Functional adaptations and metabolic interactions of undescribed Streptococcus and Rothia species during infant oral microbiome development

Early-life oral microbiome development is a complex process shaped by microbial colonization patterns that influence community assembly and long-term health outcomes. Nevertheless, the microbial interactions driving the ecological processes behind this development remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated Streptococcus and Rothia species and predict their metabolic interactions within a small network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes) involved in neutralizing reactive oxygen species (ROS). Malate and lysine were further predicted to be among the metabolites exchanged between these species, suggesting metabolic cross-feeding interactions that may support their co-occurrence. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.