Herbal and Natural Products for Antibiotic-Associated Diarrhea: A Systematic Review of Animal Studies Focusing on Molecular Microbiome and Barrier Outcomes

<b>Background/Objectives:</b> Antibiotic-associated diarrhea (AAD) arises from antibiotic-induced disruption of microbial diversity, metabolic activity, epithelial integrity, and mucosal immunity. Probiotics are widely used but often show limited efficacy under antibiotic pressure. Herbal and natural products (HNPs) may provide multi-target benefits by modulating microbiota-dependent and host-directed pathways. This review synthesized animal studies evaluating HNP or HNP-probiotic combination (HNP-C) therapies using molecular microbiome endpoints. <b>Methods:</b> Following PRISMA 2020 guidelines, controlled in vivo studies assessing HNP or HNP-C interventions for AAD were searched in Pubmed, EMBASE, Web of Science, Scopus, and CNKI through November 2025. Eligible studies reported microbial diversity, taxonomic shifts, short-chain fatty acids (SCFAs), barrier markers, or immune responses. Risk of bias was assessed using the SYRCLE tool. Due to heterogeneity, findings were narratively synthesized. <b>Results:</b> Twenty-seven studies met inclusion criteria (21 HNP, 6 HNP-C). HNP monotherapies consistently improved α-diversity, shifted β-diversity toward healthy controls, restored SCFA-producing taxa, and increased SCFA levels. They also enhanced tight junction proteins and reduced inflammatory cytokines. HNP-C interventions demonstrated more comprehensive microbial, epithelial, and immune recovery; however, only two studies included direct comparisons among HNP-only, probiotic-only, and combination groups. In these, HNP-C showed greater improvements than individual components, suggesting complementary or potentially complementary or additive effects. Other HNP-C studies were limited by absent comparator arms. <b>Conclusions:</b> HNPs appear to support recovery of microbial diversity, metabolic function, epithelial barrier integrity, and immune regulation by engaging microbiota-dependent and host-mediated mechanisms. HNP-C strategies may offer complementary benefits, although rigorously controlled comparative studies and clinical validation remain needed.