Human Milk Oligosaccharides (HMOs) & SCFAs: How Breast Milk Shapes Gut Health

The Role of Human Milk Oligosaccharides (HMOs) and Short-Chain Fatty Acids (SCFAs) in Gut Health and Overall Wellbeing

Expert insights from FerFit Dietetics & Nutrition, Melbourne

Discover how HMOs and short-chain fatty acids support infant and adult gut health. Learn how breast milk components impact immunity, digestion, and long-term wellbeing. Evidence-based insights from a Melbourne dietitian.

Q1. What are Human Milk Oligosaccharides (HMOs)?

Human Milk Oligosaccharides (HMOs) are complex carbohydrates found only in human breast milk. They are the third largest solid component, after lactose and fat. Importantly, babies cannot digest HMOs. Instead, these compounds act as prebiotics, feeding beneficial bacteria such as Bifidobacteria and Lactobacilli that protect and strengthen the developing gut microbiome. HMOs come in 200+ varieties, each with unique structures and functions that influence immunity, digestion, and microbial diversity (1,2). Infants born today face higher risks of gut dysbiosis, allergies, and infections due to modern lifestyles, antibiotics, formula feeding, and reduced microbial exposure.

Without a strong early microbiome foundation, children may be more vulnerable to long-term issues like poor immunity, digestive symptoms, and metabolic dysregulation. HMOs provide infants with the beneficial bacteria and immune-supportive compounds essential for healthy gut development.

If parents understand the role of HMOs, they can make informed choices around feeding, supplementation, and early gut health. Support from a dietitian can help optimise maternal nutrition and infant feeding approaches.

Q2. What are Short-Chain Fatty Acids (SCFAs)? How Short-Chain Fatty Acids (SCFAs) gut health?

SCFAs, including butyrate, propionate, and acetate, are produced when beneficial gut bacteria ferment HMOs. These compounds are essential for gut integrity, immune regulation, and inflammation control (3,4).

SCFAs help to:

• Strengthen the gut barrier

• Provide energy to colon cells

• Reduce inflammation

• Influence metabolic and brain function

• Support overall immune resilience

Butyrate has particularly strong anti-inflammatory and gut-repair properties, making it central to digestive and immune health. Low-fibre diets, stress, medications, and poor microbiome diversity reduce SCFA production. Insufficient SCFA levels can contribute to impaired gut barrier function, higher infection risk, and chronic inflammation. Understanding the role of HMOs and SCFAs allows parents and clinicians to build healthier microbiome foundations early in life.

SCFAs support both infant and adult health. Improving maternal diet, breastfeeding support, and targeted supplementation can boost levels for better lifelong wellbeing.

Q3. Which HMOs are most important?

Two of the most researched HMOs-2'-fucosyllactose (2'FL) and lacto-N-neotetraose (LNnT) are strongly linked with increased SCFA production and improved microbial diversity (5,6).

These HMOs:

• Reduce harmful bacteria

• Promote beneficial microbial colonisation

• Support gut maturation

• Improve immune system development

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Q4. Do all mothers produce the same HMOs?

No. HMO composition varies significantly due to:

• Genetics (especially FUT2 “secretor status”) (5)

• Parity (women with more previous births often have higher HMO concentrations) (7)

• Geography

• Dietary patterns

Interestingly, a landmark study by McGuire et al. (2017) found that maternal diet does not directly correlate with HMO levels (8). Genetics appears to have the strongest influence.

Q5. How do HMOs and SCFAs influence long-term health?

HMOs continue supporting health beyond infancy through immune modulation and microbial imprinting. Evidence suggests HMOs can:

• Reduce the severity of respiratory and gastrointestinal infections (9)

• Support immune development

• Influence allergy risk

• Strengthen gut barrier integrity

• Reduce inflammation

• Support metabolic and cognitive outcomes

SCFAs, meanwhile, play a role in:

• IBS management

• IBD inflammation modulation

• Intestinal healing

• Gut-brain signalling

• Reducing oxidative stress (10)

Chronic gut inflammation is becoming increasingly common across all age groups.

Without intervention, these gut issues may progress into more serious digestive conditions and systemic inflammation. HMOs and SCFAs represent a promising therapeutic direction for improving gut health naturally. Early intervention, personalised dietary guidance, and microbiome-focused care can gently restore gut balance at any age.

Why FerFit Dietetics & Nutrition Is Different

FerFit provides expert, personalised support for:

• Infant and maternal nutrition

• Gut health optimisation

• Microbiome assessment and dietary planning

• Complex digestive disorders (IBS, IBD, SIBO)

• Women’s health and metabolic care

• NDIS-registered dietetic support

You receive:

• Evidence-based guidance

• Clear, practical strategies

• Holistic care focusing on physical and mental wellbeing

• Specialist expertise in gut, metabolic, and women's health

• A personalised plan that adapts as your needs change

If you want to improve gut health for yourself, your baby, or through pregnancy and breastfeeding professional guidance matters. Book a consultation with FerFit Dietetics & Nutrition today and start building a healthier microbiome foundation for long-term wellbeing.

References

1. Bode, L. (2012). Human milk oligosaccharides: every baby needs a sugar mama. Glycobiology, 22(9), 1147–1162.

2. Marcobal, A., et al. (2010). Consumption of human milk oligosaccharides by gut-related microbes. Journal of Agricultural and Food Chemistry, 58(9), 5334–5340.

3. Koh, A., et al. (2016). From dietary fiber to host physiology. Cell, 165(6), 1332–1345.

4. Hamer, H. M., et al. (2008). The role of butyrate on colonic function. Alimentary Pharmacology & Therapeutics, 27(2), 104–119.

5. Goehring, K. C., et al. (2014). Evidence for the presence of HMOs in infant circulation. PLOS ONE, 9(7), e101692.

6. Kumar, H., et al. (2015). Human milk microbiota and fatty acid profiles. Frontiers in Microbiology, 6, 485.

7. De Leoz, M. L., et al. (2015). Glycomics and microbiota correlation. Journal of Proteome Research, 14(1), 491–502.

8. McGuire, M. K., et al. (2017). Oligosaccharide concentrations in breast milk globally. American Journal of Clinical Nutrition, 105(5), 1086–1100.

9. Ruiz-Palacios, G. M., et al. (2014). HMOs inhibit pathogen binding. Journal of Biological Chemistry, 278(16), 14112–14120.

10. Liu, C., et al. (2021). SCFAs in intestinal barrier function and inflammation. Pharmacological Research, 165, 105420.