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      Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

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          Abstract

          Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed. We have employed 454-pyrosequencing of a hyper-variable region of the 16S rRNA gene in combination with sample-specific barcode sequences which enables parallel in-depth analysis of hundreds of samples with limited sample processing. In silico modeling demonstrated that the method correctly describes microbial communities down to phylotypes below the genus level. Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology.

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          Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis.

          Seth Rakoff-Nahoum, Justin Paglino, Fatima Eslami-Varzaneh … (2004)
          Toll-like receptors (TLRs) play a crucial role in host defense against microbial infection. The microbial ligands recognized by TLRs are not unique to pathogens, however, and are produced by both pathogenic and commensal microorganisms. It is thought that an inflammatory response to commensal bacteria is avoided due to sequestration of microflora by surface epithelia. Here, we show that commensal bacteria are recognized by TLRs under normal steady-state conditions, and this interaction plays a crucial role in the maintenance of intestinal epithelial homeostasis. Furthermore, we find that activation of TLRs by commensal microflora is critical for the protection against gut injury and associated mortality. These findings reveal a novel function of TLRs-control of intestinal epithelial homeostasis and protection from injury-and provide a new perspective on the evolution of host-microbial interactions.
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            An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system.

            Sarkis Mazmanian, Cui Hua Liu, Arthur O Tzianabos … (2005)
            The mammalian gastrointestinal tract harbors a complex ecosystem consisting of countless bacteria in homeostasis with the host immune system. Shaped by evolution, this partnership has potential for symbiotic benefit. However, the identities of bacterial molecules mediating symbiosis remain undefined. Here we show that, during colonization of animals with the ubiquitous gut microorganism Bacteroides fragilis, a bacterial polysaccharide (PSA) directs the cellular and physical maturation of the developing immune system. Comparison with germ-free animals reveals that the immunomodulatory activities of PSA during B. fragilis colonization include correcting systemic T cell deficiencies and T(H)1/T(H)2 imbalances and directing lymphoid organogenesis. A PSA mutant of B. fragilis does not restore these immunologic functions. PSA presented by intestinal dendritic cells activates CD4+ T cells and elicits appropriate cytokine production. These findings provide a molecular basis for host-bacterial symbiosis and reveal the archetypal molecule of commensal bacteria that mediates development of the host immune system.
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              Diversity and dissimilarity coefficients: A unified approach

              C.Radhakrishna Rao (1982)
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                Author and article information

                Contributors
                : Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2008
                Publication date (Electronic): 30 July 2008
                Volume: 3
                Issue: 7
                Electronic Location Identifier: e2836
                Affiliations
                [1 ]Swedish Institute for Infectious Disease Control, Solna, Sweden
                [2 ]Department of Ecology and Evolution, Limnology, BMC, Uppsala University, Uppsala, Sweden
                [3 ]Department of Microbiology, Cell and Tumor Biology, Karolinska Institutet, Stockholm, Sweden
                [4 ]Department of Molecular and Clinical Medicine, The Sahlgrenska Center for Cardiovascular and Metabolic Research/Wallenberg Laboratory, Göteborg University, Göteborg, Sweden
                [5 ]School of Biotechnology, Albanova, KTH (Royal Institute of Technology), Stockholm, Sweden
                Centre for DNA Fingerprinting and Diagnostics, India
                Author notes

                Conceived and designed the experiments: AFA ML HJ PN LE. Performed the experiments: AFA ML HJ. Analyzed the data: AFA ML HJ FB LE. Contributed reagents/materials/analysis tools: AFA PN LE. Wrote the paper: AFA ML HJ FB PN LE.

                Article
                Publisher ID: 07-PONE-RA-02039R2
                DOI: 10.1371/journal.pone.0002836
                PMC ID: 2475661
                PubMed ID: 18665274
                SO-VID: b6fdeb43-1b8a-4dc3-82e9-b99fe48a9864
                Copyright © Andersson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                Date received : 21 August 2007
                Date accepted : 24 June 2008
                Page count
                Pages: 8
                Categories
                Subject: Research Article
                Subject: Biotechnology/Applied Microbiology
                Subject: Genetics and Genomics/Microbial Evolution and Genomics
                Subject: Microbiology/Applied Microbiology
                Subject: Microbiology/Environmental Microbiology
                Subject: Microbiology/Medical Microbiology
                Subject: Molecular Biology/Bioinformatics
                Subject: Gastroenterology and Hepatology/Gastrointestinal Infections
                Subject: Infectious Diseases/Gastrointestinal Infections

                ScienceOpen disciplines: Uncategorized
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                ScienceOpen disciplines: Uncategorized

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