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Updated: May 31, 2025
Quantitative Polymerase Chain Reaction-based Analyses of Murine Intestinal Microbiota After Oral Antibiotic Treatment
Published on: November 17, 2018
Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants
Alain J Benitez1,2, Ceylan Tanes1, Elliot S Friedman3
1Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA.
Insights
Early antibiotic exposure in infants had minimal impact on the gut microbiome, with effects being smaller than those from breastfeeding or infant age. These short-term changes did not persist long-term.
Area of Science:
- Microbiome research
- Pediatric health
- Immunology
Background:
- The infant gut microbiome is crucial for immune development and long-term health.
- Early antibiotic exposure may disrupt microbiome development, potentially leading to adverse health outcomes.
- Understanding these effects is vital for infant health strategies.
Purpose of the Study:
- To investigate the association between antibiotic exposure and the infant gut microbiome composition and bile acid profiles.
- To compare the impact of antibiotics with other factors like breastfeeding and infant age.
Main Methods:
- Prospective longitudinal birth cohort study of 323 healthy African American infants.
- Shotgun metagenomics sequencing for microbiome analysis.
- Liquid chromatography-mass spectrometry for bile acid profiling.
- Short-term substudy to assess immediate post-antibiotic effects.
Main Results:
- Antibiotic exposure showed minimal microbiome differences, with breastfeeding having a larger impact.
- Short-term effects (e.g., decreased Bifidobacterium bifidum) were observed within 2 weeks but did not persist.
- No association found between antibiotic exposure and increased antibiotic resistance genes or altered bile acid profiles.
- Infant age was associated with differences in four microbial species.
Conclusions:
- Gut microbiome perturbations from short-term and long-term antibiotic exposure are detectable but less significant than those from breastfeeding and infant age.
- The infant gut microbiome demonstrates resilience to typical antibiotic exposures.
- Further research can inform targeted interventions for infant gut health.
Background:
The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry.
Results:
Stool samples were collected at ages 4, 12, and 24 months for antibiotic-exposed (n = 170) and unexposed (n = 153) participants. A short-term substudy (n = 39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2 weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition.
Conclusions:
Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.
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