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Peer-reviewedCC BY-NC-NDNature Biotechnology

A genomic catalog of Earth’s bacterial and archaeal symbionts

  • Juan C. Villada1,2
  • Yumary M. Vasquez2,3,4
  • Gitta Szabó2
  • Ewan Whittaker-Walker2,5,6
  • Miguel F. Romero2
  • Sarina Qin7,8
  • Neha Jacob Varghese2
  • Emiley A. Eloe‐Fadrosh2
  • Nikos C. Kyrpides2
  • Ramūnas Stepanauskas9,2
  • Christopher A. Francis10,2
  • Rick Cavicchioli11,2
9 more authors
  • Trina McMahon12
  • Steven Hallam13
  • Wen‐Tso Liu14
  • Thomas Möck15
  • James M. Tiedje16
  • Jiarong Guo17
  • Axel Visel2
  • Tanja Woyke2
  • Frederik Schulz18
18 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 Life and Environmental Sciences, University of California Merced, Merced, CA, USA
  4. 4Department of Life and Environmental Sciences, University of California Merced, Merced, California, USA
  5. 5Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA, USA
  6. 6Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, USA
  7. 7School of Natural Sciences, University of California Merced, Merced, CA, USA
  8. 8School of Natural Sciences, University of California Merced, Merced, California, USA
  9. 9Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
  10. 10Earth System Science and Oceans Departments, Stanford Doerr School of Sustainability, Stanford University, Stanford, CA, USA
  11. 11School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
  12. 12Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
  13. 13Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
  14. 14Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
  15. 15School of Environmental Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, UK
  16. 16Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
  17. 17Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
  18. 18DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [email protected]
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Abstract

Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth yet remains underexplored because of culturing challenges. This study used machine learning (ML) to predict symbiotic lifestyles in more than a hundred thousand microbial genomes from diverse environmental metagenome samples and reference genomes. Predictions were performed using symclatron, an ML framework developed to identify genomic signatures of symbionts. Predictions were deposited in a catalog we established called Symbiont Genomes (SymGs). The results indicate that 15-23% of uncultivated microorganisms likely engage in symbiotic relationships with other organisms, categorized as host-associated or obligate intracellular lifestyles, and are present in half of all known bacterial and archaeal phyla. We also identify genomic signatures of symbiotic lifestyles, including the loss of certain metabolic functions and the differential presence of metabolic modules that may enable host-dependent living. The symclatron software and the SymGs catalog represent valuable resources for studying symbioses, potentially facilitating future mechanistic investigations and engineering of host-microorganism associations.

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Cite

BibTeXRIS
BibTeX
@article{villada2026genomic,
  title = {{A genomic catalog of Earth’s bacterial and archaeal symbionts}},
  author = {Juan C. Villada and Yumary M. Vasquez and Gitta Szabó and Ewan Whittaker-Walker and Miguel F. Romero and Sarina Qin and Neha Jacob Varghese and Emiley A. Eloe‐Fadrosh and Nikos C. Kyrpides and Ramūnas Stepanauskas and Christopher A. Francis and Rick Cavicchioli and Trina McMahon and Steven Hallam and Wen‐Tso Liu and Thomas Möck and James M. Tiedje and Jiarong Guo and Axel Visel and Tanja Woyke and Frederik Schulz},
  journal = {Nature Biotechnology},
  year = {2026},
  month = aug,
  doi = {10.1038/s41587-026-03213-1},
  url = {https://doi.org/10.1038/s41587-026-03213-1},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - A genomic catalog of Earth’s bacterial and archaeal symbionts
AU  - Juan C. Villada
AU  - Yumary M. Vasquez
AU  - Gitta Szabó
AU  - Ewan Whittaker-Walker
AU  - Miguel F. Romero
AU  - Sarina Qin
AU  - Neha Jacob Varghese
AU  - Emiley A. Eloe‐Fadrosh
AU  - Nikos C. Kyrpides
AU  - Ramūnas Stepanauskas
AU  - Christopher A. Francis
AU  - Rick Cavicchioli
AU  - Trina McMahon
AU  - Steven Hallam
AU  - Wen‐Tso Liu
AU  - Thomas Möck
AU  - James M. Tiedje
AU  - Jiarong Guo
AU  - Axel Visel
AU  - Tanja Woyke
AU  - Frederik Schulz
PY  - 2026
DA  - 2026/08/31
JO  - Nature Biotechnology
DO  - 10.1038/s41587-026-03213-1
UR  - https://doi.org/10.1038/s41587-026-03213-1
AB  - Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth yet remains underexplored because of culturing challenges. This study used machine learning (ML) to predict symbiotic lifestyles in more than a hundred thousand microbial genomes from diverse environmental metagenome samples and reference genomes. Predictions were performed using symclatron, an ML framework developed to identify genomic signatures of symbionts. Predictions were deposited in a catalog we established called Symbiont Genomes (SymGs). The results indicate that 15-23% of uncultivated microorganisms likely engage in symbiotic relationships with other organisms, categorized as host-associated or obligate intracellular lifestyles, and are present in half of all known bacterial and archaeal phyla. We also identify genomic signatures of symbiotic lifestyles, including the loss of certain metabolic functions and the differential presence of metabolic modules that may enable host-dependent living. The symclatron software and the SymGs catalog represent valuable resources for studying symbioses, potentially facilitating future mechanistic investigations and engineering of host-microorganism associations.
SN  - 0733-222X
SN  - 1087-0156
SN  - 1546-1696
SN  - 2331-3684
ER  -