Gut-microbiota-mediated host immune modulation: mechanisms, pathological dysbiosis, and therapeutic frontiers

Abstract

The mammalian immune system has evolved in constant dialogue with its diverse microbiota, forming an ecological and molecular partnership that is fundamental to health. This review examines how microbial communities shape immunity across developmental and functional axes, the immunological consequences of dysbiosis during infection and inflammatory disease, and emerging microbiota-targeted interventions. The host–microbiota–pathogen triad offers a framework to understand how commensals and pathogens compete for ecological niches and immune recognition, and how disturbances in this balance can cascade into chronic inflammation or infection. Microbial metabolites such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives act as key bioactive intermediaries translating microbial activity into host immune architecture, influencing epigenetic programming, cellular differentiation, and mucosal barrier function. These interactions orchestrate tolerance toward commensals while maintaining effector readiness against pathogens, particularly through regulatory T cell (Treg)–Th17 balance, B cell education, and Immunoglobulin A (IgA) responses. When perturbed, as in infections caused by Clostridioides difficile, Klebsiella pneumoniae, Salmonella enterica, or Listeria monocytogenes, the ensuing dysbiosis reinforces immune dysfunction in a self-perpetuating cycle. Therapeutic frontiers now extend beyond conventional antimicrobial strategies to include live biotherapeutics, bacteriophage therapy, fecal microbiota transplantation, and metabolite-based (postbiotic) interventions. Future efforts must reconcile inter-individual microbiome variability with precision medicine, integrating metagenomic and metabolomic profiling to design safe, effective, and personalized microbiota-centered therapeutics.