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Peer-reviewedCC BY-NC-NDNature Microbiology

Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems

  • Simon Roux1,2
  • Uri Neri2
  • Brian Bushnell2
  • Brayon J. Fremin2
  • Nikhil A. George3
  • Uri Gophna4,5
  • Laura A. Hug6,7
  • Antônio Pedro Camargo2
  • Dongying Wu2
  • Natalia Ivanova2
  • Nikos C. Kyrpides2
  • Emiley A. Eloe‐Fadrosh8,2
8 affiliations
  1. 1DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [email protected]
  2. 2DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  3. 3Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
  4. 4The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
  5. 5The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
  6. 6Department of Biology, University of Waterloo, Waterloo, Ontaria, Canada
  7. 7Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
  8. 8DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [email protected]
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Abstract

Interactions between microorganisms and their mobile genetic elements (MGEs), including viruses and plasmids, impact microbiome dynamics. CRISPR-Cas systems are important regulators of these host-MGE interactions, but a global understanding of the diversity, activity and roles of CRISPR spacers across Earth's biomes is still lacking. Here we develop a computational approach to search short-read data and collect 794 million CRISPR spacers across 367,609 public metagenomes, from which we identified 1.18 billion hits between 41 million spacers and 2.5 million viruses and plasmids. While spacers were highly variable across samples, those matching known viruses were more prevalent and conserved, consistent with a positive selection pressure associated with phage targeting. Among these, however, we find evidence suggestive of recurrent entry of phage genomes into non-host microbial cells, further blurring the line between CRISPR targeting and virus-host interactions. These results highlight key drivers of CRISPR targeting patterns likely to influence strain-level diversification and selection processes in microbiomes.

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Cite

BibTeXRIS
BibTeX
@article{roux2026planetaryscale,
  title = {{Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems}},
  author = {Simon Roux and Uri Neri and Brian Bushnell and Brayon J. Fremin and Nikhil A. George and Uri Gophna and Laura A. Hug and Antônio Pedro Camargo and Dongying Wu and Natalia Ivanova and Nikos C. Kyrpides and Emiley A. Eloe‐Fadrosh},
  journal = {Nature Microbiology},
  year = {2026},
  month = oct,
  doi = {10.1038/s41564-026-02480-7},
  url = {https://doi.org/10.1038/s41564-026-02480-7},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems
AU  - Simon Roux
AU  - Uri Neri
AU  - Brian Bushnell
AU  - Brayon J. Fremin
AU  - Nikhil A. George
AU  - Uri Gophna
AU  - Laura A. Hug
AU  - Antônio Pedro Camargo
AU  - Dongying Wu
AU  - Natalia Ivanova
AU  - Nikos C. Kyrpides
AU  - Emiley A. Eloe‐Fadrosh
PY  - 2026
DA  - 2026/10/29
JO  - Nature Microbiology
DO  - 10.1038/s41564-026-02480-7
UR  - https://doi.org/10.1038/s41564-026-02480-7
AB  - Interactions between microorganisms and their mobile genetic elements (MGEs), including viruses and plasmids, impact microbiome dynamics. CRISPR-Cas systems are important regulators of these host-MGE interactions, but a global understanding of the diversity, activity and roles of CRISPR spacers across Earth's biomes is still lacking. Here we develop a computational approach to search short-read data and collect 794 million CRISPR spacers across 367,609 public metagenomes, from which we identified 1.18 billion hits between 41 million spacers and 2.5 million viruses and plasmids. While spacers were highly variable across samples, those matching known viruses were more prevalent and conserved, consistent with a positive selection pressure associated with phage targeting. Among these, however, we find evidence suggestive of recurrent entry of phage genomes into non-host microbial cells, further blurring the line between CRISPR targeting and virus-host interactions. These results highlight key drivers of CRISPR targeting patterns likely to influence strain-level diversification and selection processes in microbiomes.
SN  - 2058-5276
ER  -