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METAHIT, microbiome of the human gut

METAHIT, microbiome de l'intestin humain

Intestinal flora can differentiate individuals (INRA press realease from the 20 April​ 2011)

Researchers in the European MetaHIT consortium coordinated by INRA and involving researchers from INRA, the CEA, CNRS, the University of Evry Val d'Essonne, Danone and the Institut Mérieux, have identified three "enterotypes", or intestinal microbial markers, which are comparable to blood groups. These markers are not specific to the individual's place of origin, age or state of health. They are primarily determined by the abundance of certain types of bacteria in the intestinal tract as well as their genetic potential (the functions coded by their genes). This research opens up a wealth of possible applications in nutrition and human health. Full results appear in the 20 April 2011 advance online edition of NATURE.

Published on 14 September 2018

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In March 2010, Researchers from the European MetaHIT project, coordinated by INRA Jouy-en-Josas, published the first set of gene sequences of bacteria hosted in the human intestinal system, or metagenome. They demonstrated that only a thousand bacterial species are usually found in large quantities in the human intestine. Each person hosts at least 170 such species, most of which are similar from one person to another.

In a new study, the consortium of researchers shows that individuals fall into one of three different groups according to the bacteria present in their intestinal tract and independently of their place of origin, their state of health (obesity or inflammatory bowel disorders), gender or age. Like a person's blood group, this classification is specific to each individual, which led researchers to use the term "enterotypes".

To demonstrate this unexpected and fundamental characteristic of human biology, the team analysed the metagenome of bacteria in intestinal samples from 39 people on three continents, of French, Danish, Italian, Spanish, American and Japanese nationality. Further analysis was carried out of 85 samples collected from Danish subjects, followed by 154 samples from American subjects, to confirm the validity of the classification in a larger dataset than the 39 initial sequences. Results indicate that all the subjects can be classified into three distinct groups according to the type of bacteria found in the digestive tube and the functions that these coded.

Scientists also used certain bacteria genes as biomarkers (1) to demonstrate the existence of correlations between these functional markers and characteristics such as age, gender, place of origin and the body mass of individuals. This provides proof of concept that intestinal flora can be studied in order to diagnose conditions such as obesity and Crohn's disease.

This study opens the door to further research on differences in the bacterial composition of intestinal flora in healthy and sick individuals. This method of classifying individuals will make it possible to establish homogenous groups for comparative analysis: notably of factors which predispose a person to conditions such as obesity or diabetes.

In the area of patient-specific medicine, the classification will help develop diagnostic tools to detect cases in which routine treatment would not be effective and adapt treatment accordingly. It will also advance nutritional studies into the effects of different foods on human health.

(1) Biomarker: A molecule which can indicate a normal or abnormal biological process or the presence of a disorder or illness.


People are in constant contact with bacteria found on all surfaces and cavities of the human body. Most of these bacteria are hosted in the intestinal tract. We have at least ten times as many bacteria accompanying us as we have cells. These complex and dynamic communities have a great influence on our physiology, our nutrition, and our immune system and its development. Bacteria perform essential functions to keep us healthy. For instance, they synthesize vitamins and help break down certain compounds that we would be unable to absorb otherwise. They play an important role in our immune system by protecting us against pathogenic bacteria. Research has shown that there are significant differences in the metagenome of healthy individuals and those who are obese or have inflammatory bowel disorders, which has led to the hypothesis that imbalances in intestinal flora could contribute to the development of diseases.​


Enterotypes of the human gut microbiome. NATURE. 

Manimozhiyan Arumugam1', Jeroen Raes1,2', Eric Pelletier3,4,5, Denis Le Paslier3,4,5, Takuji Yamada1, Daniel R. Mende1, Gabriel R. Fernandes1,6, Julien Tap1,7, Thomas Bru​ls3,4,5, Jean-Michel Batto7, Marcelo Bertalan8, Natalia Borruel9, Francesc Casellas9, Leyden Fernandez10, Laurent Gautier8, Torben Hansen11,12, Masahira Hattori13, Tetsuya Hayashi14, Michiel Kleerebezem15, Ken Kurokawa16, Marion Leclerc7, Florence Levenez7, Chaysavanh Manichanh9, H. Bjørn Nielsen8, Trine Nielsen11, Nicolas Pons7, Julie Poulain3, Junjie Qin17, Thomas Sicheritz-Ponten8,18, Sebastian Tims15, David Torrents10,19, Edgardo Ugarte3, Erwin G. Zoetendal15, JunWang17,20, Francisco Guarner9, Oluf Pedersen11,21,22,23, Willem M. de Vos15,24, Søren Brunak8, Joel Doré7, MetaHIT Consortium, Jean Weissenbach3,4,5, S. Dusko Ehrlich7 & Peer Bork1,25

1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. 
2VIB—Vrije Universiteit Brussel, 1050 Brussels, Belgium. 
3Commissariat à l'Energie Atomique, Genoscope, 91000 Evry, France.

4Centre National de la Recherche Scientifique, UMR8030, 91000 Evry, France. 
5Université d'Evry Val d'Essone 91000 Evry, France. 
6Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-901 Belo Horizonte, Minas Gerais, Brazil. 
7Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France. 
8Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark. 
9Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 08035 Barcelona, Spain.
10Barcelona Supercomputing Center, Jordi Girona 31, 08034 Barcelona, Spain. 
11Marie Krogh Center for Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark. 
12Faculty of Health Sciences, University of Southern Denmark, DK-5000 Odense, Denmark. 
13ComputationalBiology Laboratory Bld, The University of Tokyo Kashiwa Campus, Kashiwa-no-ha 5-1-5, Kashiwa, Chiba, 277-8561, Japan. 
14Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan. 
15Laboratory of Microbiology, Wageningen University, 6710BA Ede, The Netherlands. 
16Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Department of Biological Information, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa Pref. 226-8501, Japan. 
17BGI-Shenzhen, Shenzhen 518083, China. 
18Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark. 
19Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain. 
20Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark. 
21Institute of Biomedical Science, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
22Hagedorn Research Institute, DK-2820 Gentofte, Denmark. 
23Faculty of Health Sciences, University of Aarhus, DK-8000 Aarhus, Denmark. 
24University of Helsinki, FI-00014 Helsinki, Finland. 
25Max Delbrück Centre for Molecular Medicine, D-13092 Berlin, Germany.

Scientific contact:

Stanislav-Dusko Ehrlich
Département « Microbiologie et Chaîne Alimentaire »
Coordinateur du projet européen MetaHIT (Metagenomics of Human Intestinal Tract)
Centre INRA de Jouy-en-Josas
Tél : 01 34 65 25 10 ou​​