New research has found a concerning characteristic in babies that could greatly affect their health down the line.
While some gut microbiome can pass in utero, a newborn’s gut microbiome was previously thought to be nearly sterile, mostly acquiring bacteria during birth or via breastfeeding.
But new findings may prove otherwise, according to research presented at the European Society of Clinical Microbiology and Infectious Diseases Global 2026.
Researchers analyzed stool samples from 105 infants admitted to a neonatal intensive care unit within the first 72 hours of life to capture the earliest stages of microbial and genetic exposure.
Antibiotic resistance genes (ARGs) — segments of DNA that help bacteria survive the effects of antibiotics — were found in newborns, a potential contributor that could allow bacteria to evade antibiotic treatment.
The findings suggest that the newborn’s gut microbiome, which is affected by maternal and environmental factors, may be exposed to bacteria during pregnancy.
Researchers also found a variety of genes that are associated with resistance to commonly used antibiotics, including ones that break down widely used medications.
“This finding suggests that a pattern of ARGs is already established at this stage,” lead author Dr Argyro Ftergioti said in a press release.
“The neonatal gut harbors a diverse resistome, and the presence of clinically important ARGs so early in life is concerning,” he said.
The study also identified connections between resistance genes and several maternal and neonatal factors.
These included maternal hospitalization during pregnancy or central venous catheter (tube to deliver medicine or nutrition) placement within the first 24 hours of life.
The collection of antibiotic resistance genes before birth is mainly shaped by maternal transmission (the passage of bacteria or microbes from a mother to child during pregnancy, labor or breastfeeding), delivery and very early hospital exposures.
“Although some ARGs were expected, their high prevalence across the majority of samples was striking,” Ftergioti added.
While gut bacteria in new babies is crucial for developing immune, digestive and nervous systems, a healthy microbiome is necessary for protection against infections, allergies and future chronic diseases, such as asthma, ADHD and diabetes.
Earlier studies discovered newborns have much more gut bacteria than previously thought, containing some 10,000 viral species — 10 times more than the number of bacterial species in the average child.
“While further research is needed to understand how early carriage of resistance genes affects microbiome development and infection risk, these findings highlight the importance of surveillance, infection prevention and control in neonatal care,” Ftergioti said.
