Response of the bovine milk microbiome to different dry-cow treatment approaches

Most lactating cows are routinely treated in each quarter with antibiotic at drying off. This is defined as the ''blanket'' approach, and it is considered effective in preventing new infections and cure the existing infections. However, this farming practice can potentially interfere with the milk microbiota balance, as well as promote the selection for antimicrobial resistance. Therefore, the impact of this practice on the physiological milk microbiota deserves further investigation. The objective of our study was the evaluation of the possible effects that different treatments at drying-off can have on the milk microbiota of dairy cows. The study involved 5 cows from drying-off to 10 days after calving. The samples were collected at drying-off, 3 days (colostrum) and 10 days after calving, for a total of 60 samples. At drying-off, each animal received four different treatments: the left front quarter did not receive any treatment (control quarter), an internal teat sealant based on bismuth subnitrate was applied to the right front quarter, the right rear quarter received dry therapy with cefalonium and the left rear quarter was treated with another antibiotic (cloxacillin). For 16S rRNA-gene sequencing, bacterial DNA was extracted from 5 ml of milk samples, amplified using the primers for the V3-V4 hypervariable regions and sequenced in one MiSeq (Illumina) run with 2×250-base paired-end reads. There was a relatively high variability in the composition of milk microbiota between quarters already at drying-off. The variation in microbial composition among the different treatments was small. In particular, 10 days after calving there were no significant differences compared to the control quarter. In agreement with previous works, the bacterial phyla Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were relatively abundant at all sampling times.