Complete genome sequence of Spirosoma linguale type strain (1 T)

Standards in Genomic Sciences

Volumn 2, Issue 2, 2010, Pages 176-185

  Lail, Kathleen ^a   Sikorski, Johannes ^b   Saunders, Elizabeth ^c   Lapidus, Alla ^a   Glavina Del Rio, Tijana ^a   Copeland, Alex ^a   Tice, Hope ^a   Cheng, Jan Fang ^a   Lucas, Susan ^a   Nolan, Matt ^a   Bruce, David ^a,c   Goodwin, Lynne ^a,c   Pitluck, Sam ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Ovchinnikova, Galina ^a   Pati, Amrita ^a   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^a,e   Hauser, Loren ^a,e   Chang, Yun Juan ^a,e   Jeffries, Cynthia D ^a,e   Chain, Patrick ^a,f   Brettin, Thomas ^a,c   Detter, John C ^a,c   Schütze, Andrea ^b   Rohde, Manfred ^g   Tindall, Brian J ^b   Göker, Markus ^b   Bristow, Jim ^a   Eisen, Jonathan A ^a,h   Markowitz, Victor ^a   Hugenholtz, Philip ^a   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^b   Chen, Feng ^a   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

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

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

^f LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^g HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^h UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Aerobic; Cytophagaceae; Freeliving; GEBA; Non pathogenic; Oligotrophic; Psychroactive; Ringlike morphology

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); FLEXIBACTERACEAE; SPIROSOMA LINGUALE;

EID: 80053371423     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.741334     Document Type: Article

References (32)

1. 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 doi:10.1099/00207713-47-2-590
2. Raj HD. A new species - Microcyclus flavus. Int J Syst Bacteriol 1970; 20:61-81. doi:10.1099/00207713-20-1-61
3. Finster KW, Herbert RA, Lomstein BA. Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma. Int J Syst Evol Microbiol 2009; 59:839-844. PubMed doi:10.1099/ijs.0.002725-0
4. Ten LN, Xu JL, Jin FX, Im WT, Oh HM, Lee ST. Spirosoma panaciterrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:331-335. PubMed doi:10.1099/ijs.0.002436-0
5. Baik KS, Kim MS, Park SC, Lee DW, Lee SD, Ka JO, Choi SK, Seong CN. Spirosoma rigui sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2007; 57:2870-2873. PubMed doi:10.1099/ijs.0.65302-0
6. Migula W. 1900. System der Bakterien, Vol 2. Gustav Fischer, Jena.
7. Migula W. Über ein neues System der Bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235-238.
8. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. doi:10.1099/00207713-30-1-225
9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
10. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464. PubMed doi: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 doi:10.1080/10635150802429642
12. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
13. T). Stand Genomic Sci 2009; 1:133-140. doi:10.4056/sigs.19262
14. Raj HD. 1981. The genus Microcyclus and related bacteria, p. 630-44. In: Starr MP, Stolp H, Trüper HG, Balows A, HG Schlegel (eds), The Prokaryotes. A handbook on habitats, isolation and identification of bacteria, Vol 1. Springer, New York.
15. Raj HD, Maloy SR. Proposal of Cyclobacterium marinus gen. nov., comb. nov. for a marine bacterium previously assigned to the genus Flectobacillus. Int J Syst Bacteriol 1990; 40:337-347. doi:10.1099/00207713-40-4-337
16. 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 doi:10.1038/nbt1360
17. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed doi:10.1073/pnas.87.12.4576
18. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ. Taxonomic outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 11 - The Bacteria: Phyla Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Acidobacteria, Bacteroidetes, Fusobacteria, Verrucomicrobia, Dictyoglomi, Gemmatimonadetes, and Lentisphaerae. http://www.taxonomicoutline.org.
19. Woese CR, Stackebrandt E, Macke TJ, Fox GE. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 1985; 6:143-151. PubMed
20. Garrity GM, Holt JG. In: Garrity GM, Boone DR, Castenholz RW (2001) Taxonomic Outline of the Archaea and Bacteria. Bergey's Manual of Systematic Bacteriology 155-166.
21. Stanier RY. Studies on the Cytophagas. J Bacteriol 1940; 40:619-635. PubMed
22. Larkin JM, Williams PM, Taylor R. Taxonomy of the genus Microcyclus Orskov 1928: reintroduction and emendation of the genus Spirosoma Migula 1894 and proposal of a new genus, Flectobacillus. Int J Syst Bacteriol 1977; 27:147-156. doi:10.1099/00207713-27-2-147
23. Classification of Bacteria and Archaea in risk groups. www.baua.de TRBA 466.
24. Ashburner M, Ball CA, Blake JA, Botstein D, Butler 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 doi:10.1038/75556
25. Gordon RE, Mihm JM. A comparative study of some strains received as nocardiae. J Bacteriol 1957; 73:15-27. PubMed
26. Urakami T, Komagata K. Methanol-utilizing Ancylobacter strains and comparison of their cellular fatty acid compositions and quinone systems with those of Spirosoma, Flectobacillus, and Runella species. Int J Syst Bacteriol 1986; 36:415-421. doi:10.1099/00207713-36-3-415
27. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
28. 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 encyclopedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMed doi:10.1038/nature08656
29. T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
30. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
31. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods (in press).
32. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. Expert Review of Functional Annotations for Microbial Genomes. Bioinformatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393