milk metagenome Raw sequence reads. milk metagenome

Within microbial ecosystems, biotic interactions (microbe-microbe cross talks) play crucial roles in shaping the overall structure of the community and determining its functional properties such as stability and colonization resistant. To what extent such biotic interactions play role in modulating the structure of mammary gland (MG) microbiota in dairy cows remains poorly understood. The main objectives of the current study were to a) characterize bacterial communities that inhabit different ecological niches of the MG, b) determine their potential associations with the inflammatory status of the udder, and c) characterize niche-specific microbial relationships that are influential in shaping the biodiversity of the MG. To this end, aseptic quarter milk (n = 144) and their corresponding teat canal swab (n = 144) samples were collected from dairy cows with a wide range of MG inflammatory status, as determined by somatic cell counts (SCC) of the milk. Microbiota profiling was performed by sequencing the V1-V2 hypervariable regions of bacterial s16S rRNA gene.