In the study, female mice treated with two classes of widely used childhood antibiotics gained more weight and developed larger bones than untreated mice.
Both of the antibiotics also disrupted the gut microbiome, the trillions of microbes that inhabit the intestinal tract, researchers found.
Overall, the mice received three short courses of amoxicillin (a broad-spectrum antibiotic), tylosin (which isn't used in children but represents another common antibiotic class called the macrolides, which is increasingly popular in pediatrics), or a mixture of both drugs.
Martin Blaser, director of the New York University Human Microbiome Programme, and the study's senior author, said the results agree with multiple other studies pointing towards significant effects on children exposed to antibiotics early in life.
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He noted that the cumulative data could help shape guidelines governing the duration and type of paediatric prescriptions.
"We have been using antibiotics as if there was no biological cost," said Blaser.
The new study found that short, high-dose pulses of tylosin had the most pronounced and long-lasting effect on weight gain, while amoxicillin had the biggest effect on bone growth - a prerequisite for increased height.
Based on extensive DNA sequencing data, the study showed that both antibiotics also disrupted the gut microbiome.
"They changed the ecology of the microbiome in terms of the richness of the organisms, the diversity, and also what we call the community structure, or the nature of its composition," Blaser said.
"We also see that the effect is cumulative," said lead coauthor Laura M Cox, an adjunct instructor in the Department of Medicine at NYU School of Medicine.
"So the number of courses of antibiotics matters," she said.
The study was published in the journal Nature Communications.