MICROBIAL PROTEIN METABOLISM IN GASTROINTESTINAL AND ALLERGIC INFLAMMATION

Abstract

The gut microbiota is an essential modulator of host physiology, modulating mucosal barrier integrity, intestinal inflammation, and immune responses through metabolic and proteolytic activities. Disruption of these interactions has been implicated in gastrointestinal diseases, including inflammatory bowel disease (IBD), and in systemic immune responses to dietary allergens. However, the precise microbial functions that contribute to health or disease in these contexts remain incompletely understood. This thesis aimed to define how specific microbial activities, including tryptophan metabolism, proteolytic activity, and allergen degradation, influence host immunity, with the goal of identifying pathways that are targetable for therapeutic intervention. In Chapter 3, I investigated how the microbial metabolism of dietary tryptophan influences intestinal inflammation by activating the aryl hydrocarbon receptor (AhR). Using gnotobiotic and humanized mouse models, I demonstrated that enhancing dietary tryptophan availability restores AhR activation and reduces colitis severity in a microbiota-dependent manner. Furthermore, I identified that interindividual differences in AhR activation are determined by the functional capacity of the microbiota, providing the first direct evidence that the origin of impaired AhR signalling in human IBD is microbial. These findings support the development of dietary and microbial therapies tailored to the composition and function of the microbiota in IBD. In Chapter 4, I explored the contribution of microbial proteases to colitis through cleavage of the external domain of protease-activated receptor 2 (PAR2). I found that inflammation promotes the expansion of proteolytic bacteria that activate PAR2 and exacerbate barrier disruption. Using a protease-resistant PAR2 mouse model, I provided the first direct evidence that microbial proteases cleave PAR2 at its canonical activation site, triggering canonical G-protein signalling that promotes inflammation. Mice expressing this cleavage-resistant PAR2 variant were protected from colitis despite harbouring a microbiota enriched in proteolytic microbes, demonstrating that canonical PAR2 activation by microbial proteases is an important pathological mechanism and therapeutic target in intestinal inflammation. In Chapter 5, I extended our study of microbial metabolism to allergic disease by investigating whether degradation of peanut (PN) allergens by microbes modulates anaphylaxis severity. Using gnotobiotic models, I identified allergen-degrading bacteria that reduced IgE recognition and protected against severe allergic reactions. These effects occurred through two complementary mechanisms: structural degradation of immunodominant epitopes and reduced translocation of allergens across the mucosa. Colonization with bacteria such as Rothia conferred protection, while non-degrading bacteria did not. Clinical data from PN-allergic individuals undergoing oral immunotherapy further showed that higher abundance of PN-degrading oral bacteria correlated with increased PN tolerance. These findings reveal a novel microbial pathway that limits allergen exposure before immune recognition, offering potential strategies to reduce anaphylaxis severity and enhance therapeutic outcomes. Together, this work demonstrates that specific microbial metabolic and proteolytic functions are critical determinants of host immunity. By demonstrating how these pathways contribute to gastrointestinal inflammation and allergy, this thesis supports the development of microbiota- and diet-based strategies to treat gastrointestinal and allergic diseases.