Enterotypes of the human gut microbiome
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...
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| Published in | Nature (London) Vol. 473; no. 7346; pp. 174 - 180 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
12.05.2011
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0028-0836 1476-4687 1476-4687 |
| DOI | 10.1038/nature09944 |
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| Abstract | 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. |
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| AbstractList | 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. [PUBLICATION ABSTRACT] Our knowledge on species and function composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about their variation across the world. Combining 22 newly sequenced fecal metagenomes of individuals from 4 countries with previously published datasets, we identified three robust clusters (enterotypes hereafter) that are not nation or continent-specific. We confirmed the enterotypes also in two published, larger cohorts suggesting that intestinal microbiota variation is generally stratified, not continuous. This further indicates 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 for a community understanding. While 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. 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. Our knowledge on species and function composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about their variation across the world. Combining 22 newly sequenced fecal metagenomes of individuals from 4 countries with previously published datasets, we identified three robust clusters (enterotypes hereafter) that are not nation or continent-specific. We confirmed the enterotypes also in two published, larger cohorts suggesting that intestinal microbiota variation is generally stratified, not continuous. This further indicates 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 for a community understanding. While 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 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 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. 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.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. |
| Audience | Academic |
| Author | Leclerc, Marion Pons, Nicolas Zoetendal, Erwin G. Bruls, Thomas Gautier, Laurent Bork, Peer Borruel, Natalia Fernandez, Leyden Hattori, Masahira Mende, Daniel R. Sicheritz-Ponten, Thomas Casellas, Francesc Kleerebezem, Michiel Ehrlich, S. Dusko Kurokawa, Ken Nielsen, Trine Poulain, Julie Pedersen, Oluf Torrents, David Doré, Joel Ugarte, Edgardo Brunak, Søren Levenez, Florence Pelletier, Eric Fernandes, Gabriel R. Nielsen, H. Bjørn de Vos, Willem M. Qin, Junjie Weissenbach, Jean Yamada, Takuji Guarner, Francisco Wang, Jun Bertalan, Marcelo Tims, Sebastian Batto, Jean-Michel Hansen, Torben Arumugam, Manimozhiyan Hayashi, Tetsuya Manichanh, Chaysavanh Le Paslier, Denis Tap, Julien Raes, Jeroen |
| AuthorAffiliation | 1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany 8 Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark 5 Université d’Evry Val d’Essone 91000 Evry, France 20 University of Helsinki, FI-00014 Helsinki, Finland 18 Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark 14 Laboratory of Microbiology, Wageningen University, 6710BA Ede, The Netherlands 16 BGI-Shenzhen, Shenzhen 518083, China 17 Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain 12 Computational Biology Laboratory Bld, The University of Tokyo Kashiwa Campus, Kashiwa-no-ha 5-1-5, Kashiwa, Chiba, 277-8561, Japan 19 Institute of Biomedical Sciences, University of Copenhagen, Denmark 11 Hagedorn Research Institute, 2820 Gentofte, Denmark 7 Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France 4 Centre National de la Recherche Scientifique, UMR8030, 91000 Ev |
| AuthorAffiliation_xml | – name: 3 Commissariat à l’Energie Atomique, Genoscope, 91000 Evry, France – name: 13 Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan – name: 1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany – name: 4 Centre National de la Recherche Scientifique, UMR8030, 91000 Evry, France – name: 10 Barcelona Supercomputing Center, Jordi Girona 31, 08034 Barcelona, Spain – name: 17 Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain – name: 14 Laboratory of Microbiology, Wageningen University, 6710BA Ede, The Netherlands – name: 18 Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark – name: 7 Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France – name: 6 Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil – name: 15 Tokyo 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 – name: 19 Institute of Biomedical Sciences, University of Copenhagen, Denmark – name: 8 Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark – name: 5 Université d’Evry Val d’Essone 91000 Evry, France – name: 16 BGI-Shenzhen, Shenzhen 518083, China – name: 21 Max Delbrück Centre for Molecular Medicine, D-13092 Berlin, Germany – name: 2 VIB—Vrije Universiteit Brussel, 1050 Brussels, Belgium – name: 11 Hagedorn Research Institute, 2820 Gentofte, Denmark – name: 12 Computational Biology Laboratory Bld, The University of Tokyo Kashiwa Campus, Kashiwa-no-ha 5-1-5, Kashiwa, Chiba, 277-8561, Japan – name: 9 Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd, 08035 Barcelona, Spain – name: 20 University of Helsinki, FI-00014 Helsinki, Finland |
| Author_xml | – sequence: 1 givenname: Manimozhiyan surname: Arumugam fullname: Arumugam, Manimozhiyan organization: European Molecular Biology Laboratory, Meyerhofstrasse 1 – sequence: 2 givenname: Jeroen surname: Raes fullname: Raes, Jeroen organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, VIB—Vrije Universiteit Brussel – sequence: 3 givenname: Eric surname: Pelletier fullname: Pelletier, Eric organization: Commissariat à l’Energie Atomique, Genoscope, Centre National de la Recherche Scientifique, UMR8030, Université d'Evry Val d'Essone 91000 Evry – sequence: 4 givenname: Denis surname: Le Paslier fullname: Le Paslier, Denis organization: Commissariat à l’Energie Atomique, Genoscope, Centre National de la Recherche Scientifique, UMR8030, Université d'Evry Val d'Essone 91000 Evry – sequence: 5 givenname: Takuji surname: Yamada fullname: Yamada, Takuji organization: European Molecular Biology Laboratory, Meyerhofstrasse 1 – sequence: 6 givenname: Daniel R. surname: Mende fullname: Mende, Daniel R. organization: European Molecular Biology Laboratory, Meyerhofstrasse 1 – sequence: 7 givenname: Gabriel R. surname: Fernandes fullname: Fernandes, Gabriel R. organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. 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Bjørn surname: Nielsen fullname: Nielsen, H. Bjørn organization: Center for Biological Sequence Analysis, Technical University of Denmark – sequence: 25 givenname: Trine surname: Nielsen fullname: Nielsen, Trine organization: Marie Krogh Center for Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen – sequence: 26 givenname: Nicolas surname: Pons fullname: Pons, Nicolas organization: Institut National de la Recherche Agronomique – sequence: 27 givenname: Julie surname: Poulain fullname: Poulain, Julie organization: Commissariat à l’Energie Atomique, Genoscope – sequence: 28 givenname: Junjie surname: Qin fullname: Qin, Junjie organization: BGI-Shenzhen – sequence: 29 givenname: Thomas surname: Sicheritz-Ponten fullname: Sicheritz-Ponten, Thomas organization: Center for Biological Sequence Analysis, Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark – sequence: 30 givenname: Sebastian surname: Tims fullname: Tims, Sebastian organization: Laboratory of Microbiology, Wageningen University – sequence: 31 givenname: David surname: Torrents fullname: Torrents, David organization: Barcelona Supercomputing Center, Jordi Girona 31, Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23 – sequence: 32 givenname: Edgardo surname: Ugarte fullname: Ugarte, Edgardo organization: Commissariat à l’Energie Atomique, Genoscope – sequence: 33 givenname: Erwin G. surname: Zoetendal fullname: Zoetendal, Erwin G. organization: Laboratory of Microbiology, Wageningen University – sequence: 34 givenname: Jun surname: Wang fullname: Wang, Jun organization: BGI-Shenzhen, Department of Biology, University of Copenhagen – sequence: 35 givenname: Francisco surname: Guarner fullname: Guarner, Francisco organization: Digestive System Research Unit, University Hospital Vall d’Hebron, Ciberehd – sequence: 36 givenname: Oluf surname: Pedersen fullname: Pedersen, Oluf organization: Marie Krogh Center for Metabolic Research, Section of Metabolic Genetics, Faculty of Health Sciences, University of Copenhagen, Institute of Biomedical Science, Faculty of Health Sciences, University of Copenhagen, Hagedorn Research Institute, Faculty of Health Sciences, University of Aarhus – sequence: 37 givenname: Willem M. surname: de Vos fullname: de Vos, Willem M. organization: Laboratory of Microbiology, Wageningen University, University of Helsinki – sequence: 38 givenname: Søren surname: Brunak fullname: Brunak, Søren organization: Center for Biological Sequence Analysis, Technical University of Denmark – sequence: 39 givenname: Joel surname: Doré fullname: Doré, Joel organization: Institut National de la Recherche Agronomique – sequence: 41 givenname: Jean surname: Weissenbach fullname: Weissenbach, Jean organization: Commissariat à l’Energie Atomique, Genoscope, Centre National de la Recherche Scientifique, UMR8030, Université d'Evry Val d'Essone 91000 Evry – sequence: 42 givenname: S. Dusko surname: Ehrlich fullname: Ehrlich, S. Dusko email: dusko.ehrlich@jouy.inra.fr organization: Institut National de la Recherche Agronomique – sequence: 43 givenname: Peer surname: Bork fullname: Bork, Peer email: bork@embl.de organization: European Molecular Biology Laboratory, Meyerhofstrasse 1, Max Delbrück Centre for Molecular Medicine |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24128476$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/21508958$$D View this record in MEDLINE/PubMed https://hal.science/hal-03649169$$DView record in HAL |
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| CODEN | NATUAS |
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| Issue | 7346 |
| Keywords | Human Digestive system Gut Biological marker Microflora Typology Microbiome |
| Language | English |
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| Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-1 ObjectType-Feature-2 content type line 23 Lists of authors and affiliations of the additional MetaHIT members appear at the end of the paper. Author Contributions All authors are members of the Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium. Ju.W., F.G., O.P., W.M.V., S.B., J.D., Je.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. These authors contributed equally |
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| Title | Enterotypes of the human gut microbiome |
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