Effect of environmental abiotic factors on the physiology and metabolism of gut microbes

The human gut contains a diverse microbial community, known as the gut microbiota. This community affects host health through the production of a myriad of metabolites generated by the fermentation of available nutrients. The production of microbial metabolites is affected by environmental conditions within the gut, but despite the importance of these factors, their specific effects remain poorly understood. This thesis investigates how gut environmental conditions, particularly pH and substrate availability, influence microbial metabolism, with the aim of identifying strategies to promote the production of metabolites beneficial to health while limiting harmful ones.

A literature review (Manuscript I) provides an overview of how intestinal pH shapes the gut environment by regulating bacterial composition, gene expression, enzymatic activity and thereby metabolite production, with implications for health. Experimental studies explore the impact of pH on gut bacterial tryptophan metabolism using in vitro culturing, complemented by human study data linking fecal pH to microbial tryptophan metabolites (Manuscript II). Our results show that indole, a gut bacterial tryptophan metabolite and a precursor of the uremic toxin indoxyl sulfate, is inhibited under mildly acidic conditions. In Escherichia coli, this suppression occurs through downregulation of the tryptophanase gene, thereby reducing indole production. This repression redirects tryptophan to other catabolic pathways, such as Stickland fermentation in species like Clostridium sporogenes, leading to the production of beneficial metabolites like indolelactic acid and indolepropionic acid. In a separate study, another mechanism for modulating gut microbial tryptophan metabolism is demonstrated, showing that the availability of tryptophan and fermentable carbohydrates also regulates microbial tryptophan catabolism by altering microbial activity (Manuscript III). Specifically, monosaccharide cross-feeding from fibre fermentation represses tryptophanase gene expression via carbon catabolite repression, inhibiting indole production in E. coli and redirecting tryptophan metabolism toward increased Stickland fermentation. Furthermore, this thesis investigates the regulation of the bacterial tyrosine decarboxylation reaction leading to tyramine production (Manuscript IV). Our results demonstrate that this reaction is driven by both pH-mediated expression of aromatic amino acid decarboxylase genes and the abundance of producer species in vitro, supported by an inverse correlation between fecal pH and tyramine in humans.

This PhD thesis contributes to a better understanding of how gut environmental factors shape microbial metabolism, specifically influencing the production of aromatic amino acid-derived metabolites. The findings show that the production of the investigated bacterial metabolites is primarily driven by pH- and substrate-mediated changes in gene expression and metabolic activities of gut bacteria, rather than shifts in their abundance. These insights underscore the potential of targeting gut environmental conditions to modulate microbial gene expression and metabolic outputs in ways that may improve host health.