Linking ruminal microbial diversity with production traits and host genetics in dairy cattle

Abstract

Abstract The rumen microbiome plays a crucial role in controlling animal health, feed efficiency, and production sustainability. Given that certain components of the rumen microbiome are heritable, it represents a promising additional target for genetic selection. The study was based on 192 cows (180 in a genome-wide association study), housed in the same commercial free-stall barn and fed the same TMR. Rumen fluid samples were collected by rumenocentesis and analysed for microbiome composition (bacterial and archaeal fractions) using Illumina sequencing of the V3-V4 region of the 16S rRNA gene. Association analysis of bacteria abundance, production traits and animal genotypes was performed using various statistical models. Several bacterial phyla and genera were found to be associated with milk production and health parameters, with the strongest correlations observed for rumen pH, milk fat percentage, and milk urea concentration. Moreover, through a microbiome genome-wide association study (microbiome-GWAS), we demonstrated that the abundance of several microbial taxa is potentially influenced by host genetic variation, showing moderate to high heritability estimates. Overall, these results (based on a limited sample size) suggest that variation in host genetics and rumen microbiome composition is associated with variability in production traits, supporting the thesis on the potential of microbiome-informed breeding strategies. This study provides an initial foundation for integrating host genomics with rumen microbiome, aiming to improve the performance of dairy cattle.