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Background  The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility complex (BoLA) gene has been associated with susceptibility to several infectious diseases, most importantly mastitis. However, mechanisms underlying this association are yet poorly understood. In the present study, we sought to explore the association of BoLA gene polymorphism with the dynamics of mammary microbiota during the first week of lactation.    Results  Colostrum and milk samples were collected from multiparous Holstein dairy cows at the day of calving and days 1 and 6 after calving. Microbiota profiling was performed using high-throughput sequencing of the V1-V2 regions of the bacterial 16S rRNA genes and ITS2 region of the fungal ribosomal DNA. Polymorphism of BoLA genes was determined using PCR-RFLP of exon 2 of the  BoLA-DRB3 . In general, transition from colostrum to milk resulted in increased species richness and diversity of both bacterial and fungal communities. The most dominant members of intramammary microbiota included  Staphylococcus , Ruminococcaceae, and Clostridiales within the bacterial community and  Alternaria ,  Aspergillus ,  Candida , and  Cryptococcus  within the fungal community. Comparing the composition of intramammary microbiota between identified  BoLA-DRB3.2  variants ( n  = 2) revealed distinct clustering pattern on day 0, whereas this effect was not significant on the microbiota of milk samples collected on subsequent days. On day 0, proportions of several non -aureus Staphylococcus  (NAS) OTUs, including those aligned to  Staphylococcus equorum ,  Staphylococcus gallinarum ,  Staphylococcus sciuri , and  Staphylococcus haemolyticus , were enriched within the microbiota of one of the  BoLA-DRB3.2  variants, whereas lactic acid bacteria (LAB) including  Lactobacillus  and  Enterococcus  were enriched within the colostrum microbiota of the other variant.    Conclusion  Our results suggest a potential role for BoLA-gene polymorphism in modulating the composition of colostrum microbiota in dairy cows. Determining whether BoLA-mediated shifts in the composition of colostrum microbiota are regulated directly by immune system or indirectly by microbiota-derived colonization resistant can have important implications for future development of preventive/therapeutic strategies for controlling mastitis.    Electronic supplementary material  The online version of this article (10.1186/s40168-018-0586-1) contains supplementary material, which is available to authorized users.

microbiome

Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation