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Divergent immue responses to commensal Clostridia classified based on motility gene arrangement and flagellin diversity

ABSTRACT: Flagella-dependent motility is a defining feature of several species of Clostridia that colonize the intestine. The genomes of these bacteria encode varying numbers of flagellins – the basic subunits of flagella - and the machinery necessary for synthesis, assembly, and function of flagella. Although adaptive immune responses to commensal flagellins are hallmarks of Crohn’s disease, it is unclear whether flagellins themselves drive inflammation, or what defines pro-inflammatory flagellated commensals. Here, we show that the arrangement of motility loci and the diversity of encoded flagellins can separate flagellated Clostridia into at least 2 functionally distinct subgroups. Both subgroups induce tolerogenic responses at homeostasis but possess divergent capacities for TLR5 activation and induction of inflammation. We identify a hypervariable region of the flagellin D0 domain that modulates the capacity for TLR5 activation and demonstrate enrichment of bacteria in the pro-inflammatory subgroup in Crohn’s disease biopsies. Collectively, our study identified a subset of colitogenic commensals and revealed one mechanism whereby these organisms can directly initiate intestinal inflammation.

ORGANISM(S): Mus musculus

PROVIDER: GSE290365 | GEO | 2025/12/05

REPOSITORIES: GEO

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Project description:The healthy gut microbiota is composed of three different functional subgroups, symbionts, commensals and pathobionts. Additionally, infection with pathogenic bacteria can occur. Microbe Associated Molecular Patterns (MAMPs) are expressed by most members of both, microbiota and pathogens and interact with Pattern Recognition Receptors (PRRs), resulting in activation of the innate immune system. It is still unclear whether the interaction of PRRs with MAMPs of different origin, leads to a differential activation of innate immunity and whether thereby, distinction can be made between symbionts, commensals, pathobionts and pathogens. Here we addressed the question whether the interaction of flagellin with Toll-like receptor 5 (TLR5) might be a possible mechanism of the innate immune system to distinguish between the different microbial subgroups and initiate the respective immune response. To characterize distinct cellular immune responses to symbiont or pathogen derived flagellin we run transcriptomics, phosphoproteomics and proteomics of TLR5 overexpressing cells. Responses to different flagellins were characterized by differential kinetics and regulation of protein phosphorylation as well as variant protein expression patterns. In vivo experiments revealed that commensal derived flagellin mediated an inert TLR5 signal, thus not affecting Dextran-Sodium-Sulfate (DSS) induced intestinal inflammation. In vitro pathogenic derived flagellin induced a strong pro-inflammatory TLR5 response and did not ameliorate intestinal inflammation. In contrast, symbiont derived flagellin revealed an intermediate TLR5 activation and clearly ameliorated DSS induced intestinal inflammation thus shifting the host immune response in favor of mucosal immune balance. Bone marrow chimeric mice proofed that CD11c+TLR5+ intestinal lamina propria cells mediate the anti-inflammatory symbiotic effect of flagellin. We suggest that the quality of flagellin-induced TL signal might determine the balance between homeostasis and intestinal inflammation and may help the innate immune system to distinguish between symbionts, commensals, pathobionts and pathogenic microbes. We used microarrays to analyze differential expression of genes between treatments with flagellins of E. coli Nissle (EcN) and Salmonella Typhimurium SL1344 (ST).

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Divergent immue responses to commensal Clostridia classified based on motility gene arrangement and flagellin diversity

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