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Title: Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema

Abstract

Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain, H1T, was isolated in 1990 from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA, and is of interest because it enhances the degradation of cellulose when grown in co-culture with Clostridium thermocellum. Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic analyses of 16S rRNA sequences and whole genomes, and propose the reclassification of S. caldaria and two other Spirochaeta species as members of the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta possess well-distinguished genomic features related to their divergent lifestyles, the physiological and functional genomic characteristics of Spirochaeta and Treponema appear to be intermixed and are of little taxonomic value. The 3,239,340 bp long genome of strain H1T with its 2,869 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [1];  [1];  [2];  [2];  [2];  [3];  [3];  [3];  [3];  [3];  [3];  [2];  [2];  [3];  [3];  [3];  [3];  [3];  [3] more »;  [3];  [3];  [4];  [4];  [5];  [5];  [5];  [6];  [1];  [1];  [7];  [3];  [8];  [4];  [9];  [3];  [3];  [1] « less
+ Show Author Affiliations
  1. German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  6. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  7. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane, QLD (Australia)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); German Research Foundation (DFG)
OSTI Identifier:
1630591
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396; AC05-00OR22725; INST 599/1-2
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; obligately anaerobic; thermophilic; spiral-shaped; motile; periplasmic flagella; Gram-negative; chemoorganotrophic; Spirochaetaceae; Spirochaeta; Treponema; GEBA

Citation Formats

Abt, Birte, Göker, Markus, Scheuner, Carmen, Han, Cliff, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Gronow, Sabine, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Woyke, Tanja, and Klenk, Hans-Peter. Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. United States: N. p., 2013. Web. doi:10.4056/sigs.3096473.
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Abt, Birte, Göker, Markus, Scheuner, Carmen, Han, Cliff, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Gronow, Sabine, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Woyke, Tanja, & Klenk, Hans-Peter. Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema. United States. https://doi.org/10.4056/sigs.3096473
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Abt, Birte, Göker, Markus, Scheuner, Carmen, Han, Cliff, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Gronow, Sabine, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Woyke, Tanja, and Klenk, Hans-Peter. Mon . "Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema". United States. https://doi.org/10.4056/sigs.3096473. https://www.osti.gov/servlets/purl/1630591.
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@article{osti_1630591,
title = {Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema},
author = {Abt, Birte and Göker, Markus and Scheuner, Carmen and Han, Cliff and Lu, Megan and Misra, Monica and Lapidus, Alla and Nolan, Matt and Lucas, Susan and Hammon, Nancy and Deshpande, Shweta and Cheng, Jan-Fang and Tapia, Roxanne and Goodwin, Lynne A. and Pitluck, Sam and Liolios, Konstantinos and Pagani, Ioanna and Ivanova, Natalia and Mavromatis, Konstantinos and Mikhailova, Natalia and Huntemann, Marcel and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Hauser, Loren and Jeffries, Cynthia D. and Rohde, Manfred and Spring, Stefan and Gronow, Sabine and Detter, John C. and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Woyke, Tanja and Klenk, Hans-Peter},
abstractNote = {Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain, H1T, was isolated in 1990 from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA, and is of interest because it enhances the degradation of cellulose when grown in co-culture with Clostridium thermocellum. Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic analyses of 16S rRNA sequences and whole genomes, and propose the reclassification of S. caldaria and two other Spirochaeta species as members of the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta possess well-distinguished genomic features related to their divergent lifestyles, the physiological and functional genomic characteristics of Spirochaeta and Treponema appear to be intermixed and are of little taxonomic value. The 3,239,340 bp long genome of strain H1T with its 2,869 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.3096473},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 8,
place = {United States},
year = {Mon Apr 15 00:00:00 EDT 2013},
month = {Mon Apr 15 00:00:00 EDT 2013}
}
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https://doi.org/10.4056/sigs.3096473
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic tree highlighting the position of S. caldaria relative to the type strains of the other species within the family Spirochaetaceae. The tree was inferred from 1,362 aligned characters of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion. Rooting was done initially using the midpointmore » method and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 1,000 ML bootstrap replicates (left) and from 1,000 maximum-parsimony bootstrap replicates (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [19-23] (for S. thermophila, T. azotonutricium and T. primitia see CP002903, CP001841 and CP001883). Note: Spirochaeta coccoides was effectively renamed to Sphaerochaeta coccoides in [19] (see Validation List 147.)« less
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