Metaproteogenomic analyses of the gut microbiota in human and animal models: identification of changes induced by special diets in health and disease

Gut microbiota (GM) is known to have a role in immune system development, metabolism and protection from enteropathogen invasion. Characterizing the health-associated GM is key to formulate targeted interventions in case of dysbiotic states. As diet is one of the main factors with an impact on gut microbes, comprehending how it shapes the GM is also crucial. In view of this, through an integrated multi-omic approach based on 16S and shotgun metagenomics and metaproteomics, several studies were performed to obtain deeply characterized GMs in human, sheep and animal models and to shed light on specifically selected diet-GM interactions. First, the GM of a human healthy cohort and sheep were in-depth characterized, improving insights on taxonomy, active and taxon-specific functions. Further, butyrogenesis and glutamate degradation were detected as consistently active in all human subjects, becoming potential candidates for biomarkers of intestinal health. Second, the response of GM to caloric restriction (CR), and the GM possible changes at the onset of celiac disease (CD) were evaluated in animal models. Several changes solely due to CR were noted, regarding Lactobacillus spp. abundance and propionogenesis, while microbiota changes clearly related to the onset of CD were not observed. Lastly, preliminary data on two pilot studies on small human populations were reported, the first based on the analysis of different diet habits and the second as an actual dietary intervention.