Metagenomic approach to rumen, intestine and milk in relation to the environment and quality of products: the summer alpine transhumance: a case study

Transhumance is an ancient practice of pastoralism that consists of the seasonal migration of herds and shepherds in the Mediterranean and the Alps, usually in the mountainous regions there is a vertical transhumance of livestock as there is a change in altitude. It begins with the ascent to high altitude, between late May and mid-June, and ends with the moving back to the valley floor or plains in midSeptember. This herding practice shapes the relationships between people, animals, and ecosystems; it has played a key role in proper landscape management, biodiversity conservation, soil protection, and maintenance of traditions. Transhumant herders have an in-depth knowledge of the environment, ecological balance and climate change, as well as the types of handicrafts and food production that result from them; in fact, it is one of the most efficient farming methods, while coping with lower average temperature, shorter growing season, greater soil slopes, lower soil fertility and the need for longer working time. By itself, mountain animal husbandry is defined as multifunctional and multidisciplinary, it is able in addition to integrating the environmental aspect also the economic aspect that reflects on tourism and social culture of the place, still ensuring the maintenance and vitality of the mountain. The analysis of the inter-relationships among environment, pastures, animals, and food obtained is fundamental for improving our knowledge on this complex mountain farming system. Metagenomic is a recent approach, with an increasing interest, used to study the complexity of microbial populations in different sectors. Metagenomics is combined with culture-dependent methods for providing a better characterization and understanding of the microbial communities in a lot of biological samples. In dairy cows, metagenomics has been used in several studies on the microbiota of rumen, and intestinal content, and of milk and cheese. Often these studies are sectorial, analysing only one of the matrices and without identifying the relationships between the matrix studied and the others or the quality traits of food products. Therefore, the present dissertation as a general objective aims to study the metagenomics of rumen and intestinal contents on one side and metagenomics and quality of milk produced on the other side in relation to transhumance to highland pasture (and return to lowlands) as a case study. Specifically, the first two contributions (Juribello project) aim to study in detail the ruminal microbiota, the first, and the milk microbiota, the second sampled contemporarily on the same cows. In these two groups of cows from the same lowland farm were compared: a group that was moved to highland summer pastures and again to lowland, and a second (control) group that remains in indoor housing for the entire duration of the trial (June to October with monthly samplings). In the first contribution, the complex relationships among the end products of rumen fermentation, the predicted methane production, the microbiological count and the rumen metagenomics traits were investigated. While in the second contribution, the possible relationships between milk microbiota and milk quality and technological properties were studied. Special focus was reserved to bacterial taxa related to specific activities, such as cheese-making, health maintenance, milk spoilage and pathogenesis. The third and fourth contributions (Vezzena Project), on the other hand, concerns the comparison of milk from 26 cows from 4 herds during summer highland pasture and then later during indoor housing in valley floor farms. In the third contribution, individual milk metagenomics was associated with milk composition and quality, udder health, milk B vitamin content and microbiological counts. Finally, the fourth and last contribution aimed at evaluating the relationship between intestinal metagenomics and milk quality and metagenomics on the same herds and cows during the summer Alpine transhumance, and after returning to the lowland permanent valley farm. In all the 4 contributions, the microbiological, chemical and technological traits analyzed were studied one at a time, but also all together with a multivariate approach. Firstly, the heat-maps of the correlations among the analysed traits were obtained and discussed. But the large number of traits considered in each of the 4 contributions suggested the need of identifying few independent latent explanatory factors responsible of the complex relationships among the many traits analysed. Overall, the results of the thesis offer interesting point of view on the evolution of the microbiome of dairy cattle in 3 mountain areas, starting from the practice of summer transhumance, the different changes of pastures, animals’ physiology and behaviour and getting to the final products such as milk and cheese, passing through the microbial evolutions of rumen an intestinal contents. The use of this innovative approach that compares livestock data with microbiology has highlighted even more the various possible connections and interactions between the surrounding farming environment, animals and consequently the final products. The various future perspectives merit in-depth analysis and interpretations of new possible interconnections between the microorganisms (bacteria) and the other animal compartment (rumen content, intestinal content and milk) considered within this thesis and microorganisms (yeasts) and products (cheese) not included here (but under analysis)