Extracellular metabolite production by Bacteroides strains varies depending on carbohydrates used as carbon sources

The microorganisms comprising the gut microbiota perform various important functions, such as producing short-chain fatty acids (SCFAs) and other metabolites that can be taken up by the host and used as energy sources or as signaling molecules. A major nutrient for the microbiota is dietary fiber, mainly composed of complex polysaccharides that cannot be degraded by host enzymes. Species from the Bacteroidota phylum are regarded as proficient carbohydrate degraders, partly thanks to their multi-gene systems, known as polysaccharide utilization loci (PULs), encoding the necessary proteins for carbohydrate capture and cleavage. Linking which species can grow on which polysaccharides, depending on the presence of corresponding PULs encoded in their genomes, has been studied intensely in the last decades. However, little is known about which metabolites they produce from carbohydrate consumption, as previous investigations have mainly used glucose as the sole carbon source. In this study, we grew several Bacteroidota species on different carbohydrates, from monosaccharides to polysaccharides, and quantified the resulting extracellular metabolites produced. The results reveal different extracellular metabolite profiles, both intraspecies and interspecies, depending on the carbon sources. Surprisingly, in some cases, the production of extracellular metabolites differed between growth on a homopolysaccharide and its constituent monosaccharide. The results indicate that the metabolite output of gut species is not static but varies with the nutrients present, adding to the complexity of the interplay among dietary fiber, microbial ecology, and gut health.

The human gut microbiota is closely linked to health, and metabolism of different types of dietary fibers is a core activity within this community. Many studies have investigated the composition of the microbiota and sought to relate the presence and abundance of species to health or disease, often attributing a genus or species to consumption or production of a certain metabolite to explain an overall phenotype. It is known that bacteria have different carbohydrate-degrading abilities, but they may not produce a static output of metabolites from the consumption of different carbohydrates, from monosaccharides to complex polysaccharides. This study demonstrates that common bacteria in the Bacteroides genus may drastically alter their production of extracellular metabolites. The findings add another layer of complexity to the dynamics of the gut environment and are important for better understanding the interplay among diet, the microbiota, and the host.