An insight into tropical milk microbiome: Bacterial community composition of cattle milk produced in Sri Lanka

ABSTRACT This is the first study reporting the cattle milk microbiome of Sri Lanka, an island country located in the tropics. For the study, raw milk samples from 18 dairy farms (n = 90) were collected from the three different climatic zones of the country (wet, dry and intermediate). Metataxonomic characterisation performed on the Illumina MiSeq platform revealed a total of 10,918 OTUs belonging to 23 bacterial phyla, 110 orders, 381 genera and 348 known species. Macrococcus, Streptococcus, Elizabethkingia, Staphylococcus, and Enhydrobacter were the most abundant genera detected. The observed presence of Atopococcus, Helcobacillus, Millisia and Succinispira genera has not been reported previously in raw milk. The prevailing pathogens were of Streptococcus, Rothia, Enhydrobacter and Staphylococcus genera (S. agalactiae, R. nasimurium, E. aerosaccus and S. saprophyticus); their prevalence was high in the intermediate and dry zone milk. Wet zone milk had the highest species richness with lowest abundance of detected pathogens.