Association of milk microbiome in bovine clinical mastitis and their functional implications in cows in Bangladesh

Abstract Milk microbiomes impose a significant influence on the pathophysiology of bovine mastitis. To assess the association, we compared the microbiome of clinical mastitis (CM) and healthy (H) milk samples through whole metagenomic deep sequencing. A total of 483.38 million reads generated from both metagenomes were analyzed through PathoScope and MG-RAST, and mapped to 380 bacterial, 56 archaeal, and 39 viral genomes. We observed distinct shifts and differences in abundance between the microbiome of CM and H milk in phyla Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria with an inclusion of 68.04% unreported and/or opportunistic species in CM milk. Additionally, 14 archaeal and 14 viral genera were found to be solely associated with CM. The functional metagenomics identified several pathways related to…