'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 are 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.net, respectively), have prepared two rRNA datasets, currently containing more than 12,900 SSU and 1,600 LSU rRNA gene sequence entries, each representing a single type strain of a classified species, except for six species with two copies of the 16S rRNA gene that show identities below the species threshold.

Upcoming releases will be announced in the News section of the SILVA page!

Current release, February 2017: LTPs128_SSU and LTPs123_LSU

Effective publication, notification and validation of new taxa in IJSEM has been tracked up to issue 66 [6]. Newly incorporated sequences had their name with standing in nomenclature updated in LTP (Initiates file downloadcorrect_names_LTPs128_SSU.xlsx). Among multiple entries available 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 of SSU rRNA diverging in more than 2% were selected. The new LSU dataset was build from the previous LSU release and includes species with standing in nomenclature up to September 2015 (IJSEM issue 65 [9]). The LSU sequences had their names updated (Initiates file downloadcorrect_names_LTPs123_LSU.xlsx) and each represents a single type strain. The Living Tree Project datasets provide curated entries and the best quality sequences with manually checked alignments.

 

New features:

As requested by many users LTP datasets are now supplied in fasta format compatible with local blast pipelines. Also, a new field of metadata in the SSU database called phyl_ltp capitulates the phylogenetic path of each species as a sequence of monophyletic branch identifiers in the LTPs128_SSU tree. This new field aims to highlight the difference between the LTP phylogeny (phyl_ltp) and the accepted nomenclature (tax_ltp).

 

In total 1,035 new distinct species have been incorporated into the dataset of the 16S rRNA-based LTP release 128. The tree displayed is inherited from the previous released LTP 123. Newly incorporated sequences were added using the parsimony tool impremented in ARB and filtering alignment positions with less than 30% nucleotide frequency. The update of the 23S rRNA-based LTP release 123 includes 912 new distinct species. The 23S rRNA-based phylogenetic tree was re-calculated using RAxML with GTR-GAMMA distances and 'new rapid hill climbing' algorith.

Trees are dynamic structures that change on the basis of the quality and availability of data used for their calculation. Therefore, the addition of new type strain sequences in subsequent releases may help to resolve certain branching orders appearing ambiguous in this release. Partial sequences might affect the stability of tree reconstructions. Red color alerts of sensibly short sequences in LTP.arb datasets; 96 sequences shorter than 1,300 nucleotides in LTPs128_SSU and 13 sequences shorter than 2,000 nucleotides in LTPs123_LSU. We recommend to insert these sequences by parsimony into robust topologies.

Complete information with links and downloads is available in the document Initiates file downloadreadme_LTP_SSUs128_LSUs123.pdf

Downloads (release: February 2017)

Description of fields introduced by the LTPInitiates file downloadLTPs128_description_of_fields.pdf
Export filter to extract fasta files with LTP fieldsInitiates file downloadfasta_LTPs128.eft
Export filter to extract blast compatible fastasInitiates file downloadfasta_LTPs128_ncbi_blast.eft
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Effective update: June 2016LTPs128_SSU  (16S rRNA)

Release information

Initiates file downloadreadme_LTP_SSUs128_LSUs123.pdf
LTP.arb dabase extracted from SILVA s128Initiates file downloadLTPs128_SSU.arb
LTP spreadsheet databaseInitiates file downloadLTPs128_SSU.csv
SSU treeFull Tree (Initiates file downloadpdf), Full Tree (Initiates file downloadnewick, with header), Overview (Initiates file downloadpdf)
Fasta datasetTypestrains (Initiates file downloadwith alignment), Typestrains (Initiates file downloadno alignment)
Fasta dataset compatible with local blast (NEW)Typestrains_blastdb (Initiates file downloadno alignment)
List of changes in the SSU databaseInitiates file downloadchanges.xlsx
New entries with outdated submission namesInitiates file downloadcorrect_names.xlsx
List of orphan speciesInitiates file downloadorphans.xlsx
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Effective update: September 2015LTPs123_LSU  (23S rRNA)
Release informationInitiates file downloadreadme_LTP_SSUs128_LSUs123.pdf
LTP.arb dabase extracted from SILVA s123Initiates file downloadLTPs123_LSU.arb
LTP spreadsheet databaseInitiates file downloadLTPs123_LSU.csv
LSU treeFull Tree (Initiates file downloadpdf), Full Tree (Initiates file downloadnewick, with header), Overview (Initiates file downloadpdf)
Fasta datasetTypestrains (Initiates file downloadwith alignment), Typestrains (Initiates file downloadno alignment)
Fasta dataset compatible with local blast (NEW)Typestrains_blastdb (Initiates file downloadno alignment)
List of changes in the LSU databaseInitiates file downloadchanges.xlsx
New entries with outdated submission namesInitiates file downloadcorrect_names.xlsx
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Additional files and past releases available at:Opens internal link in current windowfile archive, folder [living_tree]

Paper & 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

Living Tree Project Team

Opens external link in new window Rosselló-Móra, R., Muñoz, 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


Glöckner, F.O., Amann, R.
Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany

 

 

For feedback and questions please send a message to:

living-tree (at) arb-silva.de 

Collaborators

Opens external link in new window Peplies, J., Richter, M., Yarza, P.
Ribocon GmbH. 28359 Bremen, Germany

 De Smet, W., Dawyndt, P.
Straininfo. Department of Applied Mathematics and Computer Science, Ghent University. 9000 Gent, Belgium