Abstract
Background/Objectives: Human milk oligosaccharides (HMOs) are bioactive carbohydrates abundant in human milk that shape the infant gut microbiome, yet their influence on the oral microbiome remains poorly understood. This study investigated associations between HMO concentrations and infant HMO intakes and the composition of the oral microbiome in predominantly (n = 2) and exclusively (n = 54) breastfed infants. Methods: We profiled infant oral samples collected at 2 months of age using full-length 16S rRNA gene sequencing, alongside paired milk HMO analyses from 56 mother-infant dyads from the Western Australian BLOSOM cohort. Daily HMO intakes were calculated using 24 h milk intake data. Results: Concentrations of human milk 3FL and LNFPIII were negatively associated with infant oral Shannon diversity (p = 0.027) and richness (p = 0.037), respectively. LNFPII concentration and daily intake were linked to increased abundance of Neisseria subflava (both p = 0.025), while daily intakes of DFLNT and DFLNH were positively associated with Streptococcus parasanguinis (p = 0.028 and p = 0.040). Notably, the associations observed for daily HMO intakes were modest in effect size. Conclusions: These findings demonstrate a statistically significant but biologically limited effect of HMOs on the development of the infant oral microbiome. By clarifying how specific components of human milk shape early microbial development, this work provides mechanistic insights relevant to nutritional and supportive interventions that promote breastfeeding success.