A valuable resource particularly for microbial taxonomists
After more than 1 year of work, the LTP database has been released.
The joint effort of the LTP team under the support of Elsevier, and specifically Systematic and Applied Microbiology, has resulted in the current release available at https://imedea.uib-csic.es/mmg/ltp/.
The new LTP database contains the sequences of all type strains with validly published names until December 2020, as well as all sequences of new species not yet listed in the notification lists of the IJSEM, but published in this journal.
This release has three major features:
- An improved alignment:
The LTP database in ARB format contains a new alignment that is derived from the improvement of the former universal alignment, but which has accommodated the new released sequences as well as it has been thoroughly revised. In addition, the LTP offers several conservational filters and gap and termini filters useful to reconstruct phylogenies and evaluate topologies.
- New reconstructions of the global phylogeny of the classified species:
Two trees have been prepared, one with the best sequences and another containing in addition the sequences with more compromised phylogenetic signals. According to authors, this may be the best and most robust 16S rRNA gene phylogenies yet reconstructed. The trees are the result of evaluation of multiple maximum likelihood reconstructions.
- List of taxa in the need to be evaluated:
In the accompanying manuscript that describes this release (Ludwig et al., 2021), the process of curation and tree reconstruction are explained and lists of taxa that may be susceptible of being evaluated and perhaps reclassified are provided. Taxa that do not fit in their overall taxonomic and phylogenetic framework have been highlighted.
See the information at:
Ludwig, W., Viver, T., Westram, R., Gago, J.F., Bustos-Caparros, E., Knittel, K., Amann, R., Rossello-Mora, R. (2021) Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 40: 126218. DOI: 10.1016/j.syapm.2021.126218.
Elsevier has granted this manuscript 6 months of free access for all who are interested in this new release.
Since December 2020, more than 400 species have been published and also there have been important changes in the classification (for example the Deltaproteobacteria). In about 1 month time, the LTP will be updated to offer the best proxy to the phylogeny of the classified taxa.
Enter in https://imedea.uib-csic.es/mmg/ltp/ to download the database and accompanying information, and register for a mailing list of users that want to get updated with the news and releases.