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Updated: Sep 24, 2025
Quantitative Polymerase Chain Reaction-based Analyses of Murine Intestinal Microbiota After Oral Antibiotic Treatment
Published on: November 17, 2018
Effect of antibiotics in the first week of life on faecal microbiota development
Emmy Van Daele1, Kim Kamphorst2,3, Arine M Vlieger3
1Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
Insights
Antibiotic exposure in newborn infants significantly alters gut microbiota development, impacting beneficial bacteria like Bifidobacteriaceae and increasing potentially harmful Enterobacteriaceae for up to a year. This highlights the need for strategies to restore infant gut health post-antibiotics.
Area of Science:
- Microbiome research
- Pediatric health
- Antibiotic stewardship
Background:
- Infant antibiotic exposure is common for suspected infections.
- Limited understanding of antibiotic impact on infant gut microbiota development.
- Study focuses on term-born infants' intestinal microbiota with/without early-life antibiotics.
Purpose of the Study:
- To investigate the effects of early-life antibiotic exposure on infant intestinal microbiota development.
- To compare microbiota changes in infants exposed to antibiotics versus healthy controls.
- To examine the influence of antibiotic duration, delivery mode, and feeding method on these alterations.
Main Methods:
- Analyzed fecal microbiota from birth to 2.5 years in 56 antibiotic-exposed (AB+) and 126 control (AB-) term infants.
- Utilized 16S rRNA gene amplicon sequencing.
- Compared effects of antibiotic exposure (2-3 days vs. 7 days) and duration in relation to delivery and feeding mode.
Main Results:
- Antibiotic exposure increased Enterobacteriaceae and decreased Bifidobacteriaceae in infants delivered vaginally, but not via C-section.
- Microbiota alterations persisted up to 1 year of age.
- Breastfed infants showed lower Enterobacteriaceae and faster microbiota recovery compared to formula-fed infants.
Conclusions:
- Early-life antibiotic exposure significantly alters infant fecal microbiota composition up to one year.
- These alterations may have long-term health implications.
- Further research is needed to develop methods for restoring infant gut microbiota after antibiotic treatment.
Background:
Infants are frequently exposed to antibiotics (AB) in the first week of life for suspected bacterial infections. Little is known about the effect of AB on the developing intestinal microbiota. Therefore, we studied intestinal microbiota development with and without AB exposure in the first week of life in term born infants.
Methods:
We analysed the faecal microbiota from birth until 2.5 years of age by 16S rRNA gene amplicon sequencing in a cohort with 56 term born infants, exposed to AB in the first week of life (AB+) (AB for 2-3 days (AB2, n=20), AB for 7 days (AB7, n=36)), compared with 126 healthy controls (AB-). The effects of AB and duration were examined in relation to delivery and feeding mode.
Results:
AB+ was associated with significantly increased relative abundance of Enterobacteriaceae at 3 weeks and 1 year and a decrease of Bifidobacteriaceae, from 1 week until 3 months of age only in vaginally delivered, but not in C-section born infants. Similar deviations were noted in AB7, but not in AB2. After AB, breastfed infants had lower relative abundance of potentially pathogenic Enterobacteriaceae compared with formula fed infants and recovered 2 weeks faster towards controls.
Conclusions:
AB exposure in the first week of life alters faecal microbiota development with deviations in the relative abundance of individual taxa until 1 year of age. These alterations can have long-term health consequences, which emphasises the need for future studies aiming at restoring intestinal microbiota after AB administration.
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