Sequestration of gut pathobionts in intraluminal casts, a mechanism to avoid dysregulated T cell activation by pathobionts

T cells that express the transcription factor RORg, regulatory (Treg) or conventional (Th17), are strongly influenced by intestinal symbionts. In a genetic approach to mechanisms underlying this influence, we performed a screen for microbial genes implicated, in germfree mice monocolonized with E.coli Nissle. The loss of capsule-synthesis genes impaired clonal expansion and differentiation of intestinal RORg+ T cells. Mechanistic exploration revealed that the capsule-less mutants remained able to induce specific IgA and were highly IgA-coated. They could still trigger myeloid cells, and more effectively damaged epithelial cells in vitro. Unlike wild-type microbes, capsule-less mutants were mostly engulfed in intraluminal casts, large agglomerates composed of myeloid cells extravasated into the gut lumen. We speculate that sequestration in luminal casts of potentially harmful microbes reduces the immune system’s actual exposure, preserving host-microbe equilibrium. The variable immunostimulation by microbes charted in recent years may not solely be conditioned by triggering molecules or metabolites, but also by physical limits to immunocyte exposure. To study the impact of Escherichia coli Nissle 1917 (EcN) K5 capsule on colonic CD4 T responses and activation we monocolonized Germ-Free (GF) mice with EcN wild-type and mutant lacking the K5 capsule (kfiCD). To assess the transcriptional inductions in colonic CD4 T cells, we flow-cytometrically double-sorted CD4 T cells (DAPI- CD19- CD4+ TCRβ+) from Germ-free mice (GF), EcN wild-type and EcN kfiCD mutant at day 14 post-monocolonization and performed population-level RNA-seq.