metagRoot: a comprehensive database of protein families associated with plant root microbiomes

Journal Article · Mon Sep 01 00:00:00 EDT 2025 · Nucleic Acids Research (NAR)

DOI:https://doi.org/10.1093/nar/gkaf862· OSTI ID:2997770

Chasapi, Maria N; Chasapi, Iro N; Aplakidou, Eleni; Baltoumas, Fotis A; Karatzas, Evangelos; Iliopoulos, Ioannis; Stravopodis, Dimitrios J; Emiris, Ioannis Z; Buluç, Aydin; Georgakopoulos-Soares, Ilias; Kyrpides, Nikos C; Pavlopoulos, Georgios A

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.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: US Department of Energy; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22), Scientific User Facilities Division (SC-22.3 )
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 2997770
• Journal Information: Nucleic Acids Research (NAR), Journal Name: Nucleic Acids Research (NAR) Journal Issue: D1 Vol. 54
• Country of Publication: United States
• Language: English