Microbes in Mother’s Milk Transfer to Baby

Written by: Alla Katsnelson, Ph.D | Issue # 131 | 2026

Breast milk is home to a distinct microbial community. Those bacteria are transmitted to infants through breastfeeding and help lay the foundation for infants’ gut microbiomes in the months after birth, a new study shows [1]. 

Previous work has shown that breastfeeding promotes a healthy gut microbiome in infants [2] but it remained unclear to what extent microbes in breast milk could be transferred to the infant gut and colonize it for a prolonged time [3]. But little has been known about the overall microbial makeup of breast milk and how different bacterial strains found in milk might play a role in infant microbiome development. 

The new study offers the most detailed look to date at breast milk’s cast of bacterial characters and what functional role they might play in infants’ gut. “Bacteria are transmitted to the baby during breastfeeding,” says Pamela Ferretti, a postdoctoral researcher in the lab of Ran Blekhman at the University of Chicago, who led the work.  

Ferretti and her colleagues analyzed 507 samples of breast milk and infant stool from 195 mother-infant pairs in which the mothers primarily breastfed their babies. The team had previously examined which bacterial species are transmitted to the infant from different maternal body sites such as the vagina, the gut and the mouth. But they had skipped breast milk because the relatively low levels of microbes and the high fat content made it challenging to sequence this community. “There are technical and logistical challenges in studying the milk,” says Ferretti.

Here, the researchers used a sequencing approach called metagenomics in which all bacterial DNA within a sample is sequenced comprehensively, and then analyzed to identify specific bacterial species and strains, as well as their functional potential. “We did find strains that were present between the breast milk and infant gut,” Ferretti says, “and some of those microbes were able to persist not just at one month but were still there at six months.” 

The most prominent microbial signal in the breast milk samples came from bifidobacteria, a core group of beneficial bacteria in the gut microbiome that are particularly important for infant health [4]. More than half the milk samples included the species Bifidobacterium longum (mostly as subspecies infantis), and almost all infant stool samples contained this species. 

Breast milk also contained Klebsiella pneumoniae, a bacterium that can be harmless or under certain circumstances can cause illness. “All this is transferred as a starter kit to the baby,” Ferretti says. “The mother can’t choose what to pass along – it all travels as a package.” 

The team also examined antimicrobial resistance genes found in the milk and found that babies received “quite an extensive repertoire” of these genes from breast milk, even if they had never taken antibiotics themselves.

Some previous studies had examined bacterial composition in breast milk using a cheaper, simpler approach called amplicon sequencing, which targets specific gene markers and can’t identify bacteria to the level of specific species and strains. Those studies had identified Staphylococcus and Streptococcus as the core species transferred between breast milk and the infant gut. [5] However, Ferretti notes that technique may preferentially identify those types of bacteria more easily while metagenomics tends to be less biased in detecting Staphylococcus and Streptococcus, as well as bifidobacteria. At least one previous study using metagenomics also identified a high concentration of bifidobacteria, she adds.  [6]

The bacteria that the researchers found in the infant stool samples also included species normally found on human skin or in the mouth. That may be because the milk samples the baby ingests may contain maternal skin cells from breastfeeding as well as bacteria from the baby’s own oral cavity, Ferretti explains. “The hypothesis is that microbes are not just from the breast milk to the infant, but from the infant to the breast milk,” she says. 

Ferretti and her colleagues plan to use the same data set to explore the impact of metabolites these traveling bacterial strains produce, as well as of human milk oligosaccharides and chemical contaminants such as per- and polyfluoroalkalyl substances, or PFAS, on the  infant gut microbiome and on infant health. 

“We are trying to look at breast milk from a holistic perspective,” she says – “not just who is there, but what they are doing.”

References

1. Ferretti P, Allert M, Johnson KE, Rossi M, Heisel T, Gonia S, Knights D, Fields DA, Albert FW, Demerath EW, Gale CA, Blekhman R. Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk. Nat Commun. 2025;16(1):11536. 
2. Davis EC, Castagna VP, Sela DA, Hillard MA, Lindberg S, Mantis NJ, Seppo AE, Järvinen KM. Gut microbiome and breast-feeding: Implications for early immune development. J Allergy Clin Immunol. 2022;150(3):523-534
3. Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, Adisetiyo H, Zabih S, Lincez PJ, Bittinger K, Bailey A, Bushman FD, Sleasman JW, Aldrovandi GM. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr. 2017;171(7):647-654. 
4. Saturio S, Nogacka AM, Alvarado-Jasso GM, Salazar N, de Los Reyes-Gavilán CG, Gueimonde M, Arboleya S. Role of bifidobacteria on infant health. Microorganisms. 2021 Nov 23;9(12):2415. 
5. Notarbartolo V, Giuffrè M, Montante C, Corsello G, Carta M. Composition of human breast milk microbiota and its role in children’s health. Pediatr Gastroenterol Hepatol Nutr. 2022;25(3):194-210.
6. Kordy K, Gaufin T, Mwangi M, Li F, Cerini C, Lee DJ, Adisetiyo H, Woodward C, Pannaraj PS, Tobin NH, Aldrovandi GM. Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve. PLoS One. 2020;15(1):e0219633.

Back to SPLASH!^® Home