Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium

Standards in Genomic Sciences

Volumn 9, Issue 3, 2015, Pages 704-717

  Pagnier, Isabelle ^a   Croce, Olivier ^a   Robert, Catherine ^a   Raoult, Didier ^a   La Scola, Bernard ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Fenollaria massiliensis; Genome

Indexed keywords

AMOXICILLIN; CEFOTETAN; IMIPENEM; METRONIDAZOLE; PENICILLIN DERIVATIVE; RNA 16S; VANCOMYCIN;

ANAEROBIC BACTERIUM; ANIMAL CELL; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIUM; DNA FRAGMENTATION; FENOLLARIA MASSILIENSIS; GENE NUMBER; GENE SEQUENCE; GENOME ANALYSIS; GRAM NEGATIVE BACTERIUM; HUMAN; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PROTEIN ANALYSIS; RNA GENE; TRANSMISSION ELECTRON MICROSCOPY;

EID: 84954117721     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.4056/sigs.3957647     Document Type: Article

References (37)

1. La Scola B, Fournier PE, Raoult D. Burden of emerging anaerobes in the MALDI-TOF and 16S rRNA gene sequencing era. Anaerobe 2011; 17:106-112. PubMed http://dx.doi.org/10.1016/j.anaerobe.2011.05.010
2. 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.
3. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol To-day 2006; 33:152-155.
4. 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
5. 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
6. Kokcha S, Michra 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
7. 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
8. 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
9. Lagier JC, Armougom F, Mishra AK, Nguyen 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 http://dx.doi.org/10.4056/sigs.2685971
10. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous-finished genome se-quence and description of Clostridium senegalense sp. nov. Stand Genomic Sci 2012; 6:386-395. PubMed
11. Michra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous-finished genome se-quence and description of Peptinophilus timonensis sp. nov. Stand Genomic Sci 2012; (In press).
12. Michra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous-finished genome sequence and description of Peptinophilus senegalensis sp. nov. Stand Genomic Sci 2012; (In press).
13. Ludwig W, Schleifer KH, Whitman WB. Revised road map to the phylum Firmicutes. In: Bergey's Manual of Systematic Bacteriology, 2nd ed., vol. 3 (The Firmicutes) (P. De Vos, G. Garrity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey, K.-H. Schleifer, and W.B. Whitman, eds.), Springer-Verlag, New York. (2009) pp. 1-13.
14. Mechichi T, Labat M, Garcia JL, Thomas P, Patel BK. Sporobacterium olearium gen. nov., sp. nov., a new methanethiol-producing bacterium that degrades aromatic compounds, isolated from an olive mill wastewater treatment digester. Int J Syst Bacteriol 1999; 49:1741-1748. PubMed http://dx.doi.org/10.1099/00207713-49-4-1741
15. Collins MD, Shah HN. Reclassification of Bacteroides praeacutus Tissier (Holdeman and Moore) in a new genus, Tissierella, as Tissierella praeacuta comb. nov. Int J Syst Bacteriol 1986; 36:461-463. http://dx.doi.org/10.1099/00207713-36-3-461
16. 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
17. 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 http://dx.doi.org/10.1073/pnas.87.12.4576
18. 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
19. 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.
20. 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.
21. 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
22. 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.
23. Skerman VBD, Sneath PHA. Approved list of bac-terial names. Int J Syst Bact 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
24. Prevot AR. 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.
25. 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
26. Farrow JAE, Lawson PA, Hippe H, Gauglitz U, Collins MD. Phylogenetic evidence that the Gram-negative nonsporulating bacterium Tissierella (Bacteroides) preacuta is a member of the Clostridium subphylum of the Gram-positive bacteria, and description of Tisiierella creatinini sp. nov. Int J Syst Bacteriol 1995; 45:436-440. PubMed http://dx.doi.org/10.1099/00207713-45-3-436
27. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596-1599. PubMed http://dx.doi.org/10.1093/molbev/msm092
28. Murdoch DA. Gram-positive anaerobic cocci. Clin Microbiol Rev 1998; 11:81-120. PubMed
29. 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
30. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011; 27:578-579. PubMed http://dx.doi.org/10.1093/bioinformatics/btq683
31. Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol 2012; 13:R56. PubMed http://dx.doi.org/10.1186/gb-2012-13-6-r56
32. 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
33. Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleo-tide sequences. Nucleic Acids Res 2004; 32:11-16. PubMed http://dx.doi.org/10.1093/nar/gkh152
34. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nu-cleic Acids Res 2003; 31:439-441. PubMed http://dx.doi.org/10.1093/nar/gkg006
35. 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
36. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. BMC Bioinformatics 2010; 11:119. Pub-Med http://dx.doi.org/10.1186/1471-2105-11-119
37. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed