Stanford's Outcomes Research in Kids (STORK) Virome

The virome of the human gut and its development in early life are poorly understood. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort of 53 infants from age 2 weeks to 3 years (80.7 billion reads), and from their mothers (9.8 billion reads) to describe and compare their viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary / environmental viruses, and human-host viruses, predominated by picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Novel, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As the infants aged, the phage component of the infant virome evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, infant virome development in early life is shaped predominantly by dietary, infectious, and environmental factors rather than from direct acquisition from the mother.