16S rDNA multi-amplicon sequencing and bioinformatics approaches for deciphering the animal microbiota

In recent years, new advancements in technology have significantly enhanced our understanding of the vast microbial communities residing both on and within livestock animals. These microorganisms, called microbiota, establish symbiotic relationships with their hosts, playing a crucial role in host health, performance, and adaptation in diverse environments. Indeed, a balanced microbiota is vital for animals, contributing to a correct nutritional intake, pathogen resistance, reproduction, and growth. Understanding these microbiota dynamics and enhancing the affordability and efficiency of molecular sequencing technologies, is essential to improve animal health and food production, and support conservation initiatives. Thus, this thesis aims to holistically understand the interplay between new dietary strategies, environment, and the composition and function of microbiota in several important food-producing animals. Employing a multidisciplinary approach, the study utilizes a 16S rDNA multi-amplicon sequencing approach alongside animal performance data, to generate novel advancements in animal farming practices and conservation strategies. The first contribution of this thesis included a study focused on the influence of the dietary additive, sodium butyrate, on the gut health of broiler chickens, considering as principal intrinsic factors the birds' age and sex. The study reveals that sodium butyrate dietary supplementation did not affect gut morphology or immunity in broiler chickens. The results found complex interactions between sodium butyrate and broiler caecal microbiota, with sex-specific effects. There were notable shifts in microbial composition, particularly in male broilers. These findings suggest that sodium butyrate can modulate gut microbiota and highlight the importance of considering sex in dietary interventions for poultry. The second contribution presents a study that explores the effects of wood lignocellulose addition in rabbit diets on the fermentation process and the community of microorganisms in their gut. The study reveals that under healthy conditions, adding low rates of purified lignocellulose to the diet modified the digestibility of protein, fat, and fiber without reducing the diet's nutritional value or affecting rabbit growth and feed efficiency. Although some changes in caecal fermentation were observed, there were slight impacts on gut microbiota. Whether this dietary strategy can effectively prevent digestive disorders in commercial farms with sub-optimal health conditions remains to be tested. The third contribution presents a study investigating the variations in bacterial communities between the gills of mussels (Mytilus galloprovincialis) and the surrounding water in the Scardovari Lagoon (Italy). The results present some novel insights into the composition and potential functions of microbiota in the gills of Mytilus galloprovincialis and the surrounding water in the lagoon ecosystem. We discovered that not only does the animal-mediated selective enrichment led to a bacterial community structure in gills different from that of the surrounding water source but also that such mussel-specific assemblage varies during the season both in terms of taxonomy and as predictable phenotypic traits. Moreover, the hierarchical ranking of the variables driving the change within the chosen basin, either in water or within gills, sees the temporal dimension dominate over the spatial one. These results underscore the importance of understanding native bacterial communities associated with mussels and seawater in the Po River Delta for predicting microbiota dynamics, managing mollusk production, and preserving the lagoon environment. In conclusion, the present thesis emphasizes the importance of studying the microbiota for animals health and their overall performances.