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Premature baby boy only one day old sleeps in a hospital nursery.

ST. LOUIS — Antibiotics given to premature babies in the first weeks of life could cause long-lasting damage to their gut microbiomes, according to a study released Monday in the journal Nature Microbiology.

Nearly all premature babies receive antibiotics to prevent or treat deadly bacterial infections. But the treatment damages good bacteria and increases the amount of drug-resistant bacteria long after babies leave the hospital, according to the study by Washington University School of Medicine.

Healthy gut microbiomes are linked to reduced risk of a variety of immune and metabolic disorders. The makeup of those microbes varies little after age 3, explained Dr. Guatam Dantas, professor of pathology and immunology and the study’s senior author. “If unhealthy microbes get a foothold early in life, they could stick around for a very long time.”

The study involved 41 preterm infants whose fecal samples were studied about a year and a half after their antibiotic exposure, and 17 full-term infants given no antibiotics.

The study suggests antibiotic use in preemies should be carefully tailored. The neonatal intensive care unit at St. Louis Children’s Hospital, staffed by Washington University physicians, announced it has already scaled down its use of antibiotics.

“We’re no longer saying, ‘Let’s just start them on antibiotics because it’s better to be safe than sorry,’” said newborn medicine director Dr. Barbara Warner. “We’re being much more judicious about initiating antibiotic use, and when we do start babies on antibiotics, we take them off as soon as the bacteria are cleared.”