The rumen microbial metagenome associated with high methane production in cattle

BMC Genomics, Oct 2015

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 databasefor 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× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 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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The rumen microbial metagenome associated with high methane production in cattle

Wallace et al. BMC Genomics The rumen microbial metagenome associated with high methane production in cattle R. John Wallace 1 John A. Rooke 3 Nest McKain 1 Carol-Anne Duthie 3 Jimmy J. Hyslop 3 David W. Ross 3 Anthony Waterhouse 3 Mick Watson 0 2 Rainer Roehe 0 3 0 Equal contributors 1 Rowett Institute of Nutrition and Health, University of Aberdeen , Bucksburn, Aberdeen AB21 9SB , UK 2 Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh , Easter Bush, Edinburgh EH25 9RG , UK 3 SRUC , West Mains Road, Edinburgh EH9 3JG , UK 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 databasefor 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× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 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. Archaea; Illumina; Metagenomics; Rumen; Succinovibrionaceae - Background Methane is a greenhouse gas (GHG) with a global warming potential 28-fold that of carbon dioxide [1]. It is responsible for 16 % of total anthropogenic greenhouse gas emissions [2]. Ruminants are the major producers of methane emissions from anthropogenic activities, accounting for 37 % of total GHG from agriculture in the UK [3]. Lowering methane emissions has therefore become a major priority in ruminant livestock production, with many different strategies having been proposed to mitigate emissions, including different dietary formulations, chemical and biological feed additives, chemogenomics and antimethane vaccines [4–6]. Research is also under way to determine the extent to which the animal itself has control over its ruminal microbiota, with the intention that, if the trait is heritable, low-methane livestock phenotypes may form the basis of a breeding programme to produce ruminants with a smaller environmental footprint [7]. If any of the strategies proves to be successful, benefits may be anticipated in energy retention by the animal [3, 8]. Methane, although considered to be an atmospheric pollutant, is a natural product of anaerobic microbial fermentation [9]. The rumen is an anaerobic microbial ecosystem in which a dense mixture of protozoa, bacteria and anaerobic fungi convert carbohydrates to short-chain, volatile fatty acids (VFA), which are absorbed by the animal and used in energy metabolism and protein synthesis. Hydrogen is formed as a result of fermentation, and it is used by methanogenic archaea to reduce CO2 to methane [10]. Hydrogenotrophic methane production is quantitatively the most important source of methane, although methylotrophic methanogenesis (...truncated)


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R. Wallace, John Rooke, Nest McKain, Carol-Anne Duthie, Jimmy Hyslop, David Ross, Anthony Waterhouse, Mick Watson, Rainer Roehe. The rumen microbial metagenome associated with high methane production in cattle, BMC Genomics, 2015, pp. 839, 16, DOI: 10.1186/s12864-015-2032-0