USDA-ARS dairy grand challenge project: milk microbiota from cows fed diets differing in starch-to-fiber ratios

Researchers from the United States Department of Agriculture - Agricultural Research Services (USDA-ARS) conducted a longitudinal diet intervention study of 76 healthy lactating Holstein cows in Prairie du Sac, Wisconsin. Cows were fed three diets differing in starch and fiber quantities. Cows were assigned to diet intervention groups to achieve balanced parity, dry matter intake, milk production and body weight. Details on diet intervention and study design are available at https://doi.org/10.1016/j.animal.2022.100599. Two raw milk samples were collected from each cow while on each diet. Raw milk samples were immediately stored at -10 ºC, shipped on dry ice, and stored at -70 ºC until processing. Milk samples were thawed and then centrifuged to obtain a pellet from which microbial DNA was extracted using the ZymoBIOMICS DNA Miniprep Kit. Samples with low DNA yield (below 1.9 ng/μL) were re-extracted. Extracted DNA was submitted to Dalhousie University Integrated Microbiome Resource for amplification of the 16S rRNA V4 – V5 region (using primers 515FB, GTGYCAGCMGCCGCGGTAA, and 926R, CCGYCAATTYMTTTRAGTTT) and sequencing by Illumina MiSeq with 300 bp paired-end V3 chemistry. Details on milk sample collection and processing for microbial community analysis are available at https://doi.org/10.1093/cdn/nzac086.