Enterotypes of the human gut microbiome

• Published in: Nature (London) Vol. 473; no. 7346; pp. 174 - 180
• Main Authors: Arumugam, Manimozhiyan, Raes, Jeroen, Pelletier, Eric, Le Paslier, Denis, Yamada, Takuji, Mende, Daniel R., Fernandes, Gabriel R., Tap, Julien, Bruls, Thomas, Batto, Jean-Michel, Bertalan, Marcelo, Borruel, Natalia, Casellas, Francesc, Fernandez, Leyden, Gautier, Laurent, Hansen, Torben, Hattori, Masahira, Hayashi, Tetsuya, Kleerebezem, Michiel, Kurokawa, Ken, Leclerc, Marion, Levenez, Florence, Manichanh, Chaysavanh, Nielsen, H. Bjørn, Nielsen, Trine, Pons, Nicolas, Poulain, Julie, Qin, Junjie, Sicheritz-Ponten, Thomas, Tims, Sebastian, Torrents, David, Ugarte, Edgardo, Zoetendal, Erwin G., Wang, Jun, Guarner, Francisco, Pedersen, Oluf, de Vos, Willem M., Brunak, Søren, Doré, Joel, Weissenbach, Jean, Ehrlich, S. Dusko, Bork, Peer
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 12.05.2011; Nature Publishing Group
• Subjects: 631/326/2565/2142; 692/698/2741/2135; Animal, plant and microbial ecology; Bacteria; Bacteria - classification; Bacteria - genetics; bacterial; Bacterial Typing Techniques; Bacteriology; Biodiversity; Biological and medical sciences; Biomarkers - analysis; colon; Comparative analysis; Decision trees; diversity; Europe; Feces - microbiology; Female; Fundamental and applied biological sciences. Psychology; genes; Genetic aspects; Genetic variation; Genomes; Human health and pathology; Human subjects; Humanities and Social Sciences; Humans; Hépatology and Gastroenterology; intestinal microbiota; Intestines - microbiology; Life Sciences; Male; Metagenome; Metagenomics; Microbial activity; Microbial ecology; Microbiology; Microbiology and Parasitology; Microbiota (Symbiotic organisms); Miscellaneous; mucin; multidisciplinary; Normal microflora of man and animals. Rumen; obesity; pathways; Phylogeny; Science; Science (multidisciplinary); Species composition; Studies; Europe; Germany; Human; Digestive system; Gut; Biological marker; Microflora; Typology; Microbiome
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/nature09944

Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host–microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers. Seeking order among our gut microbes The human gut microbiota consists of a huge number of species and varies greatly between individuals. A comparative metagenomic analysis of the human gut microbiomes of 39 individuals from 6 countries shows that despite this diversity, the microbiota composition can be classified into at least 3 distinct groups, or enterotypes. The enterotypes contain functional markers that correlate with individual features such as age and body mass index, a feature that may be of use in the diagnosis of numerous human disorders such as colorectal cancer and diabetes.