Complete genome sequence of leadbetterella byssophila type strain (4M15 T)

Standards in Genomic Sciences

Volumn 4, Issue 1, 2011, Pages 2-12

  Abt, Birte ^a   Teshima, Hazuki ^b,c   Lucas, Susan ^b   Lapidus, Alla ^b   del Rio, Tijana Glavina ^b   Nolan, Matt ^b   Tice, Hope ^b   Cheng, Jan Fang ^b   Pitluck, Sam ^b   Liolios, Konstantinos ^b   Pagani, Ioanna ^b   Ivanova, Natalia ^b   Mavromatis, Konstantinos ^b   Pati, Amrita ^b   Tapia, Roxane ^b,c   Han, Cliff ^b,c   Goodwin, Lynne ^b,c   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^b,e   Hauser, Loren ^b,e   Chang, Yun Juan ^b,e   Jeffries, Cynthia D ^b,e   Rohde, Manfred ^f   Göker, Markus ^a   Tindall, Brian J ^a   Detter, John C ^b,c   Woyke, Tanja ^b   Bristow, James ^b   Eisen, Jonathan A ^b,g   Markowitz, Victor ^d   Hugenholtz, Philip ^b,h   Klenk, Hans Peter ^a   Kyrpides, Nikos C ^b   more..

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

^b DOE JOINT GENOME INSTITUTE   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Aerobic; Cy tophagaceae; Flexirubin; GEBA; Gram negative; Mesophile; Non motile; Non sporulating

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDETES; FLEXIBACTERACEAE; LEADBETTERELLA; LEADBETTERELLA BYSSOPHILA; NEGIBACTERIA;

EID: 80053359202     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1413518     Document Type: Article

References (44)

1. Weon HY, Kim BY, Kwon SW, Park IC, Cha IB, Tindall BJ, Stackebrandt E, Trüper HG, Go SJ. Leadbetterella byssophila gen. nov., sp. nov., isolated from cotton waste composts for the cultivation of oyster mushroom. Int J Syst Evol Microbiol 2005; 55:2297-2302. PubMed doi:10.1099/ijs.0.63741-0
2. Ludwig W, Klenk HP. Overview: a phylogenetic backbone and taxonomic framework for proca-ryotic systematics. In: Bergey's Manual of Syste-matic Bacteriology 2001. Boone DR, Castenholz RW, Garrity GM (eds), 2nd edn, vol. 1, pp. 49-65. New York: Springer.
3. 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/index.php/toba/article/viewFile/188/220202007.
4. Lail K, Sikorski J, Saunders E, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Nolan M, et al. Complete genome sequence of Spirosoma linguale type strain (1T). Stand Genom-ic Sci 2010; 2:176-184. doi:10.4056/sigs.741334
5. Saha P, Chakrabarti T. Emticicia oligotrophica gen. nov., sp. nov., a new member of the family 'Flexibacteraceae', phylum Bacteroidetes. Int J Syst Evol Microbiol 2006; 56:991-995. PubMed doi:10.1099/ijs.0.64086-0
6. Liu QM, Ten LN, Yu HS, Jin FX, Im WT, Lee ST. Emticicia ginsengisoli sp. nov., a species of the family 'Flexibacteraceae' isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2008; 58:1100-1105. PubMed doi:10.1099/ijs.0.65386-0
7. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW. EzTaxon: a web-based tool for the iden-tification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259-2261. PubMed doi:10.1099/ijs.0.64915-0
8. Krzemieniewska H. Contribution à l'étude du ge-nre Cytophaga (Winogradsky). Arch Mikrobiol 1933; 4:394-408. doi:10.1007/BF00407552
9. Táncsics A, Kéki Z, Márialigeti K, Schumann P, Toth EM. Siphonobacter aquaeclarae gen. nov., sp. nov., a novel member of the family 'Flexibacteraceae', phylum Bacteroidetes. Int J Syst Evol Microbiol 2010; 60:2567-2571. PubMed doi:10.1099/ijs.0.019398-0
10. 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 Compatible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed doi:10.1128/AEM.03006-05
11. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
12. Li K, Guan W, Wei G, Liu B, Xu J, Zhao L, Thang Y. Phylogenetic analysis of intestinal bacteria in the Chinese mitten crab (Eriocheir sinensis). J Appl Microbiol 2007; 103:675-682. PubMed doi:10.1111/j.1365-2672.2007.03295.x
13. Li AJ, Li XY. Selective sludge discharge as the determining factor in SBR aerobic granulation: Numerical modelling and experimental verification. Water Res 2009; 43:3387-3396. PubMed doi:10.1016/j.watres.2009.05.004
14. Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W. Plant host habitat and root exudates soil bacterial community structure. ISME J 2008; 2:1221-1230. PubMed doi:10.1038/ismej.2008.80
15. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed doi:10.1093/bioinformatics/18.3.452
16. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
17. 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
18. 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. doi:10.1007/978-3-642-02008-7_13
19. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metage-nomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
20. Xie G, Bruce DC, Challacombe JF, Chertkov O, Detter JC, Gilna P, Han CS, Lucas S, Misra M, Myers GL, et al. Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. Appl Environ Microbiol 2007; 73:3536-3546. PubMed doi:10.1128/AEM.00225-07
21. Lang E, Lapidus A, Chertkov O, Brettin T, Detter JC, Han C, Copeland A, Glavina Del Rio T, Nolan M, Chen F, et al. Complete genome sequence of Dyadobacter fermentans type strain (NS114T). Stand Genomic Sci 2009; 1:133-140. doi:10.4056/sigs.19262
22. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, An-giuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
23. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms. Proposal for the do-mains Archaea and Bacteria. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed doi:10.1073/pnas.87.12.4576
24. Garrity GM, Holt J. Taxonomic outline of the Archaea and Bacteria. In: Bergey's Manual of Sys-tematic Bacteriology, 2nd ed. vol. 1. The Archaea, Deeply Branching and Phototrophic Bacteria. Garrity GM, Boone DR and Castenholz RW (eds). 2001; 155-166.
25. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacte-riol 1980; 30:225-420. doi:10.1099/00207713-30-1-225
26. Stanier RY. Studies on the Cytophagas. J Bacteriol 1940; 40:619-635. PubMed
27. Bau A. Classification of bacteria and archaea in risk groups. Bundesanstalt für Arbeitsschutz und Arbeitsmedizin, Germany. TRBA 2005; 466:84.
28. 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. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
29. Kim SJ, Weon HY, Kim YS, Yoo SH, Kim BY, Anandham R, Kwon SW. Parapedobacter luteus sp. nov. and Parapedobacter composti sp. nov., isolated from cotton waste compost. Int J Syst Evol Microbiol 2010; 60:1849-1853. PubMed doi:10.1099/ijs.0.013318-0
30. Naka T, Fujiwara N, Yano I, Maeda S, Doe M, Minamino M, Ikeda N, Kato Y, Watabe K, Kuma-zawa Y, et al. Structural analysis of sphingophos-pholipids derived from Sphingobacterium spiriti-vorum, the type species of genus Sphingobacterium. Biochim Biophys Acta 2003; 1635:83-92. PubMed
31. Weon HY, Noh HJ, Son JA, Jang HB, Kim BY, Kwon SW, Stackebrandt E. Rudanella lutea gen. nov., sp. nov., isolated from an air sample in Korea. Int J Syst Evol Microbiol 2008; 58:474-478. PubMed doi:10.1099/ijs.0.65358-0
32. Klenk HP, Goeker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed doi:10.1016/j.syapm.2010.03.003
33. 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 doi:10.1038/nature08656
34. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
35. DNA bank Network. http://www.dnabank-network.org.
36. Gemeinholzer B, Dröge G, Zetzsche H, Haszpru-nar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking (In press). DOE Joint Genome Institute. http://www.jgi.doe.gov/
37. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed doi:10.1101/gr.074492.107
38. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
39. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. HR Arabnia & H Vala-far (eds), CSREA Press. June 26-29, 2006; 141-146.
40. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
41. Hyatt D, Chen GL, LoCascio PF, Land ML, Lari-mer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
42. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene-PRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
43. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393
44. McBride MJ, Xie G, Martens EC, Lapidus A, He-nrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, et al. Novel features of the poly-saccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 2009; 75:6864-6875. PubMed doi:10.1128/AEM.01495-09