Bacillus and Ulcerative Colitis: Examining the Therapeutic Potential, and investigating the Role of Environmental Exposure in Epidemiology.

Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with a rising global burden and no definitive cure beyond proctocolectomy. It is thought to result from an aberrant immune response to the colonic microbiome, with environmental factors playing a dominant role in its pathogenesis. One prominent framework, the “old friends hypothesis”, proposes that loss of exposure to specific environmental microbes that are typical of ancestral, non-urban lifestyles contributes to this increase in incidence. The genus Bacillus has been identified as a plausible candidate within this model.
This thesis explores two central hypotheses: first, that daily administration of a Bacillus species attenuates the severity of UC; and second, that geographical variation in UC incidence may be mediated by environmental exposure to Bacillus species via the recently characterised aerobiome.
In murine models of acute and chronic UC, a specific Bacillus strain (EHv5) showed marked therapeutic efficacy. The principle bioactive component was identified as a heterogenous family of cyclic lipopeptides capable of micelle formation at higher concentrations (heterogenous lipopeptide micelles, HeLM). The requirement for HeLM was demonstrated by loss of therapeutic effect in an isogenic HeLM-deficient mutant, and further verified via the direct administration of purified HeLM with recapitulation of the therapeutic effect. Contrary to the initial hypothesis, faecal metagenomics revealed no significant or sustained changes in microbiome that could explain this therapeutic effect. Instead, HeLM was found to act as a direct Toll-like receptor 2 agonist, inducing an IL-10 mediated anti-inflammatory response, whilst also demonstrating a partial inhibition of lipopolysaccharide driven inflammation via Toll-like receptor 4. This effect was sustained in a chronic colitis model, such that it conferred protection against colitis-associated colorectal cancer.
To investigate environmental exposure pathways, a novel murine model was developed that allowed stringent control of exposure to defined aerobiomes, and was validated using culture based methods and metagenomic analysis. In this system, mice exposed to a rural aerobiome that was enriched with Bacillus and similar soil derived taxa exhibited mild but statistically significant protection against acute UC. This effect was absent in animals exposed to sterile air or an urban aerobiome. Metagenomic analysis demonstrated discrete shifts towards short chain fatty acid producing taxa in the rural exposed group, supporting a mechanistic link between aerobiome exposure, microbiome dynamics, and immuno-inflammatory states. This framework offers a potential explanation for epidemiological differences in UC incidence between rural and urban populations.
Collectively, these findings identify Bacillus derived HeLM as a potent anti-inflammatory molecule with translational potential as a therapeutic for patients with ulcerative colitis. Further, it provides a novel mechanistic framework connecting aerobiome mediated environmental microbial exposure to intestinal immune regulation and disease epidemiology.