ALL ABOUT HMOs

Every mother's milk is different

No two mothers produce identical breastmilk. HMO levels and composition vary between women, by geography, by stage of lactation, and even by the time of day.

One fascinating difference comes down to a mother's secretor status — whether she carries a functioning FUT2 gene. Mothers who do (called secretors) produce a richer, more protective set of milk sugars. Those who don't (non-secretors) produce a slightly different profile — though interestingly, non-secretors appear to have some advantages of their own, including greater resistance to certain viruses like HIV and Norovirus.

The microbiome of breastmilk itself is also shaped by how a mother gave birth, her own diet, and her weight — meaning every mother's milk is truly personalised to her circumstances.

A note on pumping

If you are expressing and bottle-feeding breastmilk, it is still hugely beneficial — but it is worth knowing that some of the bacterial benefits may be slightly reduced compared to feeding directly from the breast.

Research from the CHILD Cohort Study found that certain bacteria co-occur in mothers' milk and their babies' stool when babies feed directly, but this co-occurrence is reduced when babies receive pumped milk. Separate research found that the pumping equipment itself can influence the bacteria in expressed milk.

This is not a reason not to pump — pumped breastmilk is still vastly beneficial — but if direct feeding is possible, even some of the time, it adds an extra dimension. (Fehr et al, CHILD Cohort Study 2020; Reyes et al 2021)

Breastmilk and the brain

Emerging research is finding links between breastmilk and neurodevelopment too. A 2023 study from the University of Colorado found that breastmilk — even when given partially alongside formula — changes the chemical makeup of the infant gut in ways that positively influence brain development.

Babies who received more breastmilk had higher levels of beneficial gut metabolites, and those metabolites were associated with better scores on cognitive tests at age two. The more breastmilk, the better the cognitive outcomes — with one amusing exception (caffeine). (Chalifour et al, npj Metabolic Health and Disease 2023)

What about breastmilk's immune properties?

Breastmilk also contains immune components that actively shape the gut environment. Research from the University of Birmingham found that the proportion of regulatory T cells — key immune cells — was nearly twice as high in exclusively breastfed newborns as in formula-fed ones. Regulatory T cells are important for helping the immune system learn tolerance and avoid overreaction.

And in a fascinating discovery, scientists found that when baby's saliva mixes with breastmilk during feeding, enzymes in the saliva interact with the milk to produce hydrogen peroxide — a mild natural antiseptic. This in turn activates antimicrobial enzymes in the milk that target harmful bacteria but leave beneficial ones unharmed. This reaction only happens when the milk is fed directly from the breast — another extraordinary piece of the breastfeeding puzzle. (Sweeney et al 2018)

What about formula?

We want to be very clear here: formula saves lives, and there is no guilt in this. For many families, formula is necessary, the right choice, or the only option — and a baby fed on formula is loved and nourished. Knowledge is not judgement.

That said, the science does show real differences in what formula and breastmilk do to the infant microbiome.

Formula-fed babies are exposed to a different set of carbohydrates, bacteria and nutrients, and this leads to different patterns of gut colonisation. The oligosaccharides added to infant formula are structurally different from HMOs found in human milk, and research suggests they are unlikely to fully replicate HMOs' specific effects on the gut.

Even relatively small amounts of formula supplementation in a breastfed baby will shift the gut microbiome towards a more formula-fed pattern. And formula-fed babies tend to have:

Lower levels of Bifidobacterium and Lactobacillus
Higher levels of opportunistic bacteria including Staphylococcus aureus, Klebsiella pneumoniae, and Clostridioides difficile
Higher levels of antibiotic resistance genes in their gut bacteria — 69% higher in one 2022 study (Pärnänen et al, American Journal of Clinical Nutrition 2022)

A 2024 randomised trial comparing breastfeeding with four different formula types — including formulas supplemented with Bifidobacterium, galacto-oligosaccharides (GOS), or both — found that none of the formulas were able to fully recreate the breastmilk-related microbial environment. Interestingly, GOS-supplemented formula was more effective at sustaining Bifidobacterium levels than formula that contained Bifidobacterium directly. (Heppner et al, Cell Host & Microbe 2024)

The same research also made a completely unexpected discovery: the infant gut microbiome has its own circadian rhythm, detectable as early as two weeks after birth. The bacteria in baby's gut fluctuate in a 24-hour cycle — and this rhythm appears to be intrinsic to the bacteria themselves, not driven by light or feeding times alone. What this means for infant health is still being explored.

The longer-term picture

By around six months, the differences in gut microbiome between breastfed and formula-fed babies begin to narrow. But the early weeks and months matter enormously, because it is during this period that the immune system is being trained. As we say elsewhere on this site: we need the right bacteria, at the right time, and in the right order.

The biggest shift in the gut microbiome happens at weaning — when solid foods are introduced, the microbiome begins its journey towards an adult-like state. But breastfed babies continue to receive microbial protection and HMO benefits for as long as breastfeeding continues.

Donor milk

If breastfeeding isn't possible but you would like your baby to receive the benefits of human milk, donor milk from a milk bank is an option worth exploring. While donor milk is pasteurised (which reduces but doesn't eliminate its microbial content), it still provides many of breastmilk's remarkable benefits. Ask your midwife or health visitor about what is available in your area.

No guilt — ever

We will say it again: no guilt. The evidence about breastmilk is not a weapon, it is information. Knowing what breastmilk does is empowering — it helps us support breastfeeding better, improve formula, and understand more about what every baby needs.

If you breastfed for a day, a week, six months or two years — that mattered. If formula was what your baby needed — that was the right choice. And if you are still figuring it out — you are doing brilliantly.

Page last updated: 2025 This site is not a medical site and content is for information only. It should not be taken as medical advice. Always discuss your personal situation with your healthcare provider.