{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jvillada@lbl.gov",
    "DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA",
    "Department of Life and Environmental Sciences, University of California Merced, Merced, CA, USA",
    "Department of Life and Environmental Sciences, University of California Merced, Merced, California, USA",
    "Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA, USA",
    "Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, USA",
    "School of Natural Sciences, University of California Merced, Merced, CA, USA",
    "School of Natural Sciences, University of California Merced, Merced, California, USA",
    "Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA",
    "Earth System Science and Oceans Departments, Stanford Doerr School of Sustainability, Stanford University, Stanford, CA, USA",
    "School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia",
    "Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin-Madison, Madison, WI, USA",
    "Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada",
    "Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA",
    "School of Environmental Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, UK",
    "Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA",
    "Center of Microbiome Science, The Ohio State University, Columbus, OH, USA",
    "DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. fschulz@lbl.gov"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 21,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Juan C. Villada",
      "orcid": "0000-0003-2216-4279"
    },
    {
      "affs": [
        1,
        2,
        3
      ],
      "name": "Yumary M. Vasquez",
      "orcid": "0000-0001-6006-8873"
    },
    {
      "affs": [
        1
      ],
      "name": "Gitta Szabó",
      "orcid": "0000-0002-0397-3022"
    },
    {
      "affs": [
        1,
        4,
        5
      ],
      "name": "Ewan Whittaker-Walker"
    },
    {
      "affs": [
        1
      ],
      "name": "Miguel F. Romero"
    },
    {
      "affs": [
        6,
        7
      ],
      "name": "Sarina Qin",
      "orcid": "0000-0001-6810-7101"
    },
    {
      "affs": [
        1
      ],
      "name": "Neha Jacob Varghese",
      "orcid": "0000-0003-0580-0675"
    },
    {
      "affs": [
        1
      ],
      "name": "Emiley A. Eloe‐Fadrosh",
      "orcid": "0000-0002-8162-1276"
    },
    {
      "affs": [
        1
      ],
      "name": "Nikos C. Kyrpides",
      "orcid": "0000-0002-6131-0462"
    },
    {
      "affs": [
        8,
        1
      ],
      "name": "Ramūnas Stepanauskas",
      "orcid": "0000-0003-4458-3108"
    },
    {
      "affs": [
        9,
        1
      ],
      "name": "Christopher A. Francis",
      "orcid": "0000-0001-7557-631X"
    },
    {
      "affs": [
        10,
        1
      ],
      "name": "Rick Cavicchioli"
    },
    {
      "affs": [
        11
      ],
      "name": "Trina McMahon"
    },
    {
      "affs": [
        12
      ],
      "name": "Steven Hallam",
      "orcid": "0000-0002-4889-6876"
    },
    {
      "affs": [
        13
      ],
      "name": "Wen‐Tso Liu",
      "orcid": "0000-0002-8700-9803"
    },
    {
      "affs": [
        14
      ],
      "name": "Thomas Möck",
      "orcid": "0000-0001-9604-0362"
    },
    {
      "affs": [
        15
      ],
      "name": "James M. Tiedje",
      "orcid": "0000-0002-8992-6218"
    },
    {
      "affs": [
        16
      ],
      "name": "Jiarong Guo",
      "orcid": "0000-0002-6903-5418"
    },
    {
      "affs": [
        1
      ],
      "name": "Axel Visel",
      "orcid": "0000-0002-4130-7784"
    },
    {
      "affs": [
        1
      ],
      "name": "Tanja Woyke",
      "orcid": "0000-0002-9485-5637"
    },
    {
      "affs": [
        17
      ],
      "name": "Frederik Schulz",
      "orcid": "0000-0002-4932-4677"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/e88dk5qq39af5.bib",
  "cited_by": 10,
  "doi": "10.1038/s41587-026-03213-1",
  "fulltext_url": null,
  "id": "e88dk5qq39af5",
  "issns": [
    "0733-222X",
    "1087-0156",
    "1546-1696",
    "2331-3684"
  ],
  "landing_url": "https://doi.org/10.1038/s41587-026-03213-1",
  "language": "en",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "openalex",
      "1312|Genomics and Phylogenetic Studies"
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  "openalex": "W4410906186",
  "pdf_url": null,
  "pmcid": null,
  "pmid": "42675165",
  "published": "2026-08-31",
  "publisher": "Nature Portfolio",
  "ris": "https://research.draconitic.com/paper/e88dk5qq39af5.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:46Z",
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      "url": "https://doi.org/10.1038/s41587-026-03213-1"
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
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  ],
  "title": "A genomic catalog of Earth’s bacterial and archaeal symbionts",
  "title_text": "A genomic catalog of Earth’s bacterial and archaeal symbionts",
  "type": "peer-reviewed",
  "updated_at": "2026-11-05T13:20:47Z",
  "url": "https://research.draconitic.com/paper/e88dk5qq39af5",
  "venue": "Nature Biotechnology",
  "versions": []
}