Using HPLC to Map the Impact of Breast Milk Sugars on Infant Gut Health

Healthy bacteria in a baby's digestive system are essential for their growth and long-term health. While we know that oligosaccharides (HMOs), the special sugars in breast milk, help these good bacteria thrive, we still don't fully understand exactly how they work, especially after a baby has stopped breastfeeding. This lack of understanding has inspired a joint study conducted by researchers at The University of Turku, The University of Helsinki (both in Finland) and the University of California San Diego (La Jolla, California) which aimed to deepen the understanding of how HMOs associate with the gut microbiota composition at 3 months and at 13 months of age. Additionally, they assessed the role of HMOs as microbiome-rebalancing agents in cesarean delivered infants. By using high-performance liquid chromatography (HPLC) with fluorescent detection, they were able to determine exactly which bacteria were living in the babies' digestive system, while also measuring the amounts of a variety of healthy sugars found in the breast milk. A paper based on their research was published in The American Journal of Clinical Medicine.¹

Why are Sugars in Breast Milk So Important?

The way bacteria first settle into a baby's digestive system is very important, as it sets the stage for their gut health down the road, ultimately impacting their overall growth and well-being. Because of this, it is crucial to support the development of a healthy gut environment and to manage things that might throw it off balance, such as being born via C-section. Breast milk—especially because of the unique, healthy sugars it contains—plays a major role in building up good gut bacteria and helping to restore balance if it ever gets disrupted.^2-4 There are roughly 200 different kinds of these healthy sugars found in breast milk. Because they come in so many different shapes, they each have their own specific jobs in the body. The exact mix and amount of these sugars is completely unique to each mother—based heavily on her genetics—and naturally changes over time as her baby grows.⁵

How Was This Research Conducted?

For this study, the researchers studied over 500 babies by analyzing their stool samples at 3 months and 13 months old, along with breast milk samples taken at 3 months. Using HPLC with fluorescent detection, they identified the specific types of bacteria living in the babies' digestive systems and measured the levels of 19 different beneficial sugars within the breast milk. They then used statistical models to analyze how these specific breast milk sugars influenced the variety and groupings of bacteria in the babies' guts over time.¹

What Information Did the Research Yield?

Researchers discovered that these special breast milk sugars directly influence the types and variety of healthy bacteria in a baby's digestive system at both 3 and 13 months old, specifically:

• Different sugars work at different ages: Two specific breast milk sugars play a major role in shaping the baby's gut at 3 months. However, by the time the baby is 13 months old, a completely different breast milk sugar takes over as the main influencer.
• Mom’s genetics matter early on: A mother's natural genetics—specifically those that determine the exact makeup of the sugars in her milk—heavily impact how diverse her baby's gut bacteria is at 3 months. This maternal influence fades as the baby gets older.
• Breast milk helps C-section babies: Babies born via C-section usually have a different makeup of gut bacteria compared to those born vaginally. While no single sugar could entirely "fix" this imbalance, breast milk from mothers with a specific genetic profile helped lessen the impact of a C-section on the baby's developing gut.¹

“Our study,” write the authors of the paper,¹ “demonstrates age-dependent and structure-specific associations between HMOs and infant gut microbiota, extending beyond breastfeeding.”

The researchers noted a few imitations regarding their study:

• There was a lack of reliable details on what else the babies were eating or drinking besides breast milk.
• The researchers only looked at specific snapshots in time rather than tracking the babies continuously, and they only tested each mother's breast milk once.
• Because they could only include people who had samples available, the group might not have been a perfect representation of all mothers and babies. They also didn't test for a specific genetic trait in the mothers.
• There were too few babies born via C-section in the study to draw strong conclusions about that specific group.
• The specific type of DNA test they used to identify the gut bacteria wasn't detailed enough to show exactly how the bacteria were using the breast milk sugars.¹

Read More on Similar Topics
Characterizing Oligosaccharides in Breast Milk with Liquid Chromatography

References

1. Ovaska, M.; Tamminen, M.; Lahdenperä, M. et al. The Role of Human Milk Oligosaccharides in Shaping and Restoring Infant Gut Microbiota: Population-Based Cohort Study. Am J Clin Nutr. 2026, 16, 101318. DOI: 10.1016/j.ajcnut.2026.101318
2. Rautava, S.; Luoto, R.; Salminen, S. et al. Microbial Contact During Pregnancy, Intestinal Colonization and Human Disease. Nat Rev Gastroenterol Hepatol. 2012, 9 (10), 565-576. DOI: 10.1038/nrgastro.2012.144
3. Shao, Y.; Forster, S. C.; Tsaliki, E. et al. Stunted Microbiota and Opportunistic Pathogen Colonization in Caesarean-Section Birth. Nature 2019, 574 (7776), 117-121. DOI: 10.1038/s41586-019-1560-1
4. Dai, D. L. Y.; Petersen, C.; Hoskinson, C. et al. Breastfeeding Enrichment of B. longum subsp. infantis Mitigates the Effect of Antibiotics on the Microbiota and Childhood Asthma Risk. Med 2023, 4 (2), 92-112.e5. DOI: 10.1016/j.medj.2022.12.002
5. Bode, L. Human Milk Oligosaccharides: Every Baby Needs a Sugar Mama. Glycobiology 2012, 22 (9), 1147-1162. DOI: 10.1093/glycob/cws074