Composition of the rumen microbiome and its association with methane yield in dairy cattle raised in tropical conditions.

Background: Methane (CH) emissions from rumen fermentation are a significant contributor to global warming. Cattle with high CH emissions tend to exhibit lower efficiency in milk and meat production, as CH production represents a loss of the gross energy ingested by the animal. The objective of this study was to investigate the taxonomic and functional composition of the rumen microbiome associated with methane yield phenotype in dairy cattle raised in tropical areas.

Methods And Results: Twenty-two Girolando (F1 Holstein x Gyr) heifers were classified based on their methane yield (g CH / kg dry matter intake (DMI)) as High CH yield and Low CH yield. Rumen contents were collected and analyzed using amplicon sequencing targeting the 16 and 18S rRNA genes. The diversity indexes showed no differences for the rumen microbiota associated with the high and low methane yield groups. However, the sparse partial least squares discriminant analysis (sPLS-DA) revealed different taxonomic profiles of prokaryotes related to High and Low CH, but no difference was found for protozoa. The predicted functional profile of both prokaryotes and protozoa differed between High- and Low CH groups.

Conclusions: Our results suggest differences in rumen microbial composition between CH yield groups, with specific microorganisms being strongly associated with the Low (e.g. Veillonellaceae_UCG - 001) and High (e.g., Entodinium) CH groups. Additionally, specific microbial functions were found to be differentially more abundant in the Low CH group, such as K19341, as opposed to the High CH group, where K05352 was more prevalent. This study reinforces that identifying the key functional niches within the rumen is vital to understanding the ecological interplay that drives methane production.