Infant bacterial and viral communities more closely resemble those of their related co-twin than unrelated infants. We found that 63% of an infant’s bacterial microbiome can be traced to their mother’s gut microbiota. In contrast, only 15% of their viral communities are acquired from their mother. The delivery route did not determine how much of the bacterial microbiome or virome was shared from mother to infant. However, bacteria-bacteriophage interactions were altered by the delivery route. The maternal gut microbiome significantly influences infant gut microbiome acquisition. Vertical transmission of the bacterial microbiome is substantially higher compared to vertical transmission of the virome.