'The All-Species Living Tree' Project
Five international partners together with the journal Systematic and Applied Microbiology (SAM) started “The All-Species Living Tree" Project (LTP) to provide a valuable resource particularly for microbial taxonomists. The aim of the project is to reconstruct separate and curated 16S and 23S rRNA datasets and trees spanning all sequenced type strains of the hitherto classified species of Archaea and Bacteria.
These datasets and trees will be regularly updated by adding new species with validly published names appearing monthly in the validation and/or notification lists of the International Journal of Systematic and Evolutionary Microbiology (IJSEM). For this purpose, the SAM executive editors, together with the responsible teams of the ARB, SILVA, and LPSN projects (
www.arb-home.de, www.arb-silva.de, and www.bacterio.cict.fr, respectively), have prepared two rRNA datasets, currently containing more than 8,800 SSU and 750 LSU rRNA gene sequence entries, each representing a single type strain of a classified species.
Upcoming releases will be announced in the 
News section of the SILVA main page!
Background information for the current release (LTPs106, August 2011)
The selection of sequences has been undertaken manually due to a high error rate in the names and information fields provided for the publicly deposited entries. In addition, among multiple entries for a single type strain, the best quality sequence was selected for the project. For genomes with multiple copies of the ribosomal operon, all paralogs diverging in more than 2% were selected. The living tree datasets provide curated entries and the best quality sequences with a manually checked alignment.
In total, 274 new distinct species (
table1.pdf) have been incorporated into the dataset and tree of the 16S rRNA-based LTP release 106. Using the ARB parsimony tool, the sequences were inserted into the existing LTP_s104 tree, based on a single phylogenetic reconstruction using the maximum likelihood algorithm RAxML and a dataset containing 10,950 single entries (LTP_s100). The topology of the current tree was validated by comparing a collection of taxa-specific and broad-range trees, using different reconstruction approaches, subsets of sequences, and alignments ( Yarza et al., 2010)
No further upgrading has been carried out for the LSU dataset due to the scarce increase of 23S rRNA gene sequences in the public repositories. The 23S rRNA-based LTP release 102 ( file archive) contains 792 type strains for which adequate LSU entries exist.
Trees are dynamic structures that change on the basis of the quality and availability of the data used for their calculation. Therefore, the addition of new type strain sequences in subsequent releases may help to resolve certain branching orders that appear ambiguous in this release.
S.O.S - Sequencing the 'Orphan' Species
In the course of curating our type strain datasets, we found that about 7% of the classified species of Bacteria and Archaea with validly published names did not have a SSU gene sequence entry or the one deposited was of insufficient quality to be considered for our purposes.
Consequently, 11 international partners (DSMZ, CCUG, NBRC, CIP, LMG, CECT, ATCC, JCM, NCCB, ICMP, and BZF) have already joined us in a novel initiative to sequence these orphan type strains. It is expected that we will soon achieve the complete set of 16S rRNA gene sequences for all classified species of Bacteria and Archaea with validly published names.
Downloads (latest release)
Released: August 2011 | LTPs106 |
Release information: | |
Description of fields introduced by the LTP: | |
Export filter to extract data from LTP-ARB databases: | |
LTP datasets based on SILVA release 106 (ARB format): | |
LTP datasets (CSV format): | |
Trees SSU: | |
Alignments SSU: | |
List of changes in the SSU database (added/deleted/modified species): | |
New entries with outdated submission names: | |
Additional files and former releases are available at the |
Newick formatPaper & Citation
LTPs104_SSU release:
Munoz, R., P. Yarza, W. Ludwig, J. Euzéby, R. Amann, K.H. Schleifer, F.O. Glöckner, and R. Rosselló-Móra. 2011. Release LTPs104 of the All-Species Living Tree. Syst Appl Microbiol 34:169-170. 
doi:10.1016/j.syapm.2011.03.001
LTP, 23S rRNA paper:
Yarza, P., W. Ludwig, J. Euzeby, R. Amann, K. H. Schleifer, F. O. Glöckner, and R. Rossello-Mora. 2010. Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291-299. 
doi:10.1016/j.syapm.2010.08.001
LTP, 16S rRNA paper:
Yarza, P., M. Richter, J. Peplies, J. Euzeby, R. Amann, K. H. Schleifer, W. Ludwig, F. O. Glöckner, and R. Rossello-Mora. 2008. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241-250. 
doi:10.1016/j.syapm.2008.07.001
The Living Tree Project Partners
Rosselló-Móra, R., Yarza, P., Muńoz, R.
Institut Mediterrani d’Estudis Avançats (CSIC-UIB), E-07004 Esporles, Mallorca, Spain Schleifer, K.-H., Ludwig, W.
Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany Euzéby, J
Société de Bactériologie Systématique et Vétérinaire (SBSV) & École Nationale Vétérinaire de Toulouse (ENVT), F-31076 Toulouse cedex 03, France Glöckner, F.O., Amann, R., Richter, M.
Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany Peplies, J.
Ribocon GmbH, D-28359 Bremen, Germany
For feedback and questions please send a message to:
living-tree (at) arb-silva.de