Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome
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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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The previous study indicated that it was gene expression rather than gene abundance of methanogens that was strongly correlated with CH4 yields from sheep.
“However, the previous study indicated that it was gene expression rather than gene abundance of methanogens that was strongly correlated with CH4 yields from sheep (Shi et al., 2014).”
From Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production (2018) · cites this paper as Shi et al., 2014
Integration of different omics data types has provided novel insights missed by either approach alone, such as Shi et al. (2014) demonstrating that differences in methane production were not due to differences in abundances of genes responsible, but rather a result of their differential expression.
“This level of data integration has provided some novel insights missed by either approach alone, such as by Shi et al. (2014) who demonstrated that differences in methane production were not due to differences in the abundances of the genes responsible, but rather a result of their differential expression.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Shi et al., 2014
Metagenomics has been used to study methane emissions in cattle and sheep, biomarkers to predict ruminal methanogenesis, effects of feed-conversion-ratio, breed and host genetics on rumen microbiome composition, nutrient acquisition, diet effects, and feed additives on antimicrobial-resistance gene abundance.
“Subsequently, metagenomics has been used to study many aspects of rumen microbiology, including methane emissions in cattle (Wallace et al., 2015) and sheep (Shi et al., 2014), biomarkers to predict ruminal methanogenesis (Auffret et al., 2017b), the effect of feed-conversion-ratio, and breed and host genetics on the composition of the rumen microbiome (Roehe et al., 2016), nutrient acquisition (M”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Shi et al., 2014
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Self-citation
- 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
- 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 › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
- Physical Sciences › Engineering › Building and Construction › 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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