Non contiguous-finished genome sequence and description of Cellulomonas massiliensis sp. nov

Standards in Genomic Sciences

Volumn 7, Issue 2, 2012, Pages 258-270

  Lagier, Jean Christophe ^a   Ramasamy, Dhamodharan ^a   Rivet, Romain ^a   Raoult, Didier ^a   Fournier, Pierre Edouard ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Cellulomonas massiliensis; Genome

Indexed keywords

ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIUM EXAMINATION; BACTERIUM ISOLATION; CELLULOMONAS; CELLULOMONAS MASSILIENSIS; DNA BASE COMPOSITION; DNA SEQUENCE; GRAM STAINING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENETIC TREE; PROTEIN ANALYSIS; SEQUENCE HOMOLOGY; TRANSMISSION ELECTRON MICROSCOPY;

BACTERIA (MICROORGANISMS); CELLULOMONAS;

EID: 84872032925     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3316719     Document Type: Article

References (49)

1. Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18:1185-1193. PubMed
2. Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249-266. PubMed http://dx.doi.org/10.1099/ijs.0.016949-0
3. Genome Online Database. http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
4. Welker M, Moore ER. Applications of wholecell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 2011; 34:2-11. Pub-Med http://dx.doi.org/10.1016/j.syapm.2010.11.013
5. Lagier JC, El Karkouri K, Nguyen TT, Armougom F, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov. Stand Genomic Sci 2012; 6:116-125. PubMed http://dx.doi.org/10.4056/sigs.2415480
6. Kokcha S, Mishra AK, Lagier JC, Million M, Leroy Q, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov. Stand Genomic Sci 2012; 6:346-355. http://dx.doi.org/10.4056/sigs.2776064
7. Mishra AK, Gimenez G, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes senegalensis sp. nov. Stand Genomic Sci 2012; 6:304-314. http://dx.doi.org/10.4056/sigs.2625821
8. Lagier JC, Armougom F, Mishra AK, Ngyuen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci 2012; 6:315-324. http://dx.doi.org/10.4056/sigs.2685917
9. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov. Stand Genomic Sci 2012; 6:386-395.
10. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Peptoniphilus timonensis sp. nov. Stand Genomic Sci 2012; 7:1-11. http://dx.doi.org/10.4056/sigs.2956294
11. Mishra AK, Lagier JC, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov. Stand Genomic Sci 2012; 7:70-81. http://dx.doi.org/10.4056/sigs.3054650
12. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM. In: Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM (eds), Bergey's Manual of Determinative Bacteriology, First Edition, The Williams and Wilkins Co., Baltimore, 1923, p. 1-442.
13. Lee CM, Weon HY, Hong SB, Jeon YA, Schumann P, Kroppenstedt RM, Kwon SW, Stackebrandt E. Cellulomonas aerilata sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 2008; 58:2925-2929. PubMed http://dx.doi.org/10.1099/ijs.0.2008/002253-0
14. Jones BE, Grant WD, Duckworth AW, Schumann P, Weiss N, Stackebrandt E. Cellulomonas bogoriensis sp. nov., an alkaliphilic cellulomonad. Int J Syst Evol Microbiol 2005; 55:1711-1714. PubMed http://dx.doi.org/10.1099/ijs.0.63646-0
15. Shi Z, Luo G, Wang G. Cellulomonas carbonis sp. nov., isolated from coal mine soil. Int J Syst Evol Microbiol 2012; 62:2004-2010. PubMed http://dx.doi.org/10.1099/ijs.0.034934-0
16. Yoon MH, Ten LN, Im WT, Lee ST. Cellulomonas chitinilytica sp. nov., a chitinolytic bacterium isolated from cattle-farm compost. Int J Syst Evol Microbiol 2008; 58:1878-1884. PubMed http://dx.doi.org/10.1099/ijs.0.64768-0
17. Kang MS, Im WT, Jung HM, Kim MK, Goodfellow M, Kim KK, Yang HC, An DS, Lee ST. Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost. Int J Syst Evol Microbiol 2007; 57:1256-1260. PubMed http://dx.doi.org/10.1099/ijs.0.63974-0
18. Brown JM, Frazier RP, Morey RE, Steigerwalt AG, Pellegrini GJ, Daneshvar MI, Hollis DG, McNeil MM. Phenotypic and genetic characterization of clinical isolates of CDC coryneform group A-3: proposal of a new species of Cellulomonas, Cellulomonas denverensis sp. nov. J Clin Microbiol 2005; 43:1732-1737. PubMed http://dx.doi.org/10.1128/JCM.43.4.1732-1737.2005
19. Funke G, Ramos CP, Collins MD. Identification of some clinical strains of CDC coryneform group A-3 and A-4 bacteria as Cellulomonas species and proposal of Cellulomonas hominis sp. nov. for some group A-3 strains. J Clin Microbiol 1995; 33:2091-2097. PubMed
20. Collins MD, Pascual C. Reclassification of Actinomyces humiferus (Gledhill and Casida) as Cellulomonas humilata nom. corrig., comb. nov. Int J Syst Evol Microbiol 2000; 50:661-663. Pub-Med http://dx.doi.org/10.1099/00207713-50-2-661
21. Elberson MA, Malekzadeh F, Yazdi MT, Kameranpour N, Noori-Daloii MR, Matte MH, Shahamat M, Colwell RR, Sowers KR. Cellulomonas persica sp. nov. and Cellulomonas iranensis sp. nov., mesophilic cellulose-degrading bacteria isolated from forest soils. Int J Syst Evol Microbiol 2000; 50:993-996. PubMed http://dx.doi.org/10.1099/00207713-50-3-993
22. Rusznyák A, Toth EM, Schumann P, Sproer C, Makk J, Szabo G, Vladar P, Marialigeti K, Borsodi AK. Cellulomonas phragmiteti sp. nov., a cellulo-lytic bacterium isolated from reed (Phragmites australis) periphyton in a shallow soda pond. Int J Syst Evol Microbiol 2011; 61:1662-1666. PubMed http://dx.doi.org/10.1099/ijs.0.022608-0
23. An DS, Im WT, Yang HC, Kang MS, Kim KK, Jin L, Kim MK, Lee ST. Cellulomonas terrae sp. nov., a cellulolytic and xylanolytic bacterium isolated from soil. Int J Syst Evol Microbiol 2005; 55:1705-1709. PubMed http://dx.doi.org/10.1099/ijs.0.63696-0
24. Rivas R, Trujillo ME, Mateos PF, Martinez-Molina E, Velazquez E. Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree. Int J Syst Evol Microbiol 2004; 54:533-536. PubMed http://dx.doi.org/10.1099/ijs.0.02866-0
25. Lai PC, Chen YS, Lee SS. Infective endocarditis and osteomyelitis caused by Cellulomonas: a case report and review of the literature. Diagn Microbiol Infect Dis 2009; 65:184-187. PubMed http://dx.doi.org/10.1016/j.diagmicrobio.2009.06.001
26. Sharma S, Saffra NA, Chinyadza T, Ghitan M, Chapnick EK. Endocapsular cellulomonas as a cause of persistent postoperative endophthalmitis. Ophthalmic Surg Lasers Imaging 2008; 39:328-330. PubMed http://dx.doi.org/10.3928/15428877-20080701-16
27. Ohtaki H, Ohkusu K, Sawamura H, Ohta H, Inoue R, Iwasa J, Ito H, Murakami N, Ezaki T, Moriwaki H, Seishima M. First report of acute cholecystitis with sepsis caused by Cellulomonas denverensis. J Clin Microbiol 2009; 47:3391-3393. PubMed http://dx.doi.org/10.1128/JCM.00678-09
28. Trape JF, Tall A, Diagne N, Ndiath O, Ly AB, Faye J, Dieye-Ba F, Roucher C, Bouganali C, Badiane A, et al. Malaria morbidity and pyrethroid resistance after the introduction of insecticide-treated bednets and artemisinin-based combination therapies: a longitudinal study. Lancet Infect Dis 2011; 11:925-932. PubMed http://dx.doi.org/10.1016/S1473-3099(11)70194-3
29. 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 http://dx.doi.org/10.1073/pnas.87.12.4576
30. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
31. Stackebrandt E, Ebers J, Rainey F, Ward-Rainey N. Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479-491. http://dx.doi.org/10.1099/00207713-47-2-479
32. Skerman V, McGowan V, Sneath P. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
33. Buchanan RE. Studies in the nomenclature and classification of bacteria. II. The primary subdivisions of the Schizomycetes. J Bacteriol 1917; 2:155-164. PubMed
34. Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589-608. PubMed http://dx.doi.org/10.1099/ijs.0.65780-0
35. Stackebrandt E, Prauser H. Assignment of the genera Cellulomonas, Oerskovia, Promicromonospora, and Jonesia to Cellulomonadaceae fam. nov. Syst Appl Microbiol 1991; 14:261-265. http://dx.doi.org/10.1016/S0723-2020(11)80378-4
36. List Editor. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List no. 39. Int J Syst Bacteriol 1991; 41:580-581. PubMed http://dx.doi.org/10.1099/00207713-41-4-580
37. Stackebrandt E, Schumann P. Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae. Int J Syst Evol Microbiol 2000; 50:1279-1285. Pub-Med http://dx.doi.org/10.1099/00207713-50-3-1279
38. 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. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
39. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152-155.
40. GenBank database. http://www.ncbi.nlm.nih.gov/genbank
41. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009; 49:543-551. PubMed http://dx.doi.org/10.1086/600885
42. 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
43. Prodigal. http://prodigal.ornl.gov
44. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed
45. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100-3108. PubMed http://dx.doi.org/10.1093/nar/gkm160
46. Krogh A, Larsson B. von HG, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567-580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315
47. Bendtsen JD, Nielsen H. von HG, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783-795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028
48. T). Stand Genomic Sci 2010; 3:15-25. PubMed http://dx.doi.org/10.4056/sigs.1012662
49. Cavalier-Smith T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 2002; 52:7-76. PubMed