The occurrence of Aerococcus urinaeequi and non-aureus Staphylococci in raw milk negatively correlates with Escherichia coli clinical mastitis

Escherichia coli is a common environmental pathogen associated with clinical mastitis (CM) in dairy cattle. There is an interest in optimizing the udder microbiome to increase the resistance of dairy cattle to E. coli CM; however, the details of which members of the healthy udder microbiota may play a role in antagonizing E. coli are unknown. In this study, we characterized the bacterial community composition in raw milk collected from quarters of lactating Holstein dairy cows that developed E. coli CM during lactation, including milk from both healthy and diseased quarters (n=1,172). The milk microbiome from infected quarters was compared before, during, and after CM. A combination of 16S rRNA gene amplicon and shotgun metagenomic sequencing were used generate datasets with a high level of both depth and breadth. The microbial diversity present in raw milk significantly decreased in quarters experiencing E. coli CM, indicating that E. coli displaces other members of the microbiome. However, the diversity recovered very rapidly after infection. Two genera: Staphylococcus, Aerococcus, and the family Oscillospiraceae were significantly more abundant in healthy quarters with low inflammation. Species of these genera: Staphylococcus auricularis, Staphylococcus haemolyticus, and Aerocussus urinaeequi were identified by shotgun metagenomics. Thus, these species are of interest for optimizing the microbiome to discourage E. coli colonization without triggering inflammation. ImportanceIn this study we show that E. coli outcompetes and displaces several members of the udder microbiome during CM, but that microbial diversity recovers post-infection. In milk from quarters which remained healthy, the community composition was often highly dominated by S. auricularis, S. haemolyticus, A. urinaeequi, and S. marcescens without corresponding increases in somatic cell count (SCC). Community dominance by these organisms, without inflammation, could indicate that these species could be potential prophylactics that could contribute to colonization resistance for the pathogen and prevent future instances of E. coli CM.