Longitudinal comparison of the developing gut virome in infants and their mothers

Cell Host Microbe. 2023 Feb 8;31(2):187-198.e3. doi: 10.1016/j.chom.2023.01.003.


The human gut virome and its early life development are poorly understood. Prior studies have captured single-point assessments with the evolution of the infant virome remaining largely unexplored. 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 examine and compare viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, predominantly picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Previously undescribed, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As infants aged, the phage component evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, early life virome development is determined predominantly by dietary, infectious, and environmental factors rather than direct maternal acquisition.

Keywords: SURPI; alpha diversity; bacteriophages; beta diversity; infant gut virome; maternal virome; metagenomic sequencing; microbiome; microviruses; parechovirus; picornaviruses; principal component analysis.

MeSH terms

  • Bacteriophages* / genetics
  • Female
  • Humans
  • Metagenome
  • Metagenomics
  • Mothers
  • Virome / genetics
  • Viruses* / genetics