A human gut microbial gene catalogue established by metagenomic sequencing.
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.
Qin
Junjie
J
BGI-Shenzhen, Shenzhen 518083, China.
Li
Ruiqiang
R
Raes
Jeroen
J
Arumugam
Manimozhiyan
M
Burgdorf
Kristoffer Solvsten
KS
Manichanh
Chaysavanh
C
Nielsen
Trine
T
Pons
Nicolas
N
Levenez
Florence
F
Yamada
Takuji
T
Mende
Daniel R
DR
Li
Junhua
J
Xu
Junming
J
Li
Shaochuan
S
Li
Dongfang
D
Cao
Jianjun
J
Wang
Bo
B
Liang
Huiqing
H
Zheng
Huisong
H
Xie
Yinlong
Y
Tap
Julien
J
Lepage
Patricia
P
Bertalan
Marcelo
M
Batto
Jean-Michel
JM
Hansen
Torben
T
Le Paslier
Denis
D
Linneberg
Allan
A
Nielsen
H Bjørn
HB
Pelletier
Eric
E
Renault
Pierre
P
Sicheritz-Ponten
Thomas
T
Turner
Keith
K
Zhu
Hongmei
H
Yu
Chang
C
Li
Shengting
S
Jian
Min
M
Zhou
Yan
Y
Li
Yingrui
Y
Zhang
Xiuqing
X
Li
Songgang
S
Qin
Nan
N
Yang
Huanming
H
Wang
Jian
J
Brunak
Søren
S
Doré
Joel
J
Guarner
Francisco
F
Kristiansen
Karsten
K
Pedersen
Oluf
O
Parkhill
Julian
J
Weissenbach
Jean
J
Bork
Peer
P
Ehrlich
S Dusko
SD
Wang
Jun
J
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