FEEDING

When it comes to the infant microbiome, how a baby is fed is one of the most important factors of all. This page is about what the science tells us — about breastmilk, about formula, and about why it all matters so much. As always, this is information, not judgement. Every feeding journey is different, and whatever yours looks like, knowledge helps.

Breastmilk — a lot more than food

For a long time, breastmilk was seen as simply a source of nutrition for babies — a cocktail of fats, sugars and protein. We now know it is something far more extraordinary than that.

"Breastmilk is a perfect source of nutrition, a superfood that is actually worthy of the label…people said it's just a bag of chemicals. It's anything but that."
— Bruce German, University of California

"Breast milk is this amazing liquid that, through millions of years of evolution, has evolved to make babies healthy, particularly their immune systems."
— Dr Grace Aldrovandi, University of California, Los Angeles

Breastmilk is, in fact, a living substance. It contains bacteria, complex sugars that feed bacteria, immune components, and hundreds of bioactive molecules — all working together in ways scientists are still discovering.

Breastmilk as a source of microbes

Once thought to be sterile, breastmilk is now known to be teeming with beneficial bacteria. A baby consuming an average of 800ml of breastmilk per day receives somewhere between 100,000 and 10 million bacterial cells — every single day.

Research has found that around 30% of the beneficial bacteria in a baby's gut come directly from breastmilk, and a further 10% from the skin around the mother's nipple. These aren't random bacteria — they include exactly the kinds that a baby's gut needs most including Bifidobacterium and Lactobacillus species.
(Pannaraj et al, JAMA Pediatrics 2017)

Breastfed babies have higher levels of beneficial gut bacteria, lower rates of wheezing, and a lower risk of developing asthma as they grow older. And remarkably, any amount of breastmilk is beneficial — even feeding alongside formula, even for a short time.
(CHILD Cohort Study, Cell Host & Microbe 2020)

The magic of HMOs — breastmilk's secret weapon

Here's one of the most astonishing things about breastmilk: it contains over 200 different complex sugars called Human Milk Oligosaccharides (HMOs). They are the third most abundant ingredient in breastmilk after fat and lactose. And babies cannot digest them.

So why are they there?

They are there entirely for the microbes. HMOs are food for baby's gut bacteria — a prebiotic designed by evolution specifically to nourish the most beneficial bacteria in the infant gut. They also sometimes act as a kind of decoy system, mimicking the sugars on the gut wall that harmful bacteria attach to, so those bacteria bind to the HMOs and get flushed out instead of taking hold.

"The sugars act as a simple decoy. Cells along our intestines produce a variety of sugars that stick out like tree branches. Bacteria attach to these sugars, enabling them to hang out in the intestines like monkeys in a tree. Some of the sugars in milk are made to mimic these intestinal cell sugars so that the bacteria bind instead to the milk sugars and get flushed out into the baby's nappy. If a monkey grabs a decoy branch that is not connected to a tree, the monkey will fall to the ground." — milkgenomics.org

HMOs also directly support the gut lining, help calibrate the immune system, and may even help fight infections like Group B Streptococcus (GBS). Research has suggested that HMOs in breastmilk could one day replace antibiotics for some infant infections. (Vanderbilt University 2017)

Interestingly, HMOs even appear in amniotic fluid — meaning a baby may begin receiving their benefits before they are even born. (2018 study, Infants Are Exposed to Human Milk Oligosaccharides Already in utero)

The magic of HMOs and Breastmilk.

A great example of this is Bifidobacterium infantis...

Bifidobacterium infantis (B. infantis) and HMOs have an amazing relationship.

In healthy breastfed babies, Bifidobacterium species make up around 80% of all gut bacteria — they are absolutely dominant. And B. infantis has a unique cluster of 30 genes that no other bacterium has, allowing it to break down and use HMOs giving it an extraordinary advantage over every other microbe in the gut.

When B. infantis feeds on HMOs, something remarkable happens it:

Releases short-chain fatty acids that feed the gut cells themselves
Encourages the gut lining to seal up, keeping harmful bacteria out of the bloodstream
Produces anti-inflammatory molecules that help calibrate the immune system

But here's the crucial part — these benefits only happen when B. infantis feeds on breastmilk. If it gets lactose (as in formula) instead of HMOs, it survives, but it doesn't do any of this. The microbe's full potential is only unlocked by breastmilk.

"Over the course of human evolution, it is likely that significant selective pressure has shaped the composition of breast milk to provide the maximum advantage for the newborn… the ability of certain Bifidobacterium strains to efficiently use HMOs suggests that production of milk oligosaccharides by the mother may be a strategy to ensure the presence of this group of bacteria in the infant gut." (Marcobal & Sonnenburg, Stanford University)

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.

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 brainA 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 relationship was clear and consistent: the more breastmilk, the better the cognitive outcomes.

With one amusing exception — caffeine. Caffeine passes into breastmilk from the mother's diet through coffee, tea, chocolate and energy drinks, and the study found that caffeine metabolites in the infant gut were associated with slightly lower cognitive scores at age two, even in otherwise well-breastfed babies. This isn't a reason to stop breastfeeding — the overall cognitive benefits are considerable and far outweigh this finding — but it is a gentle nudge towards the existing guidance that moderate caffeine intake during breastfeeding is preferable. Current recommendations suggest keeping caffeine to around 200mg per day during breastfeeding, which is roughly one to two cups of coffee. So perhaps save the third cup for when baby is sleeping! ☕
(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 is the right choice for many families. For many families, formula is necessary, the right choice, or the only option. No guilt about the choice you/ a family made. So when we talk about formula, remember it's not personal. Knowledge is not judgement.

That said, the science does show real differences in what formula and breastmilk do to the infant microbiome — and it is worth understanding what those differences actually are, particularly given how misleading some formula marketing can be.

A word on formula marketing
Formula is not well regulated when it comes to health and nutrition claims. If you see a formula marketed with an added ingredient that promises a particular benefit, it is worth asking a simple question: if this ingredient genuinely worked as claimed, why don't all formulas contain it? The answer is usually that the evidence for the specific benefit isn't strong enough to require it — but it isn't strong enough to prohibit the claim either. This is a regulatory gap that formula companies have become very good at exploiting.
For independent, conflict-of-interest-free information on every infant formula available in the UK — including what each one actually contains and what claims can and cannot be substantiated — First Steps Nutrition Trust is an excellent resource: firststepsnutrition.org/parents-carers

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.

The truth about HMOs in formula
Some formula brands now include ingredients labelled as HMOs — Human Milk Oligosaccharides — and this has caused a great deal of confusion. Some parents have even assumed this means their formula contains actual breastmilk. It does not.

The HMOs in formula are laboratory-synthesised versions, manufactured to approximately 97% accuracy compared to their natural counterparts. Human breastmilk contains over 200 different HMO structures, each varying between mothers, changing across the course of lactation, and tailored in ways we don't yet fully understand to the individual mother and baby. Formula HMOs are standardised — typically just one or two specific structures — and have not been demonstrated to provide the same benefits as naturally occurring HMOs in breastmilk. If they had, all formulas would be required to contain them. As with other added ingredients, their inclusion is a marketing decision as much as a nutritional one.

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
When babies are born very prematurely and breastfeeding isn't yet possible/ not enough breastmilk is being produced, it's incredibly beneficial for babies to receive the benefits of human milk. Then 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.

Formula is not sterile — and safe preparation matters
Something many parents don't know is that powdered infant formula is not sterile. It can contain bacteria — including potentially harmful ones — which is why the way you make it up matters enormously.
Formula must always be made up using water that has been boiled and then cooled to no less than 70°C. This temperature is hot enough to kill harmful bacteria in the powder. Water that has been cooled too much, or formula made up in advance and stored incorrectly, poses a genuine risk. Formula preparation machines have also been found in independent testing to frequently not reach the required 70°C — so if you use one, it is worth checking the water temperature with a food thermometer.
Full guidance on making formula safely — including storage, sterilisation and preparation — can be found at First Steps Nutrition and on the NHS website.

A note on nipple creams
Nipple soreness is incredibly common in the early days of breastfeeding, and many mothers reach for nipple creams — most commonly lanolin-based products — as a first response. There is reasonable evidence that these can help with pain and promote moist wound healing in cases of cracked or damaged nipples.

From a microbiome perspective, though, it is worth knowing a little more about what happens on the nipple surface during breastfeeding.

The skin around the nipple and areola has its own microbiome — a community of beneficial bacteria that contributes to the bacteria baby receives during feeding, and which may even influence the bacterial community of breastmilk itself. Research has confirmed that around 10% of the bacteria in a baby's gut comes from the skin around the nipple. Applying a cream — particularly a thick occlusive one — creates a physical layer over that skin, which raises a reasonable question about whether it might affect the transfer of those bacteria to baby.
This is not yet definitively proven as a concern, and nipple creams remain an appropriate short-term option when there is genuine wound healing needed. But it is a reason to consider using them short-term only, and to think about the ingredients in the product you choose. Multi-ingredient creams with long ingredient lists may have a greater impact on the skin environment than simpler alternatives.

Alternatives to conventional lanolin-based nipple creams include:

Expressed breastmilk — rubbing a little onto the nipple and areola after feeding and allowing to air dry. This is the most microbiome-friendly option, free, and always available
Organic extra virgin olive oil — a simple, single-ingredient option with natural anti-inflammatory properties
Purslane or aloe vera preparations — both have shown effectiveness in clinical trials for nipple healing
Hydrogel pads — an alternative moist wound healing option without any ingredients applied to the skin

If nipple pain is persistent, it is always worth getting feeding support — pain is usually a sign that something about the latch or positioning can be improved, and fixing that is the most effective solution of all.

No guilt!

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.