Paradiso, Rubina (2021) GUT MICROBIOTA CHARACTERIZATION AS A MARKER TO EVALUATE THE EFFECT OF DIFFERENT DIETARY REGIMES ON WATER BUFFALO CALVES DURING THE PREWEANING PERIOD. [Tesi di dottorato]

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Growth and development of calves are highly influenced by the composition and activity of their associated gut microbiota. A classic example of the importance of the microbiota in ruminants is the rumen, where fermentation of dietary substrates due to bacteria results in the formation of short-chain fatty acids. Short-chain fatty acids are a major energy source for the host, and an important substrate for the development of the rumen epithelium. However, in newborn calves, milk is primarily digested in the small intestine, and microbes colonizing the small intestine can contribute to intestinal homeostasis, stimulation of the immune system, and enhancement of intestinal epithelium wellness and development. In particular the first three months of life result to be the most sensitive rearing period for the young calf. Calves are challenged by a series of stress factors after birth, including changes in their farming environment. Indeed, after birth, the living environment changes from the sterile uterus to natural outside conditions and, in addition, changes occur in nutrition, digestion and absorption from natural milk provided by the mother to feed that calves gain by themselves. Optimum level of nutrition in early life favors faster growth, earlier onset of puberty, enhanced productivity and colonization of gut microbiota, which can influence healthy status. Rearing healthy calves is very important as it can have a significant impact on their growth and milk production performance in adult life. Adequate calf development is therefore crucially important for the entire dairy industry. Pre-weaning calves makes them particularly vulnerable to specific diseases, such as enteritis, which, in this age group, is among the diseases causing the highest mortality rates. Colostrum quality, diet with formula milk and management, as well as calf-related hygiene practices (e.g., cleaning routine for feeding equipment, calving pens, group calf pens), can have a pronounced effect on calf health and mortality. One of the most important aspects is the establishing of a proper nutrition plan, which is fundamental for the development and health of calves. A correct and gradual transition from the neonatal phase to the subsequent phase of development ensures that the weaning phase is successfully overcome. In fact, during early life the diet may impact colonization of gut microbiota, which can influence health, leading to potential long-lasting consequences later in life. Today, there are still too many Italian farms exhibiting mortality rates higher than the physiological averages or that cannot sufficiently anticipate the weaning of calves to bring them at the next phase of growth, in a good state of health and with a rumen ready to digest fodder and concentrates,; this has led to a clear slowdown of genetic improvement in most farms. A functional diet chosen to promote the proper development of the gut microbiota is therefore a strategy to ensure animal welfare and productivity. In view of the commercial value of water buffalo milk, in addition, it has become necessary to optimize and simplify the weaning of water buffaloes calves, identifying protocols to replace breast milk without compromising the development and health of the animals themselves. This has led to use different types of feeding that consequently impacted on the development of the gastrointestinal microbiota and consequently on the health of animals, especially in calves, because in the first period of life the microbial colonization is not yet stable and therefore can be easily affected. Many studies have been conducted both in humans and in different animal species about the role of microbiota and how it changes in relation to diet. In particular, in the ruminants species, the attention was focused on the rumen microbiota, since rumen plays the main role in the digestion of the adult animal. In calves, instead, when the animal is monogastric, intestine is the site playing the most important role in the digestion so, it is important to focus attention on this organ and its microbial flora organization. Information is extremely limited on ruminant gut colonization, especially when focusing on the role of the microbiota in the early development of the gastro-intestinal (GIT) during the pre-ruminant period. Water buffalo farming is the main economic source for many families in many areas of the world: Europe, Australia, North America, South America and some African countries. For this reason it is important to invest in research in this area with the aim to integrated knowledge and to promote quality and innovation in primary productions. For these reasons the purpose of this study was to: - characterize the fecal microbiota in calves during the pre-weaning phase - determine which diet (water buffalo milk, formula milk or mixed diet) can contribute to the proper development of the gut microbiota - identify the most useful diet to promote the growth and development of calves. The results demonstrated the homogeneity in gut microbiota composition of newborn calves belonging to the same farm. In particular, consistent with what is described in dairy calves, the predominant phyla in newborn calves are: Proteobacteria, Firmicutes and Bacteroidetes. Differences are evident between samples collected at two time points and displaying maturation of the intestinal microflora in the first weeks of life. Difference occurs in groups feed with mixed diet were the microbiota structure is different and change the abundance of six genera in feces samples: Faecalibacterium, Clostridia_UCG-014, Bifidobacterium, Collinsella, Parabacteroides, Eubacterium_coprostanoligenes_group. The high-throughput sequencing demonstrated to be a suitable approach to the study of the gut microbiota of newborn calves allowing the characterization of the intestinal microbiota during the pre-weaning phase. The characterization of the gut microbiota in calves during the pre-weaning phase and monitoring changes over time could represent a useful tool for monitoring the health status of calves.

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