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PreprintCited by 438Ruminant Nutrition and Digestive PhysiologyAnaerobic Digestion and Biogas ProductionGut microbiota and health

The DOI matches its Crossref record; 64 of the 65 references it cites were found in a registry or an index.

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

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Shi, Weibing, Moon, Christina D., Leahy, Sinead C., Kang, Dongwan, Froula, Jeff, Kittelmann, Sandra, Fan, Christina, Deutsch, Samuel, Gagic, Dragana, Seedorf, Henning, Kelly, William J., Atua, Renee, Sang, Carrie, Soni, Priya, Li, Dong, Pinares-Patiño, Cesar S., McEwan, John C., Janssen, Peter H., Chen, Feng, Visel, Axel, Wang, Zhong, Attwood, Graeme T., Rubin, Edward M.·2014·Genome Research
DOI 10.1101/gr.168245.113PMC PMC4158751
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Abstract

Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH4 mitigation at the levels of microbiota composition and transcriptional regulation.

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Crossref · 10.1101/gr.168245.113

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Figures

Figure 1. The measurement of CH4 yields in sheep. (A) New Zealand sheep used for this study. (B) CH4 yields from the sheep in grams of CH4/kg dry matter intake (DMI) were measured using open-circuit respiration chambers (http://www.globalresearchalliance.org). (C) CH4 yield measurements from 22 sheep (each with two time points) sorted by mean values. Four high (red) and four low (blue) emitters are selected for further study. P-value indicates the statistical significance of the differences in CH4 yield between the two selected groups.
Figure 1. The measurement of CH4 yields in sheep. (A) New Zealand sheep used for this study. (B) CH4 yields from the sheep in grams of CH4/kg dry matter intake (DMI) were measured using open-circuit respiration chambers (http://www.globalresearchalliance.org). (C) CH4 yield measurements from 22 sheep (each with two time points) sorted by mean values. Four high (red) and four low (blue) emitters are selected for further study. P-value indicates the statistical significance of the differences in CH4 yield between the two selected groups.CC BY-NC · PubMed Central
Figure 2. Comparison of relative abundance of different microbial populations in low and high CH4 yield sheep. (A) Relative abundance of microbial domains in low and high CH4 yield sheep. (B) Relative abundance of methanogenic and nonmethanogenic archaea in low and high CH4 yield sheep. (C) Relative abundance of classes of CH4-producing Euryarchaeota in low and high CH4 yield sheep. (NS) No statistical difference in Wilcoxon rank-sum test in each subgroup.
Figure 2. Comparison of relative abundance of different microbial populations in low and high CH4 yield sheep. (A) Relative abundance of microbial domains in low and high CH4 yield sheep. (B) Relative abundance of methanogenic and nonmethanogenic archaea in low and high CH4 yield sheep. (C) Relative abundance of classes of CH4-producing Euryarchaeota in low and high CH4 yield sheep. (NS) No statistical difference in Wilcoxon rank-sum test in each subgroup.CC BY-NC · PubMed Central
Figure 3. Comparisons of gene and transcript abundance for enzymes involved in methanogenesis between high and low CH4 yield sheep. (A) Diagram of CO2/H2 methanogenesis pathway shows enzymes involved in each biochemical reaction. (B,C) Gene (B) and transcript (C) abundance for each enzyme. (D) Transcriptions per gene for each enzyme. (RPM) Reads per million; (NS) no statistical significance in Wilcoxon rank-sum test; (*) P < 0.05; (**) P < 0.01. Error bars, SE.
Figure 3. Comparisons of gene and transcript abundance for enzymes involved in methanogenesis between high and low CH4 yield sheep. (A) Diagram of CO2/H2 methanogenesis pathway shows enzymes involved in each biochemical reaction. (B,C) Gene (B) and transcript (C) abundance for each enzyme. (D) Transcriptions per gene for each enzyme. (RPM) Reads per million; (NS) no statistical significance in Wilcoxon rank-sum test; (*) P < 0.05; (**) P < 0.01. Error bars, SE.CC BY-NC · PubMed Central
Figure 4. Phylogenetic analysis of methanogens in sheep rumen. (A) A phylogenetic tree constructed based on full-length methyl coenzyme M reductase alpha subunit (McrA/MrtA) protein sequences. Known McrA/MrtA proteins from NCBI are shown in black; new ones from this study, in color. (B) Genes and transcripts for three groups of identified sheep rumen methanogens. (RPM) Reads per million; (NS) no statistical significance in Wilcoxon rank-sum test; (*) P < 0.05; (**) P < 0.01. Error bars, SE. (C) Relative contribution of each group of sheep rumen methanogens to the overall abundance (RPM) of genes and transcripts in low and high CH4 yield sheep. The sizes of each pie indicate the abundance of genes/transcripts.
Figure 4. Phylogenetic analysis of methanogens in sheep rumen. (A) A phylogenetic tree constructed based on full-length methyl coenzyme M reductase alpha subunit (McrA/MrtA) protein sequences. Known McrA/MrtA proteins from NCBI are shown in black; new ones from this study, in color. (B) Genes and transcripts for three groups of identified sheep rumen methanogens. (RPM) Reads per million; (NS) no statistical significance in Wilcoxon rank-sum test; (*) P < 0.05; (**) P < 0.01. Error bars, SE. (C) Relative contribution of each group of sheep rumen methanogens to the overall abundance (RPM) of genes and transcripts in low and high CH4 yield sheep. The sizes of each pie indicate the abundance of genes/transcripts.CC BY-NC · PubMed Central

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  1. Kunin, 2010, PyroTagger: a fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data, The Open J, 1, 1

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Authors
Shi, W., Moon, C. D., Leahy, S. C., Kang, D., Froula, J., Kittelmann, S., Fan, C., Deutsch, S., Gagic, D., Seedorf, H., Kelly, W. J., Atua, R., Sang, C., Soni, P., Li, D., Pinares-Patiño, C. S., McEwan, J. C., Janssen, P. H., Chen, F., Visel, A., Wang, Z., Attwood, G. T., & Rubin, E. M.
Affiliations
  • Lawrence Berkeley National Laboratory (US)
  • AgResearch (NZ)
Corresponding author
Rubin, Edward M.
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2014-06-06
Volume
24
Issue
9
Pages
1517-1525
ISSN
  • 1088-9051 (ISSN-L)
  • 1549-5469
DOI
10.1101/gr.168245.113
PMC
PMC4158751
OpenAlex
W2112071632
Cited by
414
References
65
Citations by year
2026: 25 · 2025: 30 · 2024: 48 · 2023: 28 · 2022: 46 · 2021: 35 · 2020: 58 · 2019: 22 · 2018: 45 · 2017: 32 · 2016: 20 · 2015: 20 · 2014: 5
Type
posted content
Language
en
Open access
Locations
  • Genome Research (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
  • HighWire Press Open Archive (submittedVersion)
Funders
Office of Science of the US Department of Energy (DE-AC02-05CH11231)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Ruminant Nutrition and Digestive Physiology
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Anaerobic Digestion and Biogas Production
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
methane yield, sheep, rumen microbiome, methanogenic archaea, gene expression, greenhouse gas emissions reduction, ruminant methane emissions, metatranscriptomics, metagenomics
MeSH terms
Animals, Archaea, Base Sequence, Methane, Molecular Sequence Data, Phenotype, Rumen, Sheep, Quantitative Trait, Heritable, Archaeal Proteins, Metagenome, Transcriptome, Microbiota

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