Healthy human gut phageome

Pilar Manrique, Benjamin Bolduc, Seth T. Walk, John van der Oost, Willem M. de Vos, Mark J. Young*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

206 Citations (Scopus)

Abstract

The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20-50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.

Original languageEnglish
Pages (from-to)10400-10405
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number37
DOIs
Publication statusPublished - 2016

Keywords

  • Gut microbiome bacteriophage
  • Gut microbiome viruses
  • Human gut viral metagenome
  • Shared microbiome viruses

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