Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea enriched microbiome characterised by lactic acid formation and utilisation

Methane yield in sheep is a heritable trait and can be used to select for sheep that produce less methane. There is evidence that the microbiomes of sheep with a low methane yield (LMY) phenotype have lower expression of genes involved in the hydrogenotrophic methanogenesis pathway compared to high methane yield (HMY) sheep and we hypothesize that this is influenced by the fermentation processes of other rumen microbes, which is governed by particle retention time and/or digesta passage rate in sheep. Here we carried out a detailed analysis of bacterial metagenome and metatranscriptome datasets from LMY and HMY sheep, and the results demonstrate strong evidence for a Sharpea-dominated, “S”-type bacterial community associated with low methane yield sheep. We also show a clear pattern of gene and transcript abundance consistent with rapid heterofermentative growth, lactate formation and subsequent metabolism of lactate to butyrate by Megasphaera. We believe these differences are the result of a smaller rumen and a higher rate of digesta turnover leading to conditions that produce less hydrogen and therefore less methane is formed. We also demonstrate that Sharpea exert direct inhibitory effects on the hydrogenotrophic methanogen, Methanobrevibacter sp. SM9, reducing methane formation in co-cultures, via an as-yet-unknown mechanism. In contrast, the HMY animals show less enrichment of specific bacterial taxa and maintain communities similar to those commonly found in other ruminants. The main difference in HMY animals is the enrichment of Type III secretion system genes and transcripts, mainly from unidentified Proteobacteria, but also found in cultivated strains of Succinivibrio dextrinosolvens. When tested in co-cultures against hydrogenotrophic and methylotrophic methanogens, S. dextrinosolvens stimulated growth of the methylotrophic methanogenic archaeon, ISO4-H5.