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Updated: Mar 17, 2026
Quantitative Polymerase Chain Reaction-based Analyses of Murine Intestinal Microbiota After Oral Antibiotic Treatment
Published on: November 17, 2018
Antibiotic perturbation of the preterm infant gut microbiome and resistome
Andrew J Gasparrini1, Terence S Crofts1,2, Molly K Gibson1
1a Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St Louis , MO , USA.
Insights
Antibiotic use in preterm infants significantly alters the gut microbiome, reducing species richness and increasing resistance genes. Early microbiome composition can predict responses to certain antibiotics, highlighting the need for further research.
Area of Science:
- Microbiology
- Neonatal Medicine
- Pharmacology
Background:
- The gut microbiota is crucial for infant health, influencing nutrient absorption and immunity.
- Early-life disruptions, especially from antibiotics, can have long-term health consequences.
- Preterm infants often receive extensive antibiotic treatment, making their gut microbiome development a critical area of study.
Purpose of the Study:
- To investigate the impact of various antibiotic treatments on the gut microbiome of preterm infants.
- To explore predictors of microbiome response to specific antibiotic therapies.
- To understand the selection of antibiotic resistance genes and multidrug-resistant organisms.
Main Methods:
- Analysis of gut microbiome composition and function in preterm infants undergoing antibiotic therapy.
- Comparison of microbiome changes associated with different antibiotics (meropenem, ticarcillin-clavulanate, cefotaxime, gentamicin, vancomycin).
- Identification of microbial species and genes that predict response to vancomycin and gentamicin.
Main Results:
- Antibiotic treatments generally decreased gut microbial species richness.
- Gentamicin and vancomycin showed variable effects on species richness, partly predictable by pre-treatment microbial factors.
- All antibiotic exposures enriched for antibiotic resistance genes and multidrug-resistant organisms.
- Different antibiotics induced unique shifts in microbial populations and selected for distinct resistance genes.
Conclusions:
- Antibiotic interventions profoundly impact the preterm infant gut microbiome, affecting diversity and promoting resistance.
- Predictive microbial markers may guide antibiotic selection in preterm infants.
- Further research is essential to understand long-term implications and optimize antibiotic strategies.
Abstract:
The gut microbiota plays important roles in nutrient absorption, immune system development, and pathogen colonization resistance. Perturbations early in life may be detrimental to host health in the short and the long-term. Antibiotics are among the many factors that influence the development of the microbiota. Because antibiotics are heavily administered during the first critical years of gut microbiota development, it is important to understand the effects of these interventions. Infants, particularly those born prematurely, represent an interesting population because they receive early and often extensive antibiotic therapy in the first months after birth. Gibson et al. recently demonstrated that antibiotic therapy in preterm infants can dramatically affect the gut microbiome. While meropenem, ticarcillin-clavulanate, and cefotaxime treatments were associated with decreased species richness, gentamicin and vancomycin had variable effects on species richness. Interestingly, the direction of species richness response could be predicted based on the abundance of 2 species and 2 genes in the microbiome prior to gentamicin or vancomycin treatment. Nonetheless, all antibiotic treatments enriched the presence of resistance genes and multidrug resistant organisms. Treatment with different antibiotics further resulted in unique population shifts of abundant organisms and selection for different sets of resistance genes. In this addendum, we provide an extended discussion of these recent findings, and outline important future directions for elucidating the interplay between antibiotics and preterm infant gut microbiota development.
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