Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases.

[1]  手塚 裕之,et al.  Regulation of IgA production by naturally occurring TNF/iNOS-producing dendritic cells , 2008 .

[2]  S. Mazmanian,et al.  A microbial symbiosis factor prevents intestinal inflammatory disease , 2008, Nature.

[3]  T. Noda,et al.  The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy. , 2008, Molecular biology of the cell.

[4]  R. Knight,et al.  Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex , 2008, Nature Methods.

[5]  Leena Peltonen,et al.  Global Transcript Profiles of Fat in Monozygotic Twins Discordant for BMI: Pathways behind Acquired Obesity , 2008, PLoS medicine.

[6]  C. Goodnow,et al.  Aberrant Mucin Assembly in Mice Causes Endoplasmic Reticulum Stress and Spontaneous Inflammation Resembling Ulcerative Colitis , 2008, PLoS medicine.

[7]  R. Flavell,et al.  An Antibiotic-Responsive Mouse Model of Fulminant Ulcerative Colitis , 2008, PLoS medicine.

[8]  Haifeng Lu,et al.  Symbiotic gut microbes modulate human metabolic phenotypes , 2008, Proceedings of the National Academy of Sciences.

[9]  R Balfour Sartor,et al.  Microbial influences in inflammatory bowel diseases. , 2008, Gastroenterology.

[10]  Elaine Holmes,et al.  Probiotic Modulation of Symbiotic Gut Microbial–host Metabolic Interactions in a Humanized Microbiome Mouse Model , 2022 .

[11]  A. Iwasaki,et al.  The autophagy gene ATG5 plays an essential role in B lymphocyte development , 2008, Autophagy.

[12]  L. Comstock,et al.  Niche-Specific Features of the Intestinal Bacteroidales , 2007, Journal of bacteriology.

[13]  M. Rescigno,et al.  Entry route of Salmonella typhimurium directs the type of induced immune response. , 2007, Immunity.

[14]  M. Peppelenbosch,et al.  Early bacterial dependent induction of inducible nitric oxide synthase (iNOS) in epithelial cells upon transfer of CD45RBhigh CD4+ T cells in a model for experimental colitis , 2007, Inflammatory bowel diseases.

[15]  C. Jobin,et al.  Dual‐association of gnotobiotic Il‐10−/− mice with 2 nonpathogenic commensal bacteria induces aggressive pancolitis , 2007, Inflammatory bowel diseases.

[16]  B. Corthésy,et al.  Secretory IgA Mediates Bacterial Translocation to Dendritic Cells in Mouse Peyer’s Patches with Restriction to Mucosal Compartment1 , 2007, The Journal of Immunology.

[17]  J. Gordon,et al.  IgA response to symbiotic bacteria as a mediator of gut homeostasis. , 2007, Cell host & microbe.

[18]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[19]  Wendy S. Garrett,et al.  Communicable Ulcerative Colitis Induced by T-bet Deficiency in the Innate Immune System , 2007, Cell.

[20]  Susan M. Huse,et al.  Microbial Population Structures in the Deep Marine Biosphere , 2007, Science.

[21]  O. Benada,et al.  Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RBhigh CD4+ T cells , 2007, Inflammatory bowel diseases.

[22]  G. Macfarlane,et al.  Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples , 2007, Applied and Environmental Microbiology.

[23]  F. Powrie,et al.  The IL23 axis plays a key role in the pathogenesis of IBD , 2007, Gut.

[24]  N. Pace,et al.  Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases , 2007, Proceedings of the National Academy of Sciences.

[25]  R. Xavier,et al.  Unravelling the pathogenesis of inflammatory bowel disease , 2007, Nature.

[26]  S. Quake,et al.  Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth , 2007, Proceedings of the National Academy of Sciences.

[27]  Daniel B. DiGiulio,et al.  Development of the Human Infant Intestinal Microbiota , 2007, PLoS biology.

[28]  A. Plebani,et al.  Intestinal bacteria trigger T cell-independent immunoglobulin A(2) class switching by inducing epithelial-cell secretion of the cytokine APRIL. , 2007, Immunity.

[29]  R. Wilson,et al.  Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut , 2007, Proceedings of the National Academy of Sciences.

[30]  R. Wilson,et al.  Evolution of Symbiotic Bacteria in the Distal Human Intestine , 2007, PLoS biology.

[31]  B. Xia,et al.  Increased susceptibility to colitis and colorectal tumors in mice lacking core 3–derived O-glycans , 2007, The Journal of experimental medicine.

[32]  R. Rappuoli,et al.  The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. , 2007, Drug discovery today.

[33]  H. Flint,et al.  Cultivable bacterial diversity from the human colon , 2007, Letters in applied microbiology.

[34]  Vincent J. Denef,et al.  Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria , 2007, Nature.

[35]  F. Theissig,et al.  Comparative study of the intestinal mucus barrier in normal and inflamed colon , 2006, Gut.

[36]  D. Bentley,et al.  Phase-variable expression of a family of glycoproteins imparts a dynamic surface to a symbiont in its human intestinal ecosystem , 2007, Proceedings of the National Academy of Sciences.

[37]  Marcy Yann,et al.  ヒト口腔からの微量の培養されないTM7微生物の単一細胞遺伝分析による生物学的「不明な物体」の詳細な分析 , 2007 .

[38]  P. Turnbaugh,et al.  Microbial ecology: Human gut microbes associated with obesity , 2006, Nature.

[39]  E. Mardis,et al.  An obesity-associated gut microbiome with increased capacity for energy harvest , 2006, Nature.

[40]  J. Gordon,et al.  Genomic and Metabolic Studies of the Impact of Probiotics on a Model Gut Symbiont and Host , 2006, PLoS biology.

[41]  Jeffrey I. Gordon,et al.  Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection , 2006, Cell.

[42]  W. Doolittle,et al.  Genomics and the bacterial species problem , 2006, Genome Biology.

[43]  F. Shanahan,et al.  Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and Targeted Bacterial Subgroups in Crohn's Disease , 2006, Journal of Clinical Microbiology.

[44]  U. Gophna,et al.  Differences between Tissue-Associated Intestinal Microfloras of Patients with Crohn's Disease and Ulcerative Colitis , 2006, Journal of Clinical Microbiology.

[45]  L. Hooper,et al.  Symbiotic Bacteria Direct Expression of an Intestinal Bactericidal Lectin , 2006, Science.

[46]  Rob Knight,et al.  UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context , 2006, BMC Bioinformatics.

[47]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[48]  R. Ley,et al.  Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine , 2006, Cell.

[49]  C. Manichanh,et al.  Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach , 2005, Gut.

[50]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[51]  Elisabeth M Bik,et al.  Molecular analysis of the bacterial microbiota in the human stomach. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[52]  R. Knight,et al.  UniFrac: a New Phylogenetic Method for Comparing Microbial Communities , 2005, Applied and Environmental Microbiology.

[53]  Jaideep P. Sundaram,et al.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[54]  S. Mazmanian,et al.  An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System , 2005, Cell.

[55]  E. Purdom,et al.  Diversity of the Human Intestinal Microbial Flora , 2005, Science.

[56]  J. Doré,et al.  Biodiversity of the Mucosa‐Associated Microbiota Is Stable Along the Distal Digestive Tract in Healthy Individuals and Patients With Ibd , 2005, Inflammatory bowel diseases.

[57]  G. Wu,et al.  How to evaluate a gastric submucosal tumour in a patient with haematemesis? , 2005, Gut.

[58]  Benjamin P. Westover,et al.  Glycan Foraging in Vivo by an Intestine-Adapted Bacterial Symbiont , 2005, Science.

[59]  S. Keilbaugh,et al.  Activation of RegIIIbeta/gamma and interferon gamma expression in the intestinal tract of SCID mice: an innate response to bacterial colonisation of the gut. , 2005, Gut.

[60]  K. Wilson,et al.  Ribosomal DNA Sequence Analysis of Mucosa-Associated Bacteria in Crohn’s Disease , 2004, Inflammatory bowel diseases.

[61]  J. Doré,et al.  Molecular inventory of faecal microflora in patients with Crohn's disease. , 2003, FEMS microbiology ecology.

[62]  A. Rudensky,et al.  Recognition of the peripheral self by naturally arising CD25+ CD4+ T cell receptors. , 2004, Immunity.

[63]  R Balfour Sartor,et al.  Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics. , 2004, Gastroenterology.

[64]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[65]  A. Macpherson,et al.  Induction of Protective IgA by Intestinal Dendritic Cells Carrying Commensal Bacteria , 2004, Science.

[66]  Keiichiro Suzuki,et al.  Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[67]  M. Kamm,et al.  Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis , 2003, Gut.

[68]  P. Brigidi,et al.  Prophylaxis of pouchitis onset with probiotic therapy: A double-blind, placebo-controlled trial , 2003 .

[69]  J. Doré,et al.  Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon , 2003, Gut.

[70]  P. Brigidi,et al.  Prophylaxis of pouchitis onset with probiotic therapy: A double‐blind, placebo‐controlled trial , 2000, Gastroenterology.

[71]  Keiichiro Suzuki,et al.  Critical Roles of Activation-Induced Cytidine Deaminase in the Homeostasis of Gut Flora , 2002, Science.

[72]  B. Nardelli,et al.  DCs induce CD40-independent immunoglobulin class switching through BLyS and APRIL , 2002, Nature Immunology.

[73]  E. Zoetendal,et al.  Mucosa-Associated Bacteria in the Human Gastrointestinal Tract Are Uniformly Distributed along the Colon and Differ from the Community Recovered from Feces , 2002, Applied and Environmental Microbiology.

[74]  Nan Yu,et al.  The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.

[75]  Laurie E. Comstock,et al.  Extensive surface diversity of a commensal microorganism by multiple DNA inversions , 2001, Nature.

[76]  T. Honjo,et al.  In situ class switching and differentiation to IgA-producing cells in the gut lamina propria , 2001, Nature.

[77]  C. Probert,et al.  Mucins in the gastrointestinal tract in health and disease. , 2001, Frontiers in bioscience : a journal and virtual library.

[78]  N. Bos,et al.  Timing, Localization, and Persistence of Colonization by Segmented Filamentous Bacteria in the Neonatal Mouse Gut Depend on Immune Status of Mothers and Pups , 2001, Infection and Immunity.

[79]  P. Toivanen,et al.  Influence of Major Histocompatibility Complex on Bacterial Composition of Fecal Flora , 2001, Infection and Immunity.

[80]  D. Kasper,et al.  Genetic Diversity of the Capsular Polysaccharide C Biosynthesis Region of Bacteroides fragilis , 2000, Infection and Immunity.

[81]  T Midtvedt,et al.  A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[82]  N. Bos,et al.  Segmented Filamentous Bacteria Are Potent Stimuli of a Physiologically Normal State of the Murine Gut Mucosal Immune System , 1999, Infection and Immunity.

[83]  F. Preffer,et al.  Suppressive Role of B Cells in Chronic Colitis of  T Cell Receptor α Mutant Mice , 1997, The Journal of experimental medicine.

[84]  D. Jewell,et al.  Altered expression of mucins throughout the colon in ulcerative colitis. , 1997, Gut.

[85]  S. Tonegawa,et al.  Alteration of a polyclonal to an oligoclonal immune response to cecal aerobic bacterial antigens in TCR alpha mutant mice with inflammatory bowel disease. , 1996, International immunology.

[86]  P. Limburg,et al.  In vivo IgA coating of anaerobic bacteria in human faeces. , 1996, Gut.

[87]  F. Kroese,et al.  B-1 cells and their reactivity with the murine intestinal microflora. , 1996, Seminars in immunology.

[88]  K. E. Shroff,et al.  Commensal enteric bacteria engender a self-limiting humoral mucosal immune response while permanently colonizing the gut , 1995, Infection and immunity.

[89]  R. Newcombe,et al.  Thickness of adherent mucus gel on colonic mucosa in humans and its relevance to colitis. , 1994, Gut.

[90]  C. Holdsworth,et al.  The assessment of faecal flora in patients with inflammatory bowel disease by a simplified bacteriological technique. , 1991, Journal of medical microbiology.

[91]  J. P. Van de Merwe,et al.  The obligate anaerobic faecal flora of patients with Crohn's disease and their first-degree relatives. , 1988, Scandinavian journal of gastroenterology.

[92]  L. Bodin,et al.  Relation between concentrations of metronidazole and Bacteroides spp in faeces of patients with Crohn's disease and healthy individuals. , 1981, Journal of clinical pathology.

[93]  D. Savage.  Microbial ecology of the gastrointestinal tract. , 1977, Annual review of microbiology.

[94]  P. Brandtzaeg,et al.  Comparative mapping of the local distribution of immunoglobulin-containing cells in ulcerative colitis and Crohn's disease of the colon. , 1975, Clinical and experimental immunology.

[95]  M. Godoy,et al.  [Fulminant ulcerative colitis]. , 1954, Revista médica de Chile (Impresa).