07/18/2026
Could breastfeeding drive unique epigenetic changes in babies?
Early-life nutrition is increasingly recognized as a critical determinant of short- and long-term health, with breastfeeding often linked to improved developmental and disease outcomes.
However, the biological mechanisms underpinning these associations remain only partially understood. Epigenetics has emerged as a promising explanatory mechanism.
Dr. Doretta Caramaschi, lecturer at the University of Exeter and co-lead author of a recent large-scale epigenetic study, is working to understand the influence of breastfeeding on epigenetic modifications. Drawing on data from thousands of individuals across international cohorts, her recent research investigated how breastfeeding may shape infant biology at the molecular level.
We spoke with Caramaschi to discuss the research.
To robustly detect epigenetic signals, Caramaschi and her colleagues conducted a meta-analysis of epigenome-wide association studies (EWAS), relying on the Pregnancy and Childhood Epigenetics consortium, which brings together datasets from across the globe. By pooling resources, the team was able to analyze thousands of samples, far exceeding what any single study could achieve.
Importance of large-scale epigenetic datasets:
👉 Large cohorts are needed to detect subtle DNA methylation changes.
👉 Consortia enable data-sharing across countries and populations.
👉 Meta-analysis reduces noise and assesses reproducibility in human studies.
The study identified several sites across the genome where DNA methylation levels differed between children who were exclusively breastfed and those who were not. These differences were modest but consistent across multiple cohorts, strengthening confidence in their validity. Some of the identified sites were located within known genes, while others were in genomic regions with unclear functions.
The annotated genes with different methylation patterns—ALAD, FNBP4, and CHFR—are related to developmental and immune processes.
Importantly, the findings also revealed a dose–response relationship: longer durations of exclusive breastfeeding were associated with more pronounced methylation differences. This pattern suggests that the exposure itself may be influencing these molecular changes rather than unrelated factors.
“The longer the exclusive breastfeeding, the more of these markers appeared,” explained Caramaschi.
To confirm that these differences were not pre-existing, the researchers also analyzed samples collected at birth. They found no evidence of methylation differences at these sites prior to breastfeeding, supporting the idea that the observed changes emerge postnatally and are likely linked to feeding practices.
Key molecular differences linked to breastfeeding:
👉 Specific DNA methylation sites differ between feeding groups.
👉 No differences in methylation at these sites were observed at birth, supporting a postnatal origin.
👉 Effects scale with breastfeeding duration.
Breastfeeding may leave detectable, albeit subtle, epigenetic signatures in infants, offering a potential molecular explanation for its health benefits. Through large-scale meta-analysis, Caramaschi and colleagues have identified DNA methylation differences associated with breastfeeding duration, reinforcing the importance of early-life exposures.
However, interpreting these findings remains challenging due to confounding factors, such as socioeconomic status, and the complexity of human development. Future work will be crucial to determine whether these molecular changes translate into meaningful health outcomes.
Key takeaways:
👉 Epigenetic mechanisms provide a plausible link between breastfeeding and long-term health.
👉 Breastfeeding-associated methylation changes are small but robust across cohorts.
👉 Socioeconomic confounding remains a major challenge in observational studies.
👉 Future research must connect epigenetic changes to functional and clinical outcomes.
👉 Expanding diversity in study populations is critical for improving global relevance.
The study titled "Breastfeeding association with DNA methylation in the pregnancy and childhood epigenetics (PACE) consortium" was published in Clinical Epigenetics.
