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

Abstract

Abstract Background Methane (CH4) emissions from rumen fermentation are a significant contributor to global warming. Cattle with high CH4 emissions tend to exhibit lower efficiency in milk and meat production, as CH4 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 (gCH4/kgDMI) as High CH4 yield and Low CH4 yield. Rumen contents were collected and analyzed using amplicon sequencing targeting the 16S and 18S rRNA genes. The diversity indexes showed no differences for the rumen microbiota associated with the methane yield phenotypes. However, the partial least squares discriminant analysis (sPLS-DA) revealed different taxonomic profiles of prokaryotes related to High- and Low CH4, but no difference was found for protozoa. The functional profile of both prokaryotes and protozoa differed between High- and Low CH4 groups.Conclusions Our results suggest differences in rumen microbial composition between CH4 yield groups, with specific microorganisms being strongly associated with the Low- and High CH4 groups (e.g. Veillonellaceae and Entodinium). Additionally, microbial functions were also differentially abundant when comparing the Low- with High CH4 animals (e.g. K19341 and K05352). This study posits that identifying the key functional niches within the rumen is vital to understanding the ecological interplay that drives methane production.