Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov

Standards in Genomic Sciences

Volumn 9, Issue 1, 2014, Pages

  Angelakis, Emmanouil ^a   Bibi, Fehmida ^b   Ramasamy, Dhamodharan ^a   Azhar, Esam I ^b   Jiman Fatani, Asif A ^c   Aboushoushah, Sally M ^b   Lagier, Jean Christophe ^a   Robert, Catherine ^a   Caputo, Aurelia ^a   Yasir, Muhammad ^b   Fournier, Pierre Edouard ^a   Raoult, Didier ^a,b  

^a CNRS   (France)

^b KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^c King Abdulaziz University   (Saudi Arabia)

Author keywords

Clostridium saudii; Culturomics; Genome; Taxono genomics

Indexed keywords

EID: 84971326486     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.1186/1944-3277-9-8     Document Type: Article

References (66)

1. Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, Trape JF, Koonin EV, La Scola B, Raoult D: Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect. 2012, 18: 1185-93. PubMed 10.1111/1469-0691.12023
2. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P: Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol. 2010, 60: 249-66. PubMed http://dx.doi.org/10.1099/ijs.0.016949-0 10.1099/ijs.0.016949-0
3. Stackebrandt E, Ebers J: Taxonomic parameters revisited: tarnished gold standards. Microbiol Today. 2006, 33: 152-5.
4. Wayne LG, Brenner DJ, Colwell PR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG: Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol. 1987, 37: 463-4. http://dx.doi.org/10.1099/00207713-37-4-463 10.1099/00207713-37-4-463
5. Rossello-Mora R: DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation. In Molecular Identification, Systematics, and population Structure of Prokaryotes. Edited by: Stackebrandt E. Berlin: Springer; 2006:23-50.
6. Welker M, Moore ER: Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol. 2011, 34: 2-11. PubMed http://dx.doi.org/10.1016/j.syapm.2010.11.013 10.1016/j.syapm.2010.11.013
7. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi-Tamisier M, Sentausa E, Raoult D, Fournier PE: A polyphasic strategy incorporating genomic data for the taxonomic description of new bacterial species. Int J Syst Evol Microbiol. 2014, 64: 384-91. PubMed http://dx.doi.org/10.1099/ijs.0.057091-0 10.1099/ijs.0.057091-0
8. 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: 346-55. PubMed http://dx.doi.org/10.4056/sigs.2776064 10.4056/sigs.2776064
9. 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: 116-25. PubMed http://dx.doi.org/10.4056/sigs.2415480 10.4056/sigs.2415480
10. 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: 304-14. http://dx.doi.org/10.4056/sigs.2625821 10.4056/sigs.2625821
11. 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: 315-24. PubMed http://dx.doi.org/10.4056/sigs.2685971 10.4056/sigs.2685971
12. 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: 386-95. PubMed
13. 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. PubMed http://dx.doi.org/10.4056/sigs.2956294
14. 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. PubMed http://dx.doi.org/10.4056/sigs.3056450 10.4056/sigs.3056450
15. Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE: Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci. 2012, 7: 200-9. PubMed
16. Kokcha S, Ramasamy D, Lagier JC, Robert C, Raoult D, Fournier PE: Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov. Stand Genomic Sci. 2012, 7: 233-45. PubMed http://dx.doi.org/10.4056/sigs.3256677 10.4056/sigs.3256677
17. Ramasamy D, Kokcha S, Lagier JC, N'Guyen TT, Raoult D, Fournier PE: Non-contiguous finished genome sequence and description of Aeromicrobiummassilense sp. nov. Stand Genomic Sci. 2012, 7: 246-57. PubMed http://dx.doi.org/10.4056/sigs.3306717 10.4056/sigs.3306717
18. Lagier JC, Ramasamy D, Rivet R, Raoult D, Fournier PE: Non-contiguous finished genome sequence and description of Cellulomonas massiliensis sp. nov. Stand Genomic Sci. 2012, 7: 258-70. PubMed http://dx.doi.org/10.4056/sigs.3316719 10.4056/sigs.3316719
19. Lagier JC, Karkouri K, Rivet R, Couderc C, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Stand Genomic Sci. 2013, 7: 343-56. PubMed http://dx.doi.org/10.4056/sigs.3246665 10.4056/sigs.3246665
20. Mishra AK, Hugon P, Nguyen TT, Robert C, Couderc C, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov. Stand Genomic Sci. 2013, 7: 357-69. PubMed http://dx.doi.org/10.4056/sigs.32766871 10.4056/sigs.32766871
21. Mishra AK, Lagier JC, Nguyen TT, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov. Stand Genomic Sci. 2013, 7: 357-69. PubMed http://dx.doi.org/10.4056/sigs.32766871 10.4056/sigs.32766871
22. Lagier JC, Karkouri K, Mishra AK, Robert C, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov. Stand Genomic Sci. 2013, 7: 399-412. PubMed http://dx.doi.org/10.4056/sigs.3396830 10.4056/sigs.3396830
23. Hugon P, Ramasamy D, Rivet R, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov. Stand Genomic Sci. 2013, 7: 427-39. PubMed http://dx.doi.org/10.4056/sigs.3336746 10.4056/sigs.3336746
24. Hugon P, Mishra AK, Nguyen TT, Raoult D, Fournier PE: Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Stand Genomic Sci. 2013, 8: 1-14. PubMed http://dx.doi.org/10.4056/sigs.3466975 10.4056/sigs.3466975
25. Mishra AK, Hugon P, Nguyen TT, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the family Coriobacteriaceae. Stand Genomic Sci. 2013, 8: 290-305. PubMed http://dx.doi.org/10.4056/sigs.3426906 10.4056/sigs.3426906
26. Ramasamy D, Lagier JC, Gorlas A, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov. Stand Genomic Sci. 2013, 8: 264-78. PubMed http://dx.doi.org/10.4056/sigs.3496989 10.4056/sigs.3496989
27. Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the family Erysipelotrichaceae. Stand Genomic Sci. 2013, 8: 336-51. PubMed http://dx.doi.org/10.4056/sigs.3567059 10.4056/sigs.3567059
28. Mishra AK, Pfleiderer A, Lagier JC, Robert C, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Bacillus massilioanorexius sp. nov. Stand Genomic Sci. 2013, 8: 465-79. PubMed http://dx.doi.org/10.4056/sigs.4087826 10.4056/sigs.4087826
29. Hugon P, Ramasamy D, Robert C, Couderc C, Raoult D, Fournier PE: Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI. Stand Genomic Sci. 2013, 8: 500-15. PubMed http://dx.doi.org/10.4056/sigs.4047997 10.4056/sigs.4047997
30. Padhmanabhan R, Lagier JC, Dangui NPM, Michelle C, Couderc C, Raoult D, Fournier PE: Non-contiguous finished genome sequence and description of Megasphaera massiliensis. Stand Genomic Sci. 2013, 8: 525-38. PubMed http://dx.doi.org/10.4056/sigs.4077819 10.4056/sigs.4077819
31. Mishra AK, Edouard S, Dangui NPM, Lagier JC, Caputo A, Blanc-Tailleur C, Ravaux I, Raoult D, Fournier PE: Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. Stand Genomic Sci. 2013, 9: 205-19. PubMed http://dx.doi.org/10.4056/sigs.4378121 10.4056/sigs.4378121
32. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE: Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcineae. Stand Genomic Sci. 2013, 8: 318-35. PubMed http://dx.doi.org/10.4056/sigs.3476977 10.4056/sigs.3476977
33. Keita MB, Diene SM, Robert C, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Bacillus massiliogorillae sp. nov. Stand Genomic Sci. 2013, 9: 93-105. PubMed http://dx.doi.org/10.4056/sigs.4388124 10.4056/sigs.4388124
34. Mediannikov O, El Karkouri K, Robert C, Fournier PE, Raoult D: Non contiguous-finished genome sequence and description of Bartonella florenciae sp. nov. Stand Genomic Sci. 2013, 9: 185-96. PubMed http://dx.doi.org/10.4056/sigs.4358060 10.4056/sigs.4358060
35. Lo CI, Mishra AK, Padhmanabhan R, Samb Ba B, Gassama Sow A, Robert C, Couderc C, Faye N, Raoult D, Fournier PE, Fenollar F: Non contiguous-finished genome sequence and description of Clostridium dakarense sp. nov. Stand Genomic Sci. 2013, 9: 14-27. PubMed http://dx.doi.org/10.4056/sigs.4097825 10.4056/sigs.4097825
36. Mishra AK, Hugon P, Robert C, Raoult D, Fournier PE: Non contiguous-finished genome sequence and description of Peptoniphilus grossensis sp. nov. Stand Genomic Sci. 2012, 7: 320-30. PubMed
37. Mediannikov O, El Karkouri K, Diatta G, Robert C, Fournier PE, Raoult D: Non contiguous-finished genome sequence and description of Bartonella senegalensis sp. nov. Stand Genomic Sci. 2013, 8: 279-89. PubMed http://dx.doi.org/10.4056/sigs.3807472 10.4056/sigs.3807472
38. Roux V, Million M, Robert C, Magne A, Raoult D: Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov. Stand Genomic Sci. 2013, 9: 370-84. doi: 10.4056/sigs.4267953 10.4056/sigs.4267953
39. Wells CL, Wilkins TD, et al.: Clostridia: Spore forming Anaerobic Bacilli. In Medical Microbiology. 4th edition. Edited by: Baron S. Galveston (TX): University of Texas Medical Branch at Galveston; 1996.
40. 16S Yourself database http://www.mediterranee-infection.com/article.php?larub=152&titre=16s-yourself
41. 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: 4576-9. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576 10.1073/pnas.87.12.4576
42. Gibbons NE, Murray RGE: Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol. 1978, 28: 1-6. http://dx.doi.org/10.1099/00207713-28-1-1 10.1099/00207713-28-1-1
43. Murray RGE: The Higher Taxa, or, a Place for Everything...? In Bergey's Manual of Systematic Bacteriology. First Edition, Volume 1 edition. Edited by: Holt JG. Baltimore: The Williams and Wilkins Co; 1984:31-4.
44. Garrity GM, Holt JG: The Road Map to the Manual. In Bergey's Manual of Systematic Bacteriology. Volume 1. 2nd edition. Edited by: Garrity GM, Boone DR, Castenholz RW. New York: Springer; 2001:119-69.
45. List of new names and new combinations previously effectively, but not validly, published. List no. 132: Int J Syst Evol Microbiol. 2010, 60: 469-72. http://dx.doi.org/10.1099/ijs.0.022855-0
46. Rainey FA, Class II: Clostridia class nov. In Bergey's Manual of Systematic Bacteriology. Second Edition, Volume 3 edition. Edited by: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB. New York: Springer; 2009:736.
47. Skerman VBD, Sneath PHA: Approved list of bacterial names. Int J Syst Bact. 1980, 30: 225-420. http://dx.doi.org/10.1099/00207713-30-1-225 10.1099/00207713-30-1-225
48. Prevot AR: Dictionnaire des Bactéries Pathogens. Edited by: Hauduroy P, Ehringer G, Guillot G, Magrou J, Prevot AR, Rosset D, Urbain A. Paris, France: Masson; 1953:1-692.
49. Pribram E: Klassification der Schizomyceten. Klassifikation der Schizomyceten (Bakterien). Leipzig: Franz Deuticke; 1933:1-143.
50. Prazmowski A Ph.D. Dissertation. In "Untersuchung Über die Entwickelungsgeschichte und Fermentwirking Einiger Bakterien-Arten". Germany: University of Leipzig; 1880:366-71.
51. Smith LDS, Hobbs G: Genus III. Clostridium Prazmowski 1880, 23. In Bergey's Manual of Determinative Bacteriology. Eighth edition. Edited by: Buchanan RE, Gibbons NE. Baltimore: The Williams and Wilkins Co; 1974:551-72.
52. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Raoult D: Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000, 25: 25-9. PubMed http://dx.doi.org/10.1038/75556 10.1038/75556
53. Seng P, Drancourt M, Gouriet F, La SB, 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: 543-51. PubMed http://dx.doi.org/10.1086/600885 10.1086/600885
54. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, et al.: The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008, 26: 541-7. PubMed http://dx.doi.org/10.1038/nbt1360 10.1038/nbt1360
55. Prodigal http://prodigal.ornl.gov/
56. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW: GenBank. Nucleic Acids Res. 2012, 40: D48-53. PubMed http://dx.doi.org/10.1093/nar/gkr1202 10.1093/nar/gkr1202
57. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25: 955-64. PubMed http://dx.doi.org/10.1093/nar/25.5.0955 10.1093/nar/25.5.0955
58. 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: 3100-8. PubMed http://dx.doi.org/10.1093/nar/gkm160 10.1093/nar/gkm160
59. Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: signalP 3.0. J Mol Biol. 2004, 340: 783-95. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028 10.1016/j.jmb.2004.05.028
60. Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001, 305: 567-80. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315 10.1006/jmbi.2000.4315
61. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS: PHAST: a fast phage search tool. Nucleic Acids Res. 2011, 39: 3W347-3W352.
62. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008, 9: 75. PubMed http://dx.doi.org/10.1186/1471-2164-9-75 10.1186/1471-2164-9-75
63. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B: Artemis: sequence visualization and annotation. Bioinformatics. 2000, 16: 944-5. PubMed http://dx.doi.org/10.1093/bioinformatics/16.10.944 10.1093/bioinformatics/16.10.944
64. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J: DNAPlotter: circular and linear interactive genome visualization. Bioinformatics. 2009, 25: 119-20. PubMed http://dx.doi.org/10.1093/bioinformatics/btn578 10.1093/bioinformatics/btn578
65. Darling AC, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14: 1394-403. PubMed http://dx.doi.org/10.1101/gr.2289704 10.1101/gr.2289704
66. Lechner M, Findeib S, Steiner L, Marz M, Stadler PF, Prohaska SJ: Proteinortho: detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics. 2011, 12: 124. PubMed http://dx.doi.org/10.1186/1471-2105-12-124 10.1186/1471-2105-12-124