Metagenome-based growth rate of bacteria and metatranscriptome analysis suggests a mechanism of butyrate formation with growth change of faecalibacterium prausnitzii in low methane yield rumen.

Boyang Zhang
Graduate (PhD)
Zhongtang Yu
Animal Sciences

1.1    Background
Methane emissions from ruminants contribute to global warming and lead to energy loss from the diet. Reducing methane emissions while increasing feed efficiency is one of the most important challenges facing the livestock industry. Previous studies have reported a difference in rumen microbiome and rumen retention time between low-methane yield (LMY) and high-methane yield (HMY) sheep. And the differences were attributed to some heterofermentative lactic acid bacteria. The objective of this study was to investigate the relationship between the growth and metabolism of rumen bacteria and methane emissions in sheep.
1.2    Results
Analysis of metagenome-based growth rates of the rumen microbiome showed that the growth rate of Faecalibacterium prausnitzii (a butyrate producer) was significantly lower in LMY sheep than in HMY sheep, whereas the relative abundance of F. prausnitzii did not differ. The relative abundance and growth rate of Bacillus tended to be higher in LMY sheep than HMY sheep. Metatranscriptomic analysis of the rumen microbiome revealed that in LMY sheep the expression of growth-related genes of F. prausnitzii was significantly downregulated, but that of energy-related genes, including those involved in butyrate production, was significantly upregulated compared to the HMY sheep. Analysis using debiased machine learning (DML) predicted a direct significant relationship between the growth rate of F. prausnitzii and methane yield, but not between the growth rate of Bacillus and methane yield. 
1.3 Conclusions
The current study suggests a proportionality between methane yield in sheep and the rumen metagenome-based growth rate of F. prausnitzii but an inverse relationship between methane yield and the expression of energy-related genes, especially the genes involved in butyrate production. The above inverse relationship corroborates the relationship reported between butyrate production and hydrogen and methane yield. The upregulated expression of the butyrate-producing pathway also concurs with the enriched lactate-producing bacteria in LMY sheep. The current study also implied a correlation between the metagenome-based growth rate of Bacillus and methane yield, attributable to microbial interactions.