Role of the normal gut microbiota

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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Pattern Recognition Receptors and Inflammation

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Human gut microbes associated with obesity

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Human gut microbiome viewed across age and geography

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Enterotypes of the human gut microbiome

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Changes of Intestinal Functions in Liver Cirrhosis

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Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

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

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

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Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

Arpaia, N., Campbell, C., Fan, X., Dikiy, S., van der Veeken, J., deRoos, P., Liu, H., Cross, J. R., Pfeffer, K., Coffer, P. J., et al. (2013) · Nature · doi:10.1038/nature12726 · Cited by 4,838 · see citing works

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774 · see citing works

Richness of human gut microbiome correlates with metabolic markers

Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662 · see citing works

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

Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works

Bioavailability and bioefficacy of polyphenols in humans. I. Review of 97 bioavailability studies

Manach, C., Williamson, G., Morand, C., Scalbert, A., & Rémésy, C. (2005) · The American Journal of Clinical Nutrition · doi:10.1093/ajcn/81.1.230s · Cited by 4,219 · see citing works

Gut microbiota in health and disease

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Lateral gene transfer and the nature of bacterial innovation

Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816 · see citing works

The gut flora as a forgotten organ

O'Hara, A. M., & Shanahan, F. (2006) · The EMBO Reports · doi:10.1038/sj.embor.7400731 · Cited by 2,791 · see citing works

Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22

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Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability

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Commensal Host-Bacterial Relationships in the Gut

Hooper, L. V., & Gordon, J. I. (2001) · Science · doi:10.1126/science.1058709 · Cited by 2,362 · see citing works

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · see citing works

Renal and Extrarenal Effects of Gum Arabic (Acacia Senegal) - What Can be Learned from Animal Experiments?

Nasir, O. (2013) · Kidney & Blood Pressure Research · doi:10.1159/000350152 · Cited by 2,331 · see citing works

Molecular Analysis of Commensal Host-Microbial Relationships in the Intestine

Hooper, L. V., Wong, M. H., Thelin, A., Hansson, L., Falk, P. G., & Gordon, J. I. (2001) · Science · doi:10.1126/science.291.5505.881 · Cited by 2,202 · see citing works

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

Johansson, M. E. V., Phillipson, M., Petersson, J., Velcich, A., Holm, L., & Hansson, G. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803124105 · Cited by 2,200 · see citing works

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

Quail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., & Gu, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-341 · Cited by 2,031 · see citing works

Regulation of short-chain fatty acid production

Macfarlane, S., & Macfarlane, G. T. (2003) · Proceedings of the Nutrition Society · doi:10.1079/pns2002207 · Cited by 1,939 · 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

Mobile genetic elements: the agents of open source evolution

Frost, L. S., Leplae, R., Summers, A. O., & Toussaint, A. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1235 · Cited by 1,859 · see citing works

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

Mariat, D., Firmesse, O., Levenez, F., Guimarăes, V., Sokol, H., Doré, J., Corthier, G., & Furet, J.-P. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-123 · Cited by 1,755 · see citing works

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

Claesson, M. J., Cusack, S., O'Sullivan, O., Greene-Diniz, R., de Weerd, H., Flannery, E., Marchesi, J. R., Falush, D., Dinan, T., Fitzgerald, G., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000097107 · Cited by 1,754 · see citing works

An ecological and evolutionary perspective on human–microbe mutualism and disease

Dethlefsen, L., McFall-Ngai, M., & Relman, D. A. (2007) · Nature · doi:10.1038/nature06245 · Cited by 1,660 · see citing works

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., Bergerat, A., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2010.118 · Cited by 1,632 · see citing works

Comparison of Next-Generation Sequencing Systems

Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lü, L., & Law, M. (2012) · BioMed Research International · doi:10.1155/2012/251364 · Cited by 1,605 · see citing works

The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota

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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

Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41

Samuel, B. S., Shaito, A., Motoike, T., Rey, F. E., Backhed, F., Manchester, J. K., Hammer, R. E., Williams, S. C., Crowley, J., Yanagisawa, M., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808567105 · Cited by 1,564 · see citing works

Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians

Biagi, E., Nylund, L., Candela, M., Ostan, R., Bucci, L., Pini, E., Nikkïla, J., Monti, D., Satokari, R., Franceschi, C., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010667 · Cited by 1,483 · see citing works

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

Intestinal Goblet Cells and Mucins in Health and Disease: Recent Insights and Progress

Kim, Y. S., & Ho, S. B. (2010) · Current Gastroenterology Reports · doi:10.1007/s11894-010-0131-2 · Cited by 1,437 · 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

Symptomatic atherosclerosis is associated with an altered gut metagenome

Karlsson, F. H., Fåk, F., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Bäckhed, F., & Nielsen, J. (2012) · Nature Communications · doi:10.1038/ncomms2266 · Cited by 1,371 · see citing works

Developmental microbial ecology of the neonatal gastrointestinal tract

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Analysis of Intestinal Flora Development in Breast-Fed and Formula-Fed Infants by Using Molecular Identification and Detection Methods

Harmsen, H. J. M., Wildeboer-Veloo, A. C. M., Raangs, G. C., Wagendorp, A. A., Klijn, N., BINDELS, J. G., & Welling, G. W. (2000) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/00005176-200001000-00019 · Cited by 1,326 · 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

Gut immune maturation depends on colonization with a host-specific microbiota

Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., Reading, N. C., Villablanca, E. J., Wang, S., Mora, J. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.037 · Cited by 1,241 · see citing works

Microbial culturomics: paradigm shift in the human gut microbiome study

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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

The first 1000 cultured species of the human gastrointestinal microbiota

Rajilić-Stojanović, M., & de Vos, W. M. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12075 · Cited by 1,182 · see citing works

Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome

Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009836 · Cited by 1,160 · see citing works

Long-term ecological impacts of antibiotic administration on the human intestinal microbiota

Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2007) · The ISME Journal · doi:10.1038/ismej.2007.3 · Cited by 1,134 · see citing works

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

Hehemann, J.-H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010) · Nature · doi:10.1038/nature08937 · Cited by 1,117 · see citing works

Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells

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Lactic Acid Permeabilizes Gram-Negative Bacteria by Disrupting the Outer Membrane

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Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation

Hemarajata, P., & Versalovic, J. (2013) · Therapeutic Advances in Gastroenterology · doi:10.1177/1756283x12459294 · Cited by 1,083 · see citing works

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

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Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives

Joossens, M., Huys, G., Cnockaert, M., De Preter, V., Verbeke, K., Rutgeerts, P., Vandamme, P., & Vermeire, S. (2011) · Gut · doi:10.1136/gut.2010.223263 · Cited by 1,063 · see citing works

Islet Amyloid Polypeptide, Islet Amyloid, and Diabetes Mellitus

Westermark, P., Andersson, A., & Westermark, G. T. (2011) · Physiological Reviews · doi:10.1152/physrev.00042.2009 · Cited by 1,044 · see citing works

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

Andersson, A. F., Lindberg, M., Jakobsson, H. E., Bäckhed, F., Nyrén, P., & Engstrand, L. G. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002836 · Cited by 1,037 · see citing works

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

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Ecology drives a global network of gene exchange connecting the human microbiome

Smillie, C. S., Smith, M. B., Friedman, J., Cordero, O. X., David, L. A., & Alm, E. J. (2011) · Nature · doi:10.1038/nature10571 · Cited by 953 · see citing works

Angiogenins: a new class of microbicidal proteins involved in innate immunity

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

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The expanding family of innate lymphoid cells: regulators and effectors of immunity and tissue remodeling

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Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

Geuking, M. B., Cahenzli, J., Lawson, M. A. E., Ng, D. C. K., Slack, E., Hapfelmeier, S., McCoy, K. D., & Macpherson, A. J. (2011) · Immunity · doi:10.1016/j.immuni.2011.03.021 · Cited by 840 · see citing works

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

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Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

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Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age

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Bioavailability of Dietary Polyphenols and Gut Microbiota Metabolism: Antimicrobial Properties

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Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

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Intestinal Alkaline Phosphatase Detoxifies Lipopolysaccharide and Prevents Inflammation in Zebrafish in Response to the Gut Microbiota

Bates, J. M., Akerlund, J., Mittge, E., & Guillemin, K. J. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2007.10.010 · Cited by 752 · 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

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

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Toll-like receptor 2 controls mucosal inflammation by regulating epithelial barrier function

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Innate Lymphoid Cells: Emerging Insights in Development, Lineage Relationships, and Function

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Human milk glycobiome and its impact on the infant gastrointestinal microbiota

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Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease

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Insights into the metabolism and microbial biotransformation of dietary flavan-3-ols and the bioactivity of their metabolites

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The gut microbiota modulates host energy and lipid metabolism in mice

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Inflammation switches the differentiation program of Ly6Chi monocytes from antiinflammatory macrophages to inflammatory dendritic cells in the colon

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Compositional and Functional Features of the Gastrointestinal Microbiome and Their Effects on Human Health

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In Vitro Metabolism of Plant Lignans: New Precursors of Mammalian Lignans Enterolactone and Enterodiol

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Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants

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Colonic metabolism of dietary polyphenols: influence of structure on microbial fermentation products

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Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases

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Bacterial biota in the human distal esophagus

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The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia

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Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies

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A Critical Review on Health Promoting Benefits of Edible Mushrooms through Gut Microbiota

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Bilirubin in the Liver–Gut Signaling Axis

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Gut Microbiota and Their Metabolites in Stroke: A Double-Edged Sword

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The Microgenderome Revealed: Sex Differences in Bidirectional Interactions between the Microbiota, Hormones, Immunity and Disease Susceptibility

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Deferasirox alleviates DSS-induced ulcerative colitis in mice by inhibiting ferroptosis and improving intestinal microbiota

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Gut Microbiota and Diarrhea: An Updated Review

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The Role of Gut Microbiota on Cholesterol Metabolism in Atherosclerosis

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Gut Microbiome–Brain Alliance: A Landscape View into Mental and Gastrointestinal Health and Disorders

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The Microbiome and Aging

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Gut Microbiota Resilience: Definition, Link to Health and Strategies for Intervention

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Intestinal Microbiome Shifts, Dysbiosis, Inflammation, and Non-alcoholic Fatty Liver Disease

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The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment

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Candida albicans induces mucosal bacterial dysbiosis that promotes invasive infection

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Microbiota in a long survival discourse with the human host

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What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases

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