TY - JOUR
T1 - Enterotypes of the human gut microbiome
AU - Arumugam, Manimozhiyan
AU - Raes, Jeroen
AU - Pelletier, Eric
AU - Paslier, Denis Le
AU - Yamada, Takuji
AU - Mende, Daniel R.
AU - Fernandes, Gabriel R.
AU - Tap, Julien
AU - Bruls, Thomas
AU - Batto, Jean Michel
AU - Bertalan, Marcelo
AU - Borruel, Natalia
AU - Casellas, Francesc
AU - Fernandez, Leyden
AU - Gautier, Laurent
AU - Hansen, Torben
AU - Hattori, Masahira
AU - Hayashi, Tetsuya
AU - Kleerebezem, Michiel
AU - Kurokawa, Ken
AU - Leclerc, Marion
AU - Levenez, Florence
AU - Manichanh, Chaysavanh
AU - Nielsen, H. Bjørn
AU - Nielsen, Trine
AU - Pons, Nicolas
AU - Poulain, Julie
AU - Qin, Junjie
AU - Sicheritz-Ponten, Thomas
AU - Tims, Sebastian
AU - Torrents, David
AU - Ugarte, Edgardo
AU - Zoetendal, Erwin G.
AU - Wang, Jun
AU - Guarner, Francisco
AU - Pedersen, Oluf
AU - de Vos, Willem M.
AU - Brunak, Søren
AU - Doré, Joel
AU - Weissenbach, Jean
AU - Ehrlich, S. Dusko
AU - Bork, Peer
AU - Antolín, María
AU - Artiguenave, François
AU - Blottiere, Hervé M.
AU - Almeida, Mathieu
AU - Brechot, Christian
AU - Cara, Carlos
AU - Chervaux, Christian
AU - Cultrone, Antonella
AU - Delorme, Christine
AU - Denariaz, Gérard
AU - Dervyn, Rozenn
AU - Foerstner, Konrad U.
AU - Friss, Carsten
AU - Guchte, Maarten van de
AU - Guedon, Eric
AU - Haimet, Florence
AU - Huber, Wolfgang
AU - Hylckama-Vlieg, Johan van
AU - Jamet, Alexandre
AU - Juste, Catherine
AU - Kaci, Ghalia
AU - Knol, Jan
AU - Kristiansen, Karsten
AU - Lakhdari, Omar
AU - Layec, Severine
AU - Roux, Karine Le
AU - Maguin, Emmanuelle
AU - Mérieux, Alexandre
AU - Minardi, Raquel Melo
AU - M’rini, Christine
AU - Muller, Jean
AU - Oozeer, Raish
AU - Parkhill, Julian
AU - Renault, Pierre
AU - Rescigno, Maria
AU - Sanchez, Nicolas
AU - Sunagawa, Shinichi
AU - Torrejon, Antonio
AU - Turner, Keith
AU - Vandemeulebrouck, Gaetana
AU - Varela, Encarna
AU - Winogradsky, Yohanan
AU - Zeller, Georg
N1 - Funding Information:
31. Woodmansey, E. J. Intestinal bacteria and ageing. J. Appl. Microbiol. 102, 1178–1186 (2007). 32. Kovacikova, G. & Skorupski, K. The alternative sigma factor sE plays an important role in intestinal survival and virulence in Vibrio cholerae. Infect. Immun. 70, 5355–5362 (2002). 33. Fujihashi, K. & Kiyono, H. Mucosal immunosenescence: new developments and vaccines to control infectious diseases. Trends Immunol. 30, 334–343 (2009). 34. Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006). 35. Raes, J., Korbel, J. O., Lercher, M. J., von Mering, C. & Bork, P. Prediction of effective genome size in metagenomic samples. Genome Biol. 8, R10 (2007). 36. Gibson, G. R. et al. Alternative pathways for hydrogen disposal during fermentation in the human colon. Gut 31, 679–683 (1990). 37. Godon, J. J., Zumstein, E., Dabert, P., Habouzit, F. & Moletta, R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 63, 2802–2813 (1997). 38. Arumugam,M.,Harrington,E.D.,Foerstner,K.U.,Raes,J.&Bork,P.SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics 26, 2977–2978 (2010). 39. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007). 40. Gianoulis, T. A. et al. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc. Natl Acad. Sci. USA 106, 1374–1379 (2009). Supplementary Information is linked to the online version of the paper at www.nature.com/nature. Acknowledgements The authors are grateful to C. Creevey, G. Falony and members of the Bork group at EMBL for discussions and assistance. We thank the EMBL IT core facility and Y. Yuan for managing the high-performance computing resources. The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013): MetaHIT, grant agreement HEALTH-F4-2007-201052, EMBL, the Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care (LuCAMP), Novo Nordisk Foundation and the International Science and Technology Cooperation Project in China (0806). Obese/non-obese volunteers for the MicroObes study were recruited from the SU.VI.MAX cohort study coordinated by P. Galan and S. Hercberg, and metagenome sequencing was funded by Agence Nationale de la Recherche (ANR);volunteers for MicroAgestudy were recruited from the CROWNALIFE cohort study coordinated by S. Silvi and A. Cresci, and metagenome sequencing was funded by GenoScope. Ciberehd is funded by the Instituto de Salud Carlos III (Spain). J.R. is supported by the Institute for the encouragement of Scientific Research and Innovation of Brussels (ISRIB) and the Odysseus programme of the Fund for Scientific Research Flanders (FWO). We are thankful to the Human Microbiome Project for generating the reference genomes from human gut microbes and the International Human Microbiome Consortium for discussions and exchange of data. Author Contributions All authors are members of the Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium. Jun W., F.G., O.P., W.M.d.V., S.B., J.D., Jean W., S.D.E. and P.B. managed the project. N.B., F.C., T.H., C.M. and T. N. performed clinical analyses. M.L. and F.L. performed DNA extraction. E.P., D.L.P., T.B., J.P. and E.U. performed DNA sequencing. M.A., J.R., S.D.E. and P.B. designed the analyses. M.A., J.R., T.Y., D.R.M., G.R.F., J.T., J.-M.B., M.B., L.F., L.G., M.K., H.B.N., N.P., J.Q., T.S.-P., S.T., D.T., E.G.Z., S.D.E. and P.B. performed the analyses. M.A., J.R., P.B. and S.D.E. wrote the manuscript. M.H., T.H., K.K. and the MetaHIT Consortium members contributed to the design and execution of the study.
PY - 2011/5/12
Y1 - 2011/5/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85027927719&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85027927719&partnerID=8YFLogxK
U2 - 10.1038/nature09944
DO - 10.1038/nature09944
M3 - Article
C2 - 21508958
AN - SCOPUS:85027927719
SN - 0028-0836
VL - 473
SP - 174
EP - 180
JO - Nature
JF - Nature
IS - 7346
ER -