Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta

Standards in Genomic Sciences

Volumn 6, Issue 2, 2012, Pages 194-209

  Abt, Birte ^c   Han, Cliff ^a,b   Scheuner, Carmen ^c   Lu, Megan ^a,b   Lapidus, Alla ^a   Nolan, Matt ^a   Lucas, Susan ^a   Hammon, Nancy ^a   Deshpande, Shweta ^a   Cheng, Jan Fang ^a   Tapia, Roxanne ^a,b   Goodwin, Lynne A ^a,b   Pitluck, Sam ^a   Liolios, Konstantinos ^a   Pagani, Ioanna ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Huntemann, Marcel ^a   Pati, Amrita ^a   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^a,e   Hauser, Loren ^a,e   Brambilla, Evelyne Marie ^c   Rohde, Manfred ^f   Spring, Stefan ^c   Gronow, Sabine ^c   Göker, Markus ^c   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,g   Markowitz, Victor ^d   Hugenholtz, Philip ^a,h   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^c   Detter, John C ^a,b   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Chemoorganotrophic; Di and oligosac charide degrading; GEBA; Gram negative; Mesophilic; Non motile; Obligately anaerobic; Sphaerochaeta; Spirochaetaceae; Termite hindgut

Indexed keywords

CELLULOSE; HEMICELLULOSE; RNA 16S;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CELL AGGREGATION; DNA ISOLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENOMICS; PHYLOGENY; SEQUENCE ANALYSIS; SPIROCHAETA; SPIROCHAETA COCCOIDES; TAXONOMIC IDENTIFICATION; UNINDEXED SEQUENCE;

BACTERIA (MICROORGANISMS); ISOPTERA; NEGIBACTERIA; NEOTERMES CASTANEUS; SPIROCHAETA; SPIROCHAETACEAE;

EID: 84863601275     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2796069     Document Type: Article

References (64)

1. Dröge S, Fröhlich J, Radek R, König H. Spirochaeta coccoides sp. nov., a novel coccoid spirochete from the hindgut of the termite Neotermes castaneus. Appl Environ Microbiol 2006; 72:392-397. PubMed http://dx.doi.org/10.1128/AEM.72.1.392-397.2006
2. Validation List No 110. Int J Syst Evol Microbiol 2006; 56:1459-1460. PubMed http://dx.doi.org/10.1099/ijs.0.64507-0
3. Euzéby JP. List of bacterial names with standing in nomenclature: A folder available on the Internet. Int J Syst Bacteriol 1997; 47:590-592. PubMed http://dx.doi.org/10.1099/00207713-47-2-590
4. Ritalahti KM, Justicia-Leon SD, Cusick KD, Ra-mos-Hernandez N, Rubin M, Dornbush J, Löffler FE. Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes. Int J Syst Evol Microbiol 2012; 62:210-216. PubMed http://dx.doi.org/10.1099/ijs.0.023986-0
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
6. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Se-bastopol, 2003
7. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compat-ible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed http://dx.doi.org/10.1128/AEM.03006-05
8. Porter MF. An algorithm for suffix stripping. Pro-gram: electronic library and information systems 1980; 14:130-137.
9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. Pub-Med http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
10. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed http://dx.doi.org/10.1093/bioinformatics/18.3.452
11. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
12. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
13. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184-200. http://dx.doi.org/10.1007/978-3-642-02008-7_13
14. Swofford DL. PAUP*: Phylogenetic Analysis Us-ing Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
15. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their as-sociated metadata. Nucleic Acids Res 2012; 40:D571-D579. PubMed http://dx.doi.org/10.1093/nar/gkr1100
16. Seshadri R, Myers GS, Tettelin H, Eisen JA, Hei-delberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, et al. Comparison of the ge-nome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci USA 2004; 101:5646-5651. PubMed http://dx.doi.org/10.1073/pnas.0307639101
17. T). Stand Genomic Sci 2011; 4:361-370. PubMed http://dx.doi.org/10.4056/sigs.1984594
18. Rosenthal AZ, Matson EG, Eldar A, Leadbetter JR. RNA-seq reveals cooperative metabolic interac-tions between two termite-gut spirochaete species in co-culture. ISME J 2011; (In press). PubMed http://dx.doi.org/10.1038/ismej.2011.3
19. T). Stand Genomic Sci 2010; 3:136-144. PubMed
20. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/10.1038/nbt1360
21. Garrity G. NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
22. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
23. Garrity G, Holt JG. Phylum B17 Spirochaetes phy. nov. Garrity and Holt. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Sys-tematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 138.
24. Judicial Commission of the International Committee on Systematics of Prokaryotes. The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol 2005; 55:517-518. PubMed http://dx.doi.org/10.1099/ijs.0.63548-0
25. Ludwig W, Euzeby J, Whitman WG. Draft taxo-nomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf. Taxonomic Outline 2008.
26. Skerman VBD, McGowan V, Sneath PHA. Ap-proved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
27. Buchanan RE. Studies in the nomenclature and classification of bacteria. II. The primary subdivi-sions of the Schizomycetes. J Bacteriol 1917; 2:155-164. PubMed
28. Swellengrebel NH. Sur la cytologie comparée des spirochètes et des spirilles. [Paris]. Ann Inst Pas-teur (Paris) 1907; 21:562-586.
29. Pikuta EV, Hoover RB, Bej AK, Marsic D, Whit-man WB, Krader P. Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bac-terium, and emended description of the genus Spirochaeta Ehrenberg 1835. Int J Syst Evol Microbiol 2009; 59:1798-1804. PubMed
30. Canale-Parola E. Genus I. Spirochaeta Ehrenberg 1835, 313. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 168-171.
31. Ehrenberg CG. Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes. Abhandlungen der Preussischen Akademie der Wissenschaften (Berlin), 1835, p. 143-336.
32. BAuA. 2010, Classification of bacteria and archaea in risk groups. http://www.baua.de TRBA 466, p. 206.
33. Ashburner M, Ball CA, Blake JA, Botstein D, But-ler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
34. Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed http://dx.doi.org/10.1016/j.syapm.2010.03.003
35. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMed http://dx.doi.org/10.1038/nature08656
36. List of growth media used at DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technolog y/list-of-media-for-microorganisms.html
37. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank 2011; 9:51-55. http://dx.doi.org/10.1089/bio.2010.0029
38. JGI website. http://www.jgi.doe.gov
39. The Phred/Phrap/Consed software package. http://www.phrap.com.
40. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed http://dx.doi.org/10.1101/gr.074492.107
41. Han C, Chain P. Finishing repeat regions auto-matically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26-29, 2006: 141-146.
42. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for us-ing ultra short reads in microbial genome assem-bly and finishing. AGBT, Marco Island, FL, 2008.
43. Hyatt D, Chen GL, LoCascio PF, Land ML, Lar-imer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. BMC Bioinformatics 2010; 11:119. Pub-Med http://dx.doi.org/10.1186/1471-2105-11-119
44. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed http://dx.doi.org/10.1038/nmeth.1457
45. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial ge-nome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393
46. Paster BJ. Phylum XV Spirochaetes Garrity and Holt 2001. In: Goodfellow MJ, Kämpfer P, Chun J, De Vos P, Rainey FA, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 471.
47. Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Móra R. Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010; 33:291-299. PubMed http://dx.doi.org/10.1016/j.syapm.2010.08.001
48. Meier-Kolthoff JP, Auch AF, Huson DH, Göker M. COPYCAT: Co-phylogenetic Analysis tool. Bioin-formatics 2007; 23:898-900. PubMed http://dx.doi.org/10.1093/bioinformatics/btm027
49. Stamatakis A, Auch AF, Meier-Kolthoff J, Göker M. AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics 2007; 8:405. PubMed http://dx.doi.org/10.1186/1471-2105-8-405
50. Legendre P, Desdevises Y, Bazen E. A Statistical Test for Host-Parasite Coevolution. Syst Biol 2002; 51:217-234. PubMed http://dx.doi.org/10.1080/10635150252899734
51. Felsenstein J. Inferring phylogenies. Sinauer Asso-ciates Inc., Sunderland, Massachusetts 2004.
52. Bermudes D, Chase D, Margulis L. Morphology as a basis for taxonomy of large spirochetes sym-biotic in wood-eating cockroaches and termites: Pillotina gen. nov., nom. rev.; Pillotina calotermitidis sp. nov., nom. rev.; Diplocalyx gen. nov., nom. rev.; Diplocalyx calotermitidis sp. nov., nom. rev.; Hollandina gen. nov., nom. rev.; Hollandina pterotermitidis sp. nov., nom. rev.; and Clevelandina reticulitermitidis gen. nov., sp. nov. Int J Syst Bacteriol 1988; 38:291-302. Pub-Med http://dx.doi.org/10.1099/00207713-38-3-291
53. Auch AF, Von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome se-quence comparison. Stand Genomic Sci 2010; 2:117-134. PubMed http://dx.doi.org/10.4056/sigs.531120
54. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome dis-tances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142-148. PubMed http://dx.doi.org/10.4056/sigs.541628
55. Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides N. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal ge-nomes. PLoS ONE 2011; 6:e20237. PubMed http://dx.doi.org/10.1371/journal.pone.0020237
56. NCBI BLAST version 2.2.17. ftp://ftp.ncbi.nih.gov/blast/execuTables/release/2.2.17
57. Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res 2003; 13:2178-2189. PubMed http://dx.doi.org/10.1101/gr.1224503
58. van Dongen S. Graph Clustering by Flow Simulation. PhD Thesis, University of Utrecht, The Netherlands, 2000 (http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm).
59. MCL version 08-312. http://micans.org/mcl
60. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792-1797. PubMed http://dx.doi.org/10.1093/nar/gkh340
61. Thompson JD, Thierry JC, Poch O. RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics 2003; 19:1155-1161. PubMed http://dx.doi.org/10.1093/bioinformatics/btg133
62. Meusemann K, von Reumont BM, Simon S, Roeding F, Strauss S, Kück P, Ebersberger I, Walzl M, Pass G, Breuers S. A Phylogenomic approach to resolve the arthropod tree oflLife. Mol Biol Evol 2010; 27:2451-2464. PubMed http://dx.doi.org/10.1093/molbev/msq130
63. Enright AJ, Van Dongen S, Ouzounis CA. An effi-cient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002; 30:1575-1584. PubMed http://dx.doi.org/10.1093/nar/30.7.1575
64. Siddall ME, Whiting MF. Long-branch abstractions. Cladistics 1999; 15:9-24. http://dx.doi.org/10.1111/j.1096-0031.1999.tb00391.x