201
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Jiao S, Chen W, Wang E, Wang J, Liu Z, Li Y, Wei G. Microbial succession in response to pollutants in batch-enrichment culture. Sci Rep 2016; 6:21791. [PMID: 26905741 PMCID: PMC4764846 DOI: 10.1038/srep21791] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/01/2016] [Indexed: 11/29/2022] Open
Abstract
As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México, D.F., Mexico
| | - Junman Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Zhenshan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Yining Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling Shaanxi 712100, P. R. China
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202
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Moor K, Wotzka SY, Toska A, Diard M, Hapfelmeier S, Slack E. Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species. Front Immunol 2016; 7:34. [PMID: 26904024 PMCID: PMC4749699 DOI: 10.3389/fimmu.2016.00034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/24/2016] [Indexed: 12/28/2022] Open
Abstract
Our mucosal surfaces are the main sites of non-vector-borne pathogen entry, as well as the main interface with our commensal microbiota. We are still only beginning to understand how mucosal adaptive immunity interacts with commensal and pathogenic microbes to influence factors such as infectivity, phenotypic diversity, and within-host evolution. This is in part due to difficulties in generating specific mucosal adaptive immune responses without disrupting the mucosal microbial ecosystem itself. Here, we present a very simple tool to generate inactivated mucosal vaccines from a broad range of culturable bacteria. Oral gavage of 1010 peracetic acid-inactivated bacteria induces high-titer-specific intestinal IgA in the absence of any measurable inflammation or species invasion. As a proof of principle, we demonstrate that this technique is sufficient to provide fully protective immunity in the murine model of invasive non-typhoidal Salmonellosis, even in the face of severe innate immune deficiency.
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Affiliation(s)
- Kathrin Moor
- Institute for Microbiology, ETH Zürich , Zürich , Switzerland
| | - Sandra Y Wotzka
- Institute for Microbiology, ETH Zürich , Zürich , Switzerland
| | - Albulena Toska
- Institute for Microbiology, ETH Zürich , Zürich , Switzerland
| | - Médéric Diard
- Institute for Microbiology, ETH Zürich , Zürich , Switzerland
| | | | - Emma Slack
- Institute for Microbiology, ETH Zürich , Zürich , Switzerland
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203
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Niu Q, Zhang L, Zhang K, Huang X, Hui F, Kan Y, Yao L. Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection. Sci Rep 2016; 6:20178. [PMID: 26830015 PMCID: PMC4735852 DOI: 10.1038/srep20178] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/23/2015] [Indexed: 12/23/2022] Open
Abstract
The effect of pathogenic bacteria on a host and its symbiotic microbiota is vital and widespread in the biotic world. The soil-dwelling opportunistic bacterium Bacillus nematocida B16 uses a "Trojan horse" mechanism to kill Caenorhabditis elegans. The alterations in the intestinal microflora that occur after B16 infection remain unknown. Here, we analyzed the intestinal bacteria presented in normal and infected worms. The gut microbial community experienced a complex change after B16 inoculation, as determined through marked differences in species diversity, structure, distribution and composition between uninfected and infected worms. Regardless of the worm's origin (i.e., from soil or rotten fruits), the diversity of the intestinal microbiome decreased after infection. Firmicutes increased sharply, whereas Proteobacteria, Actinobacteria, Cyanobacteria and Acidobacteria decreased to different degrees. Fusobacteria was only present 12 h post-infection. After 24 h of infection, 1228 and 1109 bacterial species were identified in the uninfected and infected groups, respectively. The shared species reached 21.97%. The infected group had a greater number of Bacillus species but a smaller number of Pediococcus, Halomonas, Escherichia and Shewanella species (P < 0.01). Therefore, this study provides the first evaluation of the alterations caused by pathogenic bacteria on symbiotic microbiota using C. elegans as the model species.
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Affiliation(s)
- Qiuhong Niu
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, 473000, P.R. China
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, P. R. China
| | - Lin Zhang
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, 473000, P.R. China
| | - Keqin Zhang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, P. R. China
| | - Xiaowei Huang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, P. R. China
| | - Fengli Hui
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, 473000, P.R. China
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, 473000, P.R. China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, 473000, P.R. China
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204
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Praharaj I, John SM, Bandyopadhyay R, Kang G. Probiotics, antibiotics and the immune responses to vaccines. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0144. [PMID: 25964456 DOI: 10.1098/rstb.2014.0144] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Orally delivered vaccines have been shown to perform poorly in developing countries. There are marked differences in the structure and the luminal environment of the gut in developing countries resulting in changes in immune and barrier function. Recent studies using newly developed technology and analytic methods have made it increasingly clear that the intestinal microbiota activate a multitude of pathways that control innate and adaptive immunity in the gut. Several hypotheses have been proposed for the underperformance of oral vaccines in developing countries, and modulation of the intestinal microbiota is now being tested in human clinical trials. Supplementation with specific strains of probiotics has been shown to have modulatory effects on intestinal and systemic immune responses in animal models and forms the basis for human studies with vaccines. However, most studies published so far that have evaluated the immune response to vaccines in children and adults have been small and results have varied by age, antigen, type of antibody response and probiotic strain. Use of anthelminthic drugs in children has been shown to possibly increase immunogenicity following oral cholera vaccination, lending further support to the rationale for modulation of the immune response to oral vaccination through the intestinal microbiome.
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Affiliation(s)
- Ira Praharaj
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Sushil M John
- Low Cost Effective Care Unit, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Rini Bandyopadhyay
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu 632004, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu 632004, India
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205
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Berry D, Kuzyk O, Rauch I, Heider S, Schwab C, Hainzl E, Decker T, Müller M, Strobl B, Schleper C, Urich T, Wagner M, Kenner L, Loy A. Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis. Front Microbiol 2015; 6:1408. [PMID: 26697002 PMCID: PMC4678223 DOI: 10.3389/fmicb.2015.01408] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 11/27/2015] [Indexed: 12/20/2022] Open
Abstract
Acute colitis causes alterations in the intestinal microbiota, but the microbiota is thought to recover after such events. Extreme microbiota alterations are characteristic of human chronic inflammatory bowel diseases, although alterations reported in different studies are divergent and sometimes even contradictory. To better understand the impact of periodic disturbances on the intestinal microbiota and its compositional difference between acute and relapsing colitis, we investigated the beginnings of recurrent inflammation using the dextran sodium sulfate (DSS) mouse model of chemically induced colitis. Using bacterial 16S rRNA gene-targeted pyrosequencing as well as quantitative fluorescence in situ hybridization, we profiled the intestinal and stool microbiota of mice over the course of three rounds of DSS-induced colitis and recovery. We found that characteristic inflammation-associated microbiota could be detected in recovery-phase mice. Successive inflammation episodes further drove the microbiota into an increasingly altered composition post-inflammation, and signatures of colitis history were detectable in the microbiota more sensitively than by pathology analysis. Bacterial indicators of murine colitis history were identified in intestinal and stool samples, with a high degree of consistency between both sample types. Stool may therefore be a promising non-invasive source of bacterial biomarkers that are highly sensitive to inflammation state and history.
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Affiliation(s)
- David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of ViennaVienna, Austria
| | - Orest Kuzyk
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of ViennaVienna, Austria
| | - Isabella Rauch
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of ViennaVienna, Austria
| | - Susanne Heider
- Clinical Institute of Pathology, Medical University of ViennaVienna, Austria
| | - Clarissa Schwab
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Eva Hainzl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine ViennaVienna, Austria
| | - Thomas Decker
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of ViennaVienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine ViennaVienna, Austria
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine ViennaVienna, Austria
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Tim Urich
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of ViennaVienna, Austria
| | - Lukas Kenner
- Clinical Institute of Pathology, Medical University of ViennaVienna, Austria
- Ludwig Boltzmann Institute for Cancer ResearchVienna, Austria
- Department of Laboratory Animal Pathology, University of Veterinary Medicine ViennaVienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of ViennaVienna, Austria
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206
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Becker MH, Walke JB, Cikanek S, Savage AE, Mattheus N, Santiago CN, Minbiole KPC, Harris RN, Belden LK, Gratwicke B. Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus. Proc Biol Sci 2015; 282:rspb.2014.2881. [PMID: 25788591 DOI: 10.1098/rspb.2014.2881] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Symbiotic microbes can dramatically impact host health and fitness, and recent research in a diversity of systems suggests that different symbiont community structures may result in distinct outcomes for the host. In amphibians, some symbiotic skin bacteria produce metabolites that inhibit the growth of Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen that has caused many amphibian population declines and extinctions. Treatment with beneficial bacteria (probiotics) prevents Bd infection in some amphibian species and creates optimism for conservation of species that are highly susceptible to chytridiomycosis, the disease caused by Bd. In a laboratory experiment, we used Bd-inhibitory bacteria from Bd-tolerant Panamanian amphibians in a probiotic development trial with Panamanian golden frogs, Atelopus zeteki, a species currently surviving only in captive assurance colonies. Approximately 30% of infected golden frogs survived Bd exposure by either clearing infection or maintaining low Bd loads, but this was not associated with probiotic treatment. Survival was instead related to initial composition of the skin bacterial community and metabolites present on the skin. These results suggest a strong link between the structure of these symbiotic microbial communities and amphibian host health in the face of Bd exposure and also suggest a new approach for developing amphibian probiotics.
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Affiliation(s)
- Matthew H Becker
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Jenifer B Walke
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Shawna Cikanek
- Department of Clinical Sciences, Kansas State University, Manhattan, KS, USA
| | - Anna E Savage
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Nichole Mattheus
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | | | | | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Brian Gratwicke
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
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207
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MULTIDRUG RESISTANCE IN WILD BIRD POPULATIONS: IMPORTANCE OF THE FOOD CHAIN. J Zoo Wildl Med 2015; 46:723-31. [DOI: 10.1638/2012-0212.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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208
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Mon KKZ, Saelao P, Halstead MM, Chanthavixay G, Chang HC, Garas L, Maga EA, Zhou H. Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks. Front Vet Sci 2015; 2:61. [PMID: 26664988 PMCID: PMC4672283 DOI: 10.3389/fvets.2015.00061] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 11/04/2015] [Indexed: 12/24/2022] Open
Abstract
Avian gastrointestinal (GI) tracts are highly populated with a diverse array of microorganisms that share a symbiotic relationship with their hosts and contribute to the overall health and disease state of the intestinal tract. The microbiome of the young chick is easily prone to alteration in its composition by both exogenous and endogenous factors, especially during the early posthatch period. The genetic background of the host and exposure to pathogens can impact the diversity of the microbial profile that consequently contributes to the disease progression in the host. The objective of this study was to profile the composition and structure of the gut microbiota in young chickens from two genetically distinct highly inbred lines. Furthermore, the effect of the Salmonella Enteritidis infection on altering the composition makeup of the chicken microbiome was evaluated through the 16S rRNA gene sequencing analysis. One-day-old layer chicks were challenged with S. Enteritidis and the host cecal microbiota profile as well as the degree of susceptibility to Salmonella infection was examined at 2 and 7 days post infection. Our result indicated that host genotype had a limited effect on resistance to S. Enteritidis infection. Alpha diversity, beta diversity, and overall microbiota composition were analyzed for four factors: host genotype, age, treatment, and postinfection time points. S. Enteritidis infection in young chicks was found to significantly reduce the overall diversity of the microbiota population with expansion of Enterobacteriaceae family. These changes indicated that Salmonella colonization in the GI tract of the chickens has a direct effect on altering the natural development of the GI microbiota. The impact of S. Enteritidis infection on microbial communities was also more substantial in the late stage of infection. Significant inverse correlation between Enterobacteriaceae and Lachnospiraceae family in both non-infected and infected groups, suggested possible antagonistic interaction between members of these two taxa, which could potentially influences the overall microbial population in the gut. Our results also revealed that genetic difference between two lines had minimal effect on the establishment of microbiota population. Overall, this study provided preliminary insights into the contributing role of S. Enteritidis in influencing the overall makeup of chicken’s gut microbiota.
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Affiliation(s)
- Khin K Z Mon
- Department of Animal Science, University of California Davis , Davis, CA , USA
| | - Perot Saelao
- Department of Animal Science, University of California Davis , Davis, CA , USA
| | - Michelle M Halstead
- Department of Animal Science, University of California Davis , Davis, CA , USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California Davis , Davis, CA , USA
| | - Huai-Chen Chang
- Department of Animal Science, University of California Davis , Davis, CA , USA
| | - Lydia Garas
- Department of Animal Science, University of California Davis , Davis, CA , USA
| | - Elizabeth A Maga
- Department of Animal Science, University of California Davis , Davis, CA , USA
| | - Huaijun Zhou
- Department of Animal Science, University of California Davis , Davis, CA , USA
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209
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Hoy YE, Bik EM, Lawley TD, Holmes SP, Monack DM, Theriot JA, Relman DA. Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time. PLoS One 2015; 10:e0142825. [PMID: 26565698 PMCID: PMC4643986 DOI: 10.1371/journal.pone.0142825] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/27/2015] [Indexed: 12/20/2022] Open
Abstract
Genetics, diet, and other environmental exposures are thought to be major factors in the development and composition of the intestinal microbiota of animals. However, the relative contributions of these factors in adult animals, as well as variation with time in a variety of important settings, are still not fully understood. We studied a population of inbred, female mice fed the same diet and housed under the same conditions. We collected fecal samples from 46 individual mice over two weeks, sampling four of these mice for periods as long as 236 days for a total of 190 samples, and determined the phylogenetic composition of their microbial communities after analyzing 1,849,990 high-quality pyrosequencing reads of the 16S rRNA gene V3 region. Even under these controlled conditions, we found significant inter-individual variation in community composition, as well as variation within an individual over time, including increases in alpha diversity during the first 2 months of co-habitation. Some variation was explained by mouse membership in different cage and vendor shipment groups. The differences among individual mice from the same shipment group and cage were still significant. Overall, we found that 23% of the variation in intestinal microbiota composition was explained by changes within the fecal microbiota of a mouse over time, 12% was explained by persistent differences among individual mice, 14% by cage, and 18% by shipment group. Our findings suggest that the microbiota of controlled populations of inbred laboratory animals may not be as uniform as previously thought, that animal rearing and handling may account for some variation, and that as yet unidentified factors may explain additional components of variation in the composition of the microbiota within populations and individuals over time. These findings have implications for the design and interpretation of experiments involving laboratory animals.
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Affiliation(s)
- Yana Emmy Hoy
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Elisabeth M. Bik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Trevor D. Lawley
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Denise M. Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Julie A. Theriot
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - David A. Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America
- * E-mail:
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210
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Mallon CA, Elsas JDV, Salles JF. Microbial Invasions: The Process, Patterns, and Mechanisms. Trends Microbiol 2015; 23:719-729. [DOI: 10.1016/j.tim.2015.07.013] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 07/20/2015] [Accepted: 07/31/2015] [Indexed: 01/20/2023]
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211
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Thompson JA, Oliveira RA, Djukovic A, Ubeda C, Xavier KB. Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota. Cell Rep 2015; 10:1861-71. [PMID: 25801025 DOI: 10.1016/j.celrep.2015.02.049] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/18/2015] [Accepted: 02/20/2015] [Indexed: 12/14/2022] Open
Abstract
The mammalian gut microbiota harbors a diverse ecosystem where hundreds of bacterial species interact with each other and their host. Given that bacteria use signals to communicate and regulate group behaviors (quorum sensing), we asked whether such communication between different commensal species can influence the interactions occurring in this environment. We engineered the enteric bacterium, Escherichia coli, to manipulate the levels of the interspecies quorum sensing signal, autoinducer-2 (AI-2), in the mouse intestine and investigated the effect upon antibiotic-induced gut microbiota dysbiosis. E. coli that increased intestinal AI-2 levels altered the composition of the antibiotic-treated gut microbiota, favoring the expansion of the Firmicutes phylum. This significantly increased the Firmicutes/Bacteroidetes ratio, to oppose the strong effect of the antibiotic, which had almost cleared the Firmicutes. This demonstrates that AI-2 levels influence the abundance of the major phyla of the gut microbiota, the balance of which is known to influence human health.
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212
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What Makes A Bacterial Oral Vaccine a Strong Inducer of High-Affinity IgA Responses? Antibodies (Basel) 2015. [DOI: 10.3390/antib4040295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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213
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Billeci L, Tonacci A, Tartarisco G, Ruta L, Pioggia G, Gangemi S. Association Between Atopic Dermatitis and Autism Spectrum Disorders: A Systematic Review. Am J Clin Dermatol 2015; 16:371-88. [PMID: 26254000 DOI: 10.1007/s40257-015-0145-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) is an allergic disorder caused by both immunological dysregulation and epidermal barrier defect. Several studies have investigated the association between AD and mental health disorders. Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental conditions characterized by impairments in social communication and restricted, stereotyped interests and behaviors. The concurrent increased prevalence of AD and ASD in the last decades has led many scientists to investigate the relationship between the two diseases. OBJECTIVE The aim of this systematic review was to examine the association between AD and ASD. METHODS A systematic review was performed according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. PubMed and ScienceDirect were searched up to March 2015 for all reports examining the association between ASD and AD. Descriptive statistics of the studies are reported. RESULTS The review included 18 studies assessing the association between ASD and AD. Of these studies, two focused on ASD in relation to AD alone, 14 discussed ASD in relation to both AD and other atopic disorders, and two evaluated AD in parents of children with ASD. Most of these studies found a positive association between the two disorders, although there were some studies going in the opposite direction. The entity of the association is somewhat inconsistent among the different studies given that the frequencies of AD in ASD compared with a control group ranged from 7 to 64.2%. In addition, odds ratios (ORs) or hazard ratios (HRs) gave different results as three studies found a weak association with an OR below 2 and a nonsignificant p value, and three other studies found a moderate or strong association with an OR ranging from 1.52 to 7.17 and a significant p value. When all atopic disorders were considered when evaluating the risk of ASD, the association was strong with an HR of 3.4 or an OR of 1.24 and p < 0.001. CONCLUSIONS Overall, the results of this systematic review seem to reveal an association between ASD and AD, suggesting that subjects with ASD have an increased risk of presenting with AD compared with typically developing controls, and vice versa. This association is supported by clinical/epidemiological aspects, shared genetic background and common immunological and autoimmune processes. However, the variability in study population and design, and the presence of other risk factors acting as confounding factors, sometimes contribute to inconsistent results. Further studies are needed to clarify the underlying pathophysiologic mechanism explaining the association between ASD and AD and to explore the causal association between the two conditions.
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Affiliation(s)
- Lucia Billeci
- National Research Council of Italy, Institute of Clinical Physiology, IFC-CNR, Pisa Unit, Pisa, Italy
| | - Alessandro Tonacci
- National Research Council of Italy, Institute of Clinical Physiology, IFC-CNR, Pisa Unit, Pisa, Italy
| | - Gennaro Tartarisco
- National Research Council of Italy, Institute of Clinical Physiology, IFC-CNR, Messina Unit, Via C. Valeria, SNC, 98125, Messina, Italy
| | - Liliana Ruta
- National Research Council of Italy, Institute of Clinical Physiology, IFC-CNR, Messina Unit, Via C. Valeria, SNC, 98125, Messina, Italy
- Department of Developmental Neuroscience, Stella Maris Scientific Institute, Calambrone, Pisa, Italy
| | - Giovanni Pioggia
- National Research Council of Italy, Institute of Clinical Physiology, IFC-CNR, Messina Unit, Via C. Valeria, SNC, 98125, Messina, Italy.
| | - Sebastiano Gangemi
- School and Division of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University Hospital "G. Martino", Messina, Italy
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Singh P, Teal TK, Marsh TL, Tiedje JM, Mosci R, Jernigan K, Zell A, Newton DW, Salimnia H, Lephart P, Sundin D, Khalife W, Britton RA, Rudrik JT, Manning SD. Intestinal microbial communities associated with acute enteric infections and disease recovery. MICROBIOME 2015; 3:45. [PMID: 26395244 PMCID: PMC4579588 DOI: 10.1186/s40168-015-0109-2] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/11/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion. Studies that examine differences in intestinal microbial communities across individuals with and without enteric infections are useful for identifying microbes that support or impede intestinal health. RESULTS 16S rRNA gene sequencing was conducted on stool DNA from patients with enteric infections (n = 200) and 75 healthy family members to identify differences in intestinal community composition. Stools from 13 patients were also examined post-infection to better understand how intestinal communities recover. Patient communities had lower species richness, evenness, and diversity versus uninfected communities, while principle coordinate analysis demonstrated close clustering of uninfected communities, but not the patient communities, irrespective of age, gender, and race. Differences in community composition between patients and family members were mostly due to variation in the abundance of phyla Proteobacteria, Bacteroidetes, and Firmicutes. Patient communities had significantly more Proteobacteria representing genus Escherichia relative to uninfected communities, which were dominated by Bacteroides. Intestinal communities from patients with bloody diarrhea clustered together in the neighbor-joining phylogeny, while communities from 13 patients' post-infection had a significant increase in Bacteroidetes and Firmicutes and clustered together with uninfected communities. CONCLUSIONS These data demonstrate that the intestinal communities in patients with enteric bacterial infections get altered in similar ways. Furthermore, preventing an increase in Escherichia abundance may be an important consideration for future prevention strategies.
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Affiliation(s)
- Pallavi Singh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - Tracy K Teal
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - Terence L Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - James M Tiedje
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - Rebekah Mosci
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - Katherine Jernigan
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | - Angela Zell
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
| | | | | | - Paul Lephart
- Wayne State University, Detroit, MI, 48202, USA.
| | | | | | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - James T Rudrik
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, 48913, USA.
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
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215
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Role of intestinal microbiota in the development of multiple sclerosis. Neurologia 2015; 32:175-184. [PMID: 26383059 DOI: 10.1016/j.nrl.2015.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/07/2015] [Accepted: 07/28/2015] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Multiple sclerosis (MS) is a demyelinating disease that affects young adults; in that age group, it represents the second leading cause of disability in our setting. Its precise aetiology has not been elucidated, but it is widely accepted to occur in genetically predisposed patients who are exposed to certain environmental factors. The discovery of the regulatory role played by intestinal microbiota in various autoimmune diseases has opened a new line of research in this field, which is discussed in this review. DEVELOPMENT We reviewed published studies on the role of the microbiota in the development of both MS and its animal model, experimental autoimmune encephalomyelitis (EAE). In mice, it has been shown that intestinal microorganisms regulate the polarisation of T helper cells from Th1-Th17 up to Th2, the function of regulatory T cells, and the activity of B cells; they participate in the pathogenesis of EAE and contribute to its prevention and treatment. In contrast, evidence in humans is still scarce and mainly based on case-control studies that point to the presence of differences in certain bacterial communities. CONCLUSIONS Multiple evidence points to the role of microbiota in EAE. Extrapolation of these results to MS is still in the early stages of research, and studies are needed to define which bacterial populations are associated with MS, the role they play in pathogenesis, and the therapeutic possibilities this knowledge offers us.
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216
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Kampmann C, Dicksved J, Engstrand L, Rautelin H. Composition of human faecal microbiota in resistance to Campylobacter infection. Clin Microbiol Infect 2015; 22:61.e1-61.e8. [PMID: 26369602 DOI: 10.1016/j.cmi.2015.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 01/22/2023]
Abstract
In mice, specific species composition of gut microbiota enhances susceptibility to Campylobacter jejuni but little is known about the specific composition of the human gut microbiota in providing protection from infections caused by enteropathogens. Healthy adult individuals, who travelled in groups from Sweden to destinations with an estimated high risk for acquisition of Campylobacter infection, were enrolled. Faecal samples, collected before travelling and after returning home, were cultured for bacterial enteropathogens, and analysed for Campylobacter by PCR and for the species composition of the microbiota by 16S amplicon massive parallel sequencing. The microbiota compositions were compared between persons who became infected during their travel and those who did not. A total of 63 participants completed the study; 14 became infected with Campylobacter, two with Salmonella and 47 remained negative for the enteropathogens tested. After exclusion of samples taken after antimicrobial treatment, 49 individuals were included in the final analyses. Intra-individual stability of the microbiota was demonstrated for samples taken before travelling. The original diversity of the faecal microbiota was significantly lower among individuals who later became infected compared with those who remained uninfected. The relative abundances of bacteria belonging to the family Lachnospiraceae, and more specifically its two genera Dorea and Coprococcus, were significantly higher among those who remained uninfected. The travel-related infection did not significantly modify the faecal microbiota composition. Species composition of human gut microbiota is important for colonization resistance to Campylobacter infection. Especially individuals with a lower diversity are more susceptible to Campylobacter infection.
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Affiliation(s)
- C Kampmann
- Department of Infectious Diseases, Gävle Hospital, Gävle, Sweden; Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden; Centre for Research and Development, Uppsala University/County Council of Gävleborg, Sweden.
| | - J Dicksved
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden; Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - L Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden; Science for Life Laboratory, Clinical Genomics, Stockholm, Sweden
| | - H Rautelin
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden; Department of Bacteriology and Immunology, University of Helsinki, Finland
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217
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Muszer M, Noszczyńska M, Kasperkiewicz K, Skurnik M. Human Microbiome: When a Friend Becomes an Enemy. Arch Immunol Ther Exp (Warsz) 2015; 63:287-98. [PMID: 25682593 PMCID: PMC4499106 DOI: 10.1007/s00005-015-0332-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/12/2014] [Indexed: 12/24/2022]
Abstract
The microorganisms that inhabit humans are very diverse on different body sites and tracts. Each specific niche contains a unique composition of the microorganisms that are important for a balanced human physiology. Microbial cells outnumber human cells by tenfold and they function as an invisible organ that is called the microbiome. Excessive use of antibiotics and unhealthy diets pose a serious danger to the composition of the microbiome. An imbalance in the microbial community may cause pathological conditions of the digestive system such as obesity, cancer and inflammatory bowel disease; of the skin such as atopic dermatitis, psoriasis and acne and of the cardiovascular system such as atherosclerosis. An unbalanced microbiome has also been associated with neurodevelopmental disorders such as autism and multiple sclerosis. While the microbiome has a strong impact on the development of the host immune system, it is suspected that it can also be the cause of certain autoimmune diseases, including diabetes or rheumatoid arthritis. Despite the enormous progress in the field, the interactions between the human body and its microbiome still remain largely unknown. A better characterization of the interactions may allow for a deeper understanding of human disease states and help to elucidate a possible association between the composition of the microbiome and certain pathologies. This review focuses on general findings that are related to the area and provides no detailed information about the case of study. The aim is to give some initial insight on the studies of the microbiome and its connection with human health.
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Affiliation(s)
- Magdalena Muszer
- Department of Microbiology, University of Silesia, Katowice, Poland
| | | | | | - Mikael Skurnik
- Department of Bacteriology and Immunology, Haartman Institute, Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
- University Central Hospital Laboratory Diagnostics, Helsinki, Finland
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218
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Vincent C, Manges AR. Antimicrobial Use, Human Gut Microbiota and Clostridium difficile Colonization and Infection. Antibiotics (Basel) 2015; 4:230-53. [PMID: 27025623 PMCID: PMC4790283 DOI: 10.3390/antibiotics4030230] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 12/20/2022] Open
Abstract
Clostridium difficile infection (CDI) is the most important cause of nosocomial diarrhea. Broad-spectrum antimicrobials have profound detrimental effects on the structure and diversity of the indigenous intestinal microbiota. These alterations often impair colonization resistance, allowing the establishment and proliferation of C. difficile in the gut. Studies involving animal models have begun to decipher the precise mechanisms by which the intestinal microbiota mediates colonization resistance against C. difficile and numerous investigations have described gut microbiota alterations associated with C. difficile colonization or infection in human subjects. Fecal microbiota transplantation (FMT) is a highly effective approach for the treatment of recurrent CDI that allows the restoration of a healthy intestinal ecosystem via infusion of fecal material from a healthy donor. The recovery of the intestinal microbiota after FMT has been examined in a few reports and work is being done to develop custom bacterial community preparations that could be used as a replacement for fecal material.
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Affiliation(s)
- Caroline Vincent
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada.
| | - Amee R Manges
- School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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219
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BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC Bioinformatics 2015; 16:203. [PMID: 26130132 PMCID: PMC4486701 DOI: 10.1186/s12859-015-0595-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/23/2015] [Indexed: 01/28/2023] Open
Abstract
Background Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. Results BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). Conclusion BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0595-z) contains supplementary material, which is available to authorized users.
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220
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Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Syst Appl Microbiol 2015; 38:330-9. [DOI: 10.1016/j.syapm.2015.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 05/18/2015] [Accepted: 05/26/2015] [Indexed: 01/06/2023]
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221
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Rausch P, Steck N, Suwandi A, Seidel JA, Künzel S, Bhullar K, Basic M, Bleich A, Johnsen JM, Vallance BA, Baines JF, Grassl GA. Expression of the Blood-Group-Related Gene B4galnt2 Alters Susceptibility to Salmonella Infection. PLoS Pathog 2015; 11:e1005008. [PMID: 26133982 PMCID: PMC4489644 DOI: 10.1371/journal.ppat.1005008] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/05/2015] [Indexed: 12/16/2022] Open
Abstract
Glycans play important roles in host-microbe interactions. Tissue-specific expression patterns of the blood group glycosyltransferase β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) are variable in wild mouse populations, and loss of B4galnt2 expression is associated with altered intestinal microbiota. We hypothesized that variation in B4galnt2 expression alters susceptibility to intestinal pathogens. To test this, we challenged mice genetically engineered to express different B4galnt2 tissue-specific patterns with a Salmonella Typhimurium infection model. We found B4galnt2 intestinal expression was strongly associated with bacterial community composition and increased Salmonella susceptibility as evidenced by increased intestinal inflammatory cytokines and infiltrating immune cells. Fecal transfer experiments demonstrated a crucial role of the B4galnt2-dependent microbiota in conferring susceptibility to intestinal inflammation, while epithelial B4galnt2 expression facilitated epithelial invasion of S. Typhimurium. These data support a critical role for B4galnt2 in gastrointestinal infections. We speculate that B4galnt2-specific differences in host susceptibility to intestinal pathogens underlie the strong signatures of balancing selection observed at the B4galnt2 locus in wild mouse populations.
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Affiliation(s)
- Philipp Rausch
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Natalie Steck
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
- Models of Inflammation, Research Center Borstel, Borstel, Germany
| | - Abdulhadi Suwandi
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Janice A. Seidel
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Kirandeep Bhullar
- Department of Pediatrics, Division of Gastroenterology, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marijana Basic
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Andre Bleich
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Jill M. Johnsen
- Research Institute, Puget Sound Blood Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Bruce A. Vallance
- Department of Pediatrics, Division of Gastroenterology, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - John F. Baines
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Guntram A. Grassl
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
- Models of Inflammation, Research Center Borstel, Borstel, Germany
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222
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Biggs MB, Medlock GL, Kolling GL, Papin JA. Metabolic network modeling of microbial communities. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:317-34. [PMID: 26109480 DOI: 10.1002/wsbm.1308] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 12/15/2022]
Abstract
Genome-scale metabolic network reconstructions and constraint-based analyses are powerful methods that have the potential to make functional predictions about microbial communities. Genome-scale metabolic networks are used to characterize the metabolic functions of microbial communities via several techniques including species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the 'enzyme-soup' approach, multiscale modeling, and others. There are many challenges in the field, including a need for tools that accurately assign high-level omics signals to individual community members, the need for improved automated network reconstruction methods, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be corresponding advances in the fields of ecology, health science, and microbial community engineering.
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Affiliation(s)
- Matthew B Biggs
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Gregory L Medlock
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Glynis L Kolling
- Department of Medicine, Infectious Diseases, University of Virginia, Charlottesville, VA, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
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223
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Social stress as a cause of diseases in farm animals: Current knowledge and future directions. Vet J 2015; 206:15-21. [PMID: 26160470 DOI: 10.1016/j.tvjl.2015.05.024] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
Over the past 50 years, biomedical research has established a strong linkage between psychosocial stress and disease risk in humans, which has transformed the understanding of stress and the role it plays in human lives. This research has led to personalized medicine where a reduction in daily life stress is a main goal for many people with debilitating illnesses. This review describes the supporting evidence that social stress also plays a critical role in farm animal disease prevention, and may be a mediator by which common management practices can increase disease risk. There is evidence that social factors, including deprivation of social contact ('social isolation'), reducing space allowance ('crowding') and disturbing social order ('social instability') trigger physiological and behavioral indicators of stress in livestock. Less research exists, however, linking management practices that trigger social stress with higher disease risk. Suggestions are offered for future research opportunities, and practical, evidence-based recommendations are made for reducing the negative effects of social isolation, instability and crowding. The current evidence that social factors contribute to disease risk in farm animals is not as convincing as the human literature, but remains a promising and important area for future research.
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224
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Host microbiota constantly control maturation and function of microglia in the CNS. Nat Neurosci 2015; 18:965-77. [PMID: 26030851 DOI: 10.1038/nn.4030] [Citation(s) in RCA: 2329] [Impact Index Per Article: 232.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 04/29/2015] [Indexed: 02/07/2023]
Abstract
As the tissue macrophages of the CNS, microglia are critically involved in diseases of the CNS. However, it remains unknown what controls their maturation and activation under homeostatic conditions. We observed substantial contributions of the host microbiota to microglia homeostasis, as germ-free (GF) mice displayed global defects in microglia with altered cell proportions and an immature phenotype, leading to impaired innate immune responses. Temporal eradication of host microbiota severely changed microglia properties. Limited microbiota complexity also resulted in defective microglia. In contrast, recolonization with a complex microbiota partially restored microglia features. We determined that short-chain fatty acids (SCFA), microbiota-derived bacterial fermentation products, regulated microglia homeostasis. Accordingly, mice deficient for the SCFA receptor FFAR2 mirrored microglia defects found under GF conditions. These findings suggest that host bacteria vitally regulate microglia maturation and function, whereas microglia impairment can be rectified to some extent by complex microbiota.
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225
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How the Intricate Interaction among Toll-Like Receptors, Microbiota, and Intestinal Immunity Can Influence Gastrointestinal Pathology. J Immunol Res 2015; 2015:489821. [PMID: 26090491 PMCID: PMC4452102 DOI: 10.1155/2015/489821] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 10/01/2014] [Accepted: 10/27/2014] [Indexed: 12/12/2022] Open
Abstract
The gut is able to maintain tolerance to microbial and food antigens. The intestine minimizes the number of harmful bacteria by shaping the microbiota through a symbiotic relationship. In healthy human intestine, a constant homeostasis is maintained by the perfect regulation of microbial load and the immune response generated against it. Failure of this balance may result in various pathological conditions. Innate immune sensors, such as Toll-like receptors (TLRs), may be considered an interface among intestinal epithelial barrier, microbiota, and immune system. TLRs pathway, activated by pathogens, is involved in the pathogenesis of several infectious and inflammatory diseases. The alteration of the homeostasis between physiologic and pathogenic bacteria of intestinal flora causes a condition called dysbiosis. The breakdown of homeostasis by dysbiosis may increase susceptibility to inflammatory bowel diseases. It is evident that environment, genetics, and host immunity form a highly interactive regulatory triad that controls TLR function. Imbalanced relationships within this triad may promote aberrant TLR signaling, critically contributing to acute and chronic intestinal inflammatory processes, such as in IBD, colitis, and colorectal cancer. The study of interactions between different components of the immune systems and intestinal microbiota will open new horizons in the knowledge of gut inflammation.
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226
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Disturbance of the intestinal microbial community by ursolic acid contributes to its function as a regulator of fat deposition. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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227
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Göttig S, Gruber TM, Stecher B, Wichelhaus TA, Kempf VAJ. In vivo horizontal gene transfer of the carbapenemase OXA-48 during a nosocomial outbreak. Clin Infect Dis 2015; 60:1808-15. [PMID: 25759432 DOI: 10.1093/cid/civ191] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/03/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND OXA-48 is a highly prevalent carbapenemase and has been isolated worldwide. Here, we investigate the in vivo horizontal gene transfer (HGT) of blaOXA-48 from Klebsiella pneumoniae to Escherichia coli in an infected patient. METHODS Bacterial isolates were characterized by susceptibility testing, multilocus sequence typing, DiversiLab, and plasmid analyses. Transferability of blaOXA-48 was evaluated by in vitro transconjugation using the outbreak strain and E. coli J53. In vivo transconjugation was investigated using the larvae of the greater wax moth (Galleria mellonella) and low-complexity-microbiota mice. RESULTS OXA-48-harboring K. pneumoniae isolates belonging to ST14 were isolated during a nosocomial outbreak from 6 patients. Molecular and epidemiological analyses revealed the HGT of an approximately 60-kb OXA-48-containing IncL/M-type plasmid from K. pneumoniae to E. coli belonging to the novel ST666 in a patient. In vitro conjugation experiments revealed a transconjugation frequency of 8.7 × 10(-7). HGT of OXA-48 in a newly developed in vivo model using G. mellonella larvae revealed a higher transconjugation frequency of 1.3 × 10(-4). The conjugation frequency of OXA-48 from K. pneumoniae and E. coli in the gut of low-complexity-microbiota mice was determined to be 2.9 × 10(-5). CONCLUSIONS The in vivo intergenus gene transfer of OXA-48 in the gut of an infected patient was verified in vitro and in 2 in vivo models, which both showed even higher transmission frequencies vs in vitro conditions. This implies that the current in vitro protocols might not correctly reflect the HGT of carbapenemase genes in vivo.
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Affiliation(s)
- Stephan Göttig
- Institute for Medical Microbiology and Infection Control, Hospital of Johann Wolfgang Goethe University, Frankfurt
| | - Teresa M Gruber
- Institute for Medical Microbiology and Infection Control, Hospital of Johann Wolfgang Goethe University, Frankfurt
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University German Center for Infection Research (DZIF), Munich
| | - Thomas A Wichelhaus
- Institute for Medical Microbiology and Infection Control, Hospital of Johann Wolfgang Goethe University, Frankfurt
| | - Volkhard A J Kempf
- Institute for Medical Microbiology and Infection Control, Hospital of Johann Wolfgang Goethe University, Frankfurt
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228
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Wang J, Kalyan S, Steck N, Turner LM, Harr B, Künzel S, Vallier M, Häsler R, Franke A, Oberg HH, Ibrahim SM, Grassl GA, Kabelitz D, Baines JF. Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome. Nat Commun 2015; 6:6440. [PMID: 25737238 PMCID: PMC4366507 DOI: 10.1038/ncomms7440] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 01/29/2015] [Indexed: 02/06/2023] Open
Abstract
Recent evidence suggests that natural selection operating on hosts to maintain their microbiome contributes to the emergence of new species, that is, the ‘hologenomic basis of speciation’. Here we analyse the gut microbiota of two house mice subspecies, Mus musculus musculus and M. m. domesticus, across their Central European hybrid zone, in addition to hybrids generated in the lab. Hybrid mice display widespread transgressive phenotypes (that is, exceed or fall short of parental values) in a variety of measures of bacterial community structure, which reveals the importance of stabilizing selection operating on the intestinal microbiome within species. Further genetic and immunological analyses reveal genetic incompatibilities, aberrant immune gene expression and increased intestinal pathology associated with altered community structure among hybrids. These results provide unique insight into the consequences of evolutionary divergence in a vertebrate ‘hologenome’, which may be an unrecognized contributing factor to reproductive isolation in this taxonomic group. Animal hosts and their associated microbes are largely the outcome of coevolution. Here, the authors show differences in the intestinal microbiome of hybrids compared with pure species of house mice, which suggests that host–microbiome interactions contribute to the evolution of host species.
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Affiliation(s)
- Jun Wang
- 1] Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306 Plön, Germany [2] Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Arnold-Heller-Strasse 3, D-24105 Kiel, Germany
| | - Shirin Kalyan
- Institute of Immunology, Christian-Albrechts University Kiel, Arnold-Heller-Strasse 3, Haus 17, 24105 Kiel, Germany
| | - Natalie Steck
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Arnold-Heller-Strasse 3, D-24105 Kiel, Germany
| | - Leslie M Turner
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306 Plön, Germany
| | - Bettina Harr
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306 Plön, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306 Plön, Germany
| | - Marie Vallier
- 1] Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306 Plön, Germany [2] Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Arnold-Heller-Strasse 3, D-24105 Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schittenhelmstrasse 12, D-24105 Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Schittenhelmstrasse 12, D-24105 Kiel, Germany
| | - Hans-Heinrich Oberg
- Institute of Immunology, Christian-Albrechts University Kiel, Arnold-Heller-Strasse 3, Haus 17, 24105 Kiel, Germany
| | - Saleh M Ibrahim
- Department of Dermatology, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Guntram A Grassl
- Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Arnold-Heller-Strasse 3, D-24105 Kiel, Germany
| | - Dieter Kabelitz
- Institute of Immunology, Christian-Albrechts University Kiel, Arnold-Heller-Strasse 3, Haus 17, 24105 Kiel, Germany
| | - John F Baines
- 1] Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306 Plön, Germany [2] Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Arnold-Heller-Strasse 3, D-24105 Kiel, Germany
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229
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Preidis GA, Hotez PJ. The newest "omics"--metagenomics and metabolomics--enter the battle against the neglected tropical diseases. PLoS Negl Trop Dis 2015; 9:e0003382. [PMID: 25675250 PMCID: PMC4326130 DOI: 10.1371/journal.pntd.0003382] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Geoffrey A. Preidis
- Section of Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, United States of America
- * E-mail:
| | - Peter J. Hotez
- National School of Tropical Medicine, Department of Pediatrics and Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Sabin Vaccine Institute and Texas Children’s Hospital Center for Vaccine Development, Houston, Texas, United States of America
- James A. Baker III Institute for Public Policy, Rice University, Houston, Texas, United States of America
- Department of Biology, Baylor University, Waco, Texas, United States of America
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230
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Xia X, Zhang L, Wang Y. The antimicrobial peptide cathelicidin-BF could be a potential therapeutic for Salmonella typhimurium infection. Microbiol Res 2015; 171:45-51. [DOI: 10.1016/j.micres.2014.12.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/26/2014] [Accepted: 12/26/2014] [Indexed: 12/21/2022]
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231
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Slack E, Balmer ML, Macpherson AJ. B cells as a critical node in the microbiota-host immune system network. Immunol Rev 2015; 260:50-66. [PMID: 24942681 DOI: 10.1111/imr.12179] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mutualism with our intestinal microbiota is a prerequisite for healthy existence. This requires physical separation of the majority of the microbiota from the host (by secreted antimicrobials, mucus, and the intestinal epithelium) and active immune control of the low numbers of microbes that overcome these physical and chemical barriers, even in healthy individuals. In this review, we address how B-cell responses to members of the intestinal microbiota form a robust network with mucus, epithelial integrity, follicular helper T cells, innate immunity, and gut-associated lymphoid tissues to maintain host-microbiota mutualism.
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Affiliation(s)
- Emma Slack
- Institute for Microbiology, ETH Zürich, Zurich, Switzerland
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232
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Pinn DM, Aroniadis OC, Brandt LJ. Is fecal microbiota transplantation (FMT) an effective treatment for patients with functional gastrointestinal disorders (FGID)? Neurogastroenterol Motil 2015; 27:19-29. [PMID: 25424663 DOI: 10.1111/nmo.12479] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 11/04/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Despite its high prevalence and significant effect on quality of life, the etiology of functional gastrointestinal disorders (FGID), and specifically irritable bowel syndrome (IBS), has yet to be fully elucidated. While alterations in immunity, motility, and the brain-gut axis have been implicated in disease pathogenesis, the intestinal microbiota are increasingly being shown to play a role and numerous studies have demonstrated significant differences from normal in the intestinal flora of patients with FGID, and between types of FGID. Fecal microbiota transplantation (FMT) is a curative therapy for Clostridium difficile infection (CDI), a disease hallmarked by intestinal dysbiosis, and FMT is now being explored as a means to also restore intestinal homeostasis in FGID. PURPOSE This review aims to investigate the role of intestinal microbiota in the pathogenesis of FGID, the implications of FMT for the treatment of FGID, and the challenges encountered in measuring response to a specific intervention in patients with FGID.
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Affiliation(s)
- D M Pinn
- Beth Israel Medical Center, New York, NY, USA
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233
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Malys MK, Campbell L, Malys N. Symbiotic and antibiotic interactions between gut commensal microbiota and host immune system. MEDICINA (KAUNAS, LITHUANIA) 2015; 51:69-75. [PMID: 25975874 DOI: 10.1016/j.medici.2015.03.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The human gut commensal microbiota forms a complex population of microorganisms that survive by maintaining a symbiotic relationship with the host. Amongst the metabolic benefits it brings, formation of adaptive immune system and maintenance of its homeostasis are functions that play an important role. This review discusses the integral elements of commensal microbiota that stimulate responses of different parts of the immune system and lead to health or disease. It aims to establish conditions and factors that contribute to gut commensal microbiota's transformation from symbiotic to antibiotic relationship with human. We suggest that the host-microbiota relationship has been evolved to benefit both parties and any changes that may lead to disease, are not due to unfriendly properties of the gut microbiota but due to host genetics or environmental changes such as diet or infection.
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Affiliation(s)
| | - Laura Campbell
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK
| | - Naglis Malys
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK.
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234
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Wassenaar T, Beimfohr C, Geske T, Zimmermann K. Voluntarily exposure to a single, high dose of probiotic Escherichia coli results in prolonged colonisation. Benef Microbes 2014; 5:367-75. [DOI: 10.3920/bm2013.0087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The ability of probiotic Escherichia coli to colonise the human gut was determined in a volunteer study following national (German) regulations. Five persons voluntarily took a single, high dose of Symbioflor®2, which contains 6 different probiotic E. coli genotypes, to assess tolerance of the product, after which presence of E. coli in their faeces was tested for a follow-up period of 30 weeks. Intake of the product did not result in severe side effect in any of the individuals, though mild side effects were observed. Stool analysis showed that the probiotic E. coli had colonised all five persons for a period of 10 to 30 weeks (mean: 18.7 weeks, median: 25.7 weeks). In two individuals there was evidence of competition between host E. coli and probiotic E. coli, while in two others total E. coli levels increased persistently with at least a factor of 10 as a result of the received dose. In one individual, who had lacked detectable levels of faecal E. coli at the start of the post-authorisation safety study, long-term colonisation was established, first by probiotic E. coli exclusively, which were later replaced by host E. coli strains. In four out of five individuals, total E. coli faecal counts were higher on average than at the start of the experiment, while in none total levels exceeded 5×107 cfu/g. When the specific genotypes of the 6 probiotic E. coli were analysed, it was found that one and the same common genotype was responsible for prolonged colonisation in all five individuals.
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Affiliation(s)
- T.M. Wassenaar
- Molecular Microbiology and Genomics Consultants, Tannenstrasse 7, 55576 Zotzenheim, Germany
| | - C. Beimfohr
- Vermicon AG, Emmy-Noether-Straße 2, 80992 München, Germany
| | - T. Geske
- Medical Services, Hennigsdorfer Str. 141S, 13503 Berlin, Germany
| | - K. Zimmermann
- SymbioPharm GmbH, Auf den Lüppen 8, 35745 Herborn, Germany
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235
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Manzari C, Fosso B, Marzano M, Annese A, Caprioli R, D’Erchia AM, Gissi C, Intranuovo M, Picardi E, Santamaria M, Scorrano S, Sgaramella G, Stabili L, Piraino S, Pesole G. The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0810-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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236
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Tanner SA, Chassard C, Zihler Berner A, Lacroix C. Synergistic effects of Bifidobacterium thermophilum RBL67 and selected prebiotics on inhibition of Salmonella colonization in the swine proximal colon PolyFermS model. Gut Pathog 2014; 6:44. [PMID: 25364390 PMCID: PMC4215022 DOI: 10.1186/s13099-014-0044-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/06/2014] [Indexed: 01/10/2023] Open
Abstract
Background Probiotics and prebiotics are promising strategies to counteract Salmonella prevalence in swine. In the present study, we investigated the effects of prebiotics (fructo- (FOS), galacto- (GOS) and mannan- (MOS) oligosaccharides) and the bacteriocinogenic Bifidobacterium thermophilum RBL67 (RBL67) on Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) colonization using the PolyFermS in vitro continuous fermentation model simulating the swine proximal colon. Material and methods The PolyFermS model was designed with a first-stage reactor containing immobilized fecal pig microbiota. This reactor continuously inoculated five parallel second-stage reactors, a control and four treatment reactors, all operated with proximal colon conditions. FOS and GOS (5.2 g/day), and MOS (half dosage) and RBL67 (108 copy numbers/mL applied daily) were tested on the ability of N-15 to colonize reactors, inoculated with the same microbiota. Reactor effluents were collected daily and analyzed for microbial composition (quantitative PCR and 454 pyrosequencing of 16S rRNA gene pool) and main metabolites (HPLC). Results RBL67 and N-15 were shown to stably colonize the system. Colonization of N-15 was strongly inhibited by FOS and GOS, whereas addition of RBL67 alone or combined with MOS showed intermediate results. However, the effect of FOS and GOS was enhanced when prebiotics were combined with a daily addition of RBL67. FOS and GOS increased the total short chain fatty acid production, especially acetate and propionate. RBL67 combined with FOS additionally stimulated butyrate production. Conclusions Our study demonstrates the suitability of the porcine PolyFermS in vitro model to study nutritional effects of pro- and prebiotics on gut microbiota composition and activity. It can further be used to monitor Salmonella colonization. The inhibition effects of FOS and GOS on N-15 colonization are partly due to an increased acetate production, while further antimicrobial mechanisms may contribute to an enhanced inhibition with prebiotic-RBL67 combinations. A future direction of this work could be to understand the anti-Salmonella effects of Bifidobacterium thermophilum RBL67 in the presence of prebiotics to unravel the mechanism of this probiotic:pathogen interaction. Electronic supplementary material The online version of this article (doi:10.1186/s13099-014-0044-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabine Amani Tanner
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Annina Zihler Berner
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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237
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Balmer ML, Schürch CM, Saito Y, Geuking MB, Li H, Cuenca M, Kovtonyuk LV, McCoy KD, Hapfelmeier S, Ochsenbein AF, Manz MG, Slack E, Macpherson AJ. Microbiota-derived compounds drive steady-state granulopoiesis via MyD88/TICAM signaling. THE JOURNAL OF IMMUNOLOGY 2014; 193:5273-83. [PMID: 25305320 DOI: 10.4049/jimmunol.1400762] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Neutropenia is probably the strongest known predisposition to infection with otherwise harmless environmental or microbiota-derived species. Because initial swarming of neutrophils at the site of infection occurs within minutes, rather than the hours required to induce "emergency granulopoiesis," the relevance of having high numbers of these cells available at any one time is obvious. We observed that germ-free (GF) animals show delayed clearance of an apathogenic bacterium after systemic challenge. In this article, we show that the size of the bone marrow myeloid cell pool correlates strongly with the complexity of the intestinal microbiota. The effect of colonization can be recapitulated by transferring sterile heat-treated serum from colonized mice into GF wild-type mice. TLR signaling was essential for microbiota-driven myelopoiesis, as microbiota colonization or transferring serum from colonized animals had no effect in GF MyD88(-/-)TICAM1(-/-) mice. Amplification of myelopoiesis occurred in the absence of microbiota-specific IgG production. Thus, very low concentrations of microbial Ags and TLR ligands, well below the threshold required for induction of adaptive immunity, sets the bone marrow myeloid cell pool size. Coevolution of mammals with their microbiota has probably led to a reliance on microbiota-derived signals to provide tonic stimulation to the systemic innate immune system and to maintain vigilance to infection. This suggests that microbiota changes observed in dysbiosis, obesity, or antibiotic therapy may affect the cross talk between hematopoiesis and the microbiota, potentially exacerbating inflammatory or infectious states in the host.
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Affiliation(s)
- Maria L Balmer
- Division of Gastroenterology, Department of Clinical Research, University Clinic for Visceral Surgery and Medicine, University of Bern, 3010 Bern, Switzerland
| | - Christian M Schürch
- Department of Clinical Research, Tumor Immunology, University of Bern, 3010 Bern, Switzerland
| | - Yasuyuki Saito
- Division of Hematology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Markus B Geuking
- Division of Gastroenterology, Department of Clinical Research, University Clinic for Visceral Surgery and Medicine, University of Bern, 3010 Bern, Switzerland
| | - Hai Li
- Division of Gastroenterology, Department of Clinical Research, University Clinic for Visceral Surgery and Medicine, University of Bern, 3010 Bern, Switzerland
| | - Miguelangel Cuenca
- Institute for Infectious Diseases, University of Bern, 3010 Bern, Switzerland; and
| | - Larisa V Kovtonyuk
- Division of Hematology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Kathy D McCoy
- Division of Gastroenterology, Department of Clinical Research, University Clinic for Visceral Surgery and Medicine, University of Bern, 3010 Bern, Switzerland
| | | | - Adrian F Ochsenbein
- Department of Clinical Research, Tumor Immunology, University of Bern, 3010 Bern, Switzerland
| | - Markus G Manz
- Division of Hematology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Emma Slack
- Division of Gastroenterology, Department of Clinical Research, University Clinic for Visceral Surgery and Medicine, University of Bern, 3010 Bern, Switzerland; Institute of Microbiology, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland
| | - Andrew J Macpherson
- Division of Gastroenterology, Department of Clinical Research, University Clinic for Visceral Surgery and Medicine, University of Bern, 3010 Bern, Switzerland;
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Maier L, Barthel M, Stecher B, Maier RJ, Gunn JS, Hardt WD. Salmonella Typhimurium strain ATCC14028 requires H2-hydrogenases for growth in the gut, but not at systemic sites. PLoS One 2014; 9:e110187. [PMID: 25303479 PMCID: PMC4193879 DOI: 10.1371/journal.pone.0110187] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/11/2014] [Indexed: 11/23/2022] Open
Abstract
Salmonella enterica is a common cause of diarrhea. For eliciting disease, the pathogen has to colonize the gut lumen, a site colonized by the microbiota. This process/initial stage is incompletely understood. Recent work established that one particular strain, Salmonella enterica subspecies 1 serovar Typhimurium strain SL1344, employs the hyb H2-hydrogenase for consuming microbiota-derived H2 to support gut luminal pathogen growth: Protons from the H2-splitting reaction contribute to the proton gradient across the outer bacterial membrane which can be harvested for ATP production or for import of carbon sources. However, it remained unclear, if other Salmonella strains would use the same strategy. In particular, earlier work had left unanswered if strain ATCC14028 might use H2 for growth at systemic sites. To clarify the role of the hydrogenases, it seems important to establish if H2 is used at systemic sites or in the gut and if Salmonella strains may differ with respect to the host sites where they require H2 in vivo. In order to resolve this, we constructed a strain lacking all three H2-hydrogenases of ATCC14028 (14028hyd3) and performed competitive infection experiments. Upon intragastric inoculation, 14028hyd3 was present at 100-fold lower numbers than 14028WT in the stool and at systemic sites. In contrast, i.v. inoculation led to equivalent systemic loads of 14028hyd3 and the wild type strain. However, the pathogen population spreading to the gut lumen featured again up to 100-fold attenuation of 14028hyd3. Therefore, ATCC14028 requires H2-hydrogenases for growth in the gut lumen and not at systemic sites. This extends previous work on ATCC14028 and supports the notion that H2-utilization might be a general feature of S. Typhimurium gut colonization.
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Affiliation(s)
- Lisa Maier
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Manja Barthel
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Bärbel Stecher
- Max von Pettenkofer-Institut, München, Germany
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Robert J. Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - John S. Gunn
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, Biomedical Research Tower, The Ohio State University, Columbus, Ohio, United States of America
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239
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Kortman GAM, Raffatellu M, Swinkels DW, Tjalsma H. Nutritional iron turned inside out: intestinal stress from a gut microbial perspective. FEMS Microbiol Rev 2014; 38:1202-34. [PMID: 25205464 DOI: 10.1111/1574-6976.12086] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 12/16/2022] Open
Abstract
Iron is abundantly present on earth, essential for most microorganisms and crucial for human health. Human iron deficiency that is nevertheless highly prevalent in developing regions of the world can be effectively treated by oral iron administration. Accumulating evidence indicates that excess of unabsorbed iron that enters the colonic lumen causes unwanted side effects at the intestinal host-microbiota interface. The chemical properties of iron, the luminal environment and host iron withdrawal mechanisms, especially during inflammation, can turn the intestine in a rather stressful milieu. Certain pathogenic enteric bacteria can, however, deal with this stress at the expense of other members of the gut microbiota, while their virulence also seems to be stimulated in an iron-rich intestinal environment. This review covers the multifaceted aspects of nutritional iron stress with respect to growth, composition, metabolism and pathogenicity of the gut microbiota in relation to human health. We aim to present an unpreceded view on the dynamic effects and impact of oral iron administration on intestinal host-microbiota interactions to provide leads for future research and other applications.
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Affiliation(s)
- Guus A M Kortman
- Department of Laboratory Medicine, The Radboud Institute for Molecular Life Sciences (RIMLS) of the Radboud University Medical Center, Nijmegen, The Netherlands
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240
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Susceptibility to Campylobacter infection is associated with the species composition of the human fecal microbiota. mBio 2014; 5:e01212-14. [PMID: 25227462 PMCID: PMC4172070 DOI: 10.1128/mbio.01212-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED The gut microbiota is essential for human health, but very little is known about how the composition of this ecosystem can influence and respond to bacterial infections. Here we address this by prospectively studying the gut microbiota composition before, during, and after natural Campylobacter infection in exposed poultry abattoir workers. The gut microbiota composition was analyzed with 16S amplicon sequencing of fecal samples from poultry abattoir workers during the peak season of Campylobacter infection in Sweden. The gut microbiota compositions were compared between individuals who became culture positive for Campylobacter and those who remained negative. Individuals who became Campylobacter positive had a significantly higher abundance of Bacteroides (P = 0.007) and Escherichia (P = 0.002) species than those who remained culture negative. Furthermore, this group had a significantly higher abundance of Phascolarctobacterium (P = 0.017) and Streptococcus (P = 0.034) sequences than the Campylobacter-negative group, which had an overrepresentation of Clostridiales (P = 0.017), unclassified Lachnospiraceae (P = 0.008), and Anaerovorax (P = 0.015) sequences. Intraindividual comparisons of the fecal microbiota compositions yielded small differences over time in Campylobacter-negative participants, but significant long-term changes were found in the Campylobacter-positive group (P < 0.005). The results suggest that the abundance of specific genera in the microbiota reduces resistance to Campylobacter colonization in humans and that Campylobacter infection can have long-term effects on the composition of the human fecal microbiota. IMPORTANCE Studies using mouse models have made important contributions to our understanding of the role of the gut microbiota in resistance to bacterial enteropathogen colonization. The relative abundances of Escherichia coli and Bacteroides species have been pointed out as important determinants of susceptibility to Gram-negative pathogens in general and Campylobacter infection in particular. In this study, we assessed the role of the human gut microbiota in resistance to Campylobacter colonization by studying abattoir workers that are heavily exposed to these bacteria. Individuals with a certain composition of the gut microbiota became culture positive for Campylobacter. As their microbiotas were characterized by high abundances of Bacteroides spp. and E. coli, well in line with the findings with mouse models, these bacterial species likely play an important role in colonization resistance also in humans.
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241
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Yurist-Doutsch S, Arrieta MC, Vogt SL, Finlay BB. Gastrointestinal microbiota-mediated control of enteric pathogens. Annu Rev Genet 2014; 48:361-82. [PMID: 25251855 DOI: 10.1146/annurev-genet-120213-092421] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The gastrointestinal (GI) microbiota is a complex community of microorganisms residing within the mammalian gastrointestinal tract. The GI microbiota is vital to the development of the host immune system and plays a crucial role in human health and disease. The composition of the GI microbiota differs immensely among individuals yet specific shifts in composition and diversity have been linked to inflammatory bowel disease, obesity, atopy, and susceptibility to infection. In this review, we describe the GI microbiota and its role in enteric diseases caused by pathogenic Escherichia coli, Salmonella enterica, and Clostridium difficile. We discuss the central role of the GI microbiota in protective immunity, resistance to enteric pathogens, and resolution of enteric colitis.
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Affiliation(s)
- Sophie Yurist-Doutsch
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4; , , ,
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242
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Kabat AM, Srinivasan N, Maloy KJ. Modulation of immune development and function by intestinal microbiota. Trends Immunol 2014; 35:507-17. [PMID: 25172617 DOI: 10.1016/j.it.2014.07.010] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/18/2014] [Accepted: 07/30/2014] [Indexed: 12/12/2022]
Abstract
The immune system must constantly monitor the gastrointestinal tract for the presence of pathogens while tolerating trillions of commensal microbiota. It is clear that intestinal microbiota actively modulate the immune system to maintain a mutually beneficial relation, but the mechanisms that maintain homeostasis are not fully understood. Recent advances have begun to shed light on the cellular and molecular factors involved, revealing that a range of microbiota derivatives can influence host immune functions by targeting various cell types, including intestinal epithelial cells, mononuclear phagocytes, innate lymphoid cells, and B and T lymphocytes. Here, we review these findings, highlighting open questions and important challenges to overcome in translating this knowledge into new therapies for intestinal and systemic immune disorders.
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Affiliation(s)
- Agnieszka M Kabat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Naren Srinivasan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, UK
| | - Kevin J Maloy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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243
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Food Omics Validation: Towards Understanding Key Features for Gut Microbiota, Probiotics and Human Health. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9923-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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244
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Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol 2014; 52:2813-23. [PMID: 24850358 PMCID: PMC4136157 DOI: 10.1128/jcm.00035-14] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Specific bacterial species are implicated in the pathogenesis of exacerbations of chronic obstructive pulmonary disease (COPD). However, recent studies of clinically stable COPD patients have demonstrated a greater diversity of airway microbiota, whose role in acute exacerbations is unclear. In this study, temporal changes in the airway microbiome before, at the onset of, and after an acute exacerbation were examined in 60 sputum samples collected from subjects enrolled in a longitudinal study of bacterial infection in COPD. Microbiome composition and predicted functions were examined using 16S rRNA-based culture-independent profiling methods. Shifts in the abundance (≥ 2-fold, P < 0.05) of many taxa at exacerbation and after treatment were observed. Microbiota members that were increased at exacerbation were primarily of the Proteobacteria phylum, including nontypical COPD pathogens. Changes in the bacterial composition after treatment for an exacerbation differed significantly among the therapy regimens clinically prescribed (antibiotics only, oral corticosteroids only, or both). Treatment with antibiotics alone primarily decreased the abundance of Proteobacteria, with the prolonged suppression of some microbiota members being observed. In contrast, treatment with corticosteroids alone led to enrichment for Proteobacteria and members of other phyla. Predicted metagenomes of particular microbiota members involved in these compositional shifts indicated exacerbation-associated loss of functions involved in the synthesis of antimicrobial and anti-inflammatory products, alongside enrichment in functions related to pathogen-elicited inflammation. These trends reversed upon clinical recovery. Further larger studies will be necessary to determine whether specific compositional or functional changes detected in the airway microbiome could be useful indicators of exacerbation development or outcome.
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Affiliation(s)
- Yvonne J Huang
- Division of Pulmonary/Critical Care/Allergy/Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Sanjay Sethi
- Division of Pulmonary/Critical Care/Sleep Medicine, Veterans Western New York Health System, Buffalo, New York, USA Department of Medicine, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Timothy Murphy
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Snehal Nariya
- Division of Pulmonary/Critical Care/Allergy/Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Homer A Boushey
- Division of Pulmonary/Critical Care/Allergy/Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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245
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Fecal microbiota transplantation inducing remission in Crohn's colitis and the associated changes in fecal microbial profile. J Clin Gastroenterol 2014; 48:625-8. [PMID: 24667590 DOI: 10.1097/mcg.0000000000000131] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing disorder of the intestine of unclear etiology. Increasing evidence has pointed to intestinal dysbiosis as a potential factor in a genetically susceptible individual. Fecal microbiota transplantation (FMT) has been used to treat inflammatory bowel disease with variable degrees of success. Herein, we report a patient with Crohn's colitis, previously failing an immunosuppressant, who achieved clinical, endoscopic, and histologic remission after a single fecal microbiota transplantation infusion. We have further characterized the changes in the fecal microbiota associated with this observation.
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246
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Maier L, Vyas R, Cordova CD, Lindsay H, Schmidt TSB, Brugiroux S, Periaswamy B, Bauer R, Sturm A, Schreiber F, von Mering C, Robinson MD, Stecher B, Hardt WD. Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem. Cell Host Microbe 2014; 14:641-51. [PMID: 24331462 DOI: 10.1016/j.chom.2013.11.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/01/2013] [Accepted: 11/11/2013] [Indexed: 01/09/2023]
Abstract
The intestinal microbiota features intricate metabolic interactions involving the breakdown and reuse of host- and diet-derived nutrients. The competition for these resources can limit pathogen growth. Nevertheless, some enteropathogenic bacteria can invade this niche through mechanisms that remain largely unclear. Using a mouse model for Salmonella diarrhea and a transposon mutant screen, we discovered that initial growth of Salmonella Typhimurium (S. Tm) in the unperturbed gut is powered by S. Tm hyb hydrogenase, which facilitates consumption of hydrogen (H2), a central intermediate of microbiota metabolism. In competitive infection experiments, a hyb mutant exhibited reduced growth early in infection compared to wild-type S. Tm, but these differences were lost upon antibiotic-mediated disruption of the host microbiota. Additionally, introducing H2-consuming bacteria into the microbiota interfered with hyb-dependent S. Tm growth. Thus, H2 is an Achilles' heel of microbiota metabolism that can be subverted by pathogens and might offer opportunities to prevent infection.
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Affiliation(s)
- Lisa Maier
- Institute of Microbiology, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Rounak Vyas
- SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Helen Lindsay
- SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Sandrine Brugiroux
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität Munich, 80336 Munich, Germany
| | | | - Rebekka Bauer
- Institute of Microbiology, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Alexander Sturm
- Institute of Microbiology, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Frank Schreiber
- Department of Environmental Microbiology, Eawag and Department of Environmental Systems Sciences, ETH Zurich, CH-8600 Dübendorf, Switzerland
| | - Christian von Mering
- SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität Munich, 80336 Munich, Germany
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247
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Cahenzli J, Köller Y, Wyss M, Geuking M, McCoy K. Intestinal microbial diversity during early-life colonization shapes long-term IgE levels. Cell Host Microbe 2014; 14:559-70. [PMID: 24237701 PMCID: PMC4049278 DOI: 10.1016/j.chom.2013.10.004] [Citation(s) in RCA: 426] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/11/2013] [Accepted: 10/11/2013] [Indexed: 12/22/2022]
Abstract
Microbial exposure following birth profoundly impacts mammalian immune system development. Microbiota alterations are associated with increased incidence of allergic and autoimmune disorders with elevated serum IgE as a hallmark. The previously reported abnormally high serum IgE levels in germ-free mice suggests that immunoregulatory signals from microbiota are required to control basal IgE levels. We report that germ-free mice and those with low-diversity microbiota develop elevated serum IgE levels in early life. B cells in neonatal germ-free mice undergo isotype switching to IgE at mucosal sites in a CD4 T-cell- and IL-4-dependent manner. A critical level of microbial diversity following birth is required in order to inhibit IgE induction. Elevated IgE levels in germ-free mice lead to increased mast-cell-surface-bound IgE and exaggerated oral-induced systemic anaphylaxis. Thus, appropriate intestinal microbial stimuli during early life are critical for inducing an immunoregulatory network that protects from induction of IgE at mucosal sites. Germ-free and mice with low-diversity microbiota develop high serum IgE levels B cells in germ-free mice undergo IgE class switch recombination at mucosal sites A diverse microbiota early in life is required to inhibit IgE induction Hyper IgE in germ-free mice leads to exaggerated oral-induced systemic anaphylaxis
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Affiliation(s)
- Julia Cahenzli
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3010 Bern, Switzerland
| | - Yasmin Köller
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3010 Bern, Switzerland
| | - Madeleine Wyss
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3010 Bern, Switzerland
| | - Markus B. Geuking
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3010 Bern, Switzerland
| | - Kathy D. McCoy
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, Murtenstrasse 35, University of Bern, 3010 Bern, Switzerland
- Corresponding author
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248
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Ferreyra JA, Ng KM, Sonnenburg JL. The Enteric Two-Step: nutritional strategies of bacterial pathogens within the gut. Cell Microbiol 2014; 16:993-1003. [PMID: 24720567 DOI: 10.1111/cmi.12300] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2014] [Indexed: 01/20/2023]
Abstract
The gut microbiota is a dense and diverse microbial community governed by dynamic microbe-microbe and microbe-host interactions, the status of which influences whether enteric pathogens can cause disease. Here we review recent insights into the key roles that nutrients play in bacterial pathogen exploitation of the gut microbial ecosystem. We synthesize recent findings to support a five-stage model describing the transition between a healthy microbiota and one dominated by a pathogen and disease. Within this five-stage model, two stages are critical to the pathogen: (i) an initial expansion phase that must occur in the absence of pathogen-induced inflammation, followed by (ii) pathogen-promoting physiological changes such as inflammation and diarrhoea. We discuss how this emerging paradigm of pathogen life within the lumen of the gut is giving rise to novel therapeutic strategies.
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Affiliation(s)
- Jessica A Ferreyra
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
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249
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Woodhams DC, Brandt H, Baumgartner S, Kielgast J, Küpfer E, Tobler U, Davis LR, Schmidt BR, Bel C, Hodel S, Knight R, McKenzie V. Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness. PLoS One 2014; 9:e96375. [PMID: 24789229 PMCID: PMC4005770 DOI: 10.1371/journal.pone.0096375] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/04/2014] [Indexed: 01/21/2023] Open
Abstract
Pathogenesis is strongly dependent on microbial context, but development of probiotic therapies has neglected the impact of ecological interactions. Dynamics among microbial communities, host immune responses, and environmental conditions may alter the effect of probiotics in human and veterinary medicine, agriculture and aquaculture, and the proposed treatment of emerging wildlife and zoonotic diseases such as those occurring on amphibians or vectored by mosquitoes. Here we use a holistic measure of amphibian mucosal defenses to test the effects of probiotic treatments and to assess disease risk under different ecological contexts. We developed a non-invasive assay for antifungal function of the skin mucosal ecosystem (mucosome function) integrating host immune factors and the microbial community as an alternative to pathogen exposure experiments. From approximately 8500 amphibians sampled across Europe, we compared field infection prevalence with mucosome function against the emerging fungal pathogen Batrachochytrium dendrobatidis. Four species were tested with laboratory exposure experiments, and a highly susceptible species, Alytes obstetricans, was treated with a variety of temperature and microbial conditions to test the effects of probiotic therapies and environmental conditions on mucosome function. We found that antifungal function of the amphibian skin mucosome predicts the prevalence of infection with the fungal pathogen in natural populations, and is linked to survival in laboratory exposure experiments. When altered by probiotic therapy, the mucosome increased antifungal capacity, while previous exposure to the pathogen was suppressive. In culture, antifungal properties of probiotics depended strongly on immunological and environmental context including temperature, competition, and pathogen presence. Functional changes in microbiota with shifts in temperature provide an alternative mechanistic explanation for patterns of disease susceptibility related to climate beyond direct impact on host or pathogen. This nonlethal management tool can be used to optimize and quickly assess the relative benefits of probiotic therapies under different climatic, microbial, or host conditions.
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Affiliation(s)
- Douglas C. Woodhams
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
| | - Hannelore Brandt
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Simone Baumgartner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jos Kielgast
- Section for Freshwater Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eliane Küpfer
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Evolutionary Biology, Technical University of Braunschweig, Braunschweig, Germany
| | - Ursina Tobler
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- KARCH, Neuchâtel, Switzerland
| | - Leyla R. Davis
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Benedikt R. Schmidt
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- KARCH, Neuchâtel, Switzerland
| | - Christian Bel
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Sandro Hodel
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Rob Knight
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
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250
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Daniele M, Pascual L, Barberis L. Curative effect of the probiotic strain Lactobacillus fermentum
L23 in a murine model of vaginal infection by Gardnerella vaginalis. Lett Appl Microbiol 2014; 59:93-8. [DOI: 10.1111/lam.12249] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 02/18/2014] [Accepted: 03/12/2014] [Indexed: 11/26/2022]
Affiliation(s)
- M. Daniele
- Departamento de Microbiología e Inmunología; Universidad Nacional de Río Cuarto (UNRC); Río Cuarto Argentina
| | - L. Pascual
- Departamento de Microbiología e Inmunología; Universidad Nacional de Río Cuarto (UNRC); Río Cuarto Argentina
| | - L. Barberis
- Departamento de Microbiología e Inmunología; Universidad Nacional de Río Cuarto (UNRC); Río Cuarto Argentina
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