Diet–gut microbiota interactions in immune homeostasis and food allergy

Studies during the past decade have identified correlations between abundance of certain gut
microbial taxa and disease, which further stress the need to better understand the mechanistic details of the role of the microbota in health and disease. The gut microbiome and its metabolic output is heavily influenced by environmental triggers, most notably, diet. Among various dietary components, dietary fiber is non-digestible by the host and fermentation of soluble fibers occurs in the large intestine by fiber-degrading members of the microbiome. The primary byproducts of fiber fermentation include short-chain fatty acids, which have been extensively studied in the context of immune regulation and various diseases. Nevertheless, there is an unmet need to identify additional metabolites produced by a fiber-fermenting microbiome, as this knowledge will contribute toward better unravelling the mechanistic details of the microbiome’s role in disease. Moreover, little is known about the immunological consequences of removing or limiting dietary fiber – a phenomenon that has been common in the Western world for the past decades – and its impact on both gut microbial metabolism and host immunity.
In this PhD thesis, I investigated the role of dietary fiber on gut microbial metabolism and its effect on the host immunophenotype at homeostasis. I employed distinct commerical and customized rodent diets with varying sources and content of dietary fiber, in mice with both conventional and humanized gut microbiomes to better understand how fibers alter microbial metabolism and host immunity. Using broad-scale capillary electrophoresis time-of-flight mass spectrometry-based microbial metabolomics, I identified a suit of microbial metabolites whose abudance is modulated by the microbial fermentation of dietary fiber. The main finding of this first project was that fiber deprivation leads the gut microbiome to decrease production of B vitamin synthesis and alter bile acid metabolism. This was associated with an increased immune activation in the colonic lamina propria as identified by broad immunophenotyping using time-of-flight mass cytometry of host local and systemic organs. My data show that a variety of immune cell populations are differentially affected by fiber sources and content.
In the second project of this thesis, I applied the findings that fiber deprivation induces a proinflammatory environment, which was type 2 skewed, to a disease model. Here, I evaluated the role of microbiome-mediated barrier dysfunction due to fiber deprivation in a food allergic mouse model. In mice colonized with both a conventional and artificially colonized synthetic human gut microbiota, I identified that fiber deprivation induces a colonic mucus barrier dysfunction, which led to the discovery of IgE-coated bacteria in the feces as a consequence, prior to allergic sensitization. Upon sensitization and subsequent allergen challenge, these mice exhibited more severe clinical symptoms compared to mice fed a standard laboratory chow. In a gnotobiotic model, I found that the removal of the mucin-specialist, Akkermansia muciniphila, was able to improve symptoms, and eliminate the diet effect observed in mice with a conventional as well as synthetic microbiota. This was associated with a stark decrease in type 2 inflammatory immune cell subsets within the colonic lamina propria.
These novel findings arising from my PhD thesis will help the scientific community to enhance our understanding of the functional role of the gut microbiome in modulating the immune system. The links made in the first project connecting dietary fiber and B vitamins and its role in maintaining immune homeostasis provide an additional critical factor to be considered in personalized dietary interventions. In the second project, I identify that barrier dysfunction led to the activation of an atopic environment, without any additional immunological stimulus. This generated an IgE-mediated response towards commensal bacteria. Importantly, my experiments show a clear immunomodulatory role of a mucin-specialist bacterium, A. muciniphila, in allergic disease, which provides a functional link of the gut microbial composition and physiology to food allergy sensitization