Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants (Jan 2025, n=323) Predominantly amoxicillin. Short and long-term perturbations were detectable but substantially smaller than those associated with breastfeeding and infant age Antibiotics

[Michael Harrop]

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01999-3

Abstract​

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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Amoxicillin was the most commonly prescribed antibiotic in our cohort. Amoxicillin is a narrow-spectrum beta-lactam antibiotic frequently used to treat common childhood infections, including otitis media [34]. Although prior infant microbiome studies have included subjects with amoxicillin exposure [14, 20], in most cases, antibiotic types were combined for analysis [8, 16] or the subjects encountered amoxicillin in combination with other antibiotics [13, 15, 19]. All prior studies that specifically examined amoxicillin’s association with the microbiome in infants observed a decreased relative abundance of Bifidobacterium. However, the studies differed in taxa that were observed to increase in relative abundance: several studies indicated that Enterobacteriaceae increased [14,15,16], while others reported increased relative abundance of Enterococcus [13, 19]. The results of our taxonomic analysis are consistent with the identification of Bifidobacterium, particularly B. bifidum, as a species that is decreased in association with amoxicillin use in infants.

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