Preferential sharing of virus populations between mothers and infants in early life

Maternal contributions to the establishment of the early infant microbiome play a crucial role in shaping the infant’s microbiome for life. Yet this maternal contribution in shaping the infant’s virome is not well-understood. Here, we investigated the extracellular viral fraction of the human faecal microbiome, including DNA and RNA viruses, using longitudinal samples collected from 15 healthy infant-mother pairs from pregnancy till first two years of infant development. By employing an individual mother-infant-centric approach combined with microdiversity analyses, we show that the virome of each mother-infant pair is highly distinct. Sharing of viruses within pairs is more often transient than persistent. Nonetheless, we show that a subset of vOTUs is persistently shared between mother and infants. We observed that vOTUs persistent in mothers and detected in babies undergo stronger positive selection. Interestingly, vOTUs belonging to the Class Microviricetes were significantly enriched among persistent viruses, whereas Anelloviridae were enriched among transient ones. Further, we show preferential sharing of specific viral families between pairs across the persistent and transient maternal virome pool. Our findings reveal that mother–infant virome sharing is not random but structured by specific transient and persistent viral families.