Dottorato in FARMACOLOGIA E TOSSICOLOGIA

Titolo della tesi: The impact of Colitis and Obesity on microbiota diversification in mice: a bioinformatic approach for gut bacteria population discrimination.

The skin and mucous membranes of an individual are colonized by a series of microorganisms that grow and multiply without causing infection to the host. The Gastrointestinal (GI) tract contains the greatest concentration of microorganisms, which is composed of 1000-2000 strains that encode more than 150 genes. The complex of microorganisms is called the microbiota and includes bacteria, archaea, eukaryotic microbes, bacteriophages, and eukaryotic viruses. The whole collection of the microbiota genome is defined as the microbiome GI ecosystem is dominated by bacteria, which are taxonomically classified into phyla, classes, orders, families, genera, and species. The principal phyla in the GI are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, but Firmicutes and Bacteroidetes account for 90% of the gut microbiota (GM). Many bacteria living in the GI establishes a mutualistic relationship with the host. This relationship is a gradual and dynamic process that is influenced by various factors such as childbirth, pathologies, nutrition, antibiotic intake, stress, and hygiene. This community of microorganisms is responsible for metabolizing nutrients and producing vitamins, endogenous hormones, and toxic products, as well as degrading organic compounds such as food additives, bile salts, and cholesterol. Therefore, the intestinal microbiota must be balanced and maintained to support the health of the host. This has led to the use of probiotics, which are live microorganisms that are beneficial to health when administered in adequate amounts. According to the Food and Agriculture Organization (FAO) and the World Health Organization (WHO), probiotics are live microorganisms that confer health benefits upon the host when consumed in sufficient amounts. Lactic acid bacteria (LAB) are an important and well-studied strain of probiotics, with many research studies highlighting their beneficial characteristics in the human body. Lactobacillus is one of the most important probiotics in this group of bacteria. The effects of probiotic species on the composition, diversity, and function of the GM have been studied using a variety of tools and techniques, including targeted, culture-dependent methods and metagenomics sequencing. The development of new methodologies for culturing and powerful tools for editing and modifying bacterial genomes has opened new possibilities for probiotic research. This has led to the emergence of next-generation probiotics (NGPs), also known as live biotherapeutic products (LBPs), which are designed to address specific consumer needs and issues. The potential role of NGPs includes promoting health and managing disease through mechanisms such as direct immune activation, enzyme production, and the production of molecules or drugs. Further research and development of NGPs is essential for the development of new therapies for conditions such as inflammatory bowel disease (IBD) and metabolic diseases, as well as for preventing the development of colon cancer (CC). The aim of this thesis is to highlight the potential of engineered probiotics as a novel therapeutic target for the prevention of inflammatory gastrointestinal diseases such as irritable bowel syndrome (IBS) and IBD. In addition, since these pathologies often progress to neoplasms, preliminary data on the effects of engineered probiotics in a mouse model of colitis-associated CC and obesity are included in this project. Over the course of my doctoral studies, I have focused on the production of engineered probiotics. Lactobacillus paracasei F19 has been engineered to deliver oleoylethanolamide (OEA) and palmitoylethanolamide (PEA) with a low booster of oleate or palmitate. Finally, the importance of its integration and ability to enrich the gastrointestinal flora was assessed using metagenomic analysis. The use of genetic engineering in the development of new probiotic therapies is a promising strategy for the prevention and treatment of some diseases that are becoming increasingly common in the world population. The focus of this thesis was to investigate the potential of engineered probiotics, developed in the laboratory, to prevent the development of various pathologies related to the GI tract such as IBD and metabolic diseases such as obesity. This work was primarily based on research papers and a review produced during my three-year PhD program.