Written by: Lauren Milligan Newmark, Ph.D. | Issue # 135 | 2026
- A study of 714 healthy Dutch mothers and their babies found that the mother’s gut was the largest source of colonizing bacteria for the infant’s gut microbiome.
- Strain-sharing from the vaginal and breast milk microbiomes was less frequent, although both feeding mode and delivery mode influenced the functional development of the infant’s gut microbiome.
- Breast milk was not the main route for transmitting these microbes from mothers to infants, but milk plays an important role in infant gut development by feeding beneficial bacteria with complex sugars called oligosaccharides.
- Gut bacteria from breast-fed infants had different functions than gut bacteria from formula-fed infants regarding carbohydrate digestion and subsequent production of healthy metabolites.
New mothers spare no effort when it comes to protecting their infants from germs from the outside world — pacifiers that fall to the ground are quickly sanitized, grocery cart seats and handles are wiped down before the baby can sit, and visiting guests are required to wash their hands before holding the baby. But it turns out that the ultimate shield for keeping infants healthy isn’t hand sanitizer: it’s Mom. A new study [1] reveals that the mother’s gut is the largest source of colonizing bacteria for the infant’s gut microbiome, and the ingredients from mother’s milk ensure that these beneficial gut microbes flourish to support health and immunity across the infant’s lifetime. This one-two maternal punch of defense takes the concept of the protective mother to a whole new (microscopic) level.
Researchers uncovered the details of this microscopic relationship using data from Lifelines NEXT (LLNEXT), a prospective Dutch birth cohort study. Prospective studies follow study participants for months, years, or even decades to investigate how particular variables influence future health outcomes. As a result, they collect large amounts of biological, environmental, and lifestyle data. Dr. Trishia Sinha, MD, PhD, a postdoctoral researcher at the University Medical Center Groningen, and her research team took advantage of the vast data available from the LLNEXT prospective study to investigate early life influences on the infant gut microbiome composition in 714 mother-infant pairs [1].
Gut microbiomes of mothers and their infants were characterized from fecal samples collected across ten timepoints starting in the twelfth week of pregnancy through the infant’s first birthday. In total, the study analyzed 1,587 fecal samples from mothers and 2,939 fecal samples from infants [1]. Microbial DNA was isolated from each fecal sample using shotgun metagenomics sequencing, a technique that allows for detailed identification of bacteria down to the level of the strain — almost like having a bacterial genetic fingerprint.
Sinha and her team didn’t stop with stool samples. They also applied this same sequencing method to profile the microbial populations from breast milk (n=90 samples, collected during first month) and maternal vaginal swabs (n=82 samples, collected near birth) because both mode of delivery (vaginal birth of Caesarian section) and feeding mode (human milk or formula) are important ways babies are first introduced to maternal bacteria [1-3]. Finally, to evaluate the influence of outside factors, the research team integrated their bacterial genetic data with 474 clinical and exposure variables, including location of birth, (hospital or home), maternal BMI, maternal diet, smoking history, and whether the infant had older siblings [1].
The mother’s gut microbiome was identified as the main source of pioneering microbes in the infant’s gut microbiome, whereas strain-sharing from breast milk and the vaginal microbiomes was less frequent [1]. Gut-to-gut transmission was greatest during early infancy, and the bacterial strains that were most abundant in the mother’s gut were the most likely to be shared with the infant. These findings suggest that strains that were well adapted to the mother’s gut environment may be ecologically better adapted to the infant’s gut compared with strains acquired from other sources [1, 2].
The Dutch study couldn’t pinpoint exactly how these pioneering microbes travel from the mother’s gut to baby, however. “Our results show that the maternal gut is the major reservoir of strains found in the infant gut,” explains Sinha. “But they do not allow us to determine the exact physical route by which these bacteria reach the infant.”
Could it be breast milk? Although the study did find greater mother-infant sharing in breastfed compared with formula-fed infants [1], “this does not necessarily mean that the bacteria are being transmitted through breast milk itself,” says Sinha. “In our study, direct strain-level transmission from breast milk to the infant gut was relatively rare.” Sinha suggested that the close physical contact between mothers and infants during breastfeeding could, however, promote transmission, as close physical contact within households is known to increase transmission.
Another potentially important transmission route is direct infant exposure to maternal fecal matter from the perineum during delivery. “We know from a previous study of our co-author that how you come out of the mother is more important than exposure to the vaginal tract,” shares Sinha, “which makes us even more confident it’s the exposure to maternal perineum during birth.” This previous study [4] found that infants who required an emergency Caesarian section after the mother had been in labor had similar microbial populations to those who had planned Caesarian sections and never entered the birth canal, pointing to the exit of the birth canal as the key point of microbial transmission.
Breast milk may not be the main transmission route for mom’s gut microbes, but breastfeeding may explain why some microbes flourish more than others in the infant’s gut [1-3]. Compared with formula-fed infants, breastfed infants in the LLNEXT cohort had different functional categories of microbes in their guts. Most notably, guts of breastfed infants had a higher abundance of bacteria that produced the short-chain fatty acid acetate during digestion of carbohydrates [1]. Acetate, like other short-chain fatty acids, is known to have beneficial effects on gut health and immune function and acts as a signaling molecule in the gut-brain axis [1].
Not surprisingly, breast-fed infant guts were also enriched with carbohydrate-active enzymes (CAZymes) which break down complex sugar molecules, such as human milk oligosaccharides (HMOs), into short-chain fatty acids. Not all bacteria can metabolize HMOs. Instead, CAZymes are produced by specific beneficial bacteria, such as Bifidobacterium and Bacteroides species. HMOs act as a food source for these healthy bacteria and increase their abundance in the infant gut, while at the same time increasing the numbers of their metabolic byproducts like acetate.
“Previous studies have already shown that breastfed infants are enriched for microbial functions involved in HMO and milk-glycan utilization, and individual bacteria such as Bifidobacterium and Bacteroides have well-characterized carbohydrate-active enzymes that allow them to use these substrates,” explains Sinha. “Our study…add[s] a large-scale, systematic, extensive longitudinal analysis of carbohydrate-active enzyme repertoire across infancy.”
In contrast, formula-fed infants showed decreased activity in the breakdown, or degradation, of quinolinic acid relative to breast-fed infants [1]. Gut bacteria convert dietary tryptophan, an essential amino acid, into quinolinic acid. In a healthy gut, quinolinic acid is then quickly broken down into another molecule used for cellular energy. A decrease in the rate of degradation in the gut results in the accumulation of quinolinic acid in the body, which can lead to cellular damage and inflammation, particularly in brain tissue [5].
Motherhood already comes with immense pressure to keep infants happy and healthy. Learning that the mother is primarily responsible for seeding her infant’s gut — and that breastfeeding further directs those microbes toward optimal digestion and immunity — adds a lot of physiological obligations to a mom’s already full plate. But Sinha and colleagues highlight the importance of looking at the mother’s and infant’s gut microbiome as dynamic systems with opportunities for supportive and targeted interventions rather than foregone conclusions.
“The infant microbiome remains highly dynamic and continues to change in response to exposures during the first year of life,” says Sinha. Using maternal supplements to increase the populations of beneficial bacteria early in pregnancy, adapting formula recipes to better mimic human milk HMO composition, and developing methods to safely introduce infants born by Caesarian section to maternal gut bacteria at birth to mimic vaginal delivery could take some of the burden off of the mother while providing all infants with the right microbial populations for optimal digestion and health.
References
- Sinha T, Brushett S, Fernández-Pato A, Garmaeva S, Andreu-Sánchez S, Spreckels JE, et al. Maternal influences on infant gut microbiome and health. Nature. 2026 Aug 12:1-2.
- Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018 Jul 11;24(1):133-45.
- Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, et al. Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host Microbe. 2018 Jul 11;24(1):146-54.
- Mitchell CM, Mazzoni C, Hogstrom L, Bryant A, Bergerat A, Cher A, et al. Delivery mode affects stability of early infant gut microbiota. Cell Rep Med. 2020 Dec 22;1(9).
- Vaher K, Kenny A, Parga PL, Jiménez-Sánchez L, Turner H, Smikle R, et al. From microbes to milestones: gut bacterial abundances and functional pathways associate with neurodevelopment following preterm birth. Gut Microbiol. 2026 Mar 3:100006.