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

Standards in Genomic Sciences

Volumn 9, Issue 1, 2013, Pages 14-27

  Lo, Cheikh Ibrahima ^a   Mishra, Ajay Kumar ^a   Padhmanabhan, Roshan ^a   Ba, Bissoume Samb ^b   Sow, Amy Gassama ^b   Robert, Catherine ^a   Couderc, Carine ^a   Faye, Ngor ^c   Raoult, Didier ^a   Fournier, Pierre Edouard ^a   Fenollar, Florence ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b INSTITUT PASTEUR DE DAKAR   (Senegal)

^c UNIVERSITÉ CHEIKH ANTA DIOP   (Senegal)

Author keywords

Clostridium dakarense; Culturomics; Genome; Taxono genomics

Indexed keywords

NUCLEOTIDE;

ARTICLE; BACTERIAL GROWTH; BACTERIUM ISOLATION; CELL MOTILITY; CLOSTRIDIUM; DNA ISOLATION; GASTROENTERITIS; GENE SEQUENCE; GENETIC ASSOCIATION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MAXIMUM LIKELIHOOD METHOD; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENETIC TREE; TRANSMISSION ELECTRON MICROSCOPY;

CLOSTRIDIUM; POSIBACTERIA;

EID: 84887118047     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.4097825     Document Type: Article

References (42)

1. Rossello-Mora R. DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation. In: Stackebrandt E (ed), Molecular Identification, Systematics, and popu-lation Structure of Prokaryotes. Springer, Berlin, 2006, p. 23-50.
2. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol To-day 2006; 33: 152-155.
3. Welker M, Moore ER. Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbi-ology. Syst Appl Microbiol 2011; 34: 2-11. Pub-Med http://dx. doi. org/10. 1016/j. syapm. 2010. 11. 013.
4. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of pro-karyote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60: 249-266. PubMed http://dx. doi. org/10. 1099/ijs. 0. 016949-0.
5. Kokcha S, Mishra AK, Lagier JC, Million M, Leroy Q, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Ba-cillus timonensis sp. nov. Stand Genomic Sci 2012; 6: 346-355. PubMed http://dx. doi. org/10. 4056/sigs. 2776064.
6. 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 Ge-nomic Sci 2012; 6: 116-125. PubMed http://dx. doi. org/10. 4056/sigs. 2415480.
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. PubMed.
9. Mishra AK, Lagier JC, Robert C, Raoult D, Four-nier PE. Non-contiguous finished genome se-quence and description of Clostridium senegalense sp. nov. Stand Genomic Sci 2012; 6: 386-395. PubMed.
10. Mishra AK, Lagier JC, Robert C, Raoult D, Four-nier PE. Non-contiguous finished genome se-quence and description of Peptoniphilus timonensis sp. nov. Stand Genomic Sci 2012; 7: 1-11. PubMed 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. PubMed.
12. Prazmowski A. "Untersuchung über die Entwickelungsgeschichte und Fermentwirking einiger Bakterien-Arten. " Ph. D. Dissertation, Uni-versity of Leipzig, Germany, 1880, p. 366-371.
13. List of prokaryotic names with standing with no-menclature. http://www. bacterio. net.
14. Evaluations and Standards Laboratory. "Identifica-tion of Clostridium species", 2008 pp. 14.
15. Wells CL, Wilkins TD. (1996). Clostridia: Spore forming Anaerobic Bacilli In: Baron's Medical Mi-crobiology (Baron S et al., eds.) (4th ed.). Univer-sity of Texas Medical Branch.
16. Keis S, Shaheen R, David T. Jones Emended de-scriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clos-tridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov. Int J Syst Evol Microbiol 2001; 51: 2095-2103. PubMed http://dx. doi. org/10. 1099/00207713-51-6-2095.
17. Carnahan JE, Castle JE. Nitrogen Fixation. Annu Rev Plant Physiol 1963; 14: 125-136. http://dx. doi. org/10. 1146/annurev. pp. 14. 060163. 001013.
18. 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.
19. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archae, Bacteria, and Eukarya. Proc Natl Acad Sci USA 1990; 87: 4576-4579. PubMed http://dx. doi. org/10. 1073/pnas. 87. 12. 4576.
20. 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.
21. Garrity GM, Holt JG. The Road Map to the Man-ual. 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.
22. Murray RGE. The Higher Taxa, or, a Place for Everything.? In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31-34.
23. List of new names and new combinations previ-ously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60: 469-472. http://dx. doi. org/10. 1099/ijs. 0. 022855-0.
24. Rainey FA. Class II. Clostridia class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 3, Springer-Verlag, New York, 2009, p. 736.
25. Skerman VBD, Sneath PHA. Approved list of bac-terial names. Int J Syst Bacteriol 1980; 30: 225-420. http://dx. doi. org/10. 1099/00207713-30-1-225.
26. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692.
27. Pribram E. Klassification der Schizomyceten. Klassifikation der Schizomyceten (Bakterien), Franz Deuticke, Leipzig, 1933, p. 1-143.
28. Smith LDS, Hobbs G. Genus III. Clostridium Prazmowski 1880, 23. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bac-teriology, Eighth Edition, The Williams and Wil-kins Co., Baltimore, 1974, p. 551-572.
29. 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 Con-sortium. Nat Genet 2000; 25: 25-29. PubMed http://dx. doi. org/10. 1038/75556.
30. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol To-day 2006; 33: 152-155.
31. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D. Ongoing revo-lution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ioni-zation time-of-flight mass spectrometry. Clin In-fect Dis 2009; 49: 543-551. PubMed http://dx. doi. org/10. 1086/600885.
32. 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.
33. Prodigal. http://prodigal. ornl. gov.
34. GenBank database. http://www. ncbi. nlm. nih. gov/genbank.
35. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in ge-nomic sequence. Nucleic Acids Res 1997; 25: 955-964. PubMed.
36. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucle-ic Acids Res 2007; 35: 3100-3108. PubMed http://dx. doi. org/10. 1093/nar/gkm160.
37. Bendtsen JD, Nielsen H, von Heijne G, 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.
38. 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: 567-580. PubMed http://dx. doi. org/10. 1006/jmbi. 2000. 4315.
39. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16: 944-945. PubMed http://dx. doi. org/10. 1093/bioinformatics/16. 10. 944.
40. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interac-tive genome visualization. Bioinformatics 2009; 25: 119-120. PubMed http://dx. doi. org/10. 1093/bioinformatics/btn578.
41. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14: 1394-1403. PubMed http://dx. doi. org/10. 1101/gr. 2289704.
42. Lechner M, Findeib S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinfor-matics 2011; 12: 124. PubMed http://dx. doi. org/10. 1186/1471-2105-12-124.