Metagenomics of milk before, during and after summer transhumance to highland pasture in relation to human health and cheese making properties

Summer transhumance is a traditional form of pastoralism to highland pasture in the dairy system of alpine regions and it is practiced all over the world. Positive influences can be obtained for the environment, society, tourism, animal health and welfare. The aim of this study was to analyze the evolution of the milk microbiota before, during, and after summer transhumance to highland pasture in relation to possible effects on animal / human health and cheese-making properties. The study involved 12 healthy, multiparous, mid-lactation Brown Swiss cows reared in a farm located in the Trento province (Northern East Italy). The cows were monitored from June to October and divided into two groups: six cows were used as a control group and kept in the lowland permanent farm (PF); the other six cows were moved to a temporary alpine farm (ALP) from July to September. From each milk, samples were collected every four weeks for genomic DNA extraction and microbiota characterization using community 16S rRNA amplicon (V3–V4 region) based Illumina Miseq sequencing and QIIME2 (2018.2 version). The relative abundance was analyzed after a log10 transformation and identified species were classified into two unfavorable categories: Spoilage and Pathogenic species, and two favorable categories: Probiotics and Dairy species. For the statistical analysis, we used a linear mixed model, where the combined Month × Group (MG) effect was used as fixed and the cow effect as random. The results revealed a different behavior in the ALP group compared to the PF group during the 3 months of summer transhumance. The Spoilage bacteria tended to decrease in the alpine pasture (MG effect: p < .001), with significant differences in terms of Pseudomonas, Alicyclobacillus, and Clostridiales (p < .001, p < .001, p < .05 respectively). Pathogenic did not show large differences between the two groups; instead, the Probiotic category, which includes Propionibacterium and Bifidobacterium, showed a gradual increase in the ALP group (p < .001). Dairy species also had a significant increase in the ALP group (p < .001), especially Lactococcus and Lactobacillus (both p < .001). All the microbiological changes disappeared when cows were moved back from alpine pasture to the permanent indoor farm. Summer transhumance to alpine pasture, therefore, has a favorable effect on the milk microbiota, with positive implications for both the cheese-making attitude of milk produced and its possible effect on human health