Add latest emu and lemur databases (2025) from Mike

[ppreshant]

Plan

Updated db for emu : emu_database/emu_db_mar2026.zip is in now.

• Implement the download using aria2 from github raw link (similar to lemur DB)
  • Figure out best tool for CLI download: wget vs axel
• Replace the emu/download_db module and
• archive the old one downloading from OSF?
  • (Could archive in a tag / create an OR condition to choose the old vs new module)

Context

The emu db in use is from the first publication (2023) and is definitely outdated. Eddy Huang is recently working on an update for lemur (it's not a priority as of 20/Oct/25 though)

We need to make a fresh db, especially since phyla names have been updated in 2024 (source: A Oren - npj Biofilms and Microbiomes, 2024

A few changes in phylum names summarized here from the source above

For example, the names Pseudomonadota, Bacillota, Actinomycetota, and Bacteroidota (...) were introduced for the bacterial taxa formerly known as Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, respectively. The archaeal phyla formerly known as Euryarchaeota, Crenarchaeota and Thaumarchaeota now also have validly published names: Methanobacteriota, Thermoproteota, and Nitrososphaerota, with type genera Methanobacterium Kluyver and van Niel 1936 (Approved Lists 1980), Thermoproteus Zillig and Stetter 1982, and Nitrososphaera Stieglmeier et al. 2014, respectively. The older phylum names should no longer be used, as only phyla names based on the stem of a designated type genus and the –ota ending are validly published under the rules of the ICNP. As of 3 February 2024, names of 49 phyla were validly published. ..

This should also solve issues like #33 properly

[ppreshant]

Notes

Updated db for emu : emu_database/emu_db_mar2026.zip is in now.

• Need to get it onto a downloadable place like zenodo or figure out a curl solution from the github repo?

Creating DBs in future. Implement for lemur too?
Another lab independently created a DB for emu (along with some slurm scripts to automate DB creation for the future) in UFDuttonLab/emu-database-update

A reproducible pipeline for rebuilding the EMU 16S rRNA reference database from current rrnDB and NCBI RefSeq sources. The default EMU database was built from sources downloaded in September 2020 and has not been updated since. ; this is a march 2026 update