Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov

Standards in Genomic Sciences

Volumn 8, Issue 3, 2013, Pages

  Mishra, Ajay Kumar ^a   Pfleiderer, Anne ^a   Lagier, Jean Christophe ^a   Robert, Catherine ^a   Raoult, Didier ^a   Fournier, Pierre Edouard ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

Author keywords

Bacillus massilioanorexius; Culturomics; Genome; Taxonogenomics

Indexed keywords

AMOXICILLIN; CIPROFLOXACIN; CONTIG; COTRIMOXAZOLE; DOXYCYCLINE; GENTAMICIN; METRONIDAZOLE; RIFAMPICIN; RNA 16S; VANCOMYCIN;

ANOREXIA NERVOSA; ANTIBIOTIC SENSITIVITY; ARTICLE; BACILLUS; BACILLUS MASSILIOANOREXIUS; BACTERIAL GENOME; BACTERIUM ISOLATION; CASE REPORT; CHILD; COMPARATIVE STUDY; DNA DNA HYBRIDIZATION; FEMALE; FLUOROMETRY; GENE SEQUENCE; GRAM STAINING; HUMAN; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PROTEIN ANALYSIS; SCHOOL CHILD; TRANSMISSION ELECTRON MICROSCOPY;

AEROBIC BACILLUS; POSIBACTERIA;

EID: 84881042465     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.4087826     Document Type: Article

References (58)

1. Lagier J.C, 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. [pmid:23033984]
2. Dubourg G, Lagier J.C, Armougom F, Robert C, Hamad I, Brouqui P. The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. Eur J Clin Microbiol Infect Dis 2013; 32:637-645. [doi:10.1007/s10096-012-1787-3] [pmid:23291779]
3. Pfleiderer A, Lagier J.C, Armougom F, Robert C, Vialettes B, Raoult D. Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample. [Epub ahead of print]. Eur J Clin Microbiol Infect Dis 2013. [doi:10.1007/s10096-013-1900-2] [pmid:23728738]
4. Tindall B.J, Rossello-Mora R, Busse H.J, Ludwig W, Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249-266. [doi:10.1099/ijs.0.016949-0] [pmid:19700448]
5. Genome Online Database. http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
6. The Microbial Earth Project. http://www.microbial-earth.org
7. Kokcha S, Mishra A.K, Lagier J.C, Million M, Leroy Q, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Bacillus timonensis sp. nov. Stand Genomic Sci 2012; 6:346-355. [doi:10.4056/sigs.2776064] [pmid:23408487]
8. Lagier J.C, El Karkouri K, Nguyen T.T, Armougom F, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov. Stand Genomic Sci 2012; 6:116-125. [doi:10.4056/sigs.2415480] [pmid:22675604]
9. Mishra A.K, Gimenez G, Lagier J.C, Robert C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Alistipes senegalensis sp. nov. Stand Genomic Sci 2012; 6:304-314. [doi:10.4056/sigs.2625821]
10. Lagier J.C, Armougom F, Mishra A.K, Ngyuen T.T, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci 2012; 6:315-324. [pmid:23408657]
11. Mishra A.K, Lagier J.C, Robert C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov. Stand Genomic Sci 2012; 6:386-395. [pmid:23408737]
12. Mishra A.K, Lagier J.C, Robert C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Peptoniphilus timonensis sp. nov. Stand Genomic Sci 2012; 7:1-11. [doi:10.4056/sigs.2956294] [pmid:23449949]
13. Mishra A.K, Lagier J.C, Rivet R, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov. Stand Genomic Sci 2012; 7:70-81. [pmid:23459006]
14. Lagier J.C, Gimenez G, Robert C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci 2012; 7:200-209. [pmid:23407294]
15. Roux V, El Karkouri K, Lagier J.C, Robert C, Raoult D. Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov. Stand Genomic Sci 2012; 7:221-232. [doi:10.4056/sigs.3206554] [pmid:23407462]
16. Kokcha S, Ramasamy D, Lagier J.C, Robert C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov. Stand Genomic Sci 2012; 7:233-245. [doi:10.4056/sigs.3256677] [pmid:23408786]
17. Ramasamy D, Kokcha S, Lagier J.C, N'Guyen T.T, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Aeromicrobium massilense sp. nov. Stand Genomic Sci 2012; 7:246-257. [doi:10.4056/sigs.3306717] [pmid:23408663]
18. Lagier J.C, Ramasamy D, Rivet R, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Cellulomonas massiliensis sp. nov. Stand Genomic Sci 2012; 7:258-270. [doi:10.4056/sigs.3316719] [pmid:23408774]
19. Lagier J.C, El Karkouri K, Rivet R, Couderc C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Senegalemassilia anaerobia sp. nov. Stand Genomic Sci 2013; 7:343-356. [doi:10.4056/sigs.3246665]
20. Mishra A.K, Hugon P, Lagier J.C, Nguyen TT, Robert C, Couderc C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Peptoniphilus obesi sp. nov. Stand Genomic Sci 2013; 7:357-369. [doi:10.4056/sigs.32766871]
21. Mishra A.K, Lagier JC, Nguyen T.T, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Peptoniphilus senegalensis sp. nov. Stand Genomic Sci 2013; 7:370-381. [doi:10.4056/sigs.3366764]
22. Lagier J.C, El Karkouri K, Mishra A.K, Robert C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Enterobacter massiliensis sp. nov. Stand Genomic Sci 2013; 7:399-412. [doi:10.4056/sigs.3396830]
23. Hugon P, Ramasamy D, Lagier J.C, Rivet R, Couderc C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Alistipes obesi sp. nov. Stand Genomic Sci 2013; 7:427-439.[doi:10.4056/sigs.3336746]
24. Mishra A.K, Hugon P, Robert C, Couderc C, Raoult D, Fournier P.E. Non-contiguous finished genome sequence and description of Peptoniphilus grossensis sp. nov. Stand Genomic Sci 2012; 7:320-330. [pmid:23408485]
25. Mishra A.K, Hugon P, Lagier J.C, Nguyen T.T, Couderc C, Raoult D, Fournier P.E. 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. [doi:10.4056/sigs.3426906]
26. Ramasamy D, Lagier J.C, Gorlas A, Raoult D, Fournier P.E. Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov. Stand Genomic Sci 2013; 8:336-351. [doi:10.4056/sigs.3567059]
27. Ramasamy D, Lagier J.C, Nguyen T.T, Raoult D, Fournier P.E. Non contiguous-finished genome sequence and description of of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae. Stand Genomic Sci 2013; 8:336-351. [doi:10.4056/sigs.3567059]
28. Mishra A.K, Lagier J.C, Robert C, Raoult D, Fournier PE. Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae. Stand Genomic Sci 2013; 8:318-335. [doi:10.4056/sigs.3476977]
29. Cohn F. Untersuchungen über Bakterien. Beitrage zur Biologie der Pflanzen Heft 1872; 1:127-224.
30. Mathews W.C, Caperna J, Toerner J.G, Barber R.E, Morgenstern H. Neutropenia is a risk factor for gram-negative bacillus bacteremia in human immunodeficiency virus-infected patients: results of a nested case-control study. Am J Epidemiol 1998; 48:1175-1183.25.
31. Logan N.A. Bacillus species of medical and veterinary importance. J Med Microbiol 1988; 25:157-165. [doi:10.1099/00222615-25-3-157] [pmid:3279213]
32. Jernigan J.A, Stephens D.S, Ashford D.A, Omenaca C, Topiel M.S, Galbraith M, Tapper M, Fisk T.L, Zaki S, Popovic T, et al. Bioterrorism-related inhalational anthrax: the first 10 cases reported in the United States. Emerg Infect Dis 2001; 7:933-944. [doi:10.3201/eid0706.010604] [pmid:11747719]
33. Bottone E.J. Bacillus cereus, a volatile human pathogen. Clin Microbiol Rev 2010; 23:382-398. [doi:10.1128/CMR.00073-09] [pmid:20375358]
34. Purswani J, Pozo C, Rodriguez-Diaz M, Gonzalez-Lopez J. Selection and identification of bacterial strains with methyl-tert-butyl ether, ethyl-tert-butyl ether, and tert-amyl methyl ether degrading capacities. Environ Toxicol Chem 2008; 27:2296-2303. [doi:10.1897/08-096.1] [pmid:18522454]
35. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152-155.
36. Woese C.R, Kandler O, Wheelis M.L. Towards a natural system of organisms: proposal for the domains Archae, Bacteria, and Eukarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. [doi:10.1073/pnas.87.12.4576] [pmid:2112744]
37. Gibbons N.E, Murray R.G.E. Proposals concerning the Higher Taxa of the Bacteria. Int J Syst Bacteriol 1978; 28:1-6. [doi:10.1099/00207713-28-1-1]
38. Garrity G.M, Holt J.G. 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.
39. Murray R.G.E. 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.
40. List Editor. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469-472. [doi:10.1099/ijs.0.022855-0]
41. Ludwig W, Schleifer K.H, Whitman W.B. Class I. Bacilli 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, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 19-20.
42. Skerman VBD, Sneath PHA. Approved list of bacterial names. Int J Syst Bact 1980; 30:225-420. [doi:10.1099/00207713-30-1-225]
43. Prévot A.R. Dictionnaire des bactéries pathogens. In: Hauduroy P, Ehringer G, Guillot G, Magrou J, Prevot AR, Rosset, Urbain A (eds). Paris, Masson, 1953, p.1-692.
44. Fischer A. Untersuchungen über bakterien. Jahrbücher für Wissenschaftliche Botanik 1895; 27:1-163.
45. Gibson T, Gordon R.E. Genus I. Bacillus Cohn 1872, 174; Nom. gen. cons. Nomencl. Comm. Intern. Soc. Microbiol. 1937, 28; Opin. A. Jud. Comm. 1955, 39. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 529-550.
46. Ashburner M, Ball C.A, Blake J.A, Botstein D, Butler H, Cherry J.M, Davis A.P, Dolinski K, Dwight S.S, Eppig J.T. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. [doi:10.1038/75556] [pmid:10802651]
47. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier P.E, Rolain J.M, 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. [doi:10.1086/600885] [pmid:19583519]
48. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen M.J, Angiuoli S.V, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547.[doi:10.1038/nbt1360] [pmid:18464787]
49. Prodigal. http://prodigal.ornl.gov
50. GenBank database. http://www.ncbi.nlm.nih.gov/genbank
51. 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.[pmid:9023104]
52. Lagesen K, Hallin P, Rodland E.A, Staerfeldt H.H, Rognes T, Ussery D.W. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100-3108.[doi:10.1093/nar/gkm160] [pmid:17452365]
53. Bendtsen J.D, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783-795.[doi:10.1016/j.jmb.2004.05.028] [pmid:15223320]
54. Krogh A, Larsson B, von Heijne G, Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567-580. [doi:10.1006/jmbi.2000.4315] [pmid:11152613]
55. Lechner M, Findeib S, Steiner L, Marz M, Stadler P.F, Prohaska SJ. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124.[doi:10.1186/1471-2105-12-124] [pmid:21526987]
56. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M.A, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16:944-945. [doi:10.1093/bioinformatics/16.10.944] [pmid:11120685]
57. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009; 25:119-120.[doi:10.1093/bioinformatics/btn578] [pmid:18990721]
58. Darling A.C, Mau B, Blattner F.R, Perna N.T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394-1403.[doi:10.1101/gr.2289704] [pmid:15231754]