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A metagenomic insight into our gut's microbiome
  1. Patricia Lepage1,2,
  2. Marion C Leclerc1,2,
  3. Marie Joossens3,4,5,
  4. Stanislas Mondot6,
  5. Hervé M Blottière1,2,
  6. Jeroen Raes3,4,
  7. Dusko Ehrlich1,2,
  8. Joel Doré1,2
  1. 1INRA, MICALIS UMR1319, Jouy-en-Josas, France
  2. 2AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France
  3. 3Research Group of Bioinformatics and (Eco-)systems Biology, Department of Structural Biology, VIB, Brussels, Belgium
  4. 4Microbiology Unit, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
  5. 5IBD Research Group, TARGID, Department of Gastroenterology, KU Leuven, Leuven, Belgium
  6. 6CSIRO, Division of Livestock Industries, Queensland Biosciences Precinct, St Lucia, Queensland, Australia
  1. Correspondence to Dr Patricia Lepage, MICALIS, Building 405, Domaine de Vilvert, INRA, 78350 Jouy-en-Josas, France; patricia.lepage{at}


Advances in sequencing technology and the development of metagenomic and bioinformatics methods have opened up new ways to investigate the 1014 microorganisms inhabiting the human gut. The gene composition of human gut microbiome in a large and deeply sequenced cohort highlighted an overall non-redundant genome size 150 times larger than the human genome. The in silico predictions based on metagenomic sequencing are now actively followed, compared and challenged using additional ‘omics’ technologies. Interactions between the microbiota and its host are of key interest in several pathologies and applying meta-omics to describe the human gut microbiome will give a better understanding of this crucial crosstalk at mucosal interfaces. Adding to the growing appreciation of the importance of the microbiome is the discovery that numerous phages, that is, viruses of prokaryotes infecting bacteria (bacteriophages) or archaea with a high host specificity, inhabit the human gut and impact microbial activity. In addition, gene exchanges within the gut microbiota have proved to be more frequent than anticipated. Taken together, these innovative exploratory technologies are expected to unravel new information networks critical for gut homeostasis and human health. Among the challenges faced, the in vivo validation of these networks, together with their integration into the prediction and prognosis of disease, may require further working hypothesis and collaborative efforts.

  • Bacterial interactions
  • genetics
  • IBD
  • mucus
  • intestinal microbiology
  • metagenomics
  • carbohydrates
  • anaerobic bacterial fermentation
  • molecular biology
  • mucins
  • inflammatory diseases
  • bacterial adherence
  • short chain fatty acids
  • IBD basic research
  • intestinal microbiota
  • Crohn's disease
  • stool markers
  • inflammatory bowel disease
  • intestinal bacteria
  • ribosomal RNA
  • colonic microflora
  • enteric bacterial microflora
  • RNA expression
  • gut inflammation
  • intestinal bacteria
  • immune response
  • mucosal immunology

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  • Funding The authors would like to gratefully acknowledge the financial support of the French National Agency for Research, the 7th European Framework Program (MetaHIT project and Crosstalk project). JR is supported by the Research Foundation Flanders (FWO) and the Agency for Innovation by Science and Technology (IWT).

  • Competing interests None.

  • Provenance and peer review Commissioned; internally peer reviewed.

  • Data sharing statement Available data in this paper will be shared upon request to the corresponding author.