Antibiotic impact on human microecology in low- and middle-income countries: a systematic age-stratified review of gut and respiratory microbiome and resistome

Background: Antibiotic exposure disrupts microbial communities in the gut and respiratory tract, causing functional changes that may have lasting health impacts and contribute to the spread of antibiotic resistance genes (ARGs) throughout life. However, age-stratified evidence of these effects, particularly in low- and middle-income countries (LMICs), remains limited. Objective: This systematic review assessed the impact of antibiotics on gut and respiratory microbiomes and resistomes in LMICs, with separate analyses for adults and children. Data sources: PubMed, Scopus, Web of Science, & ScienceDirect. Methods: A comprehensive literature search was conducted using a predefined search strategy and eligibility criteria to identify relevant studies from LMICs. Twenty-five studies met the inclusion criteria: 23 examined the gut microbiome, and 2 focused on the respiratory microbiome. Key outcomes included microbial diversity (alpha/beta/gamma), taxonomic shifts, resistome profiles, functional changes, and recovery potentials, stratified by age group and body site. Results: Antibiotic exposure was generally associated with reductions in microbial diversity and altered taxonomic composition, with children showing more pronounced and prolonged disruptions than adults. Analysis of resistome changes revealed a critical finding: while antibiotics consistently selected for ARGs matching the drug class administered, a substantial reservoir of non-matching, background ARGs, conferring resistance to beta-lactams, aminoglycosides, vancomycin, tetracyclines, was also highly prevalent across studies. This indicates a silent pre-existing resistome that is enriched by antibiotic pressure. ARGs were more abundant in adult resistomes, though functional changes occurred across age groups. Microbiome recovery was observed over time, but resistome recovery was limited. Conclusion: Antibiotic use significantly disturbs the gut and respiratory microbiomes and promotes ARG enrichment, especially in children, who demonstrate greater susceptibility and lower recovery potential. These findings emphasise the need for targeted antibiotic stewardship, improved microbiome recovery research, and enhanced resistome monitoring in LMICs. Trail registration: International Prospective Register of Systematic Reviews (PROSPERO), ID: CRD420250641394.