A human gut microbial gene catalogue established by metagenomic sequencing

Marcelo Bertalan Quintanilha dos Santos; Thomas Sicheritz-Pontén; Henrik Bjørn Nielsen; Søren Brunak; Junjie Qin; Ruiqiang Li; Jeroen Raes; Manimozhiyan Arumugam; Kristoffer Solvsten Burgdorf; Chaysavanh Manichanh; Trine Nielsen; Nicolas Pons; Florence Levenez; Takuji Yamada; Daniel R. Mende; Junhua Li; Junming Xu; Shaochuan Li; Dongfang Li; Jianjun Cao; Bo Wang; Huiqing Liang; Huisong Zheng; Yinlong Xie; Julien Tap; Patricia Lepage; Jean-Michel Batto; Torben Hansen; Denis Le Paslier; Allan Linneberg; Eric Pelletier; Pierre Renault; Keith Turner; Hongmei Zhu; Chang Yu; Shengting Li; Min Jian; Yan Zhou; Yingrui Li; Xiuqing Zhang; Songgang Li; Nan Qin; Huanming Yang; Jian Wang; Joel Dore; Francisco Guarner; Karsten Kristiansen; Oluf Pedersen; Julian Parkhil; Jean Weissenbach; Peer Bork; S. Dusko Ehrlich; Jun Wang

doi:10.1038/nature08821

A human gut microbial gene catalogue established by metagenomic sequencing

Marcelo Bertalan Quintanilha dos Santos, Thomas Sicheritz-Pontén, Henrik Bjørn Nielsen, Søren Brunak, Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada, Daniel R. Mende, Junhua Li, Junming Xu, Shaochuan Li, Dongfang Li, Jianjun CaoBo Wang, Huiqing Liang, Huisong Zheng, Yinlong Xie, Julien Tap, Patricia Lepage, Jean-Michel Batto, Torben Hansen, Denis Le Paslier, Allan Linneberg, Eric Pelletier, Pierre Renault, Keith Turner, Hongmei Zhu, Chang Yu, Shengting Li, Min Jian, Yan Zhou, Yingrui Li, Xiuqing Zhang, Songgang Li, Nan Qin, Huanming Yang, Jian Wang, Joel Dore, Francisco Guarner, Karsten Kristiansen, Oluf Pedersen, Julian Parkhil, Jean Weissenbach, Peer Bork, S. Dusko Ehrlich, Jun Wang

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ,150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.

Original language	English
Journal	Nature
Volume	464
Issue number	7285
Pages (from-to)	59
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature08821
Publication status	Published - 2010

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dos Santos, M. B. Q., Sicheritz-Pontén, T., Nielsen, H. B., Brunak, S., Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D. R., Li, J., Xu, J., Li, S., Li, D., ... Wang, J. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59. https://doi.org/10.1038/nature08821

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title = "A human gut microbial gene catalogue established by metagenomic sequencing",

abstract = "To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ,150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.",

author = "{dos Santos}, {Marcelo Bertalan Quintanilha} and Thomas Sicheritz-Pont{\'e}n and Nielsen, {Henrik Bj{\o}rn} and S{\o}ren Brunak and Junjie Qin and Ruiqiang Li and Jeroen Raes and Manimozhiyan Arumugam and Burgdorf, {Kristoffer Solvsten} and Chaysavanh Manichanh and Trine Nielsen and Nicolas Pons and Florence Levenez and Takuji Yamada and Mende, {Daniel R.} and Junhua Li and Junming Xu and Shaochuan Li and Dongfang Li and Jianjun Cao and Bo Wang and Huiqing Liang and Huisong Zheng and Yinlong Xie and Julien Tap and Patricia Lepage and Jean-Michel Batto and Torben Hansen and Paslier, {Denis Le} and Allan Linneberg and Eric Pelletier and Pierre Renault and Keith Turner and Hongmei Zhu and Chang Yu and Shengting Li and Min Jian and Yan Zhou and Yingrui Li and Xiuqing Zhang and Songgang Li and Nan Qin and Huanming Yang and Jian Wang and Joel Dore and Francisco Guarner and Karsten Kristiansen and Oluf Pedersen and Julian Parkhil and Jean Weissenbach and Peer Bork and Ehrlich, {S. Dusko} and Jun Wang",

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dos Santos, MBQ, Sicheritz-Pontén, T, Nielsen, HB, Brunak, S, Qin, J, Li, R, Raes, J, Arumugam, M, Burgdorf, KS, Manichanh, C, Nielsen, T, Pons, N, Levenez, F, Yamada, T, Mende, DR, Li, J, Xu, J, Li, S, Li, D, Cao, J, Wang, B, Liang, H, Zheng, H, Xie, Y, Tap, J, Lepage, P, Batto, J-M, Hansen, T, Paslier, DL, Linneberg, A, Pelletier, E, Renault, P, Turner, K, Zhu, H, Yu, C, Li, S, Jian, M, Zhou, Y, Li, Y, Zhang, X, Li, S, Qin, N, Yang, H, Wang, J, Dore, J, Guarner, F, Kristiansen, K, Pedersen, O, Parkhil, J, Weissenbach, J, Bork, P, Ehrlich, SD & Wang, J 2010, 'A human gut microbial gene catalogue established by metagenomic sequencing', Nature, vol. 464, no. 7285, pp. 59. https://doi.org/10.1038/nature08821

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T1 - A human gut microbial gene catalogue established by metagenomic sequencing

AU - dos Santos, Marcelo Bertalan Quintanilha

AU - Sicheritz-Pontén, Thomas

AU - Nielsen, Henrik Bjørn

AU - Brunak, Søren

AU - Qin, Junjie

AU - Li, Ruiqiang

AU - Raes, Jeroen

AU - Arumugam, Manimozhiyan

AU - Burgdorf, Kristoffer Solvsten

AU - Manichanh, Chaysavanh

AU - Nielsen, Trine

AU - Pons, Nicolas

AU - Levenez, Florence

AU - Yamada, Takuji

AU - Mende, Daniel R.

AU - Li, Junhua

AU - Xu, Junming

AU - Li, Shaochuan

AU - Li, Dongfang

AU - Cao, Jianjun

AU - Wang, Bo

AU - Liang, Huiqing

AU - Zheng, Huisong

AU - Xie, Yinlong

AU - Tap, Julien

AU - Lepage, Patricia

AU - Batto, Jean-Michel

AU - Hansen, Torben

AU - Paslier, Denis Le

AU - Linneberg, Allan

AU - Pelletier, Eric

AU - Renault, Pierre

AU - Turner, Keith

AU - Zhu, Hongmei

AU - Yu, Chang

AU - Li, Shengting

AU - Jian, Min

AU - Zhou, Yan

AU - Li, Yingrui

AU - Zhang, Xiuqing

AU - Li, Songgang

AU - Qin, Nan

AU - Yang, Huanming

AU - Wang, Jian

AU - Dore, Joel

AU - Guarner, Francisco

AU - Kristiansen, Karsten

AU - Pedersen, Oluf

AU - Parkhil, Julian

AU - Weissenbach, Jean

AU - Bork, Peer

AU - Ehrlich, S. Dusko

AU - Wang, Jun

PY - 2010

Y1 - 2010

N2 - To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ,150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.

AB - To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ,150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.

U2 - 10.1038/nature08821

DO - 10.1038/nature08821

M3 - Journal article

C2 - 20203603

SN - 0028-0836

VL - 464

SP - 59

JO - Nature

JF - Nature

IS - 7285

ER -

A human gut microbial gene catalogue established by metagenomic sequencing

Abstract

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