MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

Abstract

Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil a large infection network encompassing more than 6,000 interactions bridging a metagenomic assembled genomes (MAGs) and a phage sequence, allowing to study in situ phage-host ratio. Whereas three-quarter of these sequences likely correspond to dormant prophages, 5% exhibit a much higher coverage than their associated MAG, representing potentially actively replicating phages. We detected 17 sequences of members of the crAss-like phage family, whose hosts diversity remained until recently relatively elusive. For each of them, a unique bacterial host was identified, all belonging to different genus of Bacteroidetes. Therefore, metaHiC deciphers infection network of microbial population with a high-specificity paving the way to dynamic analysis of mobile genetic elements in complex ecosystems.

Data availability

Sequence data (raw reads, assemblies) have been deposited in the NCBI Sequence Read Archive under the BioProject number PRJNA627086.Code and additional data on MAGs, Bins, Contigs and Phages can be found at the following address https://github.com/mmarbout/HGP-Hi-C.

The following data sets were generated

Article and author information

Author details

  1. Martial Marbouty

    Département Génomes et Génétique, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
    For correspondence
    martial.marbouty@pasteur.fr
    Competing interests
    The authors declare that no competing interests exist.
  2. Agnès Thierry

    Département Génomes et Génétique, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Gaël A Millot

    Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Romain Koszul

    Département Génomes et Génétique, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
    For correspondence
    romain.koszul@pasteur.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3086-1173

Funding

European Research Council (771813)

  • Romain Koszul

Agence Nationale pour la Recherche (ANR-16-JPEC-0003-05)

  • Romain Koszul

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Breck A Duerkop, University of Colorado School of Medicine

Ethics

Human subjects: The work involved feces samples of healthy human individuals, stored in the Institut Pasteur biobanque (library). This research receives the ethical agreement n{degree sign}N18 from Institut Pasteur (ICAReB), and through this process we dont need informed consent from the individual donors.

Version history

  1. Received: July 1, 2020
  2. Accepted: February 20, 2021
  3. Accepted Manuscript published: February 26, 2021 (version 1)
  4. Version of Record published: March 16, 2021 (version 2)

Copyright

© 2021, Marbouty et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Martial Marbouty
  2. Agnès Thierry
  3. Gaël A Millot
  4. Romain Koszul
(2021)
MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut
eLife 10:e60608.
https://doi.org/10.7554/eLife.60608

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https://doi.org/10.7554/eLife.60608

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