Fermentation-driven interactions of gut microbes with their environment

The gut microbiome has gained a lot of attention in recent decades due to the multitude of interactions it has with the host. One of the main ways the microbiota communicates with the host is through the fermentation of dietary or host-derived nutrients. Fermentation of carbohydrates and amino acids yields structurally and compositionally different metabolites that have distinct functionality within the gut microbial community but also in the interaction with the host. The most abundant fermentation metabolites are the short-chain carboxylic acids acetate, butyrate, and propionate. While important contributions to host health have been attributed to these three, there are other compounds formed by fermentation whose relevance in the gut becomes increasingly recognized. In this essay, we will present how gut physiological properties relate to microbial fermentation capacity. We will introduce the diversity of fermentation pathways and relate functionality to the intrinsic properties of fermentation-derived metabolites. Finally, we will present strategies to restore disrupted fermentation activity.