, Papers of particular interest, published within the period of review, have been highlighted as: of special interest of outstanding interest
Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis, Nat Rev Microbiol, vol.6, pp.121-131, 2008. ,
Molecular analysis of the effect of short-chain fatty acids on intestinal cell proliferation, Proc Nutr Soc, vol.62, pp.101-106, 2003. ,
The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis, Science, vol.341, pp.569-573, 2013. ,
A human gut microbial gene catalogue established by metagenomic sequencing, Nature, vol.464, pp.59-65, 2010. ,
URL : https://hal.archives-ouvertes.fr/cea-00908974
An integrated catalog of reference genes in the human gut microbiome, Nat Biotechnol, vol.32, pp.834-841, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01195478
, The second catalog of human gut microbial genes derived from metagenomic sequencing of feces from 1267 individuals from three continents and composed of 10 million non-redundant genes
Diversity of the human intestinal microbial flora, Science, vol.308, pp.1635-1638, 2005. ,
Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut, Appl Environ Microbiol, vol.65, pp.4799-4807, 1999. ,
Evolution of mammals and their gut microbes, Science, vol.320, pp.1647-1651, 2008. ,
Towards the human intestinal microbiota phylogenetic core, Environ Microbiol, vol.11, pp.2574-2584, 2009. ,
A core gut microbiome in obese and lean twins, Nature, vol.457, pp.480-484, 2009. ,
An analysis of the ruminal bacterial microbiota in West African Dwarf sheep fed grass-and treebased diets, J Appl Microbiol, vol.116, pp.1094-1105, 2014. ,
Linking longterm dietary patterns with gut microbial enterotypes, Science, vol.334, pp.105-108, 2011. ,
Diet rapidly and reproducibly alters the human gut microbiome, Nature, vol.505, pp.559-563, 2014. ,
, A 16S ribosomal RNA-based metagenomic study showing that a shortterm diet of animal or plant products impacts on microbial community structure and functions
Exercise and associated dietary extremes impact on gut microbial diversity, Gut, vol.63, pp.1913-1920, 2014. ,
Enterotypes of the human gut microbiome, Nature, vol.473, pp.174-180, 2011. ,
URL : https://hal.archives-ouvertes.fr/cea-00903625
, An initially controversial whole metagenomic sequencing study showing a stratification of human fecal microbiome in at least three clusters named enterotypes
Factors influencing pulmonary methane excretion in man. An indirect method of studying the in situ metabolism of the methane-producing colonic bacteria, J Exp Med, vol.133, pp.572-588, 1971. ,
Stability of human methanogenic flora over 35 years and a review of insights obtained from breath methane measurements, Clin Gastroenterol Hepatol, vol.4, pp.123-129, 2006. ,
Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota, Proc Natl Acad Sci, vol.107, pp.12204-12209, 2010. ,
Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses, Immunity, vol.40, pp.608-620, 2014. ,
, A study in mice showing SFB ability to induce and stimulate intestinal lymphoid tissues that cooperate to generate potent IgA and Th17
The mucus and mucins of the goblet cells and enterocytes provide the first defense line of the gastrointestinal tract and interact with the immune system, Immunol Rev, vol.260, pp.8-20, 2014. ,
MUC1 cell surface mucin is a critical element of the mucosal barrier to infection, J Clin Invest, vol.117, pp.2313-2324, 2007. ,
The composition of the gut microbiota shapes the colon mucus barrier, EMBO Rep, vol.16, pp.164-177, 2015. ,
, A comparison of two mice colonies maintained in separate rooms and displaying different colonic mucus properties that were attributed to differences in their microbiome
PRR-signaling pathways -learning from microbial tactics, Semin Immunol, vol.27, pp.75-84, 2015. ,
The dual role of nod-like receptors in mucosal innate immunity and chronic intestinal inflammation, Front Immunol, vol.5, p.317, 2014. ,
Dynamic imaging of dendritic cell extension into the small bowel lumen in response to epithelial cell TLR engagement, J Exp Med, vol.203, pp.2841-2852, 2006. ,
Intestinal microbiota and its effects on the immune system, Cell Microbiol, vol.16, pp.1004-1013, 2014. ,
A functionally specialized population of mucosal CD103+ DCs induces Foxp3+ regulatory T cells via a TGF-b-and retinoic acid-dependent mechanism, J Exp Med, vol.204, pp.1757-1764, 2007. ,
Essential role for retinoic acid in the promotion of CD4(+) T cell effector responses via retinoic acid receptor alpha, Immunity, vol.34, pp.435-447, 2011. ,
Aryl hydrocarbon receptor: a molecular link between postnatal lymphoid follicle formation and diet, Gut Microbes, vol.3, pp.577-582, 2012. ,
Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22, Immunity, vol.39, pp.372-385, 2013. ,
, An elegant study showing that tryptophan metabolites impact on mucosal immunity through aryl-receptor dependent IL-22 production
Microbiota control of a tryptophan-AhR pathway in disease tolerance to fungi, Eur J Immunol, vol.44, pp.3192-3200, 2014. ,
Identification of a probiotic bacteria-derived activator of the aryl hydrocarbon receptor that inhibits colitis, Immunol Cell Biol, vol.92, pp.460-465, 2014. ,
Aryl hydrocarbon receptor-induced signals up-regulate IL-22 production and inhibit inflammation in the gastrointestinal tract, Gastroenterology, vol.141, pp.237-248, 2011. ,
Activation of the aryl hydrocarbon receptor pathway may ameliorate dextran sodium sulfate-induced colitis in mice, Immunol Cell Biol, vol.88, pp.685-689, 2010. ,
Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature, vol.472, pp.57-63, 2011. ,
Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide, vol.6, p.2481, 2015. ,
Food, immunity, and the microbiome, Gastroenterology, vol.148, pp.1107-1119, 2015. ,
Low counts of Faecalibacterium prausnitzii in colitis microbiota, Inflamm Bowel Dis, vol.15, pp.1183-1189, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00657435
Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii, vol.6, pp.300-315, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01226343