Novel insights into bacterial sampling by the intestinal immune system

The mammalian large intestine is home to several hundred bacterial species, forming the bacterial part of the intestinal microbiota. Yet only a fraction of these species elicits a mucosal immune response. The factors underlying immunogenicity in the gut remain poorly understood but are clearly disrupted in intestinal disorders such as Crohn’s disease and innate immunodeficiencies. Understanding these concepts is also critical for the design of oral vaccines and immunotherapies.

Sampling of antigen from the gut lumen into gut-draining lymph nodes is the first step in induction of any mucosal immune response¹. Currently this can only be directly observed using highly artificial in vitro or surgically isolated systems. To study real sampling dynamics in vivo, we critically lack good tools. Sampled bacteria are rare and rapidly killed, therefore we need to build a bacterial reporter system that is not degraded after bacterial death, is highly sensitive and can give spatially resolved information.

Lanmodulin², and other lanthium series ion-chelating proteins provide a potential solution. Lanthium series metals are very rare in intestinal microbes and tissues, are relatively non-toxic and can be easily detected by plasma-coupled mass spectrometry, CyTOF and imaging mass cytometry. In this project, you will design and test systems for over-expression and controlled expression of Lanmodulin in E.coli, Salmonella and Bacteroides species. We will also test strategies to load different isotopes in vitro, in vivo and ex vivo. Pathway engineering and directed evolution approaches will be used to improve uptake of relevant ions and to maximize Lanmodulin expression while minimizing toxicity. The overall aim is to allow robust single-cell-level detection of intestinal bacteria in gut-associated lymphoid tissues. These bacterial reporters will then be applied to probe the fundamental biology of intestinal antigen sampling. Specifically, we can investigate how bacterial factors (viability, aggregation, surface structures, oxygen-tolerance and abundance), microbiome composition, and host factors (activity of pattern-recognition receptors, epithelial integrity, circadian rhythm³, intestinal motility, IgA specificity etc) influence the rate of uptake, cellular targets and degradation rates of bacterial antigens ^4,5