Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome.
The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those associated with diseases. Moreover, we identified 8 million SNPs in the gut microbiome and observe a high similarity in microbiome SNPs between twins that slowly decreases after decades of living apart. The results shed new light on the genetic and environmental influences on the composition and function of the gut microbiome that could relate to risk of complex diseases.
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
Hailiang
H
Xie
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China.
Ruijin
R
Guo
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
Huanzi
H
Zhong
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China.
Qiang
Q
Feng
BGI-Shenzhen, Shenzhen 518083, China.
Zhou
Z
Lan
BGI-Shenzhen, Shenzhen 518083, China.
Bingcai
B
Qin
Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.
Kirsten J
KJ
Ward
Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.
Matthew A
MA
Jackson
BGI-Shenzhen, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
Yan
Y
Xia
BGI-Shenzhen, Shenzhen 518083, China; Qingdao University-BGI Joint Innovation College, Qingdao University, Qingdao 266071, China.
Xu
X
Chen
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
Bing
B
Chen
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China.
Huihua
H
Xia
BGI-Shenzhen, Shenzhen 518083, China; Qingdao University-BGI Joint Innovation College, Qingdao University, Qingdao 266071, China.
Changlu
C
Xu
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
Fei
F
Li
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
Xun
X
Xu
BGI-Shenzhen, Shenzhen 518083, China.
Jumana Yousuf
JY
Al-Aama
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
Huanming
H
Yang
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
Jian
J
Wang
BGI-Shenzhen, Shenzhen 518083, China; Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
Karsten
K
Kristiansen
BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China.
Jun
J
Wang
Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.
Claire J
CJ
Steves
Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.
Jordana T
JT
Bell
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China. Electronic address: lijunhua@genomics.cn.
Junhua
J
Li
Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK. Electronic address: tim.spector@kcl.ac.uk.
Timothy D
TD
Spector
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China; Macau University of Science and Technology, Taipa, Macau 999078, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China. Electronic address: jiahuijue@genomics.cn.
Huijue
H
Jia
SNPs; heritability; metabolic diseases; microbiome