LARGE-SCALE METAGENOMIC ANALYSIS TO IDENTIFY HUMAN GUT MICROBIOME BIOMARKERS OF CARDIOMETABOLIC HEALTH

The human gut microbiome, a complex community of microorganisms inhabiting the human gastrointestinal tract, is recognized as a critical modulator of host physiology. Imbalances in its composition have been linked with a range of human diseases, including cardiometabolic disorders. Diet is both a well-established determinant of cardiometabolic health and a major factor shaping the gut microbiome, yet many aspects of the diet–microbiome–health axis remain poorly understood, particularly regarding the presence and roles of microbial eukaryotes and the contributions of specific dietary components. This thesis investigates the connections between the human gut microbiome, diet, and cardiometabolic health through large-scale computational and multi-omic analyses. We integrate newly sequenced and publicly available metagenomic datasets with extensive metadata, including anthropometric, dietary, and clinical information, as well as serum and fecal metabolomics. As a first step, we conducted a global-scale analysis on 65,809 metagenomes, focusing on the micro-eukaryote Blastocystis, whose ecological and clinical relevance remains debated. Our findings revealed distinct prevalence patterns linked to geography, lifestyle, and diet. Notably, Blastocystis presence was associated with healthier dietary patterns, more favorable cardiometabolic markers, lower BMI, and negatively with disorders linked to altered gut ecology. In a longitudinal dietary intervention, we further observed that improvements in diet quality were accompanied by increased Blastocystis prevalence and abundance, suggesting a potentially beneficial role for Blastocystis in shaping host responses to diet. The second part of this thesis investigates, in a clinical trial with longitudinal sampling and a crossover study design on 70 individuals, how supplementation with resistant starch (RS), a type of dietary fiber, influences the gut microbiome and host lipid metabolism. We integrated shotgun metagenomics and metabolomics from stool samples to assess the effects of two RS types, RS2 and RS4. Each RS promoted distinct shifts in both the microbiome’s taxonomic composition and metabolic potential, including the upregulation of genes involved in complex carbohydrate degradation. We also observed interindividual strain-level variability in response to RS4, highlighting the importance of moving beyond species-level resolution. Finally, we identified previously uncharacterized microbial taxa linked to cholesterol metabolism and explored their potential role in mediating the effects of resistant starch on host sterol levels. Collectively, this thesis work provides novel insights into the intricate links between diet, the gut microbiome, and cardiometabolic health. By generating robust, large-scale evidence on the role of Blastocystis and identifying specific nutrient–microbe interactions, this thesis contributes to the foundation for developing microbiome-informed personalized dietary strategies for health maintenance and disease prevention.