501
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Fecal Indole as a Biomarker of Susceptibility to Cryptosporidium Infection. Infect Immun 2016; 84:2299-306. [PMID: 27245413 DOI: 10.1128/iai.00336-16] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/22/2016] [Indexed: 01/16/2023] Open
Abstract
Cryptosporidium causes significant diarrhea worldwide, especially among children and immunocompromised individuals, and no effective drug treatment is currently available for those who need it most. In this report, previous volunteer infectivity studies have been extended to examine the association between fecal indole and indole-producing (IP) gut microbiota on the outcome of a Cryptosporidium infection. Fecal indole concentrations (FICs) of 50 subjects and 19 taxa of common gut microbiota, including six IP taxa (11 subjects) were determined in stool samples collected before and after a challenge with Cryptosporidium oocysts. At the baseline, the mean FIC (± the standard deviation) was 1.66 ± 0.80 mM in those who became infected after a challenge versus 3.20 ± 1.23 mM in those who remained uninfected (P = 0.0001). Only 11.1% of the subjects with a FIC of >2.5 mM became infected after a challenge versus 65.2% of the subjects with a FIC of <2.5 mM. In contrast, the FICs of infected subjects at the baseline or during diarrhea were not correlated with infection intensity or disease severity. The relative abundances (percent) of Escherichia coli, Bacillus spp., and Clostridium spp. were greater ≥2.5-fold in volunteers with a baseline FIC of >2.5 mM, while those of Bacteroides pyogenes, B. fragilis, and Akkermansia muciniphila were greater in those with a baseline FIC of <2.5 mM. These data indicate that some IP bacteria, or perhaps indole alone, can influence the ability of Cryptosporidium to establish an infection. Thus, preexisting indole levels in the gut join the oocyst dose and immune status as important factors that determine the outcome of Cryptosporidium exposure.
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502
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Salmonella Degrades the Host Glycocalyx Leading to Altered Infection and Glycan Remodeling. Sci Rep 2016; 6:29525. [PMID: 27389966 PMCID: PMC4937416 DOI: 10.1038/srep29525] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/17/2016] [Indexed: 12/13/2022] Open
Abstract
Complex glycans cover the gut epithelial surface to protect the cell from the environment. Invasive pathogens must breach the glycan layer before initiating infection. While glycan degradation is crucial for infection, this process is inadequately understood. Salmonella contains 47 glycosyl hydrolases (GHs) that may degrade the glycan. We hypothesized that keystone genes from the entire GH complement of Salmonella are required to degrade glycans to change infection. This study determined that GHs recognize the terminal monosaccharides (N-acetylneuraminic acid (Neu5Ac), galactose, mannose, and fucose) and significantly (p < 0.05) alter infection. During infection, Salmonella used its two GHs sialidase nanH and amylase malS for internalization by targeting different glycan structures. The host glycans were altered during Salmonella association via the induction of N-glycan biosynthesis pathways leading to modification of host glycans by increasing fucosylation and mannose content, while decreasing sialylation. Gene expression analysis indicated that the host cell responded by regulating more than 50 genes resulting in remodeled glycans in response to Salmonella treatment. This study established the glycan structures on colonic epithelial cells, determined that Salmonella required two keystone GHs for internalization, and left remodeled host glycans as a result of infection. These data indicate that microbial GHs are undiscovered virulence factors.
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503
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Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol 2016; 428:3230-3252. [PMID: 27393306 DOI: 10.1016/j.jmb.2016.06.021] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023]
Abstract
Carbohydrates comprise a large fraction of the typical diet, yet humans are only able to directly process some types of starch and simple sugars. The remainder transits the large intestine where it becomes food for the commensal bacterial community. This is an environment of not only intense competition but also impressive cooperation for available glycans, as these bacteria work to maximize their energy harvest from these carbohydrates during their limited transit time through the gut. The species within the gut microbiota use a variety of strategies to process and scavenge both dietary and host-produced glycans such as mucins. Some act as generalists that are able to degrade a wide range of polysaccharides, while others are specialists that are only able to target a few select glycans. All are members of a metabolic network where substantial cross-feeding takes place, as by-products of one organism serve as important resources for another. Much of this metabolic activity influences host physiology, as secondary metabolites and fermentation end products are absorbed either by the epithelial layer or by transit via the portal vein to the liver where they can have additional effects. These microbially derived compounds influence cell proliferation and apoptosis, modulate the immune response, and can alter host metabolism. This review summarizes the molecular underpinnings of these polysaccharide degradation processes, their impact on human health, and how we can manipulate them through the use of prebiotics.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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504
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Crost EH, Tailford LE, Monestier M, Swarbreck D, Henrissat B, Crossman LC, Juge N. The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases. Gut Microbes 2016; 7:302-312. [PMID: 27223845 PMCID: PMC4988440 DOI: 10.1080/19490976.2016.1186334] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 02/07/2023] Open
Abstract
We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit.
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Affiliation(s)
- Emmanuelle H. Crost
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - Louise E. Tailford
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - Marie Monestier
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - David Swarbreck
- The Genome Analysis Center, Norwich Research Park, Norwich, United Kingdom
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université Aix-Marseille, CNRS UMR 7257, France
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lisa C. Crossman
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- SequenceAnalysis.co.uk, NRP Innovation Center, Norwich, United Kingdom
| | - Nathalie Juge
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
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505
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Wong MT, Wang W, Lacourt M, Couturier M, Edwards EA, Master ER. Substrate-Driven Convergence of the Microbial Community in Lignocellulose-Amended Enrichments of Gut Microflora from the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus). Front Microbiol 2016; 7:961. [PMID: 27446004 PMCID: PMC4914502 DOI: 10.3389/fmicb.2016.00961] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/03/2016] [Indexed: 02/01/2023] Open
Abstract
Strategic enrichment of microcosms derived from wood foragers can facilitate the discovery of key microbes that produce enzymes for the bioconversion of plant fiber (i.e., lignocellulose) into valuable chemicals and energy. In this study, lignocellulose-degrading microorganisms from the digestive systems of Canadian beaver (Castor canadensis) and North American moose (Alces americanus) were enriched under methanogenic conditions for over 3 years using various wood-derived substrates, including (i) cellulose (C), (ii) cellulose + lignosulphonate (CL), (iii) cellulose + tannic acid (CT), and (iv) poplar hydrolysate (PH). Substantial improvement in the conversion of amended organic substrates into biogas was observed in both beaver dropping and moose rumen enrichment cultures over the enrichment phases (up to 0.36–0.68 ml biogas/mg COD added), except for enrichments amended with tannic acid where conversion was approximately 0.15 ml biogas/mg COD added. Multiplex-pyrosequencing of 16S rRNA genes revealed systematic shifts in the population of Firmicutes, Bacteroidetes, Chlorobi, Spirochaetes, Chloroflexi, and Elusimicrobia in response to the enrichment. These shifts were predominantly substrate driven, not inoculum driven, as revealed by both UPGMA clustering pattern and OTU distribution. Additionally, the relative abundance of multiple OTUs from poorly defined taxonomic lineages increased from less than 1% to 25–50% in microcosms amended with lignocellulosic substrates, including OTUs from classes SJA-28, Endomicrobia, orders Bacteroidales, OPB54, and family Lachnospiraceae. This study provides the first direct comparison of shifts in microbial communities that occurred in different environmental samples in response to multiple relevant lignocellulosic carbon sources, and demonstrates the potential of enrichment to increase the abundance of key lignocellulolytic microorganisms and encoded activities.
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Affiliation(s)
- Mabel T Wong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Michael Lacourt
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Marie Couturier
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
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506
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Spring S, Bunk B, Spröer C, Schumann P, Rohde M, Tindall BJ, Klenk HP. Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. ISME JOURNAL 2016; 10:2801-2816. [PMID: 27300277 PMCID: PMC5148204 DOI: 10.1038/ismej.2016.84] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/15/2016] [Accepted: 04/21/2016] [Indexed: 12/29/2022]
Abstract
The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-ABT and related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Peter Schumann
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany
| | - Brian J Tindall
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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507
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Dwivedi R, Nothaft H, Garber J, Xin Kin L, Stahl M, Flint A, van Vliet AHM, Stintzi A, Szymanski CM. L-fucose influences chemotaxis and biofilm formation in Campylobacter jejuni. Mol Microbiol 2016; 101:575-89. [PMID: 27145048 DOI: 10.1111/mmi.13409] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 04/15/2016] [Indexed: 11/28/2022]
Abstract
Campylobacter jejuni and Campylobacter coli are zoonotic pathogens once considered asaccharolytic, but are now known to encode pathways for glucose and fucose uptake/metabolism. For C. jejuni, strains with the fuc locus possess a competitive advantage in animal colonization models. We demonstrate that this locus is present in > 50% of genome-sequenced strains and is prevalent in livestock-associated isolates of both species. To better understand how these campylobacters sense nutrient availability, we examined biofilm formation and chemotaxis to fucose. C. jejuni NCTC11168 forms less biofilms in the presence of fucose, although its fucose permease mutant (fucP) shows no change. In a newly developed chemotaxis assay, both wild-type and the fucP mutant are chemotactic towards fucose. C. jejuni 81-176 naturally lacks the fuc locus and is unable to swim towards fucose. Transfer of the NCTC11168 locus into 81-176 activated fucose uptake and chemotaxis. Fucose chemotaxis also correlated with possession of the pathway for C. jejuni RM1221 (fuc+) and 81116 (fuc-). Systematic mutation of the NCTC11168 locus revealed that Cj0485 is necessary for fucose metabolism and chemotaxis. This study suggests that components for fucose chemotaxis are encoded within the fuc locus, but downstream signals only in fuc + strains, are involved in coordinating fucose availability with biofilm development.
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Affiliation(s)
- Ritika Dwivedi
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Harald Nothaft
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Jolene Garber
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Lin Xin Kin
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Martin Stahl
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Annika Flint
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Arnoud H M van Vliet
- Institute of Food Research, Gut Health and Food Safety Programme, Norwich Research Park, Norwich, NR4 7UA, UK
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Christine M Szymanski
- Alberta Glycomics Centre and Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
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508
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Warda AK, Siezen RJ, Boekhorst J, Wells-Bennik MHJ, de Jong A, Kuipers OP, Nierop Groot MN, Abee T. Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity. PLoS One 2016; 11:e0156796. [PMID: 27272929 PMCID: PMC4896439 DOI: 10.1371/journal.pone.0156796] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/19/2016] [Indexed: 11/19/2022] Open
Abstract
We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed.
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Affiliation(s)
- Alicja K. Warda
- TI Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
- Wageningen UR Food & Biobased Research, Wageningen, The Netherlands
| | - Roland J. Siezen
- TI Food and Nutrition, Wageningen, The Netherlands
- Center for Molecular and Biomolecular Informatics, RadboudUMC, Nijmegen, The Netherlands
- Microbial Bioinformatics, Ede, The Netherlands
| | - Jos Boekhorst
- TI Food and Nutrition, Wageningen, The Netherlands
- Center for Molecular and Biomolecular Informatics, RadboudUMC, Nijmegen, The Netherlands
- NIZO Food Research B.V., Ede, The Netherlands
| | | | - Anne de Jong
- TI Food and Nutrition, Wageningen, The Netherlands
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Oscar P. Kuipers
- TI Food and Nutrition, Wageningen, The Netherlands
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Masja N. Nierop Groot
- TI Food and Nutrition, Wageningen, The Netherlands
- Wageningen UR Food & Biobased Research, Wageningen, The Netherlands
| | - Tjakko Abee
- TI Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands
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509
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Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science 2016; 352:586-9. [PMID: 27126044 DOI: 10.1126/science.aad8852] [Citation(s) in RCA: 367] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
Abstract
Fecal microbiota transplantation (FMT) has shown efficacy in treating recurrent Clostridium difficile infection and is increasingly being applied to other gastrointestinal disorders, yet the fate of native and introduced microbial strains remains largely unknown. To quantify the extent of donor microbiota colonization, we monitored strain populations in fecal samples from a recent FMT study on metabolic syndrome patients using single-nucleotide variants in metagenomes. We found extensive coexistence of donor and recipient strains, persisting 3 months after treatment. Colonization success was greater for conspecific strains than for new species, the latter falling within fluctuation levels observed in healthy individuals over a similar time frame. Furthermore, same-donor recipients displayed varying degrees of microbiota transfer, indicating individual patterns of microbiome resistance and donor-recipient compatibilities.
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Affiliation(s)
- Simone S Li
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 Sydney, Australia
| | - Ana Zhu
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Rajna Hercog
- Genomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Falk Hildebrand
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Max Nieuwdorp
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, Netherlands. Diabetes Center, Vrije University Medical Center, 1018 HV Amsterdam, Netherlands. Wallenberg Laboratory, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Jarkko Salojärvi
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland. Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Anita Y Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Willem M de Vos
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland. Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, Netherlands. Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, 00014 Helsinki, Finland.
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany. Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany. Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
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510
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McLoughlin K, Schluter J, Rakoff-Nahoum S, Smith A, Foster K. Host Selection of Microbiota via Differential Adhesion. Cell Host Microbe 2016; 19:550-9. [DOI: 10.1016/j.chom.2016.02.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/26/2016] [Accepted: 02/29/2016] [Indexed: 12/16/2022]
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511
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Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG, Henderson WA. The microbiome of the oral mucosa in irritable bowel syndrome. Gut Microbes 2016; 7:286-301. [PMID: 26963804 PMCID: PMC4988452 DOI: 10.1080/19490976.2016.1162363] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a poorly understood disorder characterized by persistent symptoms, including visceral pain. Studies have demonstrated oral microbiome differences in inflammatory bowel diseases suggesting the potential of the oral microbiome in the study of non-oral conditions. In this exploratory study we examine whether differences exist in the oral microbiome of IBS participants and healthy controls, and whether the oral microbiome relates to symptom severity. The oral buccal mucosal microbiome of 38 participants was characterized using PhyloChip microarrays. The severity of visceral pain was assessed by orally administering a gastrointestinal test solution. Participants self-reported their induced visceral pain. Pain severity was highest in IBS participants (P = 0.0002), particularly IBS-overweight participants (P = 0.02), and was robustly correlated to the abundance of 60 OTUs, 4 genera, 5 families and 4 orders of bacteria (r2 > 0.4, P < 0.001). IBS-overweight participants showed decreased richness in the phylum Bacteroidetes (P = 0.007) and the genus Bacillus (P = 0.008). Analysis of β-diversity found significant separation of the IBS-overweight group (P < 0.05). Our oral microbial results are concordant with described fecal and colonic microbiome-IBS and -weight associations. Having IBS and being overweight, rather than IBS-subtypes, was the most important factor in describing the severity of visceral pain and variation in the microbiome. Pain severity was strongly correlated to the abundance of many taxa, suggesting the potential of the oral microbiome in diagnosis and patient phenotyping. The oral microbiome has potential as a source of microbial information in IBS.
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Affiliation(s)
- Nicolaas H. Fourie
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Dan Wang
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Sarah K. Abey
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - LeeAnne B. Sherwin
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Paule V. Joseph
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Bridgett Rahim-Williams
- National Institute on Minority Health and Health Disparities, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Eric G. Ferguson
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Wendy A. Henderson
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
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512
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Zhang C, Derrien M, Levenez F, Brazeilles R, Ballal SA, Kim J, Degivry MC, Quéré G, Garault P, van Hylckama Vlieg JET, Garrett WS, Doré J, Veiga P. Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME JOURNAL 2016; 10:2235-45. [PMID: 26953599 PMCID: PMC4989305 DOI: 10.1038/ismej.2016.13] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/18/2016] [Accepted: 01/08/2016] [Indexed: 01/01/2023]
Abstract
Resident gut microbes co-exist with transient bacteria to form the gut microbiota. Despite increasing evidence suggesting a role for transient microbes on gut microbiota function, the interplay between resident and transient members of this microbial community is poorly defined. We aimed to determine the extent to which a host's autochthonous gut microbiota influences niche permissivity to transient bacteria using a fermented milk product (FMP) as a vehicle for five food-borne bacterial strains. Using conventional and gnotobiotic rats and gut microbiome analyses (16S rRNA genes pyrosequencing and reverse transcription qPCR), we demonstrated that the clearance kinetics of one FMP bacterium, Lactococcus lactis CNCM I-1631, were dependent on the structure of the resident gut microbiota. Susceptibility of the resident gut microbiota to modulation by FMP intervention correlated with increased persistence of L. lactis. We also observed gut microbiome configurations that were associated with altered stability upon exposure to transient bacteria. Our study supports the concept that allochthonous bacteria have transient and subject-specific effects on the gut microbiome that can be leveraged to re-engineer the gut microbiome and improve dysbiosis-related diseases.
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Affiliation(s)
- Chenhong Zhang
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Muriel Derrien
- Life Science, Danone Nutricia Research, Palaiseau, France
| | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | | | - Sonia A Ballal
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jason Kim
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Gaëlle Quéré
- Life Science, Danone Nutricia Research, Palaiseau, France
| | - Peggy Garault
- Life Science, Danone Nutricia Research, Palaiseau, France
| | | | | | - Joël Doré
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Patrick Veiga
- Life Science, Danone Nutricia Research, Palaiseau, France.,Harvard T. H. Chan School of Public Health, Boston, MA, USA
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513
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Derrien M, Belzer C, de Vos WM. Akkermansia muciniphila and its role in regulating host functions. Microb Pathog 2016; 106:171-181. [PMID: 26875998 DOI: 10.1016/j.micpath.2016.02.005] [Citation(s) in RCA: 636] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 02/08/2023]
Abstract
Akkermansia muciniphila is an intestinal bacterium that was isolated a decade ago from a human fecal sample. Its specialization in mucin degradation makes it a key organism at the mucosal interface between the lumen and host cells. Although it was isolated quite recently, it has rapidly raised significant interest as A. muciniphila is the only cultivated intestinal representative of the Verrucomicrobia, one of the few phyla in the human gut that can be easily detected in phylogenetic and metagenome analyses. There has also been a growing interest in A. muciniphila, due to its association with health in animals and humans. Notably, reduced levels of A. muciniphila have been observed in patients with inflammatory bowel diseases (mainly ulcerative colitis) and metabolic disorders, which suggests it may have potential anti-inflammatory properties. The aims of this review are to summarize the existing data on the intestinal distribution of A. muciniphila in health and disease, to provide insight into its ecology and its role in founding microbial networks at the mucosal interface, as well as to discuss recent research on its role in regulating host functions that are disturbed in various diseases, with a specific focus on metabolic disorders in both animals and humans.
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Affiliation(s)
- Muriel Derrien
- Danone Nutricia Research, Avenue de la Vauve, 91767 Palaiseau, France.
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands; Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland.
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514
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Karaulov AV, Gurina NN, Novikov DV, Fomina SG, Novikov VV. [Role of MUC1 Expression in Tumor Progression]. ACTA ACUST UNITED AC 2016; 71:392-6. [PMID: 29297994 DOI: 10.15690/vramn736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mucin 1 (MUC1) is a multistructural and multifunctional protein that is involved in regulating diverse cellular activities. This strongly glycosylated transmembrane protein forms a mucous gel on the surface of epithelial cells that protects the cells from injury. MUC1 acts as a signaling molecule and transcription factor modulating metabolism and resistance to bacterial-induced inflammation. This article presents a review of the relationship between structural and functional changes of the MUC1 and the characteristics of cancer cells. The alteration in MUC1 expression level, a number of structural forms, protein glycosylation and localization occurs in cancer cells. These alterations lead to metabolic reprogramming associated with proliferation, resistance to hypoxia and angiogenesis which affects the survival of cancer cells. Furthermore, cancer cells can take advantage of MUC1 interaction with adhesion molecules for invasion and metastasis. Thus, MUC1 plays a key role both in the homeostasis of epithelial cells and in cancer progression. Understanding the role of MUC1 expression in tumor cells survival is important for the development of new monitoring and therapeutic approaches for the treatment MUC1 positive maligancies.
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515
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Brahe LK, Astrup A, Larsen LH. Can We Prevent Obesity-Related Metabolic Diseases by Dietary Modulation of the Gut Microbiota? Adv Nutr 2016; 7:90-101. [PMID: 26773017 PMCID: PMC4717895 DOI: 10.3945/an.115.010587] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Obesity increases the risk of type 2 diabetes, cardiovascular diseases, and certain cancers, which are among the leading causes of death worldwide. Obesity and obesity-related metabolic diseases are characterized by specific alterations in the human gut microbiota. Experimental studies with gut microbiota transplantations in mice and in humans indicate that a specific gut microbiota composition can be the cause and not just the consequence of the obese state and metabolic disease, which suggests a potential for gut microbiota modulation in prevention and treatment of obesity-related metabolic diseases. In addition, dietary intervention studies have suggested that modulation of the gut microbiota can improve metabolic risk markers in humans, but a causal role of the gut microbiota in such studies has not yet been established. Here, we review and discuss the role of the gut microbiota in obesity-related metabolic diseases and the potential of dietary modulation of the gut microbiota in metabolic disease prevention and treatment.
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Affiliation(s)
- Lena K Brahe
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Arne Astrup
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Lesli H Larsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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516
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Glade MJ, Meguid MM. A glance at … dietary emulsifiers, the human intestinal mucus and microbiome, and dietary fiber. Nutrition 2015; 32:609-14. [PMID: 26899163 DOI: 10.1016/j.nut.2015.12.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 02/07/2023]
Affiliation(s)
| | - Michael M Meguid
- Professor Emeritus, Surgery, Neuroscience and Nutrition, Department of Surgery, University Hospital, Upstate Medical University, Syracuse, NY, USA
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517
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Antonissen G, Van Immerseel F, Pasmans F, Ducatelle R, Janssens GPJ, De Baere S, Mountzouris KC, Su S, Wong EA, De Meulenaer B, Verlinden M, Devreese M, Haesebrouck F, Novak B, Dohnal I, Martel A, Croubels S. Mycotoxins Deoxynivalenol and Fumonisins Alter the Extrinsic Component of Intestinal Barrier in Broiler Chickens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:10846-10855. [PMID: 26632976 DOI: 10.1021/acs.jafc.5b04119] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Deoxynivalenol (DON) and fumonisins (FBs) are secondary metabolites produced by Fusarium fungi that frequently contaminate broiler feed. The aim of this study was to investigate the impact of DON and/or FBs on the intestinal barrier in broiler chickens, more specifically on the mucus layer and antioxidative response to oxidative stress. One-day-old broiler chicks were divided into four groups, each consisting of eight pens of seven birds each, and were fed for 15 days either a control diet, a DON-contaminated diet (4.6 mg DON/kg feed), a FBs-contaminated diet (25.4 mg FB1 + FB2/kg feed), or a DON+FBs-contaminated diet (4.3 mg DON and 22.9 mg FB1 + FB2/kg feed). DON and FBs affected the duodenal mucus layer by suppressing intestinal mucin (MUC) 2 gene expression and altering the mucin monosaccharide composition. Both mycotoxins decreased gene expression of the intestinal zinc transporter (ZnT)-1 and regulated intracellular methionine homeostasis, which are both important for preserving the cell's critical antioxidant activity. Feeding a DON- and/or FBs-contaminated diet, at concentrations close to the European Union maximum guidance levels (5 mg DON and 20 mg FB1 + FB2/kg feed) changes the intestinal mucus layer and several intestinal epithelial antioxidative mechanisms.
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Affiliation(s)
- Gunther Antonissen
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Geert P J Janssens
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University , Heidestraat 19, 9820 Merelbeke, Belgium
| | - Siegrid De Baere
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Konstantinos C Mountzouris
- Department of Nutritional Physiology and Feeding, Agricultural University of Athens , Iera Odos 75, 11855 Athens, Greece
| | - Shengchen Su
- Department of Animal and Poultry Sciences, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Eric A Wong
- Department of Animal and Poultry Sciences, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Bruno De Meulenaer
- Department of Food Safety and Food Quality (Partner in Food2Know), Faculty of Bioscience Engineering, Ghent University , Coupure Links 653, 9000 Gent, Belgium
| | - Marc Verlinden
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Mathias Devreese
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Barbara Novak
- Biomin Research Center , Technopark 1, 3430 Tulln, Austria
| | - Ilse Dohnal
- Biomin Research Center , Technopark 1, 3430 Tulln, Austria
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Siska Croubels
- Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
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518
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De Weirdt R, Van de Wiele T. Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality. NPJ Biofilms Microbiomes 2015; 1:15026. [PMID: 28721237 PMCID: PMC5515210 DOI: 10.1038/npjbiofilms.2015.26] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/25/2015] [Accepted: 10/04/2015] [Indexed: 01/01/2023] Open
Abstract
The human gut microbiome provides us with functional features that we did not have to evolve ourselves and can be viewed as a structured microbial community that operates like a microbial organ within the human host. A minor but important part of this microbiome is the ability to colonise and thrive within the mucous layer that covers the colon epithelium. These mucosal microbes intimately interact with the intestinal tissue and seem to be important modulators of human health. Embedded in the host-secreted mucous matrix, they form a 'mucosal biofilm' with a distinct composition and functionality. In this review, we provide evidence that six specific (micro)environmental factors near the colon mucosa shape and determine mucosal biofilm formation and stability, that is, (1) mucous rigidity, (2) gradients of fluid shear, (3) radial oxygen gradients, (4) secretions of host defense molecules, (5) the presence of a rich but challenging nutrient platform and (6) the presence of niches at the colon epithelial surface. In addition, it appears that microbes actively participate in shaping their mucosal environment. Current insights into the interaction between mucosal microbes and their environment are rather limited, and many questions regarding the contribution of mucosal biofilm functionality and stability to human health remain to be answered. Yet, given the higher potency of mucosal microbes than their luminal counterparts to interact with the host, new insights can accelerate the development of novel disease-preventive or therapeutic strategies.
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Affiliation(s)
- Rosemarie De Weirdt
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Gent, Belgium
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Gent, Belgium
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519
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Swidsinski A, Loening-Baucke V, Schulz S, Manowsky J, Verstraelen H, Swidsinski S. Functional anatomy of the colonic bioreactor: Impact of antibiotics and Saccharomyces boulardii on bacterial composition in human fecal cylinders. Syst Appl Microbiol 2015; 39:67-75. [PMID: 26723852 DOI: 10.1016/j.syapm.2015.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 11/05/2015] [Accepted: 11/05/2015] [Indexed: 12/11/2022]
Abstract
Sections of fecal cylinders were analyzed using fluorescence in situ hybridization targeting 180 bacterial groups. Samples were collected from three groups of women (N=20 each) treated for bacterial vaginosis with ciprofloxacin+metronidazole. Group A only received the combined antibiotic regimen, whereas the A/Sb group received concomitant Saccharomyces boulardii CNCM I-745 treatment, and the A_Sb group received S. boulardii prophylaxis following the 14-day antibiotic course. The number of stool cylinders analyzed was 188 out of 228 in group A, 170 out of 228 in group A/Sb, and 172 out of 216 in group A_Sb. The colonic biomass was organized into a separate mucus layer with no bacteria, a 10-30μm broad unstirred transitional layer enriched with bacteria, and a patchy fermentative area that mixed digestive leftovers with bacteria. The antibiotics suppressed bacteria mainly in the fermentative area, whereas abundant bacterial clades retreated to the transitional mucus and survived. As a result, the total concentration of bacteria decreased only by one order. These effects were lasting, since the overall recovery of the microbial mass, bacterial diversity and concentrations were still below pre-antibiotic values 4 months after the end of antibiotic treatment. Sb-prophylaxis markedly reduced antibiotic effects and improved the recovery rates. Since the colon is a sophisticated bioreactor, the study indicated that the spatial anatomy of its biomass was crucial for its function.
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Affiliation(s)
- Alexander Swidsinski
- Laboratory for Molecular Genetics, Polymicrobial Infections and Biofilms, Department of Medicine, Section of Gastroenterology, Hepatology and Endocrinology, Charité University Hospital, CCM 10117 Berlin, Germany.
| | - Vera Loening-Baucke
- Laboratory for Molecular Genetics, Polymicrobial Infections and Biofilms, Department of Medicine, Section of Gastroenterology, Hepatology and Endocrinology, Charité University Hospital, CCM 10117 Berlin, Germany
| | - Stefan Schulz
- Laboratory for Molecular Genetics, Polymicrobial Infections and Biofilms, Department of Medicine, Section of Gastroenterology, Hepatology and Endocrinology, Charité University Hospital, CCM 10117 Berlin, Germany
| | - Julia Manowsky
- Department of Nutritional Biochemistry, University of Potsdam, Institute of Nutritional Science, Nuthetal, Germany
| | - Hans Verstraelen
- Department of Obstetrics and Gynaecology, Ghent University Hospital, Ghent, Belgium
| | - Sonja Swidsinski
- Department of Microbiology, Labor Berlin - Charité Vivantes GmbH, Sylter Strasse 2, 13353 Berlin, Germany
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520
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Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment. Appl Environ Microbiol 2015; 82:980-991. [PMID: 26590291 DOI: 10.1128/aem.03500-15] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bifidobacteria represent one of the dominant microbial groups that occur in the gut of various animals, being particularly prevalent during the suckling period of humans and other mammals. Their ability to compete with other gut bacteria is largely attributed to their saccharolytic features. Comparative and functional genomic as well as transcriptomic analyses have revealed the genetic background that underpins the overall saccharolytic phenotype for each of the 47 bifidobacterial (sub)species representing the genus Bifidobacterium, while also generating insightful information regarding carbohydrate resource sharing and cross-feeding among bifidobacteria. The abundance of bifidobacterial saccharolytic features in human microbiomes supports the notion that metabolic accessibility to dietary and/or host-derived glycans is a potent evolutionary force that has shaped the bifidobacterial genome.
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521
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Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Comput Biol 2015; 11:e1004573. [PMID: 26565399 PMCID: PMC4643905 DOI: 10.1371/journal.pcbi.1004573] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/29/2015] [Indexed: 12/30/2022] Open
Abstract
Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn’s disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. Microbial communities perform a wide variety of functions, from marine photosynthesis to aiding digestion in the human gut. Shotgun “metagenomic” sequencing can be used to sample millions of short DNA sequences from such communities directly, without needing to first culture its constituents in the laboratory. Using these data, researchers can survey which functions are encoded by mapping these short sequences to known protein families and pathways. Several tools for this annotation already exist. But, annotation is a multi-step process that includes identification of genes in a metagenome and determination of the type of protein each gene encodes. We currently know little about how different choices of parameters during annotation influences the final results. In this work, we systematically test how several key decisions affect the accuracy and speed of annotation, and based on these results, develop new software for annotation, which we named ShotMAP. We then use ShotMAP to functionally characterize marine communities and gut communities in a clinical cohort of inflammatory bowel disease. We find several functions are differentially represented in the gut microbiome of Crohn’s disease patients, which could be candidates for biomarkers and could also offer insight into the pathophysiology of Crohn’s. ShotMAP is freely available (https://github.com/sharpton/shotmap).
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Affiliation(s)
- Stephen Nayfach
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Patrick H. Bradley
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Stacia K. Wyman
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Timothy J. Laurent
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Alex Williams
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, UC Davis Genome Center, University of California, Davis, Davis, California, United States of America
| | - Katherine S. Pollard
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (KSP); (TJS)
| | - Thomas J. Sharpton
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
- Department of Microbiology, Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail: (KSP); (TJS)
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522
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Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation. Nat Commun 2015; 6:7624. [PMID: 26154892 PMCID: PMC4510645 DOI: 10.1038/ncomms8624] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/26/2015] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial species. Ruminococcus gnavus is a commensal anaerobe present in the gastrointestinal tract of >90% of humans and overrepresented in inflammatory bowel diseases (IBD). Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease. Mucosal sialoglycans contribute to host–microbe interactions at mucosal surfaces and impact bacterial colonization of the digestive system. Here the authors identify and characterize an intramolecular trans-sialidase produced by the gut bacterium R. gnavus ATCC 29149 that may contribute to adaptation to the mucosal environment.
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