The human gut contains 1014 bacteria and many other micro-organisms such as Archaea, viruses and fungi. This gut microbiota has co-evolved with host determinants through symbiotic and co-dependent relationships. Bacteria, which represent 10 times the number of human cells, form the most depicted part of this black box owing to new tools. Re-evaluating the gut microbiota showed how this entity participates in gut physiology and beyond this in human health. Studying and handling this real ‘hidden organ' remains a challenge for clinicians. In this review, we aimed to bring information about gut microbiota, its structure, its roles and the way to capture and measure it. After bacterial colonization in infant, intestinal microbial composition is unique for each individual although more than 95% can be assigned to 4 major phyla. Besides its biodiversity, the major characteristics of gut microbiota are stability over time and resilience after perturbation. In pathological situations, dysbiosis (i.e. imbalance in gut microbiota composition) is observed with a loss in overall diversity. Dysbiosis associated with inflammatory bowel disease was specified with the reduction in biodiversity, the decreased representation of different taxa in the Firmicutes phylum and an increase in Gammaproteobacteria. Beyond depicting gut microbial composition, metagenomics allows the description of the combined genomes of the microorganisms present in the gut, giving access to their potential functions. In fact, each individual overall microbial metagenome outnumbers the size of human genome by a factor of 150. Besides a functional core in which there is redundancy for mandatory functions assuring the robustness of the ecosystem, human gut contains an important diversity and high number of non-redundant bacterial genes. Clinical data, treatment and all the factors able to influence microbiome should enter integrated big data sets to put in light pathways of interplay within the supra organism composed of gut microbiome and host. A better understanding of dynamics within human gut microbiota and microbes-host interaction will allow new insight into gut pathophysiology especially regarding resilience mechanisms and dysbiosis onset and maintenance. This will lead to description of biomarkers of diseases, development of new probiotics/prebiotics and new therapies.

Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-214.
Haiser HJ, Turnbaugh PJ: Is it time for a metagenomic basis of therapeutics? Science 2012;336:1253-1255.
Maurice CF, Turnbaugh PJ: The human microbiome: exploring and manipulating our microbial selves; in Marco D (ed): Metagenomics: Current Innovations and Future Trends. Norfolk, UK, Caister Academic Press, 2011.
Costello EK, Lauber CL, Hamady M, et al: Bacterial community variation in human body habitats across space and time. Science 2009;326:1694-1697.
Reyes A, Wu M, McNulty NP, et al: Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc Natl Acad Sci U S A 2013;110:20236-20241.
de Muinck EJ, Stenseth NC, Sachse D, et al: Context-dependent competition in a model gut bacterial community. PLoS One 2013;8:e67210.
Martins dos Santos V, Müller M, de Vos WM: Systems biology of the gut: the interplay of food, microbiota and host at the mucosal interface. Curr Opin Biotechnol 2010;21:539-550.
Jakobsson HE, Rodríguez-Piñeiro AM, Schütte A, et al: The composition of the gut microbiota shapes the colon mucus barrier. EMBO Rep 2015;16:164-177.
Hooper LV, Wong MH, Thelin A, et al: Molecular analysis of commensal host-microbial relationships in the intestine. Science 2001;291:881-884.
Lozupone C, Faust K, Raes J, et al: Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res 2012;22:1974-1984.
Dutilh BE, Cassman N, McNair K, et al: A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun 2014;5:4498.
Mukhopadhya I, Hansen R, Meharg C, et al: The fungal microbiota of de-novo paediatric inflammatory bowel disease. Microbes Infect 2015;17:304-310.
Blais Lecours P, Marsolais D, Cormier Y, et al: Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One 2014;9:e87734.
Sokol H, Seksik P: The intestinal microbiota in inflammatory bowel diseases: time to connect with the host. Curr Opin Gastroenterol 2010;26:327-331.
Fallani M, Young D, Scott J, et al: Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. J Pediatr Gastroenterol Nutr 2010;51:77-84.
Salazar N, Arboleya S, Valdés L, et al: The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations. Front Genet 2014;5:406.
Dave M, Higgins PD, Middha S, et al: The human gut microbiome: current knowledge, challenges, and future directions. Transl Res 2012;160:246-257.
Eckburg PB, Bik EM, Bernstein CN, et al: Diversity of the human intestinal microbial flora. Science 2005;308:1635-1638.
Shanahan F: The host-microbe interface within the gut. Best Pract Res Clin Gastroenterol 2002;16:915-931.
Ley RE, Bäckhed F, Turnbaugh P, et al: Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 2005;102:11070-11075.
Belkaid Y, Hand TW: Role of the microbiota in immunity and inflammation. Cell 2014;157:121-141.
Prakash S, Rodes L, Coussa-Charley M, et al: Gut microbiota: next frontier in understanding human health and development of biotherapeutics. Biologics 2011;5:71-86.
Round JL, Mazmanian SK: The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009;9:313-323.
Collins SM, Denou E, Verdu EF, et al: The putative role of the intestinal microbiota in the irritable bowel syndrome. Dig Liver Dis 2009;41:850-853.
Turnbaugh PJ, Hamady M, Yatsunenko T, et al: A core gut microbiome in obese and lean twins. Nature 2009;457:480-484.
Seksik P, Rigottier-Gois L, Gramet G, et al: Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 2003;52:237-242.
Jumpstart Consortium Human Microbiome Project Data Generation Working Group: Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One 2012;7:e39315.
Edgar RC, Haas BJ, Clemente JC, et al: UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011;27:2194-2200.
Schloss PD, Westcott SL: Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 2011;77:3219-3226.
Sorek R, Zhu Y, Creevey CJ, et al: Genome-wide experimental determination of barriers to horizontal gene transfer. Science 2007;318:1449-1452.
Morgan XC, Huttenhower C: Meta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology 2014;146:1437-1448.e1.
Qin J, Li R, Raes J, et al: A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65.
Frias-Lopez J, Shi Y, Tyson GW, et al: Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 2008;105:3805-3810.
Wang Y, Antonopoulos DA, Zhu X, et al: Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol 2010;88:1333-1342.
Petnicki-Ocwieja T, Hrncir T, Liu YJ, et al: Nod2 is required for the regulation of commensal microbiota in the intestine. Proc Natl Acad Sci U S A 2009;106:15813-15818.
Rehman A, Sina C, Gavrilova O, et al: Nod2 is essential for temporal development of intestinal microbial communities. Gut 2011;60:1354-1362.
Cadwell K, Patel KK, Maloney NS, et al: Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine. Cell 2010;141:1135-1145.
Lepage P, Häsler R, Spehlmann ME, et al: Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011;141:227-236.
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