Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children

Nature Communications
Katri KorpelaWillem M de Vos

Abstract

Early-life antibiotic use is associated with increased risk for metabolic and immunological diseases, and mouse studies indicate a causal role of the disrupted microbiome. However, little is known about the impacts of antibiotics on the developing microbiome of children. Here we use phylogenetics, metagenomics and individual antibiotic purchase records to show that macrolide use in 2-7 year-old Finnish children (N=142; sampled at two time points) is associated with a long-lasting shift in microbiota composition and metabolism. The shift includes depletion of Actinobacteria, increase in Bacteroidetes and Proteobacteria, decrease in bile-salt hydrolase and increase in macrolide resistance. Furthermore, macrolide use in early life is associated with increased risk of asthma and predisposes to antibiotic-associated weight gain. Overweight and asthmatic children have distinct microbiota compositions. Penicillins leave a weaker mark on the microbiota than macrolides. Our results support the idea that, without compromising clinical practice, the impact on the intestinal microbiota should be considered when prescribing antibiotics.

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Datasets Mentioned

BETA
PRJEB11685

Methods Mentioned

BETA
PCR
454 Titanium sequencing
Illumina sequencing
electrophoresis

Software Mentioned

Qiime
Uchime
Uclust
MASS
R
MOCAT
BLAST
vegan

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