Manassas, VA, United States
Manassas, VA, United States

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Goker M.,DSMZ German Collection of Microorganisms and Cell Cultures GmbH | Cleland D.,ATCC American Type Culture Collection | Saunders E.,U.S. Department of Energy | Saunders E.,Los Alamos National Laboratory | And 40 more authors.
Standards in Genomic Sciences | Year: 2011

Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the genus Isosphaera. The species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the Planc-tomycetaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Isosphaera and the third of a member of the family Planctomycetaceae. The 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763 pro-tein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria and Arc-haea project.


Harmon-Smith M.,U.S. Department of Energy | Celia L.,ATCC American Type Culture Collection | Chertkov O.,Los Alamos National Laboratory | Lapidus A.,U.S. Department of Energy | And 42 more authors.
Standards in Genomic Sciences | Year: 2010

Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family 'Leptotrichiaceae'. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.


Kiss H.,Los Alamos National Laboratory | Cleland D.,ATCC American Type Culture Collection | Lapidus A.,U.S. Department of Energy | Lucas S.,U.S. Department of Energy | And 38 more authors.
Standards in Genomic Sciences | Year: 2010

'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1 T is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.


Yarza P.,CSIC - Mediterranean Institute for Advanced Studies | Yarza P.,Ribocon GmbH | Sproer C.,Leibniz Institute DSMZ | Swiderski J.,Leibniz Institute DSMZ | And 43 more authors.
Systematic and Applied Microbiology | Year: 2013

High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 " orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an 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 has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these " orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible 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 in order to help solve some of these issues. © 2013 Elsevier GmbH.

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