Microbiome-Derived RNA as a Trigger for Heritable Innate Immunity

Introduction/Rationale: The microbiome shapes host immunity, yet the molecular signals by which specific bacteria modulate innate defenses remain poorly understood. In Caenorhabditis elegans, the Intracellular Pathogen Response (IPR) is a transcriptional program activated by obligate intracellular pathogens and shares features with mammalian type I interferon responses. We aimed to identify microbiome-derived triggers of the IPR and mechanisms of host protection.

Methods: We screened twelve native bacterial isolates using an IPR GFP reporter. Reporter activation in different tissues was observed by microscopy, and bacterial inactivation or RNA treatments were used to identify the molecular triggers. Transcriptomic profiling (RNA-seq, qRT-PCR) identified host genes induced by bacterial exposure. Pathogen burden was quantified by FISH, and developmental assays measured fitness effects.

Results: Stenotrophomonas indicatrix (JUb19) robustly activated the IPR in intestine, epidermis, neurons, and somatic gonad despite residing extracellularly, making it the first non-invasive bacterium known to trigger this pathway. Heat-killed bacteria failed to induce the IPR, whereas chemical or mechanical inactivation retained activity, implicating a heat-labile trigger. Bacterial RNA contributed to IPR activation, revealing microbiome RNA as a novel immune signal. Transcriptomic analyses showed induction of IPR genes, lysozymes, and metabolic regulators that enhance resistance to intracellular pathogens, with modest fitness costs. Remarkably, protection was inherited by naïve progeny that had never been exposed to JUb19.

Conclusion: Our findings identify a previously unrecognized extracellular mechanism by which microbiome-derived RNA activates epithelial immunity and provides intergenerational protection in C. elegans, linking commensal bacteria, RNA signaling, and heritable host defense.