First-Year Evolution of Mother-Infant Microbiome and Virome in Saliva

Objectives: We utilize metagenomic sequencing to examine saliva samples from healthy mother-child dyads living in the same household, focusing on exploring the development and evolution of the maternal and infant oral microbiome and virome. This research demonstrates the feasibility of using a frozen saliva bank for these types of analyses.
Methods: Saliva samples were previously collected as part of a longitudinal study Mother and Youth Access (MAYA) healthy cohort of mother–child dyads. MAYA was a randomized clinical trial (U54DE014251) conducted in 2002–2008 aimed at reducing early childhood caries (ECC) among infants and toddlers in communities with high ECC rates, low socioeconomic status (SES), limited dental care access, and no optimally fluoridated municipal water. Data were collected at the San Ysidro Health Center, where 95% of patients are Latinx, 69% live below the federal poverty level, and 68% have caries, more than twice the national average. We tested our protocol and selected two mother-child dyads to demonstrate the feasibility of analyzing the microbiome and virome using frozen samples. To amplify DNAs from small-volume saliva samples (25 µL), we employed multiple displacement amplification (MDA) to achieve sufficient quality to support metagenomic sequencing with minimized amplification bias.
Results: Our study revealed notable shifts in bacterial and viral compositions from the prenatal stage and post-delivery in mothers. Initial comparative analyses at birth showed a conserved structure of viral and bacterial communities between mothers and their newborns. As children age, their viral and bacterial communities diversify. By four months, infants established similar the bacterial and viral communities as those in their mothers during the prenatal stage. By one year, infants developed unique and more diverse viral and bacterial patterns compared to their mothers.
Conclusions: Our findings reveal a substantial overlap in virus and bacteria species between mothers and their children at four months, diverging noticeably by the age of one year. These preliminary results underscore the potential of metagenomics in analyzing our extensive MAYA saliva bank.