Cow milk microbiota composition from 16S rRNA-gene sequencing: different dry-cow therapy treatments (two antibiotics, teat sealant, controls)

Lactating cows are routinely treated at dry-off with antibiotic infusions in each quarter for the cure and prevention of intramammary infection, which remains the most common disease in dairy herds. This approach is known as blanket dry-cow therapy, usually effective for the prevention and cure of infections, but has been shown to potentially contribute to the emergence and spreading of antibiotic resistant bacterial strains. Exploring the use of non-antibiotic treatments coupled with selective dry-cow therapy is necessary to reduce the risk of antibiotic resistance and potential interference with milk microbiota balance. The impact of selective dry cow treatment on the physiological milk microbiota needs to be carefully evaluated. In this small-scale trial, five healthy cows from dry-off to five days after calving were sampled. For every cow, each quarter received a different treatment: cephalonium dihydrate, benzathine cloxacillin, and bismuth subnitrate (internal teat sealant); the last quarter was left untreated as an experimental control. 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. Bacteriological results confirmed that the quarters were all healthy. The phyla Proteobacteria, Firmicutes, and Actinobacteria were the most abundant for all treatments and controls at all timepoints, accounting for over 80% of the entire milk microbiota. No significant differences were found between treatments and controls in terms of the major alpha and beta diversity indexes, revealing that antibiotic and non-antibiotic treatments for selective dry cow treatment did not alter significantly the milk microbiome of dairy cows. The milk microbiome showed a clear evolution over the lactation cycle and the overall changes in the milk microbiota diversity over the lactation cycle were mainly independent of treatments.