Host-microbe interactions at barrier tissues and immunomodulation: a scoping review

The intricate interactions between host microbiota and immune cells within barrier tissues—such as the gut, skin, and lungs—are central to preserving immune homeostasis, reinforcing epithelial integrity, and regulating inflammation. Key mediators, including microbial metabolites like short-chain fatty acids (SCFAs) and tryptophan derivatives, and signaling pathways involving Toll-like receptors (TLRs) and NOD-like receptors (NLRs), orchestrate immune responses that distinguish commensals from pathogens. Dysbiosis, characterized by microbial imbalance, disrupts these regulatory mechanisms and contributes to chronic conditions such as inflammatory bowel disease (IBD), atopic dermatitis, and asthma. Importantly, emerging microbiome-based therapies—including probiotics, prebiotics, postbiotics, and fecal microbiota transplantation (FMT)—offer promising strategies to restore microbial balance and improve immune function. Coupled with advances in multi-omics and artificial intelligence, these approaches support precision medicine models that tailor interventions to individual microbial and immune profiles. This review synthesizes recent evidence to highlight the therapeutic opportunities, challenges, and future directions in leveraging host–microbiome interactions for clinical immunology.