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

TLDR

Ruminant livestock are the largest anthropogenic source of methane, yet the basis for inter‑animal variation in methane emissions remains unclear. The study explores the mechanistic basis of methane production in sheep. Methane yields were measured in 22 sheep. Methane yields were found to be a reproducible quantitative trait, and deep metagenomic and metatranscriptomic analysis revealed that while methanogen abundance and pathway gene presence were similar across emitters, transcription of methanogenesis genes was markedly higher in high‑yield sheep, identifying a discrete set of methanogens whose transcription profiles correlate with yield and offering new mitigation targets.

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 CH 4 mitigation at the levels of microbiota composition and transcriptional regulation.