Impact of antimicrobial peptides and purified dietary fibres on human intestinal microbiota modulation: from screening to therapeutic potential and microbiota-based personalized medicine

Erica Bonazzi

22 November 2023

Thesis defence

Pratical info

13h00 - 23h00
Conference room Rosalind Franklin
Reduced mobility access

Under the supervision of Benoit Chassaing, team Mucosal microbiota in chronic inflammatory diseases


The gastrointestinal tract is colonized by a community of microorganisms, named the intestinal microbiota. The relationship between the host and its microbiota is symbiotic: the host provides a place for bacteria to grow and nutrients, while bacteria ensure immune development of the intestine, protection against pathogens and production of nutrients and vitamins. Composition and function of gut microbiota can be affected by several factors including diet and genetics. Deleterious changes in its composition and/or function are associated with diseases states, such as inflammatory bowel disease (IBD). Importantly, the fact that fecal microbiota transplantation from IBD patients to animals without an endogenous microbiota (germfree) is sufficient to transfer colitis susceptibility support the causal role played by the intestinal microbiota in the promotion of such chronic disorders. To control the intestinal microbial community, the host has evolved several defence mechanisms: the presence of a thick mucus layer, the secretion of immunoglobulin (sIgA), and the production of antimicrobial peptides (AMP). AMP are cationic peptides that prevent bacteria from reaching the host intestinal epithelium by permeabilizing their membrane or by limiting their aggregation. In humans, the two main AMP families are defensins and cathelicidins, and to date, several studies have reported their importance in epithelium and mucosal defence, but the exact role played by the intestinal microbiota remains controversial. During this thesis project, using an in vitro model of the gut microbiota (MBRA), I conducted a screening of select AMP for their direct impact on various human microbiotas composition and function. I then investigated the ability of one AMP (fragment HD51-9), identified as being a potent modulator of microbiota pro-inflammatory potential, to protect against DSS-induced colitis in mice. The obtained results support the hypothesis that purified AMP hold the potential to directly modulate the intestinal microbiota in a way that protects against intestinal inflammation. In addition to AMPs, dietary fibres are another important modulator of microbiota composition and function. While microbiota nourishment through dietary fibre is known to be health promoter, the impact of fermentable fibres consumption on chronic intestinal inflammation is more complex. Although epidemiological studies reported that consumption of fibre-rich diets associates with a reduced incidence of IBD, others suggest that once the disease is established, select IBD patients experience intolerance to fermentable fibre-rich foods. It has also been shown that enriching diets with inulin and psyllium remodels microbiota composition and exacerbates and alleviates, respectively, colitis in murine models. During this thesis project, the impact of inulin and psyllium on individual human microbiotas was determined in vitro as well as following transplant into germfree mice. Composition and pro-inflammatory potential of various in vitro microbiotas were highly impacted (termed “fibres-sensitive”), while others were minimally altered (termed “fibre-resistant”). Mice transplanted with fibres-sensitive microbiota harboured exacerbated and ameliorated DSS-induced colitis when fed with inulin- and psyllium-enriched diets, respectively, while the severity of colitis in mice colonized with fibres-resistant microbiota was not modulated by fibre source.  This study revealed the suitability of the MBRA model in identifying fibres-sensitive and fibres-resistant microbiotas. Moroever, it highlights that the extent to which fibres alter proneness to and/or severity of colitis is influenced by individual’s microbiota composition. Further studies appear warranted to mechanistically understand the inter-individual variability of microbiota responsiveness to a given exposure, with the ultimate goal to develop microbiota-based personalized medicine and nutrition.