A genomic catalog of Earth’s bacterial and archaeal symbionts

SymGs data consortium (2026) A genomic catalog of Earth’s bacterial and archaeal symbionts. Nature Biotechnology. ISSN 1087-0156

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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.

Item Type:	Article
Additional Information:	Data availability: All FASTA files of genomes included in the SymGs catalog are hosted in its NERSC repository for easy bulk download (https://portal.nersc.gov/cfs/nelli/symgs/) and archived on Zenodo (https://doi.org/10.5281/zenodo.20399071)103. All files are publicly available and immediately accessible for download. The symclatron database is hosted on GitHub (https://github.com/NeLLi-team/symclatron/releases/tag/db-latest). We did not generate new sequencing data for this study. All environmental DNA sequencing samples analyzed were obtained from the IMG/M database. Direct download links to the Joint Genome Institute (JGI) Data Portal for each assembly project are provided through a dedicated Zenodo archive (https://doi.org/10.5281/zenodo.20600438)104. All the assemblies of microbiome samples, from which we predicted symbionts, are individually cited in Supplementary Table 4. The JGI is a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab). To accommodate the massive scale of these datasets, the JGI Data Portal offers highly flexible and scalable retrieval methods. Users can download data manually through a web browser, transfer large-scale datasets efficiently using Globus endpoints or command line tools or access the data programmatically through the JGI API. Data providers were individually contacted in accordance with the JGI Data Policy at least 1 month before manuscript submission. The complete set of symclatron predictions and associated metadata is available in Supplementary Table 5. Code availability: The code repository for NSGTree is publicly available on GitHub (https://github.com/NeLLi-team/nsgtree). The symclatron software, along with all accompanying models, databases and comprehensive documentation, is publicly available as an open-source project on GitHub (https://github.com/NeLLi-team/symclatron). To ensure robust reproducibility and ease of use for the community, the tool supports multiple streamlined installation options through modern package managers, including pixi, mamba and conda. The software is cross-platform, natively supporting both Linux and macOS (including Apple Silicon) environments. Strict semantic versioning has been implemented through GitHub Releases (https://github.com/NeLLi-team/symclatron/releases) and system tags (the current being version 0.10.10). The exact code, neural network models and databases used to generate the findings in this study remain permanently archived and readily accessible to users and the broader scientific community.
Uncontrolled Keywords:	biotechnology,bioengineering,applied microbiology and biotechnology,biomedical engineering,molecular medicine ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School:	Faculty of Science > School of Environmental Sciences University of East Anglia Research Groups/Centres > Theme - ClimateUEA
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Centre for Ocean and Atmospheric Sciences Faculty of Science > Research Groups > Environmental Biology Faculty of Science > Research Groups > Wolfson Centre for Advanced Environmental Microbiology
Related URLs:	https://www.scopus.com/pages/publication...
Depositing User:	LivePure Connector
Date Deposited:	30 Sep 2026 13:15
Last Modified:	30 Sep 2026 13:15
URI:	https://ueaeprints.uea.ac.uk/id/eprint/104675
DOI:	10.1038/s41587-026-03213-1

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