Harnessing microbial modulators to mitigate antibiotic-induced gut dysbiosis: from phytochemicals to faecal microbiota transplantation.

Antibiotics remain indispensable for the management of infectious diseases; however, their use inevitably perturbs the gut microbiota. Advances in metagenomics and multiomics approaches have demonstrated that antibiotic exposure profoundly disrupts microbial diversity and community structure, leading to the depletion of key commensals, the expansion of opportunistic pathogens, metabolic dysfunction, and the emergence of antimicrobial resistance. These alterations are increasingly associated with a broad spectrum of dysbiosis-related diseases (DRDs), encompassing metabolic, neuropsychiatric, and immune-mediated disorders. To mitigate or reverse antibiotic-induced microbial imbalances, various microbiota-targeted interventions have emerged as promising alternatives or complementary approaches. These include dietary phytochemicals (such as polyphenols, alkaloids, and organosulfur compounds), probiotics, prebiotics, synbiotics, postbiotics, bacteriophage therapy, and faecal microbiota transplantation (FMT). Evidence from in vitro and animal studies has provided mechanistic insights into how these interventions modulate microbial composition and function; however, clinical evidence varies across intervention type. This review summarizes the composition and functional roles of the gut microbiota, outlines the consequences of antibiotic exposure, and provides an overview of the underlying mechanisms, recent evidence, and potential applications of microbiota-targeted interventions in preserving intestinal homeostasis. This review aims to provide a theoretical basis and reference framework for the development of safer and more effective alternatives or adjuncts to antibiotic therapy.