Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov.
Tóm tắt
Anaerococcus senegalensis strain JC48T sp. nov. is the type strain of A. senegalensis sp. nov. a new species within the genus Anaerococcus. This strain whose genome is described here was isolated from the fecal flora of a healthy patient. A. senegalensis is an obligate anaerobic coccus. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,790,835 bp long genome (1 chromosome but no plasmid) contains 1,721 protein-coding and 53 RNA genes including 5 rRNA genes
Tài liệu tham khảo
Rossello-Mora R. DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In: Stackebrandt E (ed.), Molecular Identification, Systematics, and population Structure of Prokaryotes. Springer, Berlin, 2006, p. 23–50.
Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155.
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
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
Ezaki T, Kawamura Y, Li N, Li ZY, Zhao L, Shu S. Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus. Int J Syst Evol Microbiol 2001; 51:1521–1528. PubMed
Jain S, Bui V, Spencer C, Yee L. Septic arthritis in a native joint due to Anaerococcus prevotii. J Clin Pathol 2007; 61:775–776. PubMed http://dx.doi.org/10.1136/jcp.2007.053421
Song Y, Liu C, Finegold SM. Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov. isolated from clinical specimens of human origin. J Clin Microbiol 2007; 45:1746–1752. PubMed http://dx.doi.org/10.1128/JCM.00213-07
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
Pépin J, Deslandes S, Giroux G, Sobéla F, Khonde N, Diakité S, Demeule S, Labbé AC, Carrier N, Frost E. The complex vaginal flora of west african women with bacterial vaginosis. PLoS ONE 2011; 6:e25082. PubMed http://dx.doi.org/10.1371/journal.pone.0025082
Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Murray PR, Green ED, et al. Topographical and temporal diversity of the human skin microbiome. Science 2009; 324:1190–1192. PubMed http://dx.doi.org/10.1126/science.1171700
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eukarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
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
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.
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.
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. http://dx.doi.org/10.1099/ijs.0.022855-0
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, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 736.
Skerman VBD, Sneath PHA. Approved list of bacterial names. Int J Syst Bacteriol 1980; 30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225
Prevot AR. In: Hauduroy P, Ehringer G, Guillot G, et al. (eds.), Dictionnaire des bactéries pathogènes, Second Edition, Masson, Paris, 1953, p. 1–692.
Garrity GM, Holt J. Taxonomic outline of the Archaea and Bacteria. In: Garrity GM, Boone DR, Castenholz RW (eds.), Bergey’s Manual of Systematic Bacteriology, Second Edition, Springer-Verlag, New York, 2003, p.155–166.
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
Seng P, Drancourta M, Gouriet F, La Scola B, Fournier PE, Jean Rolain 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. PubMed http://dx.doi.org/10.1086/600885
Prodigal. http://prodigal.ornl.gov
Lowe TM, Eddy SR. t-RNAscan-SE: a program for improved detection of transfer RNA gene in genomic sequence. Nucleic Acids Res 1997; 25:955–964. PubMed http://dx.doi.org/10.1093/nar/25.5.955
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. Complete genome sequence of Anaerococcus prevotii type strain (PC1). Nucleic Acids Res 2007; 35:3100–3108. PubMed http://dx.doi.org/10.1093/nar/gkm160
Labutti K, Pukall R, Steenblock K, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M. Complete genome sequence of type strain (PC1). Stand Genomic Sci 2009; 1:159–165. PubMed http://dx.doi.org/10.4056/sigs.24194
GenBank database. http://www.ncbi.nlm.nih.gov/genbank
URMS database. http://ifr48.timone.univmrs.fr/portail2/index.php?option=com content&ta sk=view&id=97&Itemid=54