LVTree Viewer: An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics

We describe an interactive viewer for the All-Species Living Tree (LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner. In view of the fact that the present prokaryotic systematics is largely based on 16S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla (Proteobacteria and Firmicutes) to monophyletic clusters.

[1]  S. Spring,et al.  Caldithrix palaeochoryensis sp. nov., a thermophilic, anaerobic, chemo-organotrophic bacterium from a geothermally heated sediment, and emended description of the genus Caldithrix. , 2010, International journal of systematic and evolutionary microbiology.

[2]  Guanghong Zuo,et al.  CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy , 2015, Genom. Proteom. Bioinform..

[3]  Zhao Xu,et al.  CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes , 2009, Nucleic Acids Res..

[4]  P. de Vos,et al.  Six novel Arthrobacter species isolated from deteriorated mural paintings. , 2005, International journal of systematic and evolutionary microbiology.

[5]  Raul Munoz,et al.  Release LTPs104 of the All-Species Living Tree. , 2011, Systematic and applied microbiology.

[6]  P. Lawson,et al.  Intrageneric relationships of members of the genus Fusobacterium as determined by reverse transcriptase sequencing of small-subunit rRNA. , 1991, International journal of systematic bacteriology.

[7]  W. Moore,et al.  Gemmiger formicilis, n.gen., n.sp., an Anaerobic Budding Bacterium from Intestines , 1975 .

[8]  K. Schleifer,et al.  The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. , 2008, Systematic and applied microbiology.

[9]  I. Robinson,et al.  Proposal for an Amended Classification of Anaerobic Mollicutes , 1987 .

[10]  P. Vos,et al.  Judicial Commission of the International Committee on Systematic Bacteriology; IXth International (IUMS) Congress of Bacteriology and Applied Microbiology , 2000 .

[11]  M. Collins,et al.  Reclassification of Bacteroides furcosus Veillon and Zuber (Hauduroy, Ehringer, Urbain, Guillot and Magrou) in a New Genus Anaerorhabdus, as Anaerorhabdus furcosus comb. nov. , 1986 .

[12]  S. Spring,et al.  Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGAT) , 2013, Standards in genomic sciences.

[13]  P. Lawson,et al.  Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring. , 2013, International journal of systematic and evolutionary microbiology.

[14]  S. Spring,et al.  Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage. , 2003, International journal of systematic and evolutionary microbiology.

[15]  T. Fujita,et al.  Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb , 2014, International journal of systematic and evolutionary microbiology.

[16]  J. Winter,et al.  Acetomicrobium faecalis spec, nov., a strictly anaerobic bacterium from sewage sludge, producing ethanol from pentoses , 1987 .

[17]  J. Handelsman,et al.  Status of the Microbial Census , 2004, Microbiology and Molecular Biology Reviews.

[18]  Pha Sneath,et al.  International code of nomenclature of bacteria (1990 revision). , 1992 .

[19]  Cecil M. Lewis,et al.  Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru. , 2015, Anaerobe.

[20]  K. Williams,et al.  Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. , 2013, International journal of systematic and evolutionary microbiology.

[21]  Gerhard Wanner,et al.  A New Lineage of Halophilic, Wall-Less, Contractile Bacteria from a Brine-Filled Deep of the Red Sea , 2008, Journal of bacteriology.

[22]  B. Ollivier,et al.  Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring. , 2013, International journal of systematic and evolutionary microbiology.

[23]  K. Schleifer,et al.  Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. , 2010, Systematic and applied microbiology.

[24]  O. Kandler,et al.  Acetomicrobium flavidum, gen. nov., sp. nov., a thermophilic, anaerobic bacterium from sewage sludge, forming acetate, CO2 and H2 from Glucose , 1984 .

[25]  J. Qi,et al.  Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach , 2003, Journal of Molecular Evolution.

[26]  Hélène Marchandin,et al.  Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'. , 2009, International journal of systematic and evolutionary microbiology.

[27]  J. Jalava,et al.  Phylogenetic analysis of Fusobacterium alocis and Fusobacterium sulci based on 16S rRNA gene sequences: proposal of Filifactor alocis (Cato, Moore and Moore) comb. nov. and Eubacterium sulci (Cato, Moore and Moore) comb. nov. , 1999, International journal of systematic bacteriology.

[28]  Sp Lapage,et al.  International Code of Nomenclature of Bacteria , 1992 .

[29]  R. Overbeek,et al.  The winds of (evolutionary) change: breathing new life into microbiology. , 1996, Journal of bacteriology.

[30]  Timothy Lilburn,et al.  Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names. , 2013, Systematic and applied microbiology.

[31]  P. Lawson,et al.  Genome Sequence of Thermoanaerobaculum aquaticum MP-01T, the First Cultivated Member of Acidobacteria Subdivision 23, Isolated from a Hot Spring , 2014, Genome Announcements.

[32]  Hong Luo,et al.  CVTree: a phylogenetic tree reconstruction tool based on whole genomes , 2004, Nucleic Acids Res..

[33]  E. Canale-Parola,et al.  Bacteroides pectinophilus sp. nov. and Bacteroides galacturonicus sp. nov.: two pectinolytic bacteria from the human intestinal tract , 1986, Applied and environmental microbiology.

[34]  J. Chun,et al.  Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. , 2012, International journal of systematic and evolutionary microbiology.

[35]  T. Hansen.  Bergey's Manual of Systematic Bacteriology , 2005 .

[36]  S. Spring,et al.  Complete moderate thermophile Anaerobaculum mobile type strain (NGA(T)). , 2013 .

[37]  P. Lawson,et al.  The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. , 1994, International journal of systematic bacteriology.

[38]  J. Chun,et al.  Proposal to transfer Flavobacterium oceanosedimentum Carty and Litchfield 1978 to the genus Curtobacterium as Curtobacterium oceanosedimentum comb. nov. , 2009, FEMS microbiology letters.

[39]  Donald A. Bryant,et al.  Candidatus Chloracidobacterium thermophilum: An Aerobic Phototrophic Acidobacterium , 2007, Science.

[40]  Aidan C. Parte,et al.  LPSN—list of prokaryotic names with standing in nomenclature , 2013, Nucleic Acids Res..

[41]  T. Lilburn,et al.  A Novel Lineage of Proteobacteria Involved in Formation of Marine Fe-Oxidizing Microbial Mat Communities , 2007, PloS one.

[42]  T. Naganuma,et al.  Oligoflexia, the Newest Class of the Phylum Proteobacteria, Consisting of only One Cultured Species and Uncultured Bacterial Phylotypes from Diverse Habitats , 2015 .

[43]  H. Isoda,et al.  Oligoflexus tunisiensis gen. nov., sp. nov., a Gram-negative, aerobic, filamentous bacterium of a novel proteobacterial lineage, and description of Oligoflexaceae fam. nov., Oligoflexales ord. nov. and Oligoflexia classis nov. , 2014, International journal of systematic and evolutionary microbiology.