, from the Campeche coast, Mexico. The new species is characterized by having proboscis hooks arranged in 14 to 16 longitudinal rows, with 6-7 rooted hooks per row, a trunk covered with small cuticular spines (except in the zone of gonopore or bursa), a bursa without sensory structures, and the relative position of male post-equatorial reproductive system. The prevalence of Acanthocephaloides plagiusae n. sp. from S. plagiusa was low (0-7.3%) from July to October and high (29.4-40%) in November, January, and March. Similarly, the prevalence of A. plagiusae n. sp. from Cyclopsetta chittendeni was low (1.7%) in July and high (5.8%) March. Both hosts exhibited low (0.1-3.4) mean abundance. The variation in prevalence could be explained by the seasonal freshwater discharge from rivers, which affects the dispersal of parasites and the distribution of the host. Pathology changes, such as inflammation, loss of intestinal folds, increased mucous and rodlet cells, and detachment of intestinal epithelium, were associated with the proboscis hooks and spiny surface of A. plagiusae. This is the first record of an Acanthocephaloides species from a Mexican coastal zone.

  11. Bacillus species in the intestine of termites and other soil invertebrates.

    PubMed

    König, H

    2006-09-01

    Soil invertebrates harbour a complex microbial community in their intestinal system. The total number of microbes in the hindgut of soil invertebrates can reach a titre of 10(11) ml(-1). The gut microbes play an indispensable role in the digestion of food and are of ecological importance in the global carbon cycle. The gut microbiota can include a variety of micro-organisms from the three domains Bacteria, Archaea and Eucarya. The bacterial groups from the intestinal systems are mainly affiliated to the proteobacteria, the gram-positive groups Firmicutes and Actinobacteria, the Bacteroides/Flavobacterium branch and the spirochetes. The Archaea are represented by methanogens. The eukaryotic groups consist of protozoa, yeasts and fungi. Intestinal bacteria are involved in the degradation of cellulose, hemicellulose and aromatic compounds as well as nitrogen fixation. They also contribute to the redox status of the gut. Bacilli form a significant portion of the intestinal microbial community of soil invertebrates, especially among cellulose degraders. The diversity and function of bacilli in soil invertebrates will be discussed in this paper.

  12. Synthetic Small Intestinal Scaffolds for Improved Studies of Intestinal Differentiation

    PubMed Central

    Costello, Cait M.; Hongpeng, Jia; Shaffiey, Shahab; Yu, Jiajie; Jain, Nina K.; Hackam, David

    2014-01-01

    In vitro intestinal models can provide new insights into small intestinal function, including cellular growth and proliferation mechanisms, drug absorption capabilities, and host-microbial interactions. These models are typically formed with cells cultured on 2D scaffolds or transwell inserts, but it is widely understood that epithelial cells cultured in 3D environments exhibit different phenotypes that are more reflective of native tissue. Our focus was to develop a porous, synthetic 3D tissue scaffold with villous features that could support the culture of epithelial cell types to mimic the natural microenvironment of the small intestine. We demonstrated that our scaffold could support the co-culture of Caco-2 cells with a mucus-producing cell line, HT29-MTX, as well as small intestinal crypts from mice for extended periods. By recreating the surface topography with accurately sized intestinal villi, we enable cellular differentiation along the villous axis in a similar manner to native intestines. In addition, we show that the biochemical microenvironments of the intestine can be further simulated via a combination of apical and basolateral feeding of intestinal cell types cultured on the 3D models. PMID:24390638

  13. MICROBIAL ECOLOGY OF POLLUTION ABATEMENT

    EPA Science Inventory

    My career started with Cliff Dahm at the University of New Mexico. The western United States had been experiencing a new “gold rush” using cyanide to mine previously unextractable, low-grade ore and we studied the potential to stimulate native cyanide-degrading micro...

  14. Understanding Microbial Communities: Function, Structure and Dynamics

    DTIC Science & Technology

    2015-02-11

    Park, NC 27709-2211 Conference grant, microbial ecology , biomathematics REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10...Wilmes. Challenges in Microbial Ecology : building predictive understanding, ISME Journal (06 2015) TOTAL: 1 Books Number of Manuscripts: Patents...a one day ’Open for business’ day which was attended by both industrial representatives interested in microbial ecology and academics. Final progress

  15. Population dynamics of microbial communities in the zebrafish gut

    NASA Astrophysics Data System (ADS)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Hampton, Jennifer; Rolig, Annah; Wiles, Travis; Guillemin, Karen; Parthasarathy, Raghuveer

    2015-03-01

    The vertebrate intestine is home to a diverse microbial community, which plays a crucial role in the development and health of its host. Little is known about the population dynamics and spatial structure of this ecosystem, including mechanisms of growth and interactions between species. We have constructed an experimental model system with which to explore these issues, using initially germ-free larval zebrafish inoculated with defined communities of fluorescently tagged bacteria. Using light sheet fluorescence microscopy combined with computational image analysis we observe and quantify the entire bacterial community of the intestine during the first 24 hours of colonization, during which time the bacterial population grows from tens to tens of thousands of bacteria. We identify both individual bacteria and clusters of bacteria, and quantify the growth rate and spatial distribution of these distinct subpopulations. We find that clusters of bacteria grow considerably faster than individuals and are located in specific regions of the intestine. Imaging colonization by two species reveals spatial segregation and competition. These data and their analysis highlight the importance of spatial organization in the establishment of gut microbial communities, and can provide inputs to physical models of real-world ecological dynamics.

  16. IN SITU BIOREMEDIATION OF TRICHLOROETHYLENE USING BURKHOLDERIA CEPACIA G4 PR1: ANALYSIS OF MICROBIAL ECOLOGY PARAMETERS FOR RISK ASSESSMENT (RESEARCH BRIEF)

    EPA Science Inventory

    The introduction of bacteria into aquifers for bioremediation purposes requires monitoring of the persistence and activity of microbial populations for efficacy and risk assessment purposes. Burkholderia cepacia G4 PR1 constitutively expresses a toluene ortho-monooxygenase (tom) ...

  17. Prevalence of the gastro-intestinal parasites of domestic chicken Gallus domesticus Linnaeus, 1758 in Tunisia according to the agro-ecological zones.

    PubMed

    Ben Slimane, Badreddine

    2016-09-01

    Helminthosis is a very important disease affecting the poultry industry, especially the traditionally reared free ranging chickens. In Tunisia, the poultry production is considered as the most important source of protein in as much as chickens provide 53 % of animal protein production. The traditionally reared poultry farming system exposes chickens to many types of parasites, however, very little work has been done to establish the extend of helminth infection in Tunisia. The aim of this work is to investigate various aspects of helminth infections. A significant difference (p < 0.01) was found between the prevalence rates of helminth parasites in the different agro-ecological zones. The highest prevalence was observed in lowland areas of northern Tunisia (Siliana district). This suggests that agro-ecology has a major influence on the distribution of helminth parasites. Recovered nematodes included Heterakis spp. (100 %), Ascaridia galli (53.33 %) and Acuaria hamulosa (37 %). The principal cestode species encountered were Hymenolepis spp. (73.33 %) and Raillietina spp. (33.33 %).

  18. Fermented and extruded wheat bran in piglet diets: impact on performance, intestinal morphology, microbial metabolites in chyme and blood lipid radicals.

    PubMed

    Kraler, Manuel; Schedle, Karl; Schwarz, Christiane; Domig, Konrad J; Pichler, Martin; Oppeneder, Alexander; Wetscherek, Wolfgang; Prückler, Michael; Pignitter, Marc; Pirker, Katharina F; Somoza, Veronika; Heine, Daniel; Kneifel, Wolfgang

    2015-01-01

    The aim of the present study was to evaluate the influence of native, fermented and extruded wheat bran on the performance and intestinal morphology of piglets. Additionally, short-chain fatty acids (SCFA), biogenic amines, ammonia, lactic acid, pH as well as E. coli and lactic acid bacterial counts were analysed in digesta samples from three gut sections. Furthermore, the antioxidant potential in blood samples was evaluated based on the lipid radicals formed. For this purpose, 48 newly weaned piglets (28 d old) were allocated to one of the four different dietary treatment groups: no wheat bran (Control), native wheat bran, fermented wheat bran as well as extruded wheat bran. Wheat bran variants were included at 150 g/kg into the diets. All diets were mixed to reach the calculated isonitrogenic nutrient contents. Gut tissue and digesta samples were collected from the proximal jejunum, the terminal ileum and the colon ascendens, blood samples directly at slaughter. Although none of the dietary interventions had an impact on performance parameters, the amount of goblet cells in the ileum was increased upon feeding native and extruded wheat bran, compared to fermented bran (p < 0.05). The E. coli counts in colonic chyme were significantly lower (p < 0.05) in the Control group compared to the groups fed with wheat bran. The concentration of SCFA showed differences for minor compounds (p < 0.05), while linear contrast analyses revealed a reduced concentration of total SCFA in the colon following the feeding of modified wheat bran compared to native wheat bran. This may suggest that several compounds are more easily digested already in the ileum, resulting in a reduced nutrient flow into the large intestine and therefore less unexploited digesta is available as substrate for the microorganisms there. Fermentation also resulted in a significant decrease of methylamine in the colon (p < 0.05), while other biogenic amines in the ileum and colon showed no

  19. Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure.

    PubMed

    Rungrassamee, Wanilada; Klanchui, Amornpan; Maibunkaew, Sawarot; Karoonuthaisiri, Nitsara

    2016-01-01

    . Our findings provide evidence of intestinal bacterial population altered by a presence of the pathogen in shrimp intestines and intestinal bacterial stability might provide colonization resistance against the invading pathogen in the host shrimp. Hence, intestinal microbial ecology management may potentially contribute to disease prevention in aquaculture.

  20. Intestinal Parasitoses.

    ERIC Educational Resources Information Center

    Lagardere, Bernard; Dumburgier, Elisabeth

    1994-01-01

    Intestinal parasites have become a serious public health problem in tropical countries because of the climate and the difficulty of achieving efficient hygiene. The objectives of this journal issue are to increase awareness of the individual and collective repercussions of intestinal parasites, describe the current conditions of contamination and…

  1. Effectiveness of Phytogenic Feed Additive as Alternative to Bacitracin Methylene Disalicylate on Hematological Parameters, Intestinal Histomorphology and Microbial Population and Production Performance of Japanese Quails

    PubMed Central

    Manafi, M.; Hedayati, M.; Khalaji, S.

    2016-01-01

    This study was conducted to evaluate the effects of phytogenic additive and antibiotic growth promoter in laying Japanese quails. One hundred and sixty five quails were divided into three groups of 5 replicates and 11 quails (8 females and 3 males) in each replicate. Treatment 1 was fed control diet, treatment 2 was fed control diet supplemented with 0.05% bacitracin methylene disalicylate as antibiotic growth promoter and treatment 3 was fed control diet supplemented with 0.1% phytogenic feed additive (PFA) for two periods of 3 weeks each from 37 to 42 weeks of age. Results showed that egg production, eggshell strength, eggshell weight, villus height and villus height to crypt depth ratio were significantly (p≤0.05) increased and feed consumption, feed conversion ratio, albumen, Haugh unit, cholesterol, low-density lipoprotein, alanine transaminase, gamma glutamyltransferase, alkaline phosphatase, high-density lipoprotein, triglyceride, number of goblet cell, crypt depth and intestinal bacterial population of Coliforms, Salmonella and E. coli were significantly (p≤0.05) decreased in PFA fed group. It is concluded that addition of PFA containing phytomolecules and organic acids as main ingredients could significantly improve the production parameters and the general health of laying quails as an alternative to antibiotic growth promoters. PMID:27189636

  2. Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard.

    PubMed

    Kohl, Kevin D; Brun, Antonio; Magallanes, Melisa; Brinkerhoff, Joshua; Laspiur, Alejandro; Acosta, Juan Carlos; Bordenstein, Seth R; Caviedes-Vidal, Enrique

    2016-06-15

    While herbivory is a common feeding strategy in a number of vertebrate classes, less than 4% of squamate reptiles feed primarily on plant material. It has been hypothesized that physiological or microbial limitations may constrain the evolution of herbivory in lizards. Herbivorous lizards exhibit adaptations in digestive morphology and function that allow them to better assimilate plant material. However, it is unknown whether these traits are fixed or perhaps phenotypically flexible as a result of diet. Here, we maintained a naturally omnivorous lizard, Liolaemus ruibali, on a mixed diet of 50% insects and 50% plant material, or a plant-rich diet of 90% plant material. We compared parameters of digestive performance, gut morphology and function, and gut microbial community structure between the two groups. We found that lizards fed the plant-rich diet maintained nitrogen balance and exhibited low minimum nitrogen requirements. Additionally, lizards fed the plant-rich diet exhibited significantly longer small intestines and larger hindguts, demonstrating that gut morphology is phenotypically flexible. Lizards fed the plant-rich diet harbored small intestinal communities that were more diverse and enriched in Melainabacteria and Oscillospira compared with mixed diet-fed lizards. Additionally, the relative abundance of sulfate-reducing bacteria in the small intestine significantly correlated with whole-animal fiber digestibility. Thus, we suggest that physiological and microbial limitations do not sensu stricto constrain the evolution of herbivory in lizards. Rather, ecological context and fitness consequences may be more important in driving the evolution of this feeding strategy.

  3. The Intestinal Microbiome and Health

    PubMed Central

    Tuddenham, Susan; Sears, Cynthia L.

    2015-01-01

    Purpose of Review A diverse array of microbes colonizes the human intestine. In this review we seek to outline the current state of knowledge on what characterizes a “healthy” or “normal” intestinal microbiome, what factors modify the intestinal microbiome in the healthy state and how the intestinal microbiome affects normal host physiology Recent Findings What constitutes a “normal” or “healthy” intestinal microbiome is an area of active research, but key characteristics may include diversity, richness and a microbial community’s resilience and ability to resist change. A number of factors, including age, the host immune system, host genetics, diet and antibiotic use appear to modify the intestinal microbiome in the normal state. New research shows that the microbiome likely plays a critical role in the healthy human immune system and metabolism. Summary It is clear that there is a complicated bi-directional relationship between the intestinal microbiota and host which is vital to health. An enhanced understanding of this relationship will be critical not only to maximize and maintain human health but also to shape our understanding of disease and to foster new therapeutic approaches. PMID:26237547

  4. Effects of pomegranate chemical constituents/intestinal microbial metabolites on CYP1B1 in 22Rv1 prostate cancer cells.

    PubMed

    Kasimsetty, Sashi G; Bialonska, Dobroslawa; Reddy, Muntha K; Thornton, Cammi; Willett, Kristine L; Ferreira, Daneel

    2009-11-25

    The cytochrome P450 enzyme, CYP1B1, is an established target in prostate cancer chemoprevention. Compounds inhibiting CYP1B1 activity are contemplated to exert beneficial effects at three stages of prostate cancer development, that is, initiation, progression, and development of drug resistance. Pomegranate ellagitannins/microbial metabolites were examined for their CYP1B1 inhibitory activity in a recombinant CYP1B1-mediated ethoxyresorufin-O-deethylase (EROD) assay. Urolithin A, a microbial metabolite, was the most potent uncompetitive inhibitor of CYP1B1-mediated EROD activity, exhibiting 2-fold selectivity over CYP1A1, while urolithin B was a noncompetitive inhibitor with 3-fold selectivity. The punicalins and punicalagins exhibited potent CYP1A1 inhibition with 5-10-fold selectivity over CYP1B1. Urolithins, punicalins, and punicalagins were tested for their 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced CYP1 inhibitory activity in the 22Rv1 prostate cancer cell line. Urolithins A and B showed a decrease in their CYP1-mediated EROD inhibitory IC50 values upon increasing their treatment times from 30 min to 24 h. Urolithin C, 8-O-methylurolithin A, and 8,9-di-O-methylurolithin C caused a potent CYP1-mediated EROD inhibition in 22Rv1 cells upon 24 h of incubation. Neutral red uptake assay results indicated that urolithin C, 8-O-methylurolithin A, and 8,9-di-O-methylurolithin C induced profound cytotoxicity in the proximity of their CYP1 inhibitory IC50 values. Urolithins A and B were studied for their cellular uptake and inhibition of TCDD-induced CYP1B1 expression. Cellular uptake experiments demonstrated a 5-fold increase in urolithin uptake by 22Rv1 cells. Western blots of the CYP1B1 protein indicated that the urolithins interfered with the expression of CYP1B1 protein. Thus, urolithins were found to display a dual mode mechanism by decreasing CYP1B1 activity and expression.

  5. Ecological Communities by Design

    SciTech Connect

    Fredrickson, Jim K.

    2015-06-25

    In synthetic ecology, a nascent offshoot of synthetic biology, scientists aim to design and construct microbial communities with desirable properties. Such mixed populations of microorganisms can simultaneously perform otherwise incompatible functions. Compared with individual organisms, they can also better resist losses in function as a result of environmental perturbation or invasion by other species. Synthetic ecology may thus be a promising approach for developing robust, stable biotechnological processes, such as the conversion of cellulosic biomass to biofuels. However, achieving this will require detailed knowledge of the principles that guide the structure and function of microbial communities.

  6. The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish.

    PubMed

    Stagaman, Keaton; Burns, Adam R; Guillemin, Karen; Bohannan, Brendan Jm

    2017-03-17

    All animals live in intimate association with communities of microbes, collectively referred to as their microbiota. Certain host traits can influence which microbial taxa comprise the microbiota. One potentially important trait in vertebrate animals is the adaptive immune system, which has been hypothesized to act as an ecological filter, promoting the presence of some microbial taxa over others. Here we surveyed the intestinal microbiota of 68 wild-type zebrafish, with functional adaptive immunity, and 61 rag1(-) zebrafish, lacking functional B- and T-cell receptors, to test the role of adaptive immunity as an ecological filter on the intestinal microbiota. In addition, we tested the robustness of adaptive immunity's filtering effects to host-host interaction by comparing the microbiota of fish populations segregated by genotype to those containing both genotypes. The presence of adaptive immunity individualized the gut microbiota and decreased the contributions of neutral processes to gut microbiota assembly. Although mixing genotypes led to increased phylogenetic diversity in each, there was no significant effect of adaptive immunity on gut microbiota composition in either housing condition. Interestingly, the most robust effect on microbiota composition was co-housing within a tank. In all, these results suggest that adaptive immunity has a role as an ecological filter of the zebrafish gut microbiota, but it can be overwhelmed by other factors, including transmission of microbes among hosts.The ISME Journal advance online publication, 17 March 2017; doi:10.1038/ismej.2017.28.

  7. Short communication: Modulation of the small intestinal microbial community composition over short-term or long-term administration with Lactobacillus plantarum ZDY2013.

    PubMed

    Xie, Qiong; Pan, Mingfang; Huang, Renhui; Tian, Ximei; Tao, Xueying; Shah, Nagendra P; Wei, Hua; Wan, Cuixiang

    2016-09-01

    The small intestinal (SI) microbiota has an essential role in the maintenance of human health. However, data about the indigenous bacteria in SI as affected by probiotics are limited. In our study, the short-term and long-term effects of a probiotic candidate, Lactobacillus plantarum ZDY2013, on the SI microbiota of C57BL/6J mice were investigated by the Illumina HiSeq (Novogene Bioinformatics Technology Co., Ltd., Tianjin, China) platform targeting the V4 region of the 16S rDNA. A total of 858,011 sequences in 15 samples were read. The α diversity analysis revealed that oral administration with L. plantarum ZDY2013 for 3 wk led to a significant increase in the richness and diversity of the SI bacterial community. Principal coordinate analysis and unweighted pair-group method with arithmetic means analysis showed a clear alteration in the SI microbiota composition after 3 wk of L. plantarum ZDY2013 treatment, although these changes were not found 6 wk after ceasing L. plantarum ZDY2013 administration. Species annotation showed that the dominant phyla in SI microbiota were Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia. Interestingly, operational taxonomic unit cluster analysis showed that administration with L. plantarum ZDY2013 for 3 wk significantly increased the abundance of Proteobacteria, but decreased that of Bacteroidetes. Linear discriminant analysis coupled with effect size identified 18 bacterial taxa (e.g., Ruminococcus spp. and Clostridium spp.) that overgrew in the SI microbiota of the mice administered with L. plantarum ZDY2013 for 3 wk, and most of them belonged to the phyla Bacteroidetes and Proteobacteria. However, only one bacterial taxon (e.g., Nocardioides spp.) was over-represented in the SI microbiota of mice 6 wk after L. plantarum ZDY2013 administration. Overall, this study shows that oral administration with probiotic results in an important but transient alteration in the microbiota of SI.

  8. Therapeutic modulation of intestinal dysbiosis.

    PubMed

    Walker, Alan W; Lawley, Trevor D

    2013-03-01

    The human gastrointestinal tract is home to an extremely numerous and diverse collection of microbes, collectively termed the "intestinal microbiota". This microbiota is considered to play a number of key roles in the maintenance of host health, including aiding digestion of otherwise indigestible dietary compounds, synthesis of vitamins and other beneficial metabolites, immune system regulation and enhanced resistance against colonisation by pathogenic microorganisms. Conversely, the intestinal microbiota is also a potent source of antigens and potentially harmful compounds. In health, humans can therefore be considered to exist in a state of natural balance with their microbial inhabitants. A shift in the balance of microbiota composition such that it may become deleterious to host health is termed "dysbiosis". Dysbiosis of the gut microbiota has been implicated in numerous disorders, ranging from intestinal maladies such as inflammatory bowel diseases and colorectal cancer to disorders with more systemic effects such as diabetes, metabolic syndrome and atopy. Given the far reaching influence of the intestinal microbiota on human health a clear future goal must be to develop reliable means to alter the composition of the microbiota and restore a healthy balance of microbial species. While it is clear that much fundamental research remains to be done, potentially important therapeutic options include narrow spectrum antibiotics, novel probiotics, dietary interventions and more radical techniques such as faecal transplantation, all of which aim to suppress clinical dysbiosis, restore intestinal microbiota diversity and improve host health.

  9. Probiotic Bacteria Influence the Composition and Function of the Intestinal Microbiota

    PubMed Central

    O'Toole, Paul W.; Cooney, Jakki C.

    2008-01-01

    Probiotics have a range of proposed health benefits for the consumer, which may include modulating the levels of beneficial elements in the microbiota. Recent investigations using molecular approaches have revealed a human intestinal microbiota comprising over 1000 phylotypes. Mechanisms whereby probiotics impact on the intestinal microbiota include competition for substrates, direct antagonism by inhibitory substances, competitive exclusion, and potentially host-mediated effects such as improved barrier function and altered immune response. We now have the microbial inventories and genetic blueprints to begin tackling intestinal microbial ecology at an unprecedented level of detail, aided by the understanding that dietary components may be utilized differentially by individual phylotypes. Controlled intervention studies in humans, utilizing latest molecular technologies, are required to consolidate evidence for bacterial species that impact on the microbiota. Mechanistic insights should be provided by metabolomics and other analytical techniques for small molecules. Rigorous characterization of interactions between the diet, microbiota, and probiotic bacteria will provide new opportunities for modulating the microbiota towards improving human health. PMID:19277099

  10. Effects of redox fluctuations on microbial community ecology post-wildfire in a high elevation mixed-conifer catchment in northern New Mexico.

    NASA Astrophysics Data System (ADS)

    Fairbanks, D.; Green, K.; Murphy, M. A.; Shepard, C.; Chorover, J.; Rich, V. I.; Gallery, R. E.

    2015-12-01

    Wildfires are increasing in size and severity across the western United States with impacts on regional biogeochemical cycling. The resiliency of resident soil microbial communities determines rates of nutrient transformations as well as forest structure and recovery. Redox conditions in soil determine metabolic activities of microorganisms, which first consume oxygen and a succession of alternative terminal electron acceptors to support growth and metabolism using a variety of carbon sources. Controls on redox zonation are largely unknown in dominantly oxic soils, and microbial community adaptation and response to fluctuations in redox potential in a sub-alpine forested post-disturbance catchment has not been studied. Previous work has shown that fluctuating or rising water tables result in redox-dynamic sites, which can be 'hot spots' of biogeochemical activity depending on landscape position. Fire-induced tree mortality results in altered hydrologic flow paths and decreased evapotranspiration, leading to potential for intensified hot spot activity. We are testing such coupling of microbial activity with fluctuations in redox status using field measurements and laboratory incubation experiments. The 2013 Thompson Ridge Fire in the Jemez River Basin (NM) Critical Zone Observatory provides a highly-contextualized opportunity to examine how disturbance regime affects changes in soil microbial community dynamics and fluctuations in reduction-oxidation potential (as quantified by continuous CZO measurements of O2, CO2 and Eh as a function of soil depth and landscape location). We hypothesize that areas of depositional convergence in the catchment, which have been shown to exhibit more reducing conditions, will host microbial communities that are better adapted to fluctuating redox conditions and exhibit a greater diversity in functional capabilities. In these mixed conifer forests we find shifts in redox potential status in relation to depth and topography where more

  11. Microbial interactions during carrion decomposition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This addresses the microbial ecology of carrion decomposition in the age of metagenomics. It describes what is known about the microbial communities on carrion, including a brief synopsis about the communities on other organic matter sources. It provides a description of studies using state-of-the...

  12. Intestinal Capillariasis

    DTIC Science & Technology

    1987-12-01

    bhIll inenais, the tiny nematode causing Intestinal capillariasis In humans, Is a Iunique parasite. It is one of the newest parasites that has been...Capillariaphilippinensis, the tiny nematode causing intestinal capillariasis in humans, is a unique parasite. It is one of the newest parasites that has been shown to...stichocytes surrounding the oesophagus. The posterior half of the nematode is wider than the anterior half and contains the digestive tract and the

  13. Microbial ecology of the hive and pollination landscape: Bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen that are either vertically inherited or acquired from the environment. While the core bacteria of the honey bee gut is becoming evident, the influence of the pollination environment on honey bee-associated microbial p...

  14. Microbial ecology of the watery ecosystems of Evros river in North Eastern Greece and its influence upon the cultivated soil ecosystem.

    PubMed

    Vavias, S; Alexopoulos, A; Plessas, S; Stefanis, C; Voidarou, C; Stavropoulou, E; Bezirtzoglou, E

    2011-12-01

    The aim of the present study was to evaluate the microbial ecosystem of cultivated soils along the Evros river in NE Greece. Evros river together with its derivative rivers constitute the capital source of life and sustainable development of the area. Along this riverside watery ecosystem systematic agro-cultures were developed such as wheat, corn and vegetable cultures. The evaluation of the ecosystem microbial charge was conducted in both axes which are the watery ecosystem and the riverside cultivated soil area. Considerable discrimination of water quality was observed when considering chemical and microbiological parameters of the Evros river ecosystem. Ardas river possesses a better water quality than Evros and Erythropotamos, which is mainly due to the higher quantities that these two rivers accumulate from industrial, farming and urban residues leading to higher degree of pollution. An increased microbial pollution was recorded in two of the three rivers monitored and a direct relation in microbial and chemical charging between water and cultivated-soil ecosystems was observed. The protection of these ecosystems with appropriate cultivated practices and control of human and animal activities will define the homeostasis of the environmental area.

  15. Molecular ecology of aquatic microbes

    SciTech Connect

    1994-12-31

    Abstracts of reports are presented from a meeting on Molecular Ecology of Aquatic Microbes. Topics included: opportunities offered to aquatic ecology by molecular biology; the role of aquatic microbes in biogeochemical cycles; characterization of the microbial community; the effect of the environment on aquatic microbes; and the targeting of specific biological processes.

  16. Environmental Escherichia coli: Ecology and public health implications - A review

    USGS Publications Warehouse

    Jang, Jeonghwan; Hur, Hor-Gil; Sadowsky, Michael J.; Byappanahalli, Muruleedhara; Yan, Tao; Ishii, Satoshi

    2017-01-01

    Escherichia coli is classified as a rod-shaped, Gram-negative bacterium in the family Enterobacteriaceae. The bacterium mainly inhabits the lower intestinal tract of warm-blooded animals, including humans, and is often discharged into the environment through feces or wastewater effluent. The presence of E. coli in environmental waters has long been considered as an indicator of recent fecal pollution. However, numerous recent studies have reported that some specific strains of E. coli can survive for long periods of time, and potentially reproduce, in extra-intestinal environments. This indicates that E. coli can be integrated into indigenous microbial communities in the environment. This naturalization phenomenon calls into question the reliability of E. coli as a fecal indicator bacterium (FIB). Recently, many studies reported that E. coli populations in the environment are affected by ambient environmental conditions affecting their long-term survival. Large-scale studies of population genetics provide the diversity and complexity of E. coli strains in various environments, affected by multiple environmental factors. This review examines the current knowledge on the ecology of E. coli strains in various environments in regards to its role as a FIB and as a naturalized member of indigenous microbial communities. Special emphasis is given on the growth of pathogenic E. coli in the environment, and the population genetics of environmental members of the genus Escherichia. The impact of environmental E. coli on water quality and public health is also discussed.

  17. The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment.

    PubMed

    Bastida, F; Jehmlich, N; Lima, K; Morris, B E L; Richnow, H H; Hernández, T; von Bergen, M; García, C

    2016-03-01

    The linkage between phylogenetic and functional processes may provide profound insights into the effects of hydrocarbon contamination and biodegradation processes in high-diversity environments. Here, the impacts of petroleum contamination and the bioremediation potential of compost amendment, as enhancer of the microbial activity in semiarid soils, were evaluated in a model experiment. The analysis of phospholipid fatty-acids (PLFAs) and metaproteomics allowed the study of biomass, phylogenetic and physiological responses of the microbial community in polluted semiarid soils. Petroleum pollution induced an increase of proteobacterial proteins during the contamination, while the relative abundance of Rhizobiales lowered in comparison to the non-contaminated soil. Despite only 0.55% of the metaproteome of the compost-treated soil was involved in biodegradation processes, the addition of compost promoted the removal of polycyclic aromatic hydrocarbons (PAHs) and alkanes up to 88% after 50 days. However, natural biodegradation of hydrocarbons was not significant in soils without compost. Compost-assisted bioremediation was mainly driven by Sphingomonadales and uncultured bacteria that showed an increased abundance of catabolic enzymes such as catechol 2,3-dioxygenases, cis-dihydrodiol dehydrogenase and 2-hydroxymuconic semialdehyde. For the first time, metaproteomics revealed the functional and phylogenetic relationships of petroleum contamination in soil and the microbial key players involved in the compost-assisted bioremediation.

  18. Effect of advanced oxidation on N-nitrosodimethylamine (NDMA) formation and microbial ecology during pilot-scale biological activated carbon filtration.

    PubMed

    Li, Dong; Stanford, Ben; Dickenson, Eric; Khunjar, Wendell O; Homme, Carissa L; Rosenfeldt, Erik J; Sharp, Jonathan O

    2017-04-15

    Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H2O2 followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H2O2 fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated. While microbial populations were highly similar in the upper reaches, deeper samples revealed a divergence within and between BAC filtration systems where EBCT was identified to be a significant environmental predictor for shifts in microbial populations. The abundance of Nitrospira in the top samples of both columns provides an explanation for the oxidation of nitrite and corresponding increases in nitrate concentrations during BAC transit and support interplay between nitrogen cycling with nitrosamine formation. The results of this study demonstrate that pretreatments using ozone versus UV/H2O2 impart modest differences to the overall BAC microbial population structural and functional attributes, and further highlight the need to evaluate NDMA formation prior to full-scale implementation of BAC in potable reuse applications.

  19. [Ecology and ecologies].

    PubMed

    Valera, Luca

    2011-01-01

    Ecology (from the Greek words οιχοσ, "house" and λογια "study of") is the science of the "house", since it studies the environments where we live. There are three main ways of thinking about Ecology: Ecology as the study of interactions (between humans and the environment, between humans and living beings, between all living beings, etc.), Ecology as the statistical study of interactions, Ecology as a faith, or rather as a science that requires a metaphysical view. The history of Ecology shows us how this view was released by the label of "folk sense" to gain the epistemological status of science, a science that strives to be interdisciplinary. So, the aim of Ecology is to study, through a scientific methodology, the whole natural world, answering to very different questions, that arise from several fields (Economics, Biology, Sociology, Philosophy, etc.). The plurality of issues that Ecology has to face led, during the Twentieth-century, to branch off in several different "ecologies". As a result, each one of these new approaches chose as its own field a more limited and specific portion of reality.

  20. The microbial contribution to macroecology

    PubMed Central

    Barberán, Albert; Casamayor, Emilio O.; Fierer, Noah

    2014-01-01

    There has been a recent explosion of research within the field of microbial ecology that has been fueled, in part, by methodological improvements that make it feasible to characterize microbial communities to an extent that was inconceivable only a few years ago. Furthermore, there is increasing recognition within the field of ecology that microorganisms play a critical role in the health of organisms and ecosystems. Despite these developments, an important gap still persists between the theoretical framework of macroecology and microbial ecology. We highlight two idiosyncrasies of microorganisms that are fundamental to understanding macroecological patterns and their mechanistic drivers. First, high dispersal rates provide novel opportunities to test the relative importance of niche, stochastic, and historical processes in structuring biological communities. Second, high speciation rates potentially lead to the convergence of ecological and evolutionary time scales. After reviewing these unique aspects, we discuss strategies for improving the conceptual integration of microbes into macroecology. As examples, we discuss the use of phylogenetic ecology as an integrative approach to explore patterns across the tree of life. Then we demonstrate how two general theories of biodiversity (i.e., the recently developed theory of stochastic geometry and the neutral theory) can be adapted to microorganisms. We demonstrate how conceptual models that integrate evolutionary and ecological mechanisms can contribute to the unification of microbial ecology and macroecology. PMID:24829564

  1. Helminths and Intestinal Flora Team Up to Improve Gut Health.

    PubMed

    Giacomin, Paul; Agha, Zainab; Loukas, Alex

    2016-09-01

    Inflammatory bowel diseases (IBD) are associated with impaired intestinal barrier function, chronic inflammation, and microbial dysbiosis. In a recent publication in Science, Ramanan et al. used murine and human studies to demonstrate that infections with gastrointestinal helminths can protect against IBD by provoking immune responses that alter the balance of commensal and pathogenic bacteria in the intestine.

  2. Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii.

    PubMed

    Green, Hyatt C; Fisher, Jenny C; McLellan, Sandra L; Sogin, Mitchell L; Shanks, Orin C

    2015-12-28

    The coalescence of next-generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of