New metagenomic evidence reveals how specific bacterial strains and resistance genes link breast milk to infant gut development, and challenging assumptions about how microbes are passed from mother to child.
Study: Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk. Image Credit: New Africa / Shutterstock.com
A recent study published in Nature Communications examines the relationship between the maternal milk microbiome and infant gut microbiome.
Development and function of the gut microbiome
The early-life gut microbiome is essential for developing the immune system, absorbing nutrients, and regulating metabolism. Maternal microorganisms, which are transferred to the child during and after birth, play a key role in the colonization and maturation of the infant's gut microbiome.
Human breast milk contains nutrients and bioactive compounds, such as oligosaccharides, immune cells, antibodies, and live bacteria, that influence the composition, stability, and function of the infant microbiome. In fact, evidence suggests that the milk microbiome may contribute to the protective effects of exclusive breastfeeding against chronic conditions like asthma, obesity, diabetes, and allergies.
Several bacterial groups have been isolated from human breast milk samples, including Staphylococcus, Streptococcus, Lactobacillus, Bifidobacterium, Veillonella, and Escherichia. Among these, Bifidobacteria are particularly important, as they dominate the gut of breastfed infants, supporting the digestion of human milk oligosaccharides (HMOs) and contributing to overall infant health.
Assessing the relationship between the maternal milk and infant gut microbiomes
Study participants from the Mother and Infants Linked for Health (MILk) cohort were recruited in Minneapolis, United States, for the current study. Healthy mothers between 21 and 45 years of age who delivered full-term singletons and intended to breastfeed exclusively were enrolled between 2014 and 2023. Breast milk samples were collected at one and three months postpartum using sterile techniques.
The study also included infants born at term with appropriate birth weights and who were exclusively breastfed for at least one month. Infant stool samples were collected at one and six months, either during study visits or at home.
Relevant metadata of all study participants, including ethnicity and race, were recorded.
Maternal milk microbiome influences infant gut development
A total of 507 microbiome samples from 195 mother-infant pairs were collected and sequenced. Most infants were vaginally born, approximately two-thirds remained antibiotic-naive through six months, and most were exclusively breastfed at six months.
Maternal milk exhibited a significantly lower species richness than infant stool samples. Microbial diversity in both trended upward modestly over time.
The milk microbiome was dominated by Bifidobacterium longum, along with B. breve, B. bifidum, and species associated with the skin, such as Staphylococcus epidermidis and Cutibacterium acnes, as well as those present in the oral cavity, including Streptococcus salivarius. This pattern contrasts with many prior amplicon-based studies, which have often reported milk microbiomes dominated by Staphylococcus and Streptococcus, highlighting potential methodological differences in microbiome profiling.
At one month, the infant gut microbiome was dominated by B. longum, B. breve, B. bifidum, E. coli, B. fragilis, P. vulgatus, and P. dorei. The most prevalent species in both milk and infant stool was B. longum.
Although the overall microbiome composition of milk and infant stool was distinct, both were dominated by B. longum. In milk and infant stool samples, B. longum was the most stable microorganism over time.
The prevalence and relative abundance of bifidobacteria in the infant gut increased from one to six months, particularly among exclusively breastfed infants. This trend was consistent for B. longum and its subspecies, as well as other Bifidobacterium species, despite individual variability.
Although some paired mother-infant pairs had similar bifidobacterial abundances between milk and stool samples, no significant association was detected at the population level. Strain sharing between milk and stool was more frequent at one month than six months, with no sharing observed in three-month milk samples, likely due to low microbial biomass and limited sequencing yield.
In addition to commensal species, strain sharing was also observed for potential pathobionts, including Klebsiella pneumoniae, highlighting that both beneficial and opportunistic bacteria may be shared between maternal milk and the infant gut. Shared oral-associated taxa, such as Streptococcus salivarius, Rothia mucilaginosa, and Veillonella parvula, are consistent with the possibility of retrograde transfer from the infant oral cavity into the mammary gland during breastfeeding.
Metagenomic profiling indicated that the infant gut microbiome initially contained abundant biosynthetic pathways, particularly those involved in essential amino acid synthesis, which declined by six months, particularly among infants not dominated by bifidobacteria or not exclusively breastfed. In human breast milk, biosynthetic pathways remained most abundant, with the synthesis of essential amino acids increasing at three months postpartum.
Strong correlations were observed in metabolic pathways between milk and infant stool in a few mother-infant pairs with strain sharing, but no consistent associations were identified across the cohort.
The gut and breast milk microbiomes both harbored antimicrobial resistance genes (ARGs) with distinct diversity and prevalence. Whereas maternal milk exhibited lower ARG diversity than infant stool, macrolide–lincosamide–streptogramin (MLS) resistance was most common. ARG diversity increased over time, especially in milk.
The infant gut resistome was dominated by resistance to tetracycline, MLS, aminoglycosides, and beta-lactams. Infants with bifidobacteria-dominated stool carried fewer ARGs.
Delivery mode, antibiotic exposure, diet, and feeding method did not significantly impact the carriage of ARGs. Overall, extensive ARGs were detected, even in largely antibiotic-naive infants.
No significant correlation exists between ARGs in milk and those in infant stool overall; however, the infant gut resistome at one month was positively correlated with that at six months, suggesting within-infant continuity over time. The most commonly shared ARGs confer resistance to peptides, fluoroquinolones, and MLS, with MACB, ACRD, and TETQ the most frequently shared genes.
Conclusions
Maternal breast milk contributes to the establishment, development, and stability of the infant gut microbiome and resistome during the first six months postpartum. Although the study identifies species-, strain-, and antimicrobial resistance gene overlap between milk and infant stool, its observational design and the low microbial biomass of milk samples limit the ability to confirm the direction of microbial transmission. Strain and antimicrobial resistance gene sharing between mothers and infants highlight the interconnectedness of their microbiomes.
Taken together, the study findings provide important insights into maternal-infant microbial transmission while establishing a foundation for further research investigating the role of the maternal milk microbiome in infant health.
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Genes influence the gut microbiome beyond the individual