This repository contains 18S rRNA sequences from the SILVA 138 release, nematode 18S rRNA published in GenBank, and some additional nematode 18S rRNA sequences produced in our lab. Taxonomic ranks for nematodes were fixed accoding to WoRMS database. Files include QIIME2 format (i.e., qza files) and orginal text files for sequences (.fna) and taxonomy (.tsv). Large files were zipped to reduce their size.
MeioDB v2 is the second version of the Bik lab group’s curated SILVA database, containing long (1,200 bp) and short-length (250bp-700bp) 18S rRNA reference sequences for a broad range of eukaryotes, with particular emphasis on marine nematodes (Nematoda).
MeioDB v2 builds on MeioDB v1 with additional short (250bp-700bp) reference sequences for Nematoda (primarily terrestrial nematodes) added from GenBank.
Additional sequences added: documentation/2026-02-09-additional-sequences-added-v2.csv
This is not the most updated version – please refer to the most recent release.
MeioDB v1 is the first version of the Bik lab group’s curated SILVA database, containing long (1,200 bp) and short-length (250bp-700bp) 18S rRNA reference sequences for a broad range of eukaryotes, with particular emphasis on marine nematodes (Nematoda).
This database contains the 99% sequence similarity clustered 18S rRNA OTUs from the original SILVA 138 release. Sequences that contain chimeric taxonomic labels (taxonomy strings for which the species does not match the phylum, due to SILVA’s partial curation of taxonomy at the species level but not at higher taxonomic levels) were removed. Additional short-length sequences targeting the V1-V2 region of the 18S rRNA gene generated from three studies were added (Macheriotou et al. 2019, Fonseca et al., 2012, and unpublished DNA sequences generated as part of Lallias et al., 2015). Nematode Sanger sequences initially generated by Lallias et al (2015) were published in De Santiago et al. (2025). Nematode taxonomic strings were curated using Linnaean hierarchies for standardization, following the official taxonomic nomenclature from the World Register of Marine Species (WoRMS) for reference.
Chimeric sequences removed: documentation/2026-02-09-chimeric-sequences-removed-v1.csv
Additional sequences added: documentation/2026-02-09-additional-sequences-added-v1.csv
References:
- Fonseca, V. G., B. Nichols, D. Lallias, et al. 2012. “Sample Richness and Genetic Diversity as Drivers of Chimera Formation in nSSU Metagenetic Analyses.” Nucleic Acids Research 40, no. 9: e66.
- Lallias, D., J. G. Hiddink, V. G. Fonseca, et al. 2015. “Environmental Metabarcoding Reveals Heterogeneous Drivers of Microbial Eukaryote Diversity in Contrasting Estuarine Ecosystems.” ISME Journal 9, no. 5:1208–1221.
- Macheriotou, L., K. Guilini, T. N. Bezerra, et al. 2019. “Metabarcoding Free-Living Marine Nematodes Using Curated 18S and CO1 Reference Sequence Databases for Species-Level Taxonomic Assignments.” Ecology and Evolution 9, no. 3: 1211–1226.
- WoRMS Editorial Board (2024). World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. Accessed 2024-05-01. doi:10.14284/170
- De Santiago, A., Pereira, T. J., Ferrero, T. J., Barnes, N., Lallias, D., Creer, S., & Bik, H. M. (2025). Persistent gaps and errors in reference databases impede ecologically meaningful taxonomy assignments in 18S rRNA studies: A case study of terrestrial and marine nematodes. Environmental DNA (Hoboken, N.J.), 7(2), e70080.