Antibiotic Exposure and Gut Microbiota in Childhood Health

Antibiotic use during pregnancy, at birth and throughout early childhood exerts profound effects on the developing gut microbial community, with implications for metabolic, immunological and neuroendocrine health. By altering the composition, diversity and functional capacity of intestinal bacteria, early antibiotic exposure can disrupt the critical window in which host–microbiota symbiosis is established. Consequences include reduced abundance of beneficial taxa such as Bifidobacteria, overgrowth of opportunistic Proteobacteria, weakened barrier integrity, aberrant immune maturation and altered energy harvest. Epidemiological studies link cumulative antibiotic courses with increased risks of asthma, allergies, obesity and non-alcoholic fatty liver disease, while mechanistic work in animal models reveals pathways by which microbial metabolites shape epithelial, immune and metabolic functions. Recognition of antibiotic-induced dysbiosis has prompted exploration of mitigation strategies, from targeted microbial restoration to refined prescribing guidelines, underscoring the global importance of preserving early-life microbial health for lifelong well-being.

Research from Nature Portfolio

Recent studies have demonstrated that antibiotic administration in the neonatal period is associated with enduring perturbations of gut microbiota and impaired growth trajectories in male children. Neonatal courses diminish Bifidobacteria richness and overall microbial diversity for up to two years, and transfer of antibiotic-exposed microbiota into germ-free male mice recapitulates growth deficits. In addition, investigation of intrapartum and postnatal antibiotic regimens in full-term, vaginally delivered infants has revealed that both interventions comparably alter initial gut colonisation patterns, delay succession of protective commensals and increase the prevalence of resistance genes. These effects persist at six months of age despite probiotic supplementation, highlighting the need to re-evaluate perinatal antibiotic protocols and to develop interventions that support microbiota recovery.

Antibiotic Exposure and Gut Microbiota in Childhood Health publication trend

The graph below shows the total number of articles in antibiotic exposure and gut microbiota in childhood health across all publications each year (not limited to Nature Index journals).

Technical terms

Gut microbiota: The community of microorganisms residing in the gastrointestinal tract.

Dysbiosis: An imbalance in the composition or function of the gut microbiota.

Enterocyte barrier: The layer of intestinal epithelial cells that regulates absorption and prevents translocation of microbes and toxins.

Microbial metabolite: A bioactive small molecule produced by gut microbes that can influence host physiology.

Intrapartum antimicrobial prophylaxis (IAP): Antibiotic administration to a mother during labour to prevent neonatal infection.

References

1. Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization. Nature Communications (2021).
2. Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants. Scientific Reports (2019).
3. An early-life microbiota metabolite protects against obesity by regulating intestinal lipid metabolism. Cell Host & Microbe (2023).
4. Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk. Gut Microbes (2023).