Where does a baby’s first gut microbiome come from?

Researchers have now followed hundreds of mothers and babies from pregnancy through the first year of life—and the answer appears to involve rather more of Mum’s gut than previously appreciated.

In a large Dutch study published in Nature, the maternal gut microbiome emerged as the main reservoir of bacterial strains shared with infants. Direct strain sharing from breast milk and the vaginal microbiome occurred, but much less often.

Delivery method and feeding also influenced how the infant microbiome developed. Researchers additionally found an association between features of the mother’s gut microbiome and eczema during the baby’s first year.

That eczema finding is fascinating, but it is observational, reported for the first time and requires replication. The study did not give mothers probiotics, did not deliberately alter anyone’s microbiome and did not prove that taking a probiotic during pregnancy prevents eczema.

The microbiome may be a family hand-me-down. It is not yet a prescription wearing a baby bonnet.

How was the maternal gut microbiome studied?

The study used data from Lifelines NEXT, a long-term birth cohort in the northern Netherlands.

Researchers analysed 4,526 faecal samples from 714 mother–infant pairs. Samples were collected from 12 weeks of pregnancy until the baby reached one year old.

The researchers also considered 474 clinical, lifestyle, dietary and environmental variables. These included pregnancy factors, delivery circumstances, feeding, antibiotic exposure, maternal diet, smoking history, infections and infant health.

For smaller groups of mothers, the investigators performed ultra-deep sequencing of:

• 82 vaginal microbiome samples collected close to birth; and
• 90 breast-milk microbiome samples collected during the first month.

This allowed the team to compare bacterial strains found in the baby’s gut with strains detected at several maternal body sites.

This was not a supplement trial. It was a detailed observation of what happened naturally across pregnancy, birth and infancy.

There was also an impressive quantity of stool collection. Nothing says cutting-edge science quite like 4,526 carefully labelled poo samples.

The maternal gut microbiome was the main bacterial reservoir

The central finding was that the maternal gut microbiome contained many of the same bacterial strains later detected in the infant gut.

Researchers did not merely identify the same bacterial species. They used strain-level analysis to look for closely matching genetic versions of those bacteria.

Across 81 sufficiently common bacterial species, the researchers detected thousands of mother–infant strain-sharing events. In the earliest period, a substantial proportion of bacterial strains detected in babies matched strains found in their mothers.

Higher abundance of a particular bacterium in the mother’s gut was associated with a greater likelihood of that strain being shared with her baby. Several maternally shared strains also appeared more likely to persist during infancy.

This makes the maternal gut microbiome look less like a passive collection of microscopic passengers and more like an important starter library for the infant gut ecosystem.

It does not, however, establish one simple physical route of transfer for every organism. Families share close contact, skin, hands, food environments and rather a lot of bodily reality that parenting books occasionally describe with suspicious delicacy.

What about the vaginal microbiome?

The researchers found fewer shared species between maternal vaginal samples and infant gut samples than between maternal and infant gut samples.

Some vaginal-to-infant strain transmission still occurred. A notable example involved Bifidobacterium breve, where matching strains were found in the infants of the small number of mothers whose vaginal samples contained a reconstructable strain.

The correct conclusion is therefore not “the vaginal microbiome does nothing”. It is that, in this cohort and with these methods, the mother’s gut appeared to be the larger reservoir of strains that became established in the infant gut.

Microbiology rarely enjoys an all-or-nothing answer. It prefers to leave several doors open and then hide the keys in a supplementary table.

Does this mean breast milk is unimportant?

Absolutely not.

The study found that direct sharing of dominant bacterial strains from breast milk to the infant gut was comparatively infrequent. That answers one narrow question about the source of matching strains.

It does not place breast milk in competition with the maternal gut microbiome. These are different biological influences doing different jobs.

It also does not measure the total value of breastfeeding.

Breast milk supplies nutrition, immune components and human milk oligosaccharides that can feed selected infant gut bacteria. Feeding mode was one of the strongest influences on infant microbiome development in this study.

Breast milk has therefore not been fired. It simply turned out not to be the main warehouse from which most shared bacterial strains were dispatched.

Families who cannot breastfeed or who use formula should not interpret microbiome differences as evidence of inferior parenting. Feeding decisions are shaped by health, milk supply, medicines, work, access and family circumstances. A microbial pattern is not a moral scorecard.

How did strain sharing change during the first year?

Mother–infant gut strain sharing was highest early in life.

The median proportion of shared strains was approximately 65% at two weeks and one month, falling to about 25% by 12 months.

That decline makes biological sense. As babies grow, they encounter:

• other family members;
• food;
• pets;
• different environments;
• medicines;
• illnesses; and
• an impressive range of objects they apparently need to lick.

The early maternal gut microbiome contribution was therefore important, but it did not permanently dictate the baby’s final microbial community.

In fact, the microbiome pattern seen at two weeks did not reliably determine what the child’s microbiome would look like later in the first year.

A baby’s microbiome is a developing ecosystem, not a tattoo applied at birth.

Delivery method influenced microbiome development

Delivery method was one of the strongest biological factors associated with infant gut microbiome patterns.

Infants born by caesarean section and those born vaginally showed differences in several bacterial groups, including Bacteroides. Some differences persisted across the first year.

This does not mean caesarean birth is “bad for the microbiome”. Caesareans are often medically necessary and can be life-saving for mothers and babies.

The study also does not establish that parents should attempt vaginal seeding after caesarean birth. Deliberately transferring vaginal fluids can expose a newborn to harmful organisms and should not be improvised from instructions discovered online.

Delivery decisions belong with the mother and maternity-care team—not with a bacterium wearing a cape on social media.

Feeding influenced which microbes and functions developed

Feeding mode was another major influence on the infant microbiome and its functional potential.

Breastfeeding was associated with bacterial functions involved in using human milk glycans and other complex carbohydrates. As complementary foods were introduced, the infant microbiome gained organisms and functions suited to a broader diet.

By 12 months, bacteria capable of fermenting a wider range of carbohydrates had become more prominent.

This is normal development: first milk, then food, then the glorious day when a lovingly prepared meal is rejected in favour of a floor crumb of uncertain origin.

What did the study find about infant eczema?

The most headline-friendly result was an association between the maternal gut microbiome and eczema during the infant’s first year.

Mothers whose babies developed eczema had lower average gut microbial diversity. The association remained statistically significant in an analysis that included maternal smoking history and a family history of allergic disease.

The researchers also built experimental prediction models using maternal bacterial composition, microbial pathways and diversity. These models performed better than chance, but they are research tools—not clinical eczema tests ready for the antenatal clinic.

Most importantly, this was the first report of this particular association. The authors themselves called for replication in other populations and investigation of possible causal pathways.

How strong is the evidence?

The study has substantial strengths. It followed mothers and babies repeatedly, used strain-level metagenomic analysis and combined microbiome findings with hundreds of health and exposure variables.

However, several limitations matter when interpreting the maternal gut microbiome findings:

• This was an observational cohort, so it can identify associations but cannot prove cause and effect.
• The participants formed a comparatively healthy Dutch cohort, and the results may differ in more diverse or higher-risk populations.
• The breast-milk and vaginal comparisons involved much smaller subsets than the main gut analysis.
• The strain-analysis method focused on dominant strains and may have missed less abundant secondary strains.
• The precise physical and biological routes of mother-to-infant transfer were not established.
• The eczema association was reported for the first time and has not yet been independently replicated.
• Prediction-model performance does not make the maternal microbiome a diagnostic test.

The Lifelines NEXT cohort received funding from several public and private sources, including Philips and Société des Produits Nestlé. Two authors reported Nestlé affiliations, and one senior author reported speaker fees from Nestlé and AVOLA. The remaining authors declared no competing interests.

Commercial involvement does not automatically invalidate the work. It is still worth disclosing openly before anyone tries to hide it behind the cot.

Association is not prevention

The eczema result does not show that a less diverse maternal gut microbiome caused eczema.

It also does not show that increasing microbial diversity would prevent eczema.

Observational associations may be influenced by factors including:

• maternal genetics;
• infant genetics;
• shared family environment;
• diet;
• medicines and antibiotics;
• smoking exposure;
• maternal health;
• delivery and feeding circumstances; and
• other factors that were not measured completely.

Statistical adjustment can reduce some confounding. It cannot turn an observational cohort into a randomised prevention trial while nobody is looking.

This study therefore does not prove that taking probiotics during pregnancy prevents infant eczema. It did not test a probiotic product, strain, dose or treatment schedule.

Any headline that jumps directly from “maternal microbiome associated with eczema” to “take this probiotic to protect your baby’s skin” has skipped several flights of scientific stairs.

Can changing the maternal gut microbiome prevent eczema?

Probiotics have been studied during pregnancy and early infancy for possible allergy and eczema prevention. Results have varied according to the strains, combinations, timing, participants and outcomes examined.

Some reviews have found small preventive signals for selected regimens, while clinical recommendations remain cautious or inconsistent because no universal strain and schedule has been established.

The new Nature paper does not settle that broader question. It strengthens our understanding of the maternal gut microbiome, but it cannot be used as evidence for a particular probiotic product.

Pregnant women should discuss medicines and supplements with their doctor, midwife or pharmacist, particularly when they have a high-risk pregnancy, serious illness or weakened immune function.

Sensible ways to support maternal gut health

There is no proven recipe for manufacturing a “perfect” maternal gut microbiome. Microbiomes differ naturally, and greater diversity is not automatically better in every body site or every situation.

General maternal health can be supported with familiar, decidedly unmagical habits:

• eat a varied diet that includes vegetables, fruit, legumes, whole grains, nuts and seeds where suitable;
• increase fibre gradually if current intake is low;
• drink adequate fluids;
• include suitable fermented foods if they are tolerated;
• remain physically active within pregnancy-care recommendations;
• avoid smoking and alcohol during pregnancy;
• use antibiotics when they are genuinely needed and exactly as prescribed; and
• review supplements with a healthcare professional.

Please do not begin a heroic pregnancy cleanse. Your liver, kidneys and placenta already have job descriptions, and none requested assistance from celery foam.

Should babies be given probiotics?

This study does not support routine probiotic supplementation for every newborn.

Infant probiotic decisions depend on age, gestational age, health, feeding, the exact strain and the reason for use. Premature, medically fragile or immunocompromised infants require particular caution because serious infections caused by probiotic organisms have occasionally occurred.

Do not give a newborn a probiotic simply because the mother–infant microbiome connection sounds appealing. Discuss it with the baby’s doctor or an appropriately qualified healthcare professional.

Newborns are not small adults with better cheeks.

Where do Noster ProBiotics fit?

Noster ProBiotics are refrigerated, live-culture probiotics intended to support everyday gut and microbial balance.

Noster ProBiotics were not tested in this study. The research cannot be used to claim that Noster changes an infant’s microbiome, prevents eczema or produces the strain-sharing patterns observed in the Dutch cohort.

A pregnant or breastfeeding woman considering a probiotic should discuss her individual circumstances with her doctor, midwife or pharmacist. An infant should receive a probiotic only with appropriate professional guidance.

The study matters to Noster because it demonstrates the significance of the maternal gut microbiome during early microbial development. It gives us excellent biology—not permission to borrow the finding and glue “prevents eczema” onto a bottle.

For adults seeking general digestive and microbial support, you can learn more about Noster Live Culture Probiotic Capsules.

Pop it in the fridge. Take it daily. Keep pregnancy and infant claims on a very short scientific leash.

When infant eczema needs medical attention

Baby rashes have many possible causes and should not automatically be diagnosed as eczema from a photograph or social-media post.

Arrange an assessment if your baby develops a persistent, itchy or recurring rash. Seek prompt medical advice if the skin:

• becomes blistered, crusted or leaks fluid;
• develops pus-filled spots;
• becomes painful, swollen or warm;
• suddenly worsens or spreads;
• bleeds extensively; or
• is accompanied by fever, poor feeding or an unwell baby.

Probiotics should not replace moisturisers, prescribed treatment, allergy assessment or medical care.

Frequently asked questions

Is a baby’s gut microbiome inherited from the mother?

A baby does not genetically inherit the microbiome in the same way as eye colour. However, this study found that many early infant gut strains closely matched strains in the mother’s gut. Microbes are also acquired from feeding, family contact, food and the wider environment.

Was the vaginal microbiome unimportant?

No. Some strain transmission from the vaginal microbiome occurred, and delivery mode influenced infant gut development. The study found that the maternal gut was the larger reservoir of shared dominant strains; it did not show that the vaginal microbiome had no role.

Did breast milk contribute no bacteria?

Some breast-milk-to-infant strain sharing was detected, but it occurred less frequently than maternal-gut-to-infant sharing. Breast milk also influences the infant microbiome through nutrition, immune components and human milk oligosaccharides. Its importance cannot be judged only by direct bacterial strain transfer.

Does caesarean birth damage a baby’s microbiome permanently?

No. Delivery mode was associated with differences, but the microbiome continued changing throughout infancy. Caesarean births may be medically necessary and life-saving. This study does not justify avoiding a recommended caesarean or attempting unapproved microbial-transfer procedures. Elective Caesarean births are not recommended as the travel down the birth canal does provide the baby with its first microbiome.

Does the maternal microbiome cause infant eczema?

The study found an association between maternal gut microbial features and infant eczema. It did not establish causation. The finding was reported for the first time and needs replication in diverse populations.

Should I take probiotics during pregnancy to prevent eczema?

This study provides no basis for doing so because it did not test probiotics. Research on pregnancy probiotics and eczema prevention is mixed and strain-specific. Discuss the possible benefits and risks of any supplement with your pregnancy-care professional.

Was Noster ProBiotics studied?

No. Noster ProBiotics were not used in this observational study, and its results cannot be attributed to the Noster formulation.

The friendly pharmacist’s final word

This impressive study places the maternal gut microbiome near the centre of early infant gut development.

Many bacterial strains found in babies matched strains in their mothers’ guts, particularly during the earliest months. Delivery and feeding then helped shape the developing microbial community as the baby encountered a wider world.

The eczema association deserves serious follow-up, but it does not prove cause and effect—and it certainly does not prove that a pregnancy probiotic prevents eczema.

The practical message is reassuringly ordinary: support maternal health, use medicines and supplements sensibly, feed babies according to sound healthcare guidance and avoid turning microbiome findings into another competitive event for exhausted mothers.

Mum contributes a remarkable microbial starting point. The baby, family, food, and environment continue to write the story.

Resources

• Nature: Maternal influences on infant gut microbiome and health
• World Health Organization: Infant and young-child feeding
• NIAID: Eczema-prevention research
• American Academy of Dermatology: Probiotics and childhood eczema
• NCCIH: Probiotic usefulness and safety
• NHS Inform: Atopic eczema and warning signs

This article provides general educational information and does not replace individual advice from your doctor, midwife, pharmacist, paediatrician or other qualified healthcare professional.