Pediatrics

October 7, 2025

Human milk pasteurization method impacts preterm infant microbiome

Researchers used whole-metagenome sequencing to assess the composition, diversity and functional enrichment of the preterm infant gut microbiome — the microorganisms that aid digestion, immune function and metabolism.

Preterm infants in the neonatal intensive care unit are often fed donor human milk when mother’s own milk is not available. In extremely preterm infants, feeding human milk — compared to formula — is associated with improved rates of complications such as bronchopulmonary dysplasia and necrotizing enterocolitis. 

Donor human milk is pasteurized for safety, which can reduce macronutrients and bioactive compounds, but the effects of different pasteurization methods on the preterm infant gut microbiome — the microorganisms that aid digestion, immune function and metabolism — are unknown. 

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Seesandra Rajagopala, PhD, Jörn-Hendrik Weitkamp, MD, and colleagues have now demonstrated that the type of pasteurization used for donor human milk influences the gut microbiome and its function in preterm infants. Their study was published in the journal Pediatric Research

The investigators analyzed stool samples collected from 150 infants born from 25 to 31 weeks’ gestation and admitted to the NICU at Monroe Carell Jr. Children’s Hospital at Vanderbilt. The infants were fed exclusively retort-pasteurized (80 infants) or Holder-pasteurized (54 infants) donor human milk, or mother’s own milk (16 infants). 

The researchers used whole-metagenome sequencing to assess microbiome composition, diversity and functional enrichment. They found that compared to infants fed retort-pasteurized donor human milk, infants fed Holder-pasteurized donor human milk had higher microbial diversity, a higher abundance of beneficial microbes, and functional differences in carbohydrate metabolism, transport systems and regulatory pathways. 

In contrast to feeding retort-pasteurized donor human milk, feeding Holder-pasteurized donor human milk generated an infant gut microbiome similar to feeding mother’s own milk, the researchers reported. 

Although short-term clinical outcomes were not significantly different between the feeding groups, the observed microbial shifts could have implications for long-term health, supporting the need for further investigation, the authors noted. 

Rajagopala, research assistant professor of Medicine in the Division of Infectious Diseases, and Weitkamp, professor of Pediatrics in the Mildred Stahlman Division of Neonatology, are co-corresponding authors of the study. Other contributors are first author Claudia Ocampo-Chih, MD, Hope Hendricks, MD, Selin Weitkamp, Nidhi Gowda, Harinder Singh, PhD, and Ritu Banerjee, MD, PhD. The research was supported by the National Institutes of Health (grants UL1TR002243 and R21AI168832).