Quantifying metabolic diversity in Bacteroides uniformis and Phocaeicola vulgatus: From type strains to species heterogeneity

Abstract

The human gut microbiota plays a central role in host physiology, with metabolic interactions between the microbiota and host being a critical determinant of health and disease. However, understanding metabolic diversity at the strain level, the level at which microbes are selected as therapeutics, remains incomplete. Among the omics techniques, metabolomics is considered the field most directly related to phenotypes, as metabolites act as direct regulators of biological processes. In chapter 2, I established a GC-MS/MS method for the quantification of 120 gut microbiota-derived metabolites with high precision in complex biological matrices. This targeted metabolomics approach provides the sensitivity and specificity necessary for strain-level functional studies. The metabolic potential of the gut microbiome determines its significance in host health and diseases. In Chapter 3, I applied the developed method to characterize how B. uniformis and P. vulgatus metabolic outputs vary with nutrient availability. Substrate composition determined which metabolic pathways were activated, revealing that core metabolic pathways are present across strains but engaged differently depending on available substrates. Since the core metabolism of gut strains is analogous to higher living organisms, they represent the genetically distinct, fundamental functional units of the gut ecosystem. The contribution of the gut microbiome to human metabolic diseases and healthy state must be carried out at the strain level. In Chapter 4, I extended metabolic profiling to a panel of 107 strains (59 B. uniformis and 48 P. vulgatus), revealing surprising strain-level functional diversity that was not predicted by genomic similarity. Phylogenetically similar strains produced dramatically different metabolic outputs, with phenotypes that has completely different preference in nutrients to consume or metabolites to secrete. Together, these studies establish a quantitative understanding of the extent to which metabolic specialization and substrate-dependent activity operate at the strain- and species level in key gut commensals. This work suggests that microbiome research should move beyond simply identifying species-level presence and instead prioritize strain-level, phenotype-based resolution to understand the functional mechanisms driving host health and disease.

Die Dissertation ist gesperrt bis zum 10. Juli 2028 !