Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits

Haiying / HY Wang, Huiru Zheng, Fiona Browne, Rainer Roeheb, Richard J. Dewhurst, Felix Engel, Matthias Hemmje, Xiangwu Lu, Paul Walsh

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Methane is one of the major contributors to global warming. The rumen microbiota is directly involved in methane production in cattle. The link between variation in rumen microbial communities and host genetics has important applications and implications in bioscience. Having the potential to reveal the full extent of microbial gene diversity and complex microbial interactions, integrated metagenomics and network analysis holds great promise in this endeavour. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions is to develop a random matrix theory-based approach to automatically determining the correlation threshold used to construct the co-abundance network. The resulting network, consisting of 549 microbial genes and 3349 connections, exhibits a clear modular structure with certain trait-specific genes highly over-represented in modules. More specifically, all the 20 genes previously identified to be associated with methane emissions are found in a module (hypergeometric test, p <10−11). One third of genes are involved in methane metabolism pathways. The further examination of abundance profiles across 8 samples of genes highlights that the revealed pattern of metagenomics abundance has a strong association with methane emissions. Furthermore, the module is significantly enriched with microbial genes encoding enzymes that are directly involved in methanogenesis (hypergeometric test, p <10−9).
LanguageEnglish
Pages108-119
JournalMethods
Volume124
Early online date9 Jun 2017
DOIs
Publication statusE-pub ahead of print - 9 Jun 2017

Fingerprint

Microbial Genes
Metagenomics
Microbiota
Rumen
Methane
Genes
Microbial Interactions
Global Warming
Gene encoding
Global warming
Electric network analysis
Metabolism
Enzymes

Keywords

  • Ru­men mi­cro­bial com­mu­nity
  • Metage­nomics
  • Net­work-based ap­proaches
  • Ran­dom ma­trix the­ory

Cite this

Wang, Haiying / HY ; Zheng, Huiru ; Browne, Fiona ; Roeheb, Rainer ; Dewhurst, Richard J. ; Engel, Felix ; Hemmje, Matthias ; Lu, Xiangwu ; Walsh, Paul. / Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits. 2017 ; Vol. 124. pp. 108-119.
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abstract = "Methane is one of the major contributors to global warming. The rumen microbiota is directly involved in methane production in cattle. The link between variation in rumen microbial communities and host genetics has important applications and implications in bioscience. Having the potential to reveal the full extent of microbial gene diversity and complex microbial interactions, integrated metagenomics and network analysis holds great promise in this endeavour. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions is to develop a random matrix theory-based approach to automatically determining the correlation threshold used to construct the co-abundance network. The resulting network, consisting of 549 microbial genes and 3349 connections, exhibits a clear modular structure with certain trait-specific genes highly over-represented in modules. More specifically, all the 20 genes previously identified to be associated with methane emissions are found in a module (hypergeometric test, p <10−11). One third of genes are involved in methane metabolism pathways. The further examination of abundance profiles across 8 samples of genes highlights that the revealed pattern of metagenomics abundance has a strong association with methane emissions. Furthermore, the module is significantly enriched with microbial genes encoding enzymes that are directly involved in methanogenesis (hypergeometric test, p <10−9).",
keywords = "Ru­men mi­cro­bial com­mu­nity, Metage­nomics, Net­work-based ap­proaches, Ran­dom ma­trix the­ory",
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Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits. / Wang, Haiying / HY; Zheng, Huiru; Browne, Fiona; Roeheb, Rainer; Dewhurst, Richard J.; Engel, Felix; Hemmje, Matthias; Lu, Xiangwu; Walsh, Paul.

Vol. 124, 09.06.2017, p. 108-119.

Research output: Contribution to journalArticle

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AU - Wang, Haiying / HY

AU - Zheng, Huiru

AU - Browne, Fiona

AU - Roeheb, Rainer

AU - Dewhurst, Richard J.

AU - Engel, Felix

AU - Hemmje, Matthias

AU - Lu, Xiangwu

AU - Walsh, Paul

N1 - Highlights •RMT-based approach can be used to construct condition-specific co-abundance networks. •The constructed co-abundance network exhibits a clear modular structure. •Certain trait-specific genes are highly over-represented in modules. • Key biological mechanisms associated with methane emission were revealed.

PY - 2017/6/9

Y1 - 2017/6/9

N2 - Methane is one of the major contributors to global warming. The rumen microbiota is directly involved in methane production in cattle. The link between variation in rumen microbial communities and host genetics has important applications and implications in bioscience. Having the potential to reveal the full extent of microbial gene diversity and complex microbial interactions, integrated metagenomics and network analysis holds great promise in this endeavour. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions is to develop a random matrix theory-based approach to automatically determining the correlation threshold used to construct the co-abundance network. The resulting network, consisting of 549 microbial genes and 3349 connections, exhibits a clear modular structure with certain trait-specific genes highly over-represented in modules. More specifically, all the 20 genes previously identified to be associated with methane emissions are found in a module (hypergeometric test, p <10−11). One third of genes are involved in methane metabolism pathways. The further examination of abundance profiles across 8 samples of genes highlights that the revealed pattern of metagenomics abundance has a strong association with methane emissions. Furthermore, the module is significantly enriched with microbial genes encoding enzymes that are directly involved in methanogenesis (hypergeometric test, p <10−9).

AB - Methane is one of the major contributors to global warming. The rumen microbiota is directly involved in methane production in cattle. The link between variation in rumen microbial communities and host genetics has important applications and implications in bioscience. Having the potential to reveal the full extent of microbial gene diversity and complex microbial interactions, integrated metagenomics and network analysis holds great promise in this endeavour. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions is to develop a random matrix theory-based approach to automatically determining the correlation threshold used to construct the co-abundance network. The resulting network, consisting of 549 microbial genes and 3349 connections, exhibits a clear modular structure with certain trait-specific genes highly over-represented in modules. More specifically, all the 20 genes previously identified to be associated with methane emissions are found in a module (hypergeometric test, p <10−11). One third of genes are involved in methane metabolism pathways. The further examination of abundance profiles across 8 samples of genes highlights that the revealed pattern of metagenomics abundance has a strong association with methane emissions. Furthermore, the module is significantly enriched with microbial genes encoding enzymes that are directly involved in methanogenesis (hypergeometric test, p <10−9).

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KW - Net­work-based ap­proaches

KW - Ran­dom ma­trix the­ory

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