Mechanisms and consequences of intestinal dysbiosis

The “Golden Age” of Probiotics: A Systematic Review and Meta-Analysis of Randomized and Observational Studies in Preterm Infants

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

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Human gut microbes associated with obesity

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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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Metabolic Endotoxemia Initiates Obesity and Insulin Resistance

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Linking long-term dietary patterns with gut microbial enterotypes

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The gut microbiota as an environmental factor that regulates fat storage

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Obesity alters gut microbial ecology

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

De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579

Regulatory T Cells and Immune Tolerance

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Breastfeeding and the Use of Human Milk

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

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Richness of human gut microbiome correlates with metabolic markers

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Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

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Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

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

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Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

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Overweight, obesity and cancer: epidemiological evidence and proposed mechanisms

Calle, E. E., & Kaaks, R. (2004) · Nature reviews. Cancer · doi:10.1038/nrc1408 · Cited by 3,613

Gut flora in health and disease

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Short chain fatty acids in human large intestine, portal, hepatic and venous blood

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Mechanisms underlying the resistance to diet-induced obesity in germ-free mice

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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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Fusobacterium nucleatum Promotes Colorectal Carcinogenesis by Modulating E-Cadherin/β-Catenin Signaling via its FadA Adhesin

Rubinstein, M. R., Wang, X., Liu, W., Hao, Y., Cai, G., & Han, Y. W. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.07.012 · Cited by 2,476

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

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The Orphan G Protein-coupled Receptors GPR41 and GPR43 Are Activated by Propionate and Other Short Chain Carboxylic Acids

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Bacteriocins: Developing innate immunity for food

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Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis

Singh, N., Gurav, A., Sivaprakasam, S., Brady, E., Padia, R., Shi, H., Thangaraju, M., Prasad, P. D., Manicassamy, S., Munn, D. H., et al. (2014) · Immunity · doi:10.1016/j.immuni.2013.12.007 · Cited by 2,368

Intestinal inflammation targets cancer-inducing activity of the microbiota

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Diet–microbiota interactions as moderators of human metabolism

Sonnenburg, J. L., & Bäckhed, F. (2016) · Nature · doi:10.1038/nature18846 · Cited by 2,257

Bile acids induce energy expenditure by promoting intracellular thyroid hormone activation

Watanabe, M., Houten, S. M., Mataki, C., Christoffolete, M. A., Kim, B. W., Sato, H., Messaddeq, N., Harney, J. W., Ezaki, O., Kodama, T., et al. (2006) · Nature · doi:10.1038/nature04330 · Cited by 2,220

Necrotizing Enterocolitis

Neu, J., & Walker, W. A. (2011) · New England Journal of Medicine · doi:10.1056/nejmra1005408 · Cited by 2,141

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

MetaHIT consortium, Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., et al. (2015) · Nature · doi:10.1038/nature15766 · Cited by 2,116

Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium

Derrien, M., Vaughan, E. E., Plugge, C. M., & de Vos, W. M. (2004) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijs.0.02873-0 · Cited by 2,094

Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

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Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

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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

The microbiome and innate immunity

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Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens

Zheng, Y., Valdez, P. A., Danilenko, D. M., Hu, Y., Susan, M. L., Gong, Q., Abbas, A. R., Modrusan, Z. D., Ghilardi, N., de Sauvage, F. J., et al. (2008) · Nature Medicine · doi:10.1038/nm1720 · Cited by 1,972

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

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

Wen, L., Ley, R. E., Volchkov, P. Y., Stranges, P. B., Avanesyan, L., Stonebraker, A. C., Hu, C., Wong, F. S., Szot, G. L., Bluestone, J. A., et al. (2008) · Nature · doi:10.1038/nature07336 · Cited by 1,921

The microbiota in adaptive immune homeostasis and disease

Honda, K., & Littman, D. R. (2016) · Nature · doi:10.1038/nature18848 · Cited by 1,846

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

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A protocol for generating a high-quality genome-scale metabolic reconstruction

Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789

The microbiome and cancer

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Functional Characterization of Human Receptors for Short Chain Fatty Acids and Their Role in Polymorphonuclear Cell Activation

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

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Bacteria as vitamin suppliers to their host: A gut microbiota perspective

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Breast milk and neonatal necrotising enterocolitis

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The population genetics of commensal Escherichia coli

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

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Immune adaptations that maintain homeostasis with the intestinal microbiota

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The chemistry of peroxynitrite: A product from the reaction of nitric oxide with superoxide

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Gut/brain axis and the microbiota

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The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses

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Targeting bile‐acid signalling for metabolic diseases

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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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Host-Mediated Inflammation Disrupts the Intestinal Microbiota and Promotes the Overgrowth of Enterobacteriaceae

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

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Gut inflammation provides a respiratory electron acceptor for Salmonella

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Differential Alteration in Intestinal Epithelial Cell Expression of Toll-Like Receptor 3 (TLR3) and TLR4 in Inflammatory Bowel Disease

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Enteric defensins are essential regulators of intestinal microbial ecology

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Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity

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Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

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Responses of Gut Microbiota and Glucose and Lipid Metabolism to Prebiotics in Genetic Obese and Diet-Induced Leptin-Resistant Mice

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The influence of diet on the gut microbiota

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Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

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Rifaximin Therapy for Patients with Irritable Bowel Syndrome without Constipation

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

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Reduced Paneth cell α-defensins in ileal Crohn's disease

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Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut

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Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

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Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling

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

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Human Gut Microbiome and Risk for Colorectal Cancer

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Bacteriophage adhering to mucus provide a non–host-derived immunity

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The human gut virome: inter-individual variation and dynamic response to diet

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

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The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

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Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells

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Gut Microbiota Orchestrates Energy Homeostasis during Cold

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High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health

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Short-chain fatty acids stimulate leptin production in adipocytes through the G protein-coupled receptor GPR41

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Infections as a major preventable cause of human cancer

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High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

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