Carbohydrate utilization and metabolite production by diverse members of the phylum Bacteroidota

Doctoral thesis, 2026

The human microbiota consists of a huge number of microorganisms. Countless metabolic pathways within the microbiota help sustain the microbes themselves, but also contribute positive effects to the host, in a highly dynamic and complex interplay. The gut microbiota contains the highest number of microorganisms in mammals, and complex carbohydrates from dietary fiber represent a major nutrient source in this environment. The degradation of carbohydrates in mammalian guts thus relies on species that possess efficient carbohydrate-active enzymes (CAZymes). Some species, particularly from the phylum Bacteroidota, cluster CAZyme encoding genes in so-called polysaccharide utilization loci (PULs), which are large gene clusters that encode the necessary proteins to bind, transport, and break down specific polysaccharides. As a result of carbohydrate metabolism, many gut species are known to produce various profiles of metabolites such as organic acids (OAs) that in turn can be utilized by the host, and these are linked to multiple health benefits. However, whether metabolism of different types of carbohydrates results in production of static or variable OA output remains poorly understood.

In this thesis, I have investigated bacterial consumption of various carbohydrates and the resulting production of extracellular metabolite profiles. Biochemical characterization of individual CAZymes involved in breakdown of complex glycans was additionally done to assess unexpected poor degradation abilities in select species. Lastly, a system to transfer entire PULs between species was established, which enables modification of which carbohydrates a species can grow on. I show through metabolite profiling of species from the Bacteroides genus and the Prevotellaceae family that different carbohydrates indeed lead to different metabolite profiles both within and across species. Biochemical characterization of α-glucuronidases encoded by the poorly studied species Paraprevotella clara showed that while it does not readily grow on glucuronoxylan, it encodes functional xylan-active enzymes. Finally, the developed PUL transfer method enabled hemicellulose conversion in the model species Bacteroides thetaiotaomicron as well as deeper studies of a PUL sourced from a metagenome. In summary, this thesis contributes to fundamental knowledge regarding carbohydrate utilization by gut microorganisms, which has implications for improved human gut health.