The rumen microbial metagenome associated with high methane production in cattle

R. John Wallace*, John A. Rooke, Nest McKain, Carol-Anne Duthie, Jimmy J. Hyslop, David W. Ross, Anthony Waterhouse, Mick Watson, Rainer Roehe

*Corresponding author for this work

Research output: Contribution to journalArticle

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Abstract

Background: Methane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high-and low-methane-emitting cattle phenotypes.

Methods: Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes database for functional analysis.

Results: Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5 x more numerous (rho = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; rho = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence.

Conclusions: The abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high-and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation.

Original languageEnglish
Article number839
Number of pages14
JournalBMC Genomics
Volume16
DOIs
Publication statusPublished - 23 Oct 2015

Keywords

  • archaea
  • illumina
  • metagenomics
  • rumen
  • succinovibrionaceae
  • bovine rumen
  • SP-NOV.
  • methanogenic archaea
  • sheep rumen
  • beef-cattle
  • gen. nov.
  • emissions
  • community
  • reveals
  • library

Cite this

Wallace, R. J., Rooke, J. A., McKain, N., Duthie, C-A., Hyslop, J. J., Ross, D. W., ... Roehe, R. (2015). The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics, 16, [839]. https://doi.org/10.1186/s12864-015-2032-0

The rumen microbial metagenome associated with high methane production in cattle. / Wallace, R. John; Rooke, John A.; McKain, Nest; Duthie, Carol-Anne; Hyslop, Jimmy J.; Ross, David W.; Waterhouse, Anthony; Watson, Mick; Roehe, Rainer.

In: BMC Genomics, Vol. 16, 839, 23.10.2015.

Research output: Contribution to journalArticle

Wallace, RJ, Rooke, JA, McKain, N, Duthie, C-A, Hyslop, JJ, Ross, DW, Waterhouse, A, Watson, M & Roehe, R 2015, 'The rumen microbial metagenome associated with high methane production in cattle', BMC Genomics, vol. 16, 839. https://doi.org/10.1186/s12864-015-2032-0
Wallace, R. John ; Rooke, John A. ; McKain, Nest ; Duthie, Carol-Anne ; Hyslop, Jimmy J. ; Ross, David W. ; Waterhouse, Anthony ; Watson, Mick ; Roehe, Rainer. / The rumen microbial metagenome associated with high methane production in cattle. In: BMC Genomics. 2015 ; Vol. 16.
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abstract = "Background: Methane represents 16 {\%} of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 {\%} of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high-and low-methane-emitting cattle phenotypes.Methods: Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes database for functional analysis.Results: Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5 x more numerous (rho = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 {\%}; rho = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 {\%} identity with a publicly available protein sequence.Conclusions: The abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high-and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation.",
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author = "Wallace, {R. John} and Rooke, {John A.} and Nest McKain and Carol-Anne Duthie and Hyslop, {Jimmy J.} and Ross, {David W.} and Anthony Waterhouse and Mick Watson and Rainer Roehe",
note = "Acknowledgements The Rowett Institute of Nutrition and Health and SRUC are funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The project was supported by Defra and the DA funded Agricultural Greenhouse Gas Inventory Research Platform, the Technology Strategy Board (Project No: TP 5903–40240) and the Biotechnology and Biological Sciences Research Council (BBSRC; BB/J004243/1, BB/J004235/1). Our thanks are due to the excellent support staff at the SRUC Beef and Sheep Research Centre, Edinburgh, and to Silvia Ramos Garcia for help in interrogating the data. MW and RR contributed equally to the paper and should be considered as joint last authors.",
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TY - JOUR

T1 - The rumen microbial metagenome associated with high methane production in cattle

AU - Wallace, R. John

AU - Rooke, John A.

AU - McKain, Nest

AU - Duthie, Carol-Anne

AU - Hyslop, Jimmy J.

AU - Ross, David W.

AU - Waterhouse, Anthony

AU - Watson, Mick

AU - Roehe, Rainer

N1 - Acknowledgements The Rowett Institute of Nutrition and Health and SRUC are funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The project was supported by Defra and the DA funded Agricultural Greenhouse Gas Inventory Research Platform, the Technology Strategy Board (Project No: TP 5903–40240) and the Biotechnology and Biological Sciences Research Council (BBSRC; BB/J004243/1, BB/J004235/1). Our thanks are due to the excellent support staff at the SRUC Beef and Sheep Research Centre, Edinburgh, and to Silvia Ramos Garcia for help in interrogating the data. MW and RR contributed equally to the paper and should be considered as joint last authors.

PY - 2015/10/23

Y1 - 2015/10/23

N2 - Background: Methane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high-and low-methane-emitting cattle phenotypes.Methods: Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes database for functional analysis.Results: Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5 x more numerous (rho = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; rho = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence.Conclusions: The abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high-and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation.

AB - Background: Methane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high-and low-methane-emitting cattle phenotypes.Methods: Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes database for functional analysis.Results: Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5 x more numerous (rho = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; rho = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence.Conclusions: The abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high-and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation.

KW - archaea

KW - illumina

KW - metagenomics

KW - rumen

KW - succinovibrionaceae

KW - bovine rumen

KW - SP-NOV.

KW - methanogenic archaea

KW - sheep rumen

KW - beef-cattle

KW - gen. nov.

KW - emissions

KW - community

KW - reveals

KW - library

U2 - 10.1186/s12864-015-2032-0

DO - 10.1186/s12864-015-2032-0

M3 - Article

VL - 16

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 839

ER -