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, approximately 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.
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Qin
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.forename: Manimozhiyan
authors.initials: M
authors.lastname: Arumugam
authors.forename: Kristoffer Solvsten
authors.initials: KS
authors.lastname: Burgdorf
authors.forename: Chaysavanh
authors.initials: C
authors.lastname: Manichanh
authors.forename: Trine
authors.initials: T
authors.lastname: Nielsen
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pons
authors.forename: Florence
authors.initials: F
authors.lastname: Levenez
authors.forename: Takuji
authors.initials: T
authors.lastname: Yamada
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Mende
authors.forename: Junhua
authors.initials: J
authors.lastname: Li
authors.forename: Junming
authors.initials: J
authors.lastname: Xu
authors.forename: Shaochuan
authors.initials: S
authors.lastname: Li
authors.forename: Dongfang
authors.initials: D
authors.lastname: Li
authors.forename: Jianjun
authors.initials: J
authors.lastname: Cao
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.forename: Huiqing
authors.initials: H
authors.lastname: Liang
authors.forename: Huisong
authors.initials: H
authors.lastname: Zheng
authors.forename: Yinlong
authors.initials: Y
authors.lastname: Xie
authors.forename: Julien
authors.initials: J
authors.lastname: Tap
authors.forename: Patricia
authors.initials: P
authors.lastname: Lepage
authors.forename: Marcelo
authors.initials: M
authors.lastname: Bertalan
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Batto
authors.forename: Torben
authors.initials: T
authors.lastname: Hansen
authors.forename: Denis
authors.initials: D
authors.lastname: Le Paslier
authors.forename: Allan
authors.initials: A
authors.lastname: Linneberg
authors.forename: H Bjørn
authors.initials: HB
authors.lastname: Nielsen
authors.forename: Eric
authors.initials: E
authors.lastname: Pelletier
authors.forename: Pierre
authors.initials: P
authors.lastname: Renault
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Ponten
authors.forename: Keith
authors.initials: K
authors.lastname: Turner
authors.forename: Hongmei
authors.initials: H
authors.lastname: Zhu
authors.forename: Chang
authors.initials: C
authors.lastname: Yu
authors.forename: Shengting
authors.initials: S
authors.lastname: Li
authors.forename: Min
authors.initials: M
authors.lastname: Jian
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhou
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.forename: Songgang
authors.initials: S
authors.lastname: Li
authors.forename: Nan
authors.initials: N
authors.lastname: Qin
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Joel
authors.initials: J
authors.lastname: Doré
authors.forename: Francisco
authors.initials: F
authors.lastname: Guarner
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristiansen
authors.forename: Oluf
authors.initials: O
authors.lastname: Pedersen
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Jean
authors.initials: J
authors.lastname: Weissenbach
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: S Dusko
authors.initials: SD
authors.lastname: Ehrlich
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D000328:Adult; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D015331:Cohort Studies; D020451:Contig Mapping; D003718:Denmark; D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000382:microbiology*; D005798:Genes, Bacterial / Q000235:genetics; D020043:Genes, Essential / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D006262:Health; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics; D054892:Metagenome / Q000235:genetics*; D009765:Obesity / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D050177:Overweight / Q000235:genetics; D017422:Sequence Analysis, DNA; D013030:Spain