A comprehensive genetic study of the vaginal microbiota composition of Holstein cows

The vaginal microbiota is a potentially important component of the bovine reproductive tract and has been associated with fertility, health, and production-related traits in cattle. However, the impact of host genetics on the bovine vaginal microbiota and its genetic correlations with animal performance remain largely unexplored. To investigate this, we performed a comprehensive genetic study of the vaginal microbiota in Holstein cows. Vaginal swabs from 681 lactating cows across 18 herds in Northern France were collected, along with records of fertility, milk production, and health traits. The microbiota samples were sequenced for the 16S rRNA gene, generating count tables of amplicon sequence variants (ASV). We estimated genetic parameters for vaginal microbiota -diversity (Chao1, Shannon, and Simpson indices) and {beta}-diversity (Bray-Curtis dissimilarity matrix), as well as the centered log-ratio (CLR)-transformed abundances of taxa present in more than 50% of samples. Across the 173 analyzed taxa, heritability estimates ranged from low to moderate (h2 = 0.09 to 0.38) for five genera, three families, eight orders, three classes, and one phylum. Notably, the order Flavobacteriales exhibited the highest heritability estimate. The study also highlighted genetic correlations between heritable microbiota traits and host phenotypes related to fertility, production, and health. Sequence-based genome-wide association studies (GWAS) identified biologically relevant signals, including a quantitative trait locus (QTL) for the genus Alloprevotella on chromosome 6, with lead variants located within the NAF1 gene. Additionally, two signals on chromosome 17 for the Bacteroidales order and the Bacteroida class co-localized with IL15. Our findings show that host genetics contributes to variation in specific components of the bovine vaginal microbiota and suggest that microbiome-related traits may warrant further investigation as potential indicators in dairy cattle breeding and management research.