Abstract
Dry and early lactation periods represent the most critical phases for udder health in cattle, especially in highly productive breeds, such as the Holstein Friesian (HF). On the other hand, some autochthonous cattle breeds, such as the Rendena (REN), have a lower prevalence of mastitis and other transition-related diseases. In this study, milk microbiota of 6 HF and 3 REN cows, all raised on the same farm under the same conditions, was compared. A special focus was placed on the transition period to define bacterial groups’ prevalence with a plausible effect on mammary gland health. Four time points (dry-off, 1 d, 7–10 d and 30 d after calving) were considered. Through 16S rRNA sequencing, we characterized the microbiota composition for 117 out of the 144 milk samples initially collected, keeping only the healthy quarters, in order to focus on physiological microbiome changes and avoid shifts due to suspected diseases. Microbial populations were very different in the two breeds along all the time points, with REN milk showing a significantly lower microbial biodiversity. The taxonomic profiles of both cosmopolitan and local breeds were dominated by Firmicutes, mostly represented by the Streptococcus genus, although in very different proportions (HF 27.5%, REN 68.6%). Large differences in HF and REN cows were, also, evident from the metabolic predictive analysis from microbiome data. Finally, only HF milk displayed significant changes in the microbial composition along the transition period, while REN maintained a more stable microbiota. In conclusion, in addition to the influence on the final characteristics of dairy products obtained from milk of the two breeds, differences in the milk microbiome might, also, have an impact on their mammary gland health.
Highlights
The complex variety of microbes inhabiting living animals and the reciprocal interactions they entertain among themselves and with their hosts have been increasingly pointed out by the evolution of molecular and “-omics” technologies [1]
Thirteen samples were positive for pathogenic bacteria and 6 had a somatic cell counts (SCC) at either T3 or T4 above 200,000 cell/ml
From the 125 remaining milk quarter samples, 8 samples were, further, excluded, since their microbiota was almost exclusively constituted by only one (i.e.: Escherichia spp.) or few environmental (i.e.: Pseudomonas spp.) and opportunistic (i.e.: Staphylococcus spp.) microorganisms representing more than 35% of the relative bacterial abundance (S1 Fig)
Summary
The complex variety of microbes inhabiting living animals and the reciprocal interactions they entertain among themselves and with their hosts have been increasingly pointed out by the evolution of molecular and “-omics” technologies [1] Among these new technologies, metagenomics enables the characterization of a microbial population in a culture-independent manner [2], providing a powerful tool for identifying dominant and subdominant microbes and their dynamics in highly complex ecosystems. Metagenomics enables the characterization of a microbial population in a culture-independent manner [2], providing a powerful tool for identifying dominant and subdominant microbes and their dynamics in highly complex ecosystems On their skin, in gut, oro-pharyngeal, urinary, and genital tracts, all animals host a broad diversity of microbial communities that, through intricate mutualistic interactions, have evolved with them and play crucial roles in their biology and health [3]. Various authors described the ability of some microbes to move from intestinal lumen to the mammary gland through an enteromammary pathway [1,7]
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