'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 10,000 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 page!

Background information for the current release (LTPs115, March 2014)

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 (Initiates file downloadtable2.pdf). 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 597 new distinct species (Initiates file downloadtable1.pdf) have been incorporated into the dataset of the 16S rRNA-based LTP release 115. The tree displayed is inherited from the previous released LTP 111 and newly incorporated sequences were added using the parsimony tool impremented by ARB, filtering nucleotide positions below 10% identity. Other changes on the dataset can be found in the document Initiates file downloadreadme_LTPs115.pdf.

As a new feature, the field 'NJ_support_pk4_ltp' has been included. Entries labeled in this field are a selection of good quality sequences representing most taxa along the Living Tree. We recommend to include this set of 758 species (Initiates file downloadtable3.pdf) in Neighbour Joining analysis to correct distance biases generated when different taxa are unevenly populated in a sample. This method is described in The Prokaryotes Fourth Edition (PK4), in chapter 'Harmonizing trees for pk4' (Munoz et al. in press).

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.

The 23S rRNA-based LTP release 102 (Opens external link in new windowfile archive) contains 792 type strains for which adequate LSU entries exist.

S.O.S - Sequencing the 'Orphan' Species

During the last few years the Living Tree Project revealed that in total 552 “orphan” species had to be excluded from the reference trees. Among them, 322 type strains were not represented by a SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team coordinated a network of researchers and culture collections to improve the situation by (re)-sequencing the type strains of these “orphan” species.

We have accomplished the 16S rRNA gene sequencing of 351 type strains. 201 species could not be sequenced because either cultivable type strains were not available (121), or the cultures had either been lost or were never deposited in first place (66), or due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms to help solve some of these issues.

SOS Consortium partners:  ATCC, BZF (at University of Hamburg), CECT, CIP, CCUG, DSMZ, JCM, ICMP, BCCM/LMG, NBRC, NCCB, and LTP team.

 

Reference: Yarza P, Spröer C, Swiderski J, et al. 2013. Sequencing Orphan Species initiative (SOS): filling the gaps in the 16S rRNA gene sequence database for all species with validly published names. Syst Appl Microbiol 36:69-73. Opens external link in new windowdoi:10.1016/j.syapm.2012.12.006

Downloads (latest release)

Released: March 2014 LTPs115
Release information:Initiates file downloadreadme_LTP_s115.pdf

Description of fields introduced by the LTP:

NEW FIELD

 

Initiates file downloadLTP_description_of_fields.pdf
Export filter to extract data from LTP-ARB databases:Initiates file downloadexport_filter
LTP datasets based on SILVA release 115 (ARB format):   Initiates file downloadLTPs115_SSU.arb
LTP datasets (CSV format):Initiates file downloadLTPs111_SSU.csv
Trees SSU:Initiates file downloadFull Tree (pdf), Initiates file downloadOverview (pdf), Initiates file downloadNewick format.

Alignments SSU:

Initiates file downloadTypestrains (aligned), Initiates file downloadTypestrains (compressed)
List of changes in the SSU database (added/deleted/modified species):Initiates file downloadTable1.pdf

New entries with outdated submission names:

Support sequences for Neighbour-Joining analyses:

Initiates file downloadTable2.pdf

Initiates file downloadTable3.pdf

Additional files and former releases are available at theOpens external link in new windowfile archive

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., Yarza, P., 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
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.
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.
Ribocon GmbH. 28359 Bremen, Germany

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