Host genetic regulation of specific functional groups in the rumen microbiome of dairy cows: Implications for...

Ruminants play a pivotal role in our society by transforming non-consumable substances from industrial by-products and plant fibers into valuable resources such as meat and milk. This remarkable conversion ability is primarily attributed to the rumen microbiota, which is influenced by various factors, including diet, climate, and geographical location. In recent years, increasing research has shown that host factors (breed, genetic variation, etc.) also play vital roles in shaping rumen microbial composition and function in cattle.

This study aims to provide a theoretical basis and an opportunity for further investigating the regulation of lactation traits in dairy cows through host genetics and the interaction with the rumen microbiota.

To investigate the interactions between host genotype, rumen microbiota, and animal phenotype, we curated and analyzed the dairy herd improvement data, single nucleotide polymorphisms (SNPs) genotypes, and 16S rumen microbiota data from 1,169 Holstein dairy cows. Heritability and microbiability estimation, along with genome-wide association studies, were performed to identify candidate microorganisms and host genetic loci.

We identified thirty-one heritable taxa, whose functions were predominantly enriched in carbohydrate metabolism and energy metabolism. The genome-wide association study revealed that nine heritable bacteria were significantly associated with forty-three SNPs. Functional genes located within or near these SNPs were primarily associated with rumen epithelial development. Additionally, these nine heritable bacteria were primarily annotated as complex polysaccharide degraders and butyrate producers, such as Fibrobacter sp900143055 and Pseudoruminococcus massiliensis, which showed significant associations with milk yield and milk fat percentage. Compared to previous studies, we newly discovered the existence of a high heritability of Olsenella umbonate, Butyrivibrio hungatei, among others.

This study identified thirty-one heritable bacterial taxa in Holstein dairy cows' rumen microbiota, with nine showing significant associations with forty-three SNPs related to rumen epithelial development. The discovery of novel heritable species and their correlations with lactation traits provides valuable insights for future breeding strategies aimed at improving dairy cattle productivity through the manipulation of host genetics and rumen microbiota.