A decline in taxonomic diversity of milk microbiome is linked to clinical mastitis and physiological states of cow

Abstract

Using 16S rRNA gene amplicon sequencing, longitudinal shifts in the microbial composition during dry-off, calving, the early, middle and late lactation state of healthy and mastitis cows were examined. Compared to healthy cow milk, fewer bacteria taxa were found for mastitis cow milk. Throughout the dry-off, calving, the early, middle, and late lactation phases, the taxonomic diversity of bacteria in both groups were declined. At dry-off, post-calving, early, middle, and late lactation periods, the percentage of bacteria species that were shared by milk samples of healthy and mastitis cows was 71.1, 65.8, 80.3, 52.6, and 44.3 %, respectively. From dry-off to late lactation periods, the core unique bacteria species of mastitis cow milk rose from 13 to 34 taxa, while the core unique species for healthy cow milk declined from 31 to 20 taxa. In the milk samples of healthy/mastitis cows the majority of microorganisms were represented by the phylum Proteobacteria as 52.9/9.1 %; 38.5/95.4 %; 24.0/19.2 %; 92.9/43.5 %; 46.8/57.1 %; the phylum Firmicutes as 16.5/50.7 %; 35.9/1.4 %; 28.6/11.3 %; 3.1/11.4 %; 7.0/2.7 % at dry-off, post-calving, early, middle and late lactation period, respectively. Taxonomic profile of 40 most abundant bacterial genera of milk samples were comparable in the both group of healthy and mastitis animals at all physiological states. There are prevalence of positive/negative correlation between the number of microorganisms of clinically important species in milk of healthy/mastitis cows, respectively, from dry-off to the late lactation periods.