A study of 714 mother-infant pairs found that a mother’s gut is a major source of her baby’s gut bacteria, while birth and feeding strongly shape microbiome development.
A large Nature study suggests that a mother’s gut microbiome may play a major role in establishing her baby’s gut bacteria and could even help identify infants at higher risk of eczema. (1✔ ✔Trusted Source
Maternal influences on infant gut microbiome and health
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The study also found that delivery method and feeding were the strongest factors influencing how the infant gut microbiome developed during the first year of life.
The research analyzed 4,526 longitudinal stool samples from 714 mother-infant pairs in the Dutch Lifelines NEXT birth cohort.
Researchers combined microbiome data with 474 clinical, dietary, and environmental variables and also performed detailed sequencing of breast milk and vaginal microbiomes. (1✔ ✔Trusted Source
Maternal influences on infant gut microbiome and health
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What Did the Study Reveal About Mother-to-Baby Microbiome Transfer?
The researchers found that the maternal gut was the major reservoir of bacterial strains found in the infant gut. Although bacteria from breast milk and the vaginal microbiome could occasionally be transmitted, gut-to-gut transmission appeared to be much more prominent.
The scale of transmission was substantial. Across 81 bacterial species that could be assessed in more than 20 mother-infant pairs, researchers identified 7,345 strain-sharing events across 15,462 comparisons.
All of the species examined showed at least one instance of strain sharing between a mother and her infant.
The sharing was strongest early in life. The median proportion of infant bacterial species sharing the same strain with the mother was 65% at two weeks and one month, falling to 25% by 12 months. Researchers suggest that this decline may occur as infants acquire bacteria from their wider environment and other social contacts.
Importantly, the amount of a particular bacterial species in the mother’s gut also mattered. Higher maternal abundance increased the likelihood that the strain would be transmitted to the infant, while transmitted strains were more likely to persist during infancy.
Some of these strains carried genes involved in carbohydrate metabolism, coenzyme metabolism, and immune-related functions.
The researchers also found that the vaginal and breast milk microbiomes were not the dominant sources of infant gut strains. However, they did identify specific examples of possible vaginal transmission.
For instance, the same Bifidobacterium breve strain was detected in the vaginal microbiome and infant gut in five mothers for whom the strain could be reconstructed, providing evidence of transmission around birth in those cases.
These findings build on earlier research showing that birth mode, breastfeeding, and other early-life exposures influence infant microbiome development, but the new study provides a much broader, strain-level view of how maternal and infant microbiomes are connected.
The authors specifically note that previous work had not fully established the maternal sources and routes responsible for this transmission.
Could a Mother’s Gut Microbiome Predict Eczema in Her Baby?
One of the most notable findings was the link between the maternal gut microbiome and infant eczema.
The study found that mothers whose infants developed eczema during the first year had lower gut microbial alpha diversity.
This association remained significant after researchers accounted for maternal smoking history and family history of allergic disease. Maternal alpha diversity was the only one of these factors that remained significantly associated with infant eczema in the multivariable analysis.
The researchers then tested whether information from the mother’s gut microbiome could actually help predict eczema. Three models were evaluated using maternal microbiome characteristics measured around birth:
- Bacterial composition: AUC 0.74
- Functional microbial pathways: AUC 0.73
- Microbial alpha diversity: AUC 0.68
Among the bacterial features contributing to the prediction model, Dialister invisus ranked highest and was associated with a lower risk of eczema in infants.
However, the findings show an association and predictive potential, not proof that the maternal microbiome causes eczema. The mechanisms behind the relationship still need to be established.
The study also found that maternal gut diversity was associated with several aspects of maternal health and lifestyle, including pre-pregnancy BMI, smoking, diet, infections, and other health characteristics. This suggests that the maternal microbiome may reflect a combination of biological and environmental influences rather than acting as an isolated factor.
Why Do Birth and Feeding Matter So Much for the Infant Microbiome?
Although maternal bacteria played an important role in transmission, the researchers found that delivery mode and feeding mode were the strongest biological factors shaping the infant gut microbiome over time.
Infants born vaginally showed greater representation of certain Bacteroides bacteria, while babies born by caesarean section showed reduced Bacteroides colonisation that remained detectable through the first year. Delivery mode emerged as the strongest biological factor associated with two of the major microbiome patterns identified by the researchers.
Feeding was another major influence. Breastfeeding and formula feeding were associated with different bacterial and metabolic profiles, although these differences became less pronounced after solid foods were introduced.
The study also found differences in microbial pathways linked to carbohydrate metabolism and gut-brain-related metabolic potential according to feeding mode.
Interestingly, the researchers found that the microbiome at two weeks of age did not reliably predict its composition at six, nine, or 12 months. This suggests that early colonization is not a fixed blueprint for the infant’s later microbiome. Instead, the microbial community continues to change substantially throughout infancy.
The study also found that maternal diet, pregnancy infections, pre-pregnancy smoking, parity, and infant diet were associated with aspects of microbiome development.
After accounting for delivery and feeding, several dietary factors continued to show associations with microbial pathways, highlighting the potential contribution of maternal and infant nutrition.
Overall, the findings suggest that a baby’s microbiome is built through a constantly changing interaction between maternal microbes, birth, feeding, diet, and other environmental exposures.
The research provides a stronger understanding of this process, but it does not mean that altering a mother’s microbiome can currently prevent eczema or other infant diseases. Further studies will be needed to determine whether these microbial associations can eventually be translated into preventive strategies.
Reference:
- Nature. Maternal influences on infant gut microbiome and health
(https://www.nature.com/articles/s41586-026-10922-9)
Source-Medindia