HMOs exhibit age-dependent and structure-specific associations with infant gut microbiota, extending beyond breastfeeding, with disialyllacto-N-tetraose and lacto-N-sialyllactose b notable at 3 months and fucodisialyllacto-N-hexaose associated with multiple gut microbiota metrics at 13 months.
Key Findings
Results
HMOs were associated with gut microbiota fecal community types, diversity measures, and bacterial genera at both 3 and 13 months of age.
Fecal samples were analyzed from infants at 3 months (n = 517) and 13 months (n = 522), along with human milk samples at 3 months.
Gut microbiota was profiled by 16S rRNA sequencing and 19 HMOs were quantified by high-performance liquid chromatography with fluorescent detection.
Dirichlet multinomial mixtures clustering was used to identify bacterial fecal community types (FCTs) and multinomial logistic regression models to study associations between HMOs and FCTs.
Permutational multivariate analysis of variance and linear regression models were used to associate HMOs with gut microbiota diversity measures, and Spearman correlation to bacterial genera.
Results
At 3 months of age, disialyllacto-N-tetraose (DSLNT) and the structurally related lacto-N-sialyllactose b (LSTb) showed notable associations with the gut microbiota.
These two sialylated HMOs were identified as having particularly notable associations with gut microbiota composition at 3 months.
DSLNT and LSTb are structurally related molecules, suggesting that structural features of HMOs may underlie their differential effects on the microbiota.
These associations were identified from a panel of 19 quantified HMOs.
The population-based cohort design allowed for assessment of these associations in a real-world infant feeding context.
Results
At 13 months of age, fucodisialyllacto-N-hexaose (FDSLNH) was associated with multiple gut microbiota metrics.
FDSLNH showed associations with multiple gut microbiota metrics at 13 months, indicating a distinct HMO-microbiota relationship at this later age compared to 3 months.
The shift in which HMOs were most prominently associated at different time points demonstrates age-dependent HMO-microbiota relationships.
This finding was based on fecal samples from n = 522 infants at 13 months of age.
The associations at 13 months extended beyond the period of active breastfeeding, suggesting lasting effects of early HMO exposure.
Results
Maternal secretor status was associated with infant gut microbiota beta diversity and decreased Shannon diversity at 3 months, with diminishing associations at 13 months.
Maternal secretor status was associated with gut microbiota beta diversity (R2 = 0.003, P < 0.05) at 3 months.
Maternal secretor status was associated with decreased Shannon diversity (b = -0.24, P < 0.05) at 3 months.
At 13 months, the association was diminished, with only observed richness remaining significant (b = -11, P < 0.05).
Secretor status determines which fucosylated HMOs a mother produces, thereby influencing the HMO composition of her breast milk.
Results
No individual HMOs showed microbiome-rebalancing effects in cesarean-born infants compared to vaginally-born infants.
The study specifically examined whether HMOs could act as microbiome-rebalancing agents in cesarean-delivered infants, whose gut microbiota colonization is known to differ from vaginally-born infants.
Despite testing 19 HMOs, none individually demonstrated a significant microbiome-rebalancing effect in cesarean-born infants.
This null finding was one of the explicit aims of the study.
Results
Infants born by cesarean section and fed by nonsecretor mothers exhibited stronger cesarean-related microbiota patterns compared with those fed by secretor mothers.
This finding suggests that secretor-status-dependent HMOs may partially mitigate the microbiota differences associated with cesarean delivery.
Nonsecretor mothers produce a different HMO profile, lacking certain fucosylated HMOs such as 2'-fucosyllactose.
The result implies that HMO composition, determined in part by maternal secretor status, modulates the impact of delivery mode on infant gut microbiota.
This was observed in the context of a population-based cohort study design.
Results
HMO associations with infant gut microbiota extended beyond the breastfeeding period, indicating lasting effects.
Associations between HMOs measured in milk at 3 months and gut microbiota were detectable at 13 months of age.
This persistence of association suggests that early HMO exposure may have durable effects on microbiota composition.
The authors noted that HMO effects 'extending beyond breastfeeding' represent a key finding of the study.
The study used a longitudinal design with fecal samples collected at both 3 and 13 months to capture these temporal dynamics.
What This Means
This research suggests that specific sugars found in breast milk, called human milk oligosaccharides (HMOs), shape the community of bacteria living in an infant's gut in ways that are both dependent on the infant's age and on the specific chemical structure of each sugar. The study followed over 500 infants at 3 months and 13 months of age, measuring 19 different HMOs in mothers' milk and analyzing the gut bacteria of their infants. At 3 months, two structurally related sialylated HMOs (DSLNT and LSTb) were most strongly linked to the types of bacteria present, while at 13 months a different HMO (FDSLNH) was most prominent, showing that the relationship between breast milk sugars and gut bacteria changes as infants grow.
The study also found that whether a mother is a 'secretor' — a genetic trait that determines which specific HMOs she produces — affected her infant's gut bacterial diversity, particularly at 3 months of age. Notably, cesarean-born infants fed by nonsecretor mothers showed more pronounced differences in gut bacteria compared to vaginally born infants than those whose mothers were secretors. However, no single HMO was able to fully 'rebalance' the gut microbiota of cesarean-born infants to resemble that of vaginally born infants.
This research suggests that the effects of breast milk sugars on infant gut health are more complex and longer-lasting than previously appreciated, with certain HMOs continuing to show associations with gut bacteria composition even at 13 months, beyond the typical period of active breastfeeding. These findings could have implications for understanding how early feeding shapes long-term gut health and for the development of infant formula supplemented with specific HMOs.
Ovaska M, Tamminen M, Lahdenperä M, Rautava S, Jeevannavar A, Isokääntä H, et al.. (2026). The role of human milk oligosaccharides in shaping and restoring infant gut microbiota: population-based cohort study.. The American journal of clinical nutrition. https://doi.org/10.1016/j.ajcnut.2026.101318