Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases

An obesity-associated gut microbiome with increased capacity for energy harvest

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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

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Human gut microbes associated with obesity

Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785 · see citing works

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227 · see citing works

Diversity of the Human Intestinal Microbial Flora

Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · see citing works

ARB: a software environment for sequence data

Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,649 · see citing works

The human microbiome project

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Metagenomic Analysis of the Human Distal Gut Microbiome

Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., & Nelson, K. E. (2006) · Science · doi:10.1126/science.1124234 · Cited by 4,699 · see citing works

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

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Unravelling the pathogenesis of inflammatory bowel disease

Xavier, R. J., & Podolsky, D. K. (2007) · Nature · doi:10.1038/nature06005 · Cited by 4,364 · see citing works

Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine

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An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System

Mazmanian, S. K., Liu, C. H., Tzianabos, A. O., & Kasper, D. L. (2005) · Cell · doi:10.1016/j.cell.2005.05.007 · Cited by 2,910 · see citing works

Development of the Human Infant Intestinal Microbiota

Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050177 · Cited by 2,877 · see citing works

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial “pan-genome”

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MICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT

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A microbial symbiosis factor prevents intestinal inflammatory disease

Mazmanian, S. K., Round, J. L., & Kasper, D. L. (2008) · Nature · doi:10.1038/nature07008 · Cited by 2,340 · see citing works

Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach

Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., et al. (2006) · Gut · doi:10.1136/gut.2005.073817 · Cited by 2,277 · see citing works

Microbial Influences in Inflammatory Bowel Diseases

Sartor, R. B. (2008) · Gastroenterology · doi:10.1053/j.gastro.2007.11.059 · Cited by 1,927 · see citing works

The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

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Induction of Protective IgA by Intestinal Dendritic Cells Carrying Commensal Bacteria

Macpherson, A. J., & Uhr, T. (2004) · Science · doi:10.1126/science.1091334 · Cited by 1,584 · see citing works

UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context

Lozupone, C., Hamady, M., & Knight, R. D. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-371 · Cited by 1,454 · see citing works

Symbiotic bacteria direct expression of an intestinal bactericidal lectin

Cash, H. L., Whitham, C. V., Behrendt, C. L., & Hooper, L. V. (2006) · Science · doi:10.1126/science.1127119 · Cited by 1,432 · see citing works

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J., & Knight, R. (2008) · Nature Methods · doi:10.1038/nmeth.1184 · Cited by 1,310 · see citing works

Glycan foraging in vivo by an intestine-adapted bacterial symbiont

Sonnenburg, J. L., Xu, J., Leip, D. D., Chen, C.-H., Westover, B. P., Weatherford, J., Buhler, J. D., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1109051 · Cited by 1,184 · see citing works

Molecular analysis of the bacterial microbiota in the human stomach

Bik, E. M., Eckburg, P. B., Gill, S. R., Nelson, K. E., Purdom, E. A., François, F., Perez-Perez, G., Blaser, M. J., & Relman, D. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506655103 · Cited by 1,160 · see citing works

Prophylaxis of pouchitis onset with probiotic therapy: a double-blind, placebo-controlled trial

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Symbiotic gut microbes modulate human metabolic phenotypes

Li, M., Wang, B., Zhang, M., Rantalainen, M., Wang, S., Zhou, H., Zhang, Y., Shen, J., Pang, X., Zhang, M., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712038105 · Cited by 1,144 · see citing works

The Atg16L Complex Specifies the Site of LC3 Lipidation for Membrane Biogenesis in Autophagy

Fujita, N., Itoh, T., Omori, H., Fukuda, M., Noda, T., & Yoshimori, T. (2008) · Molecular Biology of the Cell · doi:10.1091/mbc.e07-12-1257 · Cited by 1,083 · see citing works

Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics

Sartor, R. B. (2004) · Gastroenterology · doi:10.1053/j.gastro.2004.03.024 · Cited by 1,053 · see citing works

Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection

Rawls, J. F., Mahowald, M. A., Ley, R. E., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.08.043 · Cited by 962 · see citing works

Communicable Ulcerative Colitis Induced by T-bet Deficiency in the Innate Immune System

Garrett, W. S., Lord, G. M., Punit, S., Lugo‐Villarino, G., Mazmanian, S. K., Ito, S., Glickman, J. N., & Glimcher, L. H. (2007) · Cell · doi:10.1016/j.cell.2007.08.017 · Cited by 918 · see citing works

Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis

Mimura, T., Rizzello, F., Helwig, U., Poggioli, G., Schreiber, S., Talbot, I. C., Nicholls, R. J., Gionchetti, P., Campieri, M., & Kamm, M. A. (2003) · Gut · doi:10.1136/gut.53.1.108 · Cited by 912 · see citing works

Microbial Population Structures in the Deep Marine Biosphere

Huber, J. A., Welch, D. B. M., Morrison, H. G., Huse, S. M., Neal, P. R., Butterfield, D. A., & Sogin, M. L. (2007) · Science · doi:10.1126/science.1146689 · Cited by 887 · see citing works

Mucosa-Associated Bacteria in the Human Gastrointestinal Tract Are Uniformly Distributed along the Colon and Differ from the Community Recovered from Feces

Zoetendal, E. G., von Wright, A., Vilpponen-Salmela, T., Ben-Amor, K., Akkermans, A. D. L., & de Vos, W. M. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.7.3401-3407.2002 · Cited by 868 · see citing works

IgA Response to Symbiotic Bacteria as a Mediator of Gut Homeostasis

Peterson, D. A., McNulty, N. P., Guruge, J. L., & Gordon, J. I. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2007.09.013 · Cited by 828 · see citing works

Intestinal Bacteria Trigger T Cell-Independent Immunoglobulin A2 Class Switching by Inducing Epithelial-Cell Secretion of the Cytokine APRIL

He, B., Xu, W., Santini, P. A., Polydorides, A. D., Chiu, A., Estrella, J. S., Shan, M., Chadburn, A., Villanacci, V., Plebani, A., et al. (2007) · Immunity · doi:10.1016/j.immuni.2007.04.014 · Cited by 748 · see citing works

Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon

Seksik, P., Rigottier‐Gois, L., Gramet, G., BRIEND‐SUTREN, M., Pochart, P., Marteau, P. R., Jian, R., & Dore, J. M. (2003) · Gut · doi:10.1136/gut.52.2.237 · Cited by 746 · see citing works

Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut

Suzuki, K., Meek, B., Doi, Y., Muramatsu, M., Chiba, T., Honjo, T., & Fagarasan, S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307317101 · Cited by 721 · see citing works

Recognition of the Peripheral Self by Naturally Arising CD25+ CD4+ T Cell Receptors

Hsieh, C., Liang, Y., Tyznik, A. J., Self, S. G., Liggitt, D., & Rudensky, A. Y. (2004) · Immunity · doi:10.1016/j.immuni.2004.07.009 · Cited by 719 · see citing works

Aberrant Mucin Assembly in Mice Causes Endoplasmic Reticulum Stress and Spontaneous Inflammation Resembling Ulcerative Colitis

Heazlewood, C. K., Cook, M. C., Eri, R., Price, G. R., Tauro, S. B., Taupin, D., Thornton, D. J., Png, C. W., Crockford, T. L., Cornall, R. J., et al. (2008) · PLoS Medicine · doi:10.1371/journal.pmed.0050054 · Cited by 701 · see citing works

Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

Marcy, Y., Ouverney, C., Bik, E. M., Lösekann, T., Ivanova, N., Martín, H. G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D. A., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704662104 · Cited by 632 · see citing works

Critical Roles of Activation-Induced Cytidine Deaminase in the Homeostasis of Gut Flora

Fagarasan, S., Muramatsu, M., Suzuki, K., Nagaoka, H., Hiai, H., & Honjo, T. (2002) · Science · doi:10.1126/science.1077336 · Cited by 590 · see citing works

Evolution of Symbiotic Bacteria in the Distal Human Intestine

Xu, J., Mahowald, M. A., Ley, R. E., Lozupone, C., Hamady, M., Martens, E. C., Henrissat, B., Coutinho, P. M., Minx, P. J., Latreille, P., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050156 · Cited by 585 · see citing works

Genomic and metabolic adaptations of <i>Methanobrevibacter smithii</i> to the human gut

Samuel, B. S., Hansen, E. E., Manchester, J. K., Coutinho, P. M., Henrissat, B., Fulton, R., Latreille, P., Kim, K., Wilson, R. K., & Gordon, J. I. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704189104 · Cited by 549 · see citing works

Differences between Tissue-Associated Intestinal Microfloras of Patients with Crohn's Disease and Ulcerative Colitis

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A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem

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Thickness of adherent mucus gel on colonic mucosa in humans and its relevance to colitis.

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In situ class switching and differentiation to IgA-producing cells in the gut lamina propria

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Genomic and Metabolic Studies of the Impact of Probiotics on a Model Gut Symbiont and Host

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Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model

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Regulation of IgA production by naturally occurring TNF/iNOS-producing dendritic cells

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Segmented filamentous bacteria are potent stimuli of a physiologically normal state of the murine gut mucosal immune system

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Commensal enteric bacteria engender a self-limiting humoral mucosal immune response while permanently colonizing the gut

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Comparative study of the intestinal mucus barrier in normal and inflamed colon

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Extensive surface diversity of a commensal microorganism by multiple DNA inversions

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Increased susceptibility to colitis and colorectal tumors in mice lacking core 3–derived O-glycans

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The autophagy gene <i>ATG5</i> plays an essential role in B lymphocyte development

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Suppressive Role of B Cells in Chronic Colitis of T Cell Receptor α Mutant Mice

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Mucins in the gastrointestinal tract in health and disease

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Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and Targeted Bacterial Subgroups in Crohn's Disease

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Regulation of IgA production by naturally occurring TNF/iNOS-producing dendritic cells

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Global Transcript Profiles of Fat in Monozygotic Twins Discordant for BMI: Pathways behind Acquired Obesity

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Cultivable bacterial diversity from the human colon

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Biodiversity of the Mucosa-Associated Microbiota Is Stable Along the Distal Digestive Tract in Healthy Individuals and Patients With Ibd

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Genomics and the bacterial species problem.

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Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples

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The IL23 axis plays a key role in the pathogenesis of IBD: Figure 1

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Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

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In vivo IgA coating of anaerobic bacteria in human faeces.

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Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RBhigh CD4+ T cells

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Influence of Major Histocompatibility Complex on Bacterial Composition of Fecal Flora

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Secretory IgA Mediates Bacterial Translocation to Dendritic Cells in Mouse Peyer’s Patches with Restriction to Mucosal Compartment

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Molecular inventory of faecal microflora in patients with Crohn's disease.

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Entry Route of Salmonella typhimurium Directs the Type of Induced Immune Response

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Dual-association of gnotobiotic Il-10−/− mice with 2 nonpathogenic commensal bacteria induces aggressive pancolitis

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The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials

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An Antibiotic-Responsive Mouse Model of Fulminant Ulcerative Colitis

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