Phages with a broad host range are common across ecosystems

Amaury Bignaud, Devon E. Conti, Agnès Thierry, Jacques Serizay, Karine Labadie, Julie Poulain, Olivia Cheny, Maritrini Colón-González, Laurent Debarbieux, Marianna Guerrero-Osornio, Sophie Helaine, Peter Hill, Gwenaelle Le Tinier, Gael A. Millot, Lucia Morales, Andrés Parada, Nadia Riera, Gregorio Iraola, Romain Koszul, Martial Marbouty

Nature Microbiology10(10): 2537-2549 1 September 2025

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Abstract

Phages are diverse and abundant within microbial communities, where they play major roles in their evolution and adaptation. Phage replication, and multiplication, is generally thought to be restricted within a single or narrow host range. Here we use published and newly generated proximity-ligation-based metagenomic Hi-C (metaHiC) data from various environments to explore virus–host interactions. We reconstructed 4,975 microbial and 6,572 phage genomes of medium quality or higher. MetaHiC yielded a contact network between genomes and enabled assignment of approximately half of phage genomes to their hosts, revealing that a substantial proportion of these phages interact with multiple species in environments as diverse as the oceanic water column or the human gut. This observation challenges the traditional view of a narrow host spectrum of phages by unveiling that multihost associations are common across ecosystems, with implications for how they might impact ecology and evolution and phage therapy approaches.

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Bignaud A, Conti DE, Thierry A, Serizay J, Labadie K, Poulain J, et al. Phages with a broad host range are common across ecosystems. Nature Microbiology. 2025;10(10):2537-2549. doi:10.1038/s41564-025-02108-2

@article{bignaud_natmicro_2025,
  author  = {Bignaud, Amaury and Conti, Devon E. and Thierry, Agnès and Serizay, Jacques and Labadie, Karine and Poulain, Julie and Cheny, Olivia and Colón-González, Maritrini and Debarbieux, Laurent and Guerrero-Osornio, Marianna and Helaine, Sophie and Hill, Peter and Le Tinier, Gwenaelle and Millot, Gael A. and Morales, Lucia and Parada, Andrés and Riera, Nadia and Iraola, Gregorio and Koszul, Romain and Marbouty, Martial},
  title   = {{Phages with a broad host range are common across ecosystems}},
  journal = {Nature Microbiology},
  year    = {2025},
  volume  = {10},
  number  = {10},
  pages   = {2537--2549},
  doi     = {10.1038/s41564-025-02108-2},
  url     = {https://doi.org/10.1038/s41564-025-02108-2}
}

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