Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium

Standards in Genomic Sciences

Volumn 9, Issue 3, 2015, Pages 794-806

  Cassir, Nadim ^a   Croce, Olivier ^a   Pagnier, Isabelle ^a   Benamar, Samia ^a   Couderc, Carine ^a   Robert, Catherine ^a   Raoult, Didier ^a   La Scola, Bernard ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Bacteroides neonati; Genome

Indexed keywords

ALKALINE PHOSPHATASE; AMOXICILLIN PLUS CLAVULANIC ACID; CATALASE; GELATINASE; IMIPENEM; METRONIDAZOLE; RIBOSOME RNA;

ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM COLONY; BACTEROIDES; BACTEROIDES NEONATI; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA DNA HYBRIDIZATION; DNA ISOLATION; ENZYME ACTIVITY; FECES ANALYSIS; GENE SEQUENCE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR GENETICS; NECROTIZING ENTEROCOLITIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; SCORING SYSTEM; SEQUENCE HOMOLOGY; TRANSMISSION ELECTRON MICROSCOPY;

EID: 84954114424     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.4056/sigs.5159098     Document Type: Article

References (53)

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, 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
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, 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
9. Michra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous-finished genome se-quence and description of Clostridium senegalenses sp. nov. Stand Genomic Sci 2012; 6:386-395. PubMed
10. 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; 7:1-11. PubMed
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 http://dx.doi.org/10.4056/sigs.3056450
12. Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome se-quence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci 2012; 7:200-209; 10.4056/sigs.3086474. PubMed
13. Roux V, El Karkouri K, Lagier JC, Robert C, Raoult D. Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov. Stand Genomic Sci 2012; 7:221-232. PubMed http://dx.doi.org/10.4056/sigs.3206554
14. 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 Ge-nomic Sci 2012; 7:233-245. PubMed http://dx.doi.org/10.4056/sigs.3256677
15. Ramasamy D, Kokcha S, Lagier JC, N'Guyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Aeromicrobium massilense sp. nov. Stand Ge-nomic Sci 2012; 7:246-257. PubMed http://dx.doi.org/10.4056/sigs.3306717
16. Lagier JC, Ramasamy D, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genome se-quence and description of Cellulomonas massiliensis sp. nov. Stand Genomic Sci 2012; 7:258-270. PubMed http://dx.doi.org/10.4056/sigs.3316719
17. Lagier JC, El Karkouri K, Rivet R, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Senegalemassilia anaerobia sp. nov. Stand Ge-nomic Sci 2013; 7:343-356. PubMed http://dx.doi.org/10.4056/sigs.3246665
18. Mishra AK, Hugon P, Lagier JC, Nguyen TT, Robert C, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and de-scription of Peptoniphilus obesi sp. nov. Stand Genomic Sci 2013; 7:357-369. PubMed http://dx.doi.org/10.4056/sigs.32766871
19. Mishra AK, Lagier JC, Nguyen TT, Raoult D, Fournier PE. Non-contiguous finished genome se-quence and description of Peptoniphilus senegalensis sp. nov. Stand Genomic Sci 2013; 7:370-381. PubMed http://dx.doi.org/10.4056/sigs.3366764
20. Lagier JC, El 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
21. Hugon P, Ramasamy D, Lagier JC, Rivet R, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and de-scription of Alistipes obesi sp. nov. Stand Ge-nomic Sci 2013; 7:427-439. PubMed http://dx.doi.org/10.4056/sigs.3336746
22. Mishra AK, Hugon P, Robert C, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Peptoniphilus grossensis sp. nov. Stand Genomic Sci 2012; 7:320-330. PubMed
23. Nishiyama T, Ueki A, Kaku N, Watanabe K, Ueki K. Bacteroides graminisolvens sp. nov., a xylanolytic anaerobe isolated from a methanogenic reactor treating cattle waste. Int J Syst Evol Microbiol 2009; 59:1901-1907. PubMed http://dx.doi.org/10.1099/ijs.0.008268-0
24. Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y. Bacteroides intestinalis sp. nov., iso-lated from human feces. Int J Syst Evol Microbiol 2006; 56:151-154. PubMed http://dx.doi.org/10.1099/ijs.0.63914-0
25. 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
26. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eukarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
27. Editor L. Validation List No. 143. Int J Syst Evol Microbiol 2012; 62:1-4.
28. Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York, 2011, p. 25.
29. Krieg NR. Class I. Bacteroidia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York, 2011, p. 25.
30. Krieg NR. Order I. Bacteroidales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Pas-ter BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York, 2011, p. 25.
31. 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
32. Pribram E. Klassification der Schizomyceten. Klassifikation der Schizomyceten (Bakterien), Franz Deuticke, Leipzig, 1933, p. 1-143.
33. Castellani A, Chalmers AJ. Genus Bacteroides Castellani and Chalmers, 1918. Manual of Tropi-cal Medicine, Third Edition, Williams, Wood and Co., New York, 1919, p. 959-960.
34. Holdeman LV, Moore WEC. Genus I. Bacteroides Castellani and Chalmers 1919, 959. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Deter-minative Bacteriology, Eighth Edition, The Wil-liams and Wilkins Co., Baltimore, 1974, p. 385-404.
35. Cato EP, Kelley RW, Moore WEC, Holdeman LV. Bacteroides zoogleoformans (Weinberg, Nativelle, and Prévot 1937) corrig. comb. nov.: emended description. Int J Syst Bacteriol 1982; 32:271-274. http://dx.doi.org/10.1099/00207713-32-3-271
36. Shah HN, Collins MD. Proposal to restrict the ge-nus Bacteroides (Castellani and Chalmers) to Bacteroides fragilis and closely related species. Int J Syst Bacteriol 1989; 39:85-87. http://dx.doi.org/10.1099/00207713-39-1-85
37. 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 Con-sortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
38. Schloss PD, Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev 2004; 68:686-691. PubMed http://dx.doi.org/10.1128/MMBR.68.4.686-691.2004
39. 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
40. Murdoch DA. Gram-positive anaerobic cocci. Clin Microbiol Rev 1998; 11:81-120. PubMed
41. 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
42. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004; 14:1147-1159. PubMed http://dx.doi.org/10.1101/gr.1917404
43. Gao S, Sung WK, Nagarajan N. Opera: recon-structing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 2011; 18:1681-1691. PubMed http://dx.doi.org/10.1089/cmb.2011.0170
44. 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
45. 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
46. 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
47. 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
48. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al. The Pfam protein families data-base. Nucleic Acids Res 2012; 40:D290-D301. PubMed http://dx.doi.org/10.1093/nar/gkr1065
49. 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
50. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: ar-chitecture and applications. BMC Bioinformatics 2009; 10:421. PubMed http://dx.doi.org/10.1186/1471-2105-10-421
51. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW. Gen Bank. Nucleic Acids Res 2012; 40:D48-D53. PubMed http://dx.doi.org/10.1093/nar/gkr1202
52. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genomoe-scale analysis of protein functions and evolution. Nu-cleic Acids Res 2000; 28:33-36. PubMed http://dx.doi.org/10.1093/nar/28.1.33
53. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997; 278:631-637. PubMed http://dx.doi.org/10.1126/science.278.5338.631