The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as
ARB, SILVA rRNA database project, and
LPSN
List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclature ...
, with the aim of assembling a database of
16S rRNA 16S rRNA may refer to:
* 16S ribosomal RNA
16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.
The g ...
sequences of all validly published species of ''
Bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
'' and ''
Archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
''.
At one stage,
23S
The 23S rRNA is a 2,904 nucleotide long (in ''Escherichia coli, E. coli'') component of the large subunit (50S) of the bacterial/archean ribosome and makes up the peptidyl transferase center (PTC). The 23S rRNA is divided into six secondary st ...
sequences were also collected,
but this has since stopped.
Currently there are over 10,950 species in the aligned dataset and several more are being added either as new species are discovered or species that are not represented in the database are sequenced. Initially the latter group consisted of 7% of species.
Similar (and more recent) projects include the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which focused on whole genome sequencing of bacteria and archaea.
Tree
The tree was created by
maximum likelihood
In statistics, maximum likelihood estimation (MLE) is a method of estimation theory, estimating the Statistical parameter, parameters of an assumed probability distribution, given some observed data. This is achieved by Mathematical optimization, ...
analysis without bootstrap: consequently accuracy is traded off for size and many phylum level clades are not correctly resolved (such as the Firmicutes). (Eukaryotes not present in analysis). This phylogeny is a summary of the 16S rRNA based LTP_01_2022 and contains all type species with validly published names up to January 2022.
See also
*
Branching order of bacterial phyla (Woese, 1987)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.
The branching order proposed by Carl Woese was based on molecular phylogeny, which was considered revolutionary as all p ...
*
Branching order of bacterial phyla (Gupta, 2001)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic ex ...
*
Branching order of bacterial phyla (Cavalier-Smith, 2002)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2002 and 2004 by Thomas Cavalier-Smith. In this frame of work, the branching order of the major lineage of bacteria are determined based on some mor ...
*
*
Branching order of bacterial phyla (Battistuzzi et al.,2004)
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2004 by Battistuzzi and Hedges, note the coinage of the taxa Terrabacteria and Hydrobacteria.
See also
* Branching order of bacterial phyla (Woes ...
*
Branching order of bacterial phyla (Ciccarelli et al., 2006)
*
*
Bacterial phyla
*
List of Archaea genera
This article lists the genera of the Archaea. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI).
Phylogeny
National Center for ...
*
List of bacteria genera This article lists the genera of the bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI). However many taxonomic names are ...
*
List of bacterial orders
This article lists the orders of the Bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI)
and the phylogeny is based on 16S ...
*
LPSN
List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclature ...
, list of accepted bacterial and archaeal names
References
External links
* http://www.arb-silva.de/projects/living-tree/
{{DEFAULTSORT:All-Species Living Tree Project
Bacteria
Bacteriology
Microbiology
Taxonomy (biology)
Systems of bacterial taxonomy