show Abstracthide AbstractThe earliest microbial colonizers of the human gut could have life-long consequences for their hosts. To better understand how the maternal microbiome influences acquisition of the infant gut microbiome, we studied the early life bacterial microbiome and virome of 28 infant twin-pairs and their mothers. Only 63% of an infant's bacterial and 15% of their viral communities mapped to their respective mothers. Infants shared bacterial and viral communities that more closely resembled those of their related co-twin than to an unrelated infant. Thus, this study portrays the differences of the inter-generation transmissibility at birth between the major kingdoms of microbes.