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

Andrea C Granados, Catherine Ley, William A. Walters, Scot Federman, Yale Santos, Thomas Haggerty, Alicia Sotomayor-Gonzalez, Venice Servellita, Ruth E Ley, Julie Parsonnet, View ORCID ProfileCharles Y Chiu
doi: https://doi.org/10.1101/2022.05.13.491764
Andrea C Granados
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
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Catherine Ley
3Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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William A. Walters
4Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
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Scot Federman
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
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Yale Santos
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
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Thomas Haggerty
3Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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Alicia Sotomayor-Gonzalez
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
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Venice Servellita
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
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Ruth E Ley
4Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
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Julie Parsonnet
3Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
5Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
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Charles Y Chiu
1Department of Laboratory Medicine, University of California, San Francisco, CA, USA
2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
6Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, CA, USA
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  • ORCID record for Charles Y Chiu
  • For correspondence: charles.chiu@ucsf.edu
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Abstract

The virome of the human gut and its development in early life are poorly understood. Here we performed viral metagenomic sequencing on stool samples from a multiethnic, socioeconomically diverse cohort of 53 infants collected longitudinally over their first 3 years of life and their mothers to investigate and compare their viromes. The asymptomatic infant virome consisted of bacteriophages, dietary/environmental viruses, and human pathogenic viruses, in contrast to the material virome, in which sequence reads from human pathogenic viruses were absent or present at extremely low levels. Picornaviruses and phages in the family Microviridae (microviruses) dominated the infant virome, while microviruses and tomato mosaic virus dominated the maternal virome. As the infants aged, the human pathogenic and dietary/environmental virus components remained distinct from the materal virome, while the phage component evolved to become more similar. However, the composition of the evolving infant virome was not determined by the mother and was still maturing to the adult virome at three years of age.

Importance The development of the human gut virome in early childhood is poorly understood. Here we use viral metagenomic sequencing in a cohort of 53 infants to the characterize their gut viromes and compare them to their mothers’.. This study finds that the infant virome consists of phages and human pathogenic viruses in asymptomatic individuals and is still maturing into the adult virome at three years of age.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* co-senior authors

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 13, 2022.
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Longitudinal comparison of the developing gut virome in infants and their mothers
Andrea C Granados, Catherine Ley, William A. Walters, Scot Federman, Yale Santos, Thomas Haggerty, Alicia Sotomayor-Gonzalez, Venice Servellita, Ruth E Ley, Julie Parsonnet, Charles Y Chiu
bioRxiv 2022.05.13.491764; doi: https://doi.org/10.1101/2022.05.13.491764
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Longitudinal comparison of the developing gut virome in infants and their mothers
Andrea C Granados, Catherine Ley, William A. Walters, Scot Federman, Yale Santos, Thomas Haggerty, Alicia Sotomayor-Gonzalez, Venice Servellita, Ruth E Ley, Julie Parsonnet, Charles Y Chiu
bioRxiv 2022.05.13.491764; doi: https://doi.org/10.1101/2022.05.13.491764

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