The human gut microbiota begins forming at birth and continues evolving through early childhood. This microbial community plays a critical role in digestion, immunity, and metabolic processes.
However, early-life exposure to antibiotics, particularly during the neonatal period, can significantly disrupt this delicate microbial balance, leading to long-lasting health consequences.
Antibiotic administration during infancy, especially in the neonatal intensive care unit (NICU), has been consistently linked to reduced gut microbial diversity and dysbiosis – a shift away from the beneficial bacterial populations normally seen in healthy infants.
Fjalstad et al. (2018) systematically reviewed how neonatal antibiotic therapy perturbs the microbial landscape, showing decreases in commensal genera such as Bifidobacterium and Lactobacillus, accompanied by increases in opportunistic pathogens like Klebsiella and Enterobacter.
Gibson et al. (2015, 2016) further emphasized that these shifts not only affect diversity but also enhance the gut’s antibiotic resistome – the collection of all antibiotic resistance genes in a microbial community. Their studies found that antibiotic exposure led to persistent colonization by multidrug-resistant bacteria, including strains known to cause hospital-acquired infections.
Beyond bacterial populations, antibiotic use also influences the gut mycobiota (fungal microbiota).
Ventin-Holmberg et al. (2022) revealed that infants receiving antibiotics had a significantly higher abundance of Candida species, with increased fungal richness and diversity. This shift may increase susceptibility to mucosal inflammation and chronic inflammatory diseases later in life.
The downstream effects of early-life gut microbiota disruption are extensive. Morreale et al. (2023) reported associations between perinatal antibiotic exposure and long-term gastrointestinal and immunological issues, including an increased risk for inflammatory bowel disease (IBD), asthma, and food allergies.
Antibiotic-induced dysbiosis is also suspected to contribute to neurocognitive disorders. Ramirez et al. (2020) proposed that gut-brain axis dysregulation caused by microbiota alterations could underlie increased risks for anxiety, depression, and behavioral disorders in later childhood.
Furthermore, Kwon et al. (2022) demonstrated that post-antibiotic gut environments in infants are slower to return to baseline, especially when not supported by microbial restoration strategies, suggesting that even short-term treatments can have persistent consequences.
Antibiotic use in infancy, though sometimes necessary, poses a serious risk to the developing gut microbiota.
The resulting dysbiosis is linked to microbial resistance, fungal overgrowth, and lifelong health impacts.
Clinical protocols should prioritize antibiotic stewardship and consider microbiota-supportive interventions to mitigate these effects.
References
Fjalstad, J., Esaiassen, E., Juvet, L., Van Den Anker, J., & Klingenberg, C. (2018). Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review. Journal of Antimicrobial Chemotherapy, 73, 569–580. https://doi.org/10.1093/jac/dkx426
Gibson, M., Crofts, T., & Dantas, G. (2015). Antibiotics and the developing infant gut microbiota and resistome. Current Opinion in Microbiology, 27, 51–56. https://doi.org/10.1016/j.mib.2015.07.007
Gibson, M. K., Wang, B., Ahmadi, S., Burnham, C. A., Tarr, P. I., Warner, B. B., & Dantas, G. (2016). Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nature microbiology, 1, 16024. https://doi.org/10.1038/nmicrobiol.2016.24
Kwon, Y., Cho, Y. S., Lee, Y. M., Kim, S. J., Bae, J., & Jeong, S. J. (2022). Changes to Gut Microbiota Following Systemic Antibiotic Administration in Infants. Antibiotics (Basel, Switzerland), 11(4), 470. https://doi.org/10.3390/antibiotics11040470
Morreale, C., Giaroni, C., Baj, A., Folgori, L., Barcellini, L., Dhami, A., Agosti, M., & Bresesti, I. (2023). Effects of Perinatal Antibiotic Exposure and Neonatal Gut Microbiota. Antibiotics (Basel, Switzerland), 12(2), 258. https://doi.org/10.3390/antibiotics12020258
Ramirez, J., Guarner, F., Bustos Fernandez, L., Maruy, A., Sdepanian, V. L., & Cohen, H. (2020). Antibiotics as Major Disruptors of Gut Microbiota. Frontiers in cellular and infection microbiology, 10, 572912. https://doi.org/10.3389/fcimb.2020.572912
Ventin-Holmberg, R., Saqib, S., Korpela, K., Nikkonen, A., Peltola, V., Salonen, A., de Vos, W. M., & Kolho, K. L. (2022). The Effect of Antibiotics on the Infant Gut Fungal Microbiota. Journal of fungi (Basel, Switzerland), 8(4), 328. https://doi.org/10.3390/jof8040328