metagRoot: a comprehensive database of protein families associated with plant root microbiomes
The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.
Authors
- Nikos C. Kyrpides (ORCID: https://orcid.org/0000-0002-6131-0462)
- Dimitrios J. Stravopodis (ORCID: https://orcid.org/0000-0002-9535-2134)
- Eleni Aplakidou (ORCID: https://orcid.org/0009-0002-0737-4817)
- Aydın Buluç (ORCID: https://orcid.org/0000-0001-7253-9038)
- Fotis A. Baltoumas (ORCID: https://orcid.org/0000-0002-2870-2931)
- Evangelos Karatzas (ORCID: https://orcid.org/0000-0001-9132-8981)
- Ilias Georgakopoulos‐Soares (ORCID: https://orcid.org/0000-0003-3641-1488)
- Ioannis Iliopoulos (ORCID: https://orcid.org/0000-0002-9079-0565)
- Ioannis Z. Emiris (ORCID: https://orcid.org/0000-0002-2339-5303)
- Georgios A. Pavlopoulos (ORCID: https://orcid.org/0000-0002-4577-8276)
- Maria N Chasapi
- Iro N Chasapi
Institutions
- University of Crete (GR)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- National and Kapodistrian University of Athens (GR)
- Czech Academy of Sciences, Institute of Chemical Process Fundamentals (CZ)
- Bioinformatics Institute (RU)
- Athena Research and Innovation Center In Information Communication & Knowledge Technologies (GR)
- Alexander Fleming Biomedical Sciences Research Center (GR)
- Penn State Milton S. Hershey Medical Center (US)
- University of California, Berkeley (US)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-08-16
- DOI
- https://doi.org/10.1093/nar/gkaf862
- Citations
- 1
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- Hellenic Foundation for Research and Innovation
- Office of Science
- Huck Institutes of the Life Sciences
- Penn State College of Medicine