Published in Nature, the study followed 714 mother–infant pairs from pregnancy through the first year after birth to track how the infant gut microbiome develops and where its bacterial strains originate.
Strains more abundant in the maternal gut were more likely to be passed on and tended to persist longer in infants. Delivery and feeding mode also strongly influenced infant gut microbiome development.
The researchers additionally found an association between the maternal gut microbiome and infant eczema, although they said the result needs to be replicated and the underlying mechanism remains unclear.
“The clearest takeaway is that the maternal gut microbiome is the main reservoir seeding the infant gut, rather than the vaginal or breast milk microbiomes,” a Nestlé corporate spokesperson told NutraIngredients.
“The study also suggests that this transmission is quantitative: maternally derived strains are more likely to be in higher abundance in infants and persist longer,” the spokesperson added.
Maternal gut as main reservoir
The researchers analyzed 4,526 fecal samples from mothers and infants in the Dutch Lifelines NEXT cohort, beginning at 12 weeks of pregnancy and continuing until 1 year postpartum.
They also used vaginal and breast milk samples from smaller groups of mothers to compare possible sources of bacteria found in the infant gut.
“Our analysis further highlighted the critical role of the maternal gut microbiome in seeding and shaping the infant gut microbiome,” the researchers wrote.
They reported that a substantial proportion of strains found in infants were identical to maternal gut strains, while transmission from the vaginal and breast milk microbiomes occurred less frequently. Higher abundance of a species in the mother also increased its likelihood of transmission.
Delivery and feeding practices were associated with mother–infant strain sharing and remained the main factors shaping the infant gut microbiome throughout the first year.
“The findings point researchers further upstream, towards understanding and potentially supporting the maternal gut microbiome before and during pregnancy,” the Nestlé spokesperson said.
“At the same time, the study confirms that mode of birth and feeding remain major influences on an infant’s early microbiome development.”
Maternal diet was among the factors associated with the maternal microbiome, along with infections, pre-pregnancy smoking and BMI.
Nestlé said further research is needed before the results can be translated into maternal nutrition interventions.
“The study supports a ‘maternal-first’ approach as a promising direction for future research, but the evidence is not yet sufficient,” the spokesperson said.
“It shows a clear biological link between the maternal and infant gut microbiomes, but it does not demonstrate that a maternal supplement will improve an infant’s health...that possibility now needs to be tested in well-controlled clinical trials,” the spokesperson added.
Link with infant eczema
The study also found that mothers of infants who developed eczema had lower gut microbial diversity.
The association remained significant after accounting for maternal smoking history and family history of allergic disease, and maternal microbiome composition around the time of birth showed some ability to predict which infants developed eczema.
“While the underlying mechanism remains unclear, previous research suggests that the maternal gut microbiome may influence the developing fetal immune system through microbial metabolites during pregnancy or direct transfer of antibodies or cytokines,” the researchers wrote.
They noted that this was the first report of the association and called for replication in more diverse populations and further research into possible causal pathways.
“This is a promising and novel finding, but it is still at an early research stage and is not ready for use as a clinical tool,” the Nestlé spokesperson said.
Nestlé said the next step is to identify which maternal strains transfer reliably and persist in infants and to better understand how maternal diet affects the process.
“The highest-priority next step is to translate these findings into clinical research...identifying maternal strains that transfer reliably and persist in the infant gut, and understanding how maternal diet influences this process, are both important,” the spokesperson said.
“Ultimately, however, targeted nutritional approaches will need to be tested in well-designed clinical trials that measure not only changes in the microbiome but also meaningful infant health outcomes,” they added.
Source: Nature. doi: 10.1038/s41586-026-10922-9 “Maternal influences on infant gut microbiome and health”. Authors: Sinha, T. et al.
