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

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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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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: Shi, Weibing
Moon, Christina D.
Leahy, Sinead C.
Kang, Dongwan
Froula, Jeff
Kittelmann, Sandra
Deutsch, Samuel
Seedorf, Henning
Kelly, William J.
Sang, Carrie
Pinares-Patiño, Cesar S.
McEwan, John C.
Janssen, Peter H.
Chen, Feng
Visel, Axel
Attwood, Graeme T.
Rubin, Edward M.
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: bronze
doi.org
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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Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

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