Insights Into the Human Gut Microbiome and its Link with Obesity and Cardiometabolic Diseases

The gut microbiome is a complex microbial community that inhabits the gastrointestinal tract comprising archaea, bacteria, viruses and fungi. This community lies at the interface between our environment and our cells. As such, it plays an important role in multiple nutritional, physiological and immune processes, including the synthesis of vitamins and other compounds, the energy harvest from food, and the tight regulation of innate and adaptive immunity. The gut microbiome is implicated in the pathophysiology of obesity, type 2 diabetes and cardiovascular disease. This is of particular relevance in the context of the epidemiologic and dietary transition that characterizes westernization, a process in which low- and middle-income countries shift towards increased consumption of processed foods and reduced physical activity with a concomitant increase in non-communicable diseases. This thesis contributes to our understanding of the role of the gut microbiome in cardiometabolic disease and obesity In chapter I, studied the gut microbiome of adults from multiple populations to describe the association between the host's age and sex and the gut microbial diversity using 16S rRNA gene sequencing. I showed that the microbiome diversity increased with age until 40 years of age, and that young, but not middle-aged adult women had higher gut microbial diversity than men. These observations were robust to the use of antibiotics or the cardiometabolic health of the subjects. However, the pattern was not universal since it was not observed in all studied populations. In chapter II, I described the diversity, ecological distribution and genomic characteristics of the archaeal order Methanomassiliicoccales, which have potential as microbiome-based therapeutics. I carried out genomic and phylogenetic comparisons and confirmed that the Methanomassiliicoccales order forms two large phylogenetic clades. Based on abundance across host-associated and environmental metagenomes, I showed that the clades largely differ in environment preference and genomic potential. Chapter III introduces a modular pipeline that aids with the retrieval of microbial genomes from public databases, which are then used to create custom databases for several metagenome profiler programs. Here I carried out benchmark analyses on synthetic and real datasets and showed that the use of custom databases result in an increase of mappability of sequencing reads. Databases created using this pipeline were used in other chapters of this dissertation. For chapter IV, I evaluated the functional potential of the gut microbiome of a cohort of Colombian adults to detect variation in the microbiome associated with obesity or cardiometabolic health. I used shotgun gut metagenomes from the Colombian cohort to test the reproducibility of a set of functional characteristics previously reported to be associated with cardiometabolic conditions in other populations. Using host metadata, I classified subjects according to their obesity and cardiometabolic status, and identified which microbiome functions were uniquely associated with each condition. I found that obesity drives associations of the microbiome with cardiometabolic disease when both are present. Chapter V describes the retrieval of genomes from the Colombian gut microbiome using the metagenome sequence data I collected in the previous chapter. I evaluated the quality of the genome assemblies, performed the taxonomic classification, established their taxonomic novelty compared to what is currently reported, and annotated functional and genomic characteristics. All in all, the works presented in this thesis advance our knowledge of the role of the gut microbiome in obesity and cardiometabolic disease. I expect this will help guide future studies that use metagenomics to look into the associations and mechanisms of the microbiome with these non-communicable conditions