SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity
Maria S. Chuvochina, Jan Gerken, Martinique Frentrup, Yeliz Sandikci, Robin Goldmann, Heike M. Freese et al. · 2025 · 106 citationsRead the paper
Since 2007, the SILVA database (https://www.arb-silva.de/) has served as a comprehensive resource providing quality-checked, aligned, and classified ribosomal RNA sequences for the scientific community worldwide. The database provides manually curated taxonomic classifications for the three domains of life, standardized reference datasets, and tools for classifying microbial diversity. SILVA's impact has been recognized in its designation as ELIXIR Core Data Resource and Global Core Biodata Resource. The integration of SILVA into the DSMZ Digital Diversity consortium (D3; https://hub.dsmz.de) in 2023 marked a significant update, ensuring the long-term sustainability and continued development of the resource. Apart from moving to a new hosting institution, this integration facilitates data interoperability and standardization among SILVA, LPSN, StrainInfo, and other D3 databases. New developments this year include a redesigned website consistent with the DSMZ corporate identity, DOI assignments for all SILVA releases to enhance data citation and support the FAIR data principles, and the provisioning of QIIME2, DADA2, and KRAKEN2 classifiers. Additionally, the EukMap application has been redeveloped as a curation and visualization tool called TaxMap. In anticipation of the next data release, we outline recent developments and the current state of the database, its relation with other D3 resources, and its future directions.
What the full text shows
Deployed in practice- Implementation of nonredundant reference datasets (Ref NR 99) for SSU and LSU to improve computational efficiency and tree clarity. — 99% identity threshold (Starting from release 115 for SSU and 138.1 for LSU)
- Creation of Incertae sedis placeholder taxa for unassigned sequences or those known only from environmental sequences. — 2726 total taxa (1524 genera, 776 families, 279 orders, 112 classes, 12 phyla) (Starting from release 138.2)
- Adoption of validly published phylum names for Bacteria and Archaea under the ICNP. — 43 phylum names (Starting from release 138.2)
- Transition of clustering tool from UCLUST to VSEARCH for improved accuracy and transparency. (SILVA release 138)
- Setup
- Global rRNA database covering three domains of life, integrated into the DSMZ Digital Diversity (D3) consortium.
- How
- The resource integrates manually curated taxonomic classifications from LPSN, GTDB, and UniEuk with rRNA sequences. It employs VSEARCH for 99% identity clustering to create nonredundant reference sets and utilizes the de.NBI cloud for scalable job processing.
- Limitations
- 16S rRNA is insufficient as a species-specific marker in some lineages due to evolutionary stasis, limiting classification to the genus level. · TaxMap does not fetch LPSN data continuously, relying on periodic snapshots. · TaxMap cannot import taxa with missing descendants due to technical constraints.
Summarized by Gemma 4 from the open-access full text · 13 Oct 2026. Read it