Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome

Hailiang Xie; Ruijin Guo; Huanzi Zhong; Qiang Feng; Zhou Lan; Bingcai Qin; Kirsten J. Ward; Matthew A. Jackson; Yan Xia; Xu Chen; Bing Chen; Huihua Xia; Changlu Xu; Fei Li; Xun Xu; Jumana Yousuf Al-Aama; Huanming Yang; Jian Wang; Karsten Kristiansen; Jun Wang; Claire J. Steves; Jordana T. Bell; Junhua Li; Timothy D. Spector; Huijue Jia

doi:10.1016/j.cels.2016.10.004

Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome

Hailiang Xie, Ruijin Guo, Huanzi Zhong, Qiang Feng, Zhou Lan, Bingcai Qin, Kirsten J. Ward, Matthew A. Jackson, Yan Xia, Xu Chen, Bing Chen, Huihua Xia, Changlu Xu, Fei Li, Xun Xu, Jumana Yousuf Al-Aama, Huanming Yang, Jian Wang, Karsten Kristiansen, Jun WangClaire J. Steves, Jordana T. Bell, Junhua Li^*, Timothy D. Spector, Huijue Jia

^*Corresponding author for this work

Genome Research and Molecular Bio Medicine

111 Citations (Scopus)

Abstract

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.

Original language	English
Journal	Cell Systems
Volume	3
Issue number	6
Pages (from-to)	572-584.e3
Number of pages	13
ISSN	2405-4712
DOIs	https://doi.org/10.1016/j.cels.2016.10.004
Publication status	Published - 2016

Keywords

heritability
metabolic diseases
microbiome
SNPs

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.cels.2016.10.004

http://www.cell.com/article/S2405471216303234/pdf

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Xie, H., Guo, R., Zhong, H., Feng, Q., Lan, Z., Qin, B., Ward, K. J., Jackson, M. A., Xia, Y., Chen, X., Chen, B., Xia, H., Xu, C., Li, F., Xu, X., Al-Aama, J. Y., Yang, H., Wang, J., Kristiansen, K., ... Jia, H. (2016). Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome. Cell Systems, 3(6), 572-584.e3. https://doi.org/10.1016/j.cels.2016.10.004

Xie, H, Guo, R, Zhong, H, Feng, Q, Lan, Z, Qin, B, Ward, KJ, Jackson, MA, Xia, Y, Chen, X, Chen, B, Xia, H, Xu, C, Li, F, Xu, X, Al-Aama, JY, Yang, H, Wang, J, Kristiansen, K, Wang, J, Steves, CJ, Bell, JT, Li, J, Spector, TD & Jia, H 2016, 'Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome', Cell Systems, vol. 3, no. 6, pp. 572-584.e3. https://doi.org/10.1016/j.cels.2016.10.004

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title = "Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome",

abstract = "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.",

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author = "Hailiang Xie and Ruijin Guo and Huanzi Zhong and Qiang Feng and Zhou Lan and Bingcai Qin and Ward, {Kirsten J.} and Jackson, {Matthew A.} and Yan Xia and Xu Chen and Bing Chen and Huihua Xia and Changlu Xu and Fei Li and Xun Xu and Al-Aama, {Jumana Yousuf} and Huanming Yang and Jian Wang and Karsten Kristiansen and Jun Wang and Steves, {Claire J.} and Bell, {Jordana T.} and Junhua Li and Spector, {Timothy D.} and Huijue Jia",

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T1 - Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome

AU - Xie, Hailiang

AU - Guo, Ruijin

AU - Zhong, Huanzi

AU - Feng, Qiang

AU - Lan, Zhou

AU - Qin, Bingcai

AU - Ward, Kirsten J.

AU - Jackson, Matthew A.

AU - Xia, Yan

AU - Chen, Xu

AU - Chen, Bing

AU - Xia, Huihua

AU - Xu, Changlu

AU - Li, Fei

AU - Xu, Xun

AU - Al-Aama, Jumana Yousuf

AU - Yang, Huanming

AU - Wang, Jian

AU - Kristiansen, Karsten

AU - Wang, Jun

AU - Steves, Claire J.

AU - Bell, Jordana T.

AU - Li, Junhua

AU - Spector, Timothy D.

AU - Jia, Huijue

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - heritability

KW - metabolic diseases

KW - microbiome

KW - SNPs

U2 - 10.1016/j.cels.2016.10.004

DO - 10.1016/j.cels.2016.10.004

M3 - Journal article

C2 - 27818083

AN - SCOPUS:85006105634

SN - 2405-4712

VL - 3

SP - 572-584.e3

JO - Cell Systems

JF - Cell Systems

IS - 6

ER -

Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome

Abstract

Keywords

UN SDGs

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