Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20 t)

Standards in Genomic Sciences

Volumn 5, Issue 1, 2011, Pages 41-49

  Pati, Amrita ^a   Gronow, Sabine ^b   Lu, Megan ^a,c   Lapidus, Alla ^a   Nolan, Matt ^a   Lucas, Susan ^a   Hammon, Nancy ^a   Deshpande, Shweta ^a   Cheng, Jan Fang ^a   Tapia, Roxanne ^a,c   Han, Cliff ^a,c   Goodwin, Lynne ^a,c   Pitluck, Sam ^a   Liolios, Konstantinos ^a   Pagani, Ioanna ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Huntemann, Marcel ^a   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^a,e   Hauser, Loren ^a,c   Detter, John C ^a   Brambilla, Evelyne Marie ^b   Rohde, Manfred ^f   Göker, Markus ^b   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 ^b   Ivanova, Natalia ^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 HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Chemoorganotroph ic; GEBA; Gram negative; Mesophilic; Non motile; Obligately anaerobic; Opportunistic pathogen; Prevotellaceae

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; PREVOTELLA; PREVOTELLA MULTISACCHARIVORAX; PREVOTELLACEAE;

EID: 80054856529     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2164949     Document Type: Article

References (37)

1. Garrity G. NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
2. Sakamoto M, Umeda M, Ishikawa I, Benno Y. Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque. Int J Syst Evol Microbiol 2005; 55:1839-1843. PubMed doi:10.1099/ijs.0.63739-0
3. Preza D, Olsen I, Aas JA, Willumsen T, Grinde B, Paster BJ. Bacterial profiles of root caries in elder-ly patients. J Clin Microbiol 2008; 46:2015-2021. PubMed doi:10.1128/JCM.02411-07
4. Rôças IN, Siqueira JF, Jr. Prevalence of new can-didate pathogens Prevotella baroniae, Prevotella multisaccharivorax and as-yet-uncultivated Bacte-roidetes clone X083 in primary endodontic infec-tions. J Endod 2009; 35:1359-1362. PubMed doi:10.1016/j.joen.2009.05.033
5. Siqueira JF, Jr., Rôças IN. The oral microbiota: general overview, taxonomy, and nucleic acid techniques. Methods Mol Biol 2010; 666:55-69. PubMed doi:10.1007/978-1-60761-820-1_5
6. Altschul SF, Gish W, Miller W, Myers EW, Lip-man DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
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 doi: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. 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
10. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
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. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. doi: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. doi: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. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes OnLine 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
16. Purushe J, Foulds DE, Morrison M, White BA, Mackie RI. North American Consortium for Ru-men Bacteria, Coultinho PM, Henrissat G, Nelson KE. Comparative genome anaylsis of Prevotella ruminicola and Prevotella bryantii: insight into their environmental niche. Microb Ecol 2010; 60:721-729. PubMed doi:10.1007/s00248-010-9692-8
17. 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
18. 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 doi:10.1073/pnas.87.12.4576
19. Garrity GM, Holt JG. The Road Map to the Ma-nual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriolo-gy, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
20. Ludwig W, Euzeby J, Whitman WG. Draft tax-onomic outline of the Bacteroidetes, Planctomy-cetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf. Taxonomic Outline 2008.
21. Garrity GM, Holt JG. 2001. Taxonomic outline of the Archaea and Bacteria, p. 155-166. In: Garrity GM, Boone RR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, 2nd ed, vol. 1. Springer, New York.
22. Shah HN, Collins DM. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacte-roides. Int J Syst Bacteriol 1990; 40:205-208. PubMed doi:10.1099/00207713-40-2-205
23. Willems A, Collins MD. 16S rRNA gene similari-ties indicate that Hallella seregens (Moore and Moore) and Mitsuokella dentalis (Haapasalo et al.) are genealogically highly related and are mem-bers of the genus Prevotella: emended description of the genus Prevotella (Shah and Collins) and de-scription of Prevotella dentalis comb. nov. Int J Syst Bacteriol 1995; 45:832-836. PubMed doi:10.1099/00207713-45-4-832
24. BAuA. Classification of bacteria and archaea in risk groups. TRBA 2010; 466:173.
25. 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 doi:10.1038/75556
26. Klenk HP, Göker 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
27. 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
28. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
29. 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 2011; 9:51-55. doi:10.1089/bio.2010.0029
30. The DOE Joint Genome Institute. http://www.jgi.doe.gov
31. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
32. 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
33. Han C, Chain P. 2006. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinfor-matics & computational biology. Arabnia HR, Va-lafar H (eds), CSREA Press. June 26-29, 2006: 141-146
34. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assem-bly and finishing. AGBT, Marco Island, FL, 2008.
35. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer 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
36. 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
37. 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 doi:10.1093/bioinformatics/btp393