Inflammatory bowel diseases (IBD) and the microbiome-searching the crime scene for clues

Structure, function and diversity of the healthy human microbiome

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A human gut microbial gene catalogue established by metagenomic sequencing

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Diet rapidly and reproducibly alters the human gut microbiome

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Untitled work

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Diversity of the Human Intestinal Microbial Flora

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Human gut microbiome viewed across age and geography

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Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

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Revised Estimates for the Number of Human and Bacteria Cells in the Body

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The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T _reg Cell Homeostasis

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A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease

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Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

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

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Autophagy and Viruses: Adversaries or Allies?

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<i>Faecalibacterium prausnitzii</i> is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

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Induction of Colonic Regulatory T Cells by Indigenous <i>Clostridium</i> Species

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Evolution of mammals and their gut microbes

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Antimicrobial Autophagy: A Conserved Innate Immune Response in Drosophila

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Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

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Microfluidic organs-on-chips

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The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

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Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism

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Development of the Human Infant Intestinal Microbiota

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Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

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Bile salt biotransformations by human intestinal bacteria

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Colonic Health: Fermentation and Short Chain Fatty Acids

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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

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Genetics and pathogenesis of inflammatory bowel disease

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Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

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The gut microbiota and host health: a new clinical frontier

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The Long-Term Stability of the Human Gut Microbiota

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NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

Elinav, E., Strowig, T., Kau, A. L., Henao-Mejia, J., Thaiss, C. A., Booth, C. J., Peaper, D. R., Bertin, J., Eisenbarth, S. C., Gordon, J. I., et al. (2011) · Cell · doi:10.1016/j.cell.2011.04.022 · Cited by 2,024 · see citing works

The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota

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Regulation of short-chain fatty acid production

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Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice

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A decrease of the butyrate-producing species <i>Roseburia hominis</i> and <i>Faecalibacterium prausnitzii</i> defines dysbiosis in patients with ulcerative colitis

Machiels, K., Joossens, M., Sabino, J., De Preter, V., Arijs, I., Eeckhaut, V., Ballet, V., Claes, K., Van Immerseel, F., Verbeke, K., et al. (2014) · Gut · doi:10.1136/gutjnl-2013-304833 · Cited by 1,904 · see citing works

Dietary fiber and prebiotics and the gastrointestinal microbiota

Holscher, H. D. (2017) · Gut Microbes · doi:10.1080/19490976.2017.1290756 · Cited by 1,808 · see citing works

Gut microbiota and IBD: causation or correlation?

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Nod2-Dependent Regulation of Innate and Adaptive Immunity in the Intestinal Tract

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Dysbiosis of the gut microbiota in disease

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Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

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High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease

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A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

Cadwell, K., Liu, J. Y., Brown, S. L., Miyoshi, H., Loh, J., Lennerz, J. K., Kishi, C., Kc, W., Carrero, J. A., Hunt, S., et al. (2008) · Nature · doi:10.1038/nature07416 · Cited by 1,542 · see citing works

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

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CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands

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Antibiotics, birth mode, and diet shape microbiome maturation during early life

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The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host–microbial interactions

Johansson, M., Larsson, J. M. H., & Hansson, G. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006451107 · Cited by 1,459 · see citing works

Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor

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Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

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Mucosal flora in inflammatory bowel disease

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Fungal microbiota dysbiosis in IBD

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Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

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Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease

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Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

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Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial

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Understanding and Preventing the Global Increase of Inflammatory Bowel Disease

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Diet dominates host genotype in shaping the murine gut microbiota

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Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis

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

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Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

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Host-Derived Nitrate Boosts Growth of <i>E. coli</i> in the Inflamed Gut

Winter, S. E., Winter, M. G., Xavier, M. N., Thiennimitr, P., Poon, V., Keestra, A. M., Laughlin, R. C., Gomez, G., Wu, J., Lawhon, S. D., et al. (2013) · Science · doi:10.1126/science.1232467 · Cited by 1,019 · see citing works

Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months

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Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis

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Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

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Bile Acid Is a Host Factor That Regulates the Composition of the Cecal Microbiota in Rats

Islam, K. B. M. S., Fukiya, S., Hagio, M., Fujii, N., Ishizuka, S., Ooka, T., Ogura, Y., Hayashi, T., & Yokota, A. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.07.046 · Cited by 918 · see citing works

Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease

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Farnesoid X receptor activation inhibits inflammation and preserves the intestinal barrier in inflammatory bowel disease

Gadaleta, R. M., van Erpecum, K. J., Oldenburg, B., Willemsen, E. C. L., Renooij, W., Murzilli, S., Klomp, L. W. J., Siersema, P. D., Schipper, M. E. I., Danese, S., et al. (2011) · Gut · doi:10.1136/gut.2010.212159 · Cited by 870 · see citing works

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation

Sinha, S. R., Haileselassie, Y., Nguyen, L. P., Tropini, C., Wang, M., Becker, L. S., Sim, D., Jarr, K. J., Bishop, E. S., Singh, G., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2020.01.021 · Cited by 857 · see citing works

Keeping It All Going—Complement Meets Metabolism

Kolev, M. V., & Kemper, C. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00001 · Cited by 819 · see citing works

The Human Microbiome and Child Growth – First 1000 Days and Beyond

Robertson, R. C., Manges, A. R., Finlay, B. B., & Prendergast, A. J. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2018.09.008 · Cited by 793 · see citing works

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

Imhann, F., Vich Vila, A., Bonder, M. J., Fu, J., Gevers, D., Visschedijk, M. C., Spekhorst, L. M., Alberts, R., Franke, L., van Dullemen, H. M., et al. (2018) · Gut · doi:10.1136/gutjnl-2016-312135 · Cited by 788 · see citing works

Alteration of gut microbiota in inflammatory bowel disease (IBD): cause or consequence? IBD treatment targeting the gut microbiome

Khan, I., Ullah, N., Zha, L., Bai, Y., Khan, A., Zhao, T., Che, T., & Zhang, C. (2019) · Pathogens · doi:10.3390/pathogens8030126 · Cited by 771 · see citing works

Synbiotic therapy ( <i>Bifidobacterium longum</i> /Synergy 1) initiates resolution of inflammation in patients with active ulcerative colitis: a randomised controlled pilot trial

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Enhanced Escherichia coli adherence and invasion in Crohn’s disease and colon cancer 1 1The authors thank Professor T. K. Korhonen (Division of General Microbiology, University of Helsinki, Finland), who kindly donated Escherichia coli IH11165; Professor J.-F. Colombel (Laboratoire de Recherche sur les Maladies Inflammatoire de l’Intestine, Centre Hospitalier Universitaire, Lille, France) and Professor A. Darfeuille-Michaud (Faculte de Pharmacie, Clermont-Ferrand, France), who kindly donated the Crohn’s disease ileal isolates LF10 and LF82; and Dr. Keith Leiper (Gastroenterology Unit, Royal Liverpool & Broadgreen University Hospitals Trust, Liverpool, UK) for his cooperation in obtaining colorectal tissue specimens.As a consequence of the work described herein, a patent application has been filed by the University of Liverpool regarding the use of soluble plantain fiber in Crohn’s disease.

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Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration

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The mycobiota: interactions between commensal fungi and the host immune system

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