Genome sequence and description of Bacteroides timonensis sp. nov

Standards in Genomic Sciences

Volumn 9, Issue 3, 2015, Pages 1181-1197

  Ramasamy, Dhamodharan ^a   Lagier, Jean Christophe ^a   Rossi Tamisier, Morgane ^a   Pfleiderer, Anne ^a   Michelle, Caroline ^a   Couderc, Carine ^a   Raoult, Didier ^a,b   Fournier, Pierre Edouard ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Bacteroides timonensis; Culturomics; Genome; Taxono genomics

Indexed keywords

ADULT; ARTICLE; BACTERIAL GENETICS; BACTEROIDES; BACTEROIDES CELLULOSILYTICUS; BACTEROIDES FINEGOLDII; BACTEROIDES FRAGILIS; BACTEROIDES HELCOGENES; BACTEROIDES INTESTINALIS; BACTEROIDES SALANITRONIS; BACTEROIDES THETAIOTAOMICRON; BACTEROIDES TIMONENSIS AP1; BACTEROIDES UNIFORMIS; BACTEROIDES VULGATUS; COMPARATIVE STUDY; CONTROLLED STUDY; DNA ISOLATION; FECES MICROFLORA; FEMALE; GENE SEQUENCE; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; TRANSMISSION ELECTRON MICROSCOPY; YOUNG ADULT;

EID: 84954187047     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.4056/sigs.5389564     Document Type: Article

References (80)

1. Lagier JC, 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. PubMed
2. Tindall BJ, Rosselló-Móra 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
3. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152-155.
4. Wayne LG, Brenner DJ, Colwell PR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, et al. Report of the ad hoc committee on reconcilia-tion of approaches to bacterial systematic. Int J Syst Bacteriol 1987; 37:463-464. http://dx.doi.org/10.1099/00207713-37-4-463
5. 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.
6. 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
7. Kokcha S, Mishra AK, Lagier JC, Million M, Leroy Q, Raoult D, Fournier PE. Non-contiguous finished genome sequence and de-scription of Bacillus timonensis sp. nov. Stand Genomic Sci 2012; 6:346-355. PubMed http://dx.doi.org/10.4056/sigs.2776064
8. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi-Tamisier M, Sentausa E, Raoult D, Fournier PE. A polyphasic strategy incorpo-rating genomic data for the taxonomic descrip-tion of new bacterial species. Int J Syst Evol Microbiol 2013; 64:384-391 . PubMed http://dx.doi.org/10.1099/ijs.0.057091-0
9. Lagier JC, El Karkouri K, Nguyen TT, Armougom F, Raoult D, Fournier PE. Non-contiguous fin-ished 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
10. 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
11. 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 http://dx.doi.org/10.4056/sigs.2685971
12. 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
13. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier 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
14. Mishra AK, Lagier JC, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genome se-quence and description of Paenibacillus senegalensis sp. nov. Stand Genomic Sci 2012; 7:70-81. PubMed http://dx.doi.org/10.4056/sigs.3056450
15. Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci 2012; 7:200-209. PubMed
16. 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
17. Ramasamy D, Kokcha S, Lagier JC, N'Guyen TT, Raoult D, Fournier PE. Non-contiguous fin-ished 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
18. Lagier JC, Ramasamy D, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genomesequence and description of Cellulomonas massiliensis sp. nov. Stand Genomic Sci 2012; 7:258-270. PubMed http://dx.doi.org/10.4056/sigs.3316719
19. Lagier JC, Karkouri K, Rivet R, Couderc C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Stand Genomic Sci 2013; 7:343-356. PubMed http://dx.doi.org/10.4056/sigs.3246665
20. Mishra AK, Hugon P, Nguyen TT, Robert C, Couderc C, Raoult D, Fournier PE. Non contig-uous-finished genome sequence and descrip-tion of Peptoniphilus obesi sp. nov. Stand Ge-nomic Sci 2013; 7:357-369. PubMed http://dx.doi.org/10.4056/sigs.32766871
21. Mishra AK, Lagier JC, Nguyen TT, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov. Stand Genomic Sci 2013; 7:370-381. PubMed http://dx.doi.org/10.4056/sigs.3366764
22. Lagier JC, Karkouri K, Mishra AK, Robert C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov. Stand Ge-nomic Sci 2013; 7:399-412. PubMed http://dx.doi.org/10.4056/sigs.3396830
23. Hugon P, Ramasamy D, Rivet R, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov. Stand Genomic Sci 2013; 7:427-439. PubMed http://dx.doi.org/10.4056/sigs.3336746
24. Hugon P, Mishra AK, Nguyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Stand Genomic Sci 2013; 8:1-14. PubMed http://dx.doi.org/10.4056/sigs.3466975
25. Mishra AK, Hugon P, Nguyen TT, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae. Stand Ge-nomic Sci 2013; 8:290-305. PubMed http://dx.doi.org/10.4056/sigs.3426906
26. Ramasamy D, Lagier JC, Gorlas A, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. Nov. Stand Genomic Sci 2013; 8:264-278. PubMed http://dx.doi.org/10.4056/sigs.3496989
27. Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Fami-ly Erysipelotrichaceae. Stand Genomic Sci 2013; 8:336-351. PubMed http://dx.doi.org/10.4056/sigs.3567059
28. Mishra AK, Pfleiderer A, Lagier JC, Robert C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massilioanorexius sp. nov. Stand Genomic Sci 2013; 8:465-479. PubMed http://dx.doi.org/10.4056/sigs.4087826
29. Hugon P, Ramasamy D, Robert C, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI. Stand Genomic Sci 2013; 8:500-515. PubMed http://dx.doi.org/10.4056/sigs.4047997
30. Padmanabhan R, Lagier JC, Dangui NPM, Michelle C, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Megasphaera massiliensis. Stand Genomic Sci 2013; 8:525-538. PubMed http://dx.doi.org/10.4056/sigs.4077819
31. Mishra AK, Edouard S, Dangui NPM, Lagier JC, Caputo A, Blanc-Tailleur C, Ravaux I, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. Stand Genomic Sci 2013; 9:205-219. PubMed http://dx.doi.org/10.4056/sigs.4378121
32. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcineae. Stand Genomic Sci 2013; 8:318-335. PubMed http://dx.doi.org/10.4056/sigs.3476977
33. Keita MB, Diene SM, Robert C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massiliogorillae sp. nov. Stand Genomic Sci 2013; 9:93-105. PubMed http://dx.doi.org/10.4056/sigs.4388124
34. Mediannikov O, El Karkouri K, Robert C, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Bartonella florenciae sp. nov. Stand Genomic Sci 2013; 9:185-196. PubMed http://dx.doi.org/10.4056/sigs.4358060
35. Lo CI, Mishra AK, Padhmanabhan R, Samb Ba B, Gassama Sow A, Robert C, Couderc C, Faye N, Raoult D, Fournier PE, Fenollar F. Non con-tiguous-finished genome sequence and descrip-tion of Clostridium dakarense sp. nov. Stand Genomic Sci 2013; 9:14-27. PubMed http://dx.doi.org/10.4056/sigs.4097825
36. Mishra AK, Hugon P, Robert 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
37. Mediannikov O, El Karkouri K, Diatta G, Robert C, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Bartonella senegalensis sp. nov. Stand Genomic Sci 2013; 8:279-289. PubMed http://dx.doi.org/10.4056/sigs.3807472
38. Garrity GM, Holt JG. Taxonomic Outline of the Archaea and Bacteria. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Vol-ume 1, Springer, New York, 2001, p. 155-166.
39. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science 2005; 308:1635-1638. PubMed http://dx.doi.org/10.1126/science.1110591
40. List of Prokaryotic names with standing nomenclature (LPSN). http://www.bacterio.cict.fr.
41. Smith CJ, Rocha ER, Paster BJ. 2005. The medically important Bacteroides spp. in health and disease. In The Prokaryotes, an evolving electronic resource for the microbiological community, Release 3.19 (18.3.2005) (http://141-150-157-117:8080/prokPUB/index.htm). Edited by M. Dworkin. New York: Springer.
42. Finegold SM, George WL. 1989. Anaerobic In-fections in Humans. San Diego: Academic Press.
43. 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) speci-fication. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/10.1038/nbt1360
44. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. Pub-Med http://dx.doi.org/10.1073/pnas.87.12.4576
45. Validation List No. 143. Int J Syst Evol Microbiol 2012; 62:1-4. http://dx.doi.org/10.1099/ijs.0.039487-0
46. 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, Second Edition, Volume 4, Springer, New York, 2011, p. 25.
47. 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 Bacteriol-ogy, Second Edition, Volume 4, Springer, New York, 2011, p. 25.
48. Krieg NR. Order I. Bacteroidales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriol-ogy, Second Edition, Volume 4, Springer, New York, 2011, p. 25.
49. Skerman VBD, McGowan V, Sneath PHA. Ap-proved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
50. Pribram E. Klassification der Schizomyceten. Klassifikation der Schizomyceten (Bakterien), Franz Deuticke, Leipzig, 1933, p. 1-143.
51. Castellani A, Chalmers AJ. Genus Bacteroides Castellani and Chalmers, 1918. Manual of Tropical Medicine, Third Edition, Williams, Wood and Co., New York, 1919, p. 959-960.
52. Holdeman LV, Moore WEC. Genus I. Bacteroides Castellani and Chalmers 1919, 959. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Balti-more, 1974, p. 385-404.
53. 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
54. Shah HN, Collins MD. Proposal to restrict the genus 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
55. 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 Ontol-ogy Consortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
56. 16S Yourself database. (http://www.mediterranee-infection.com/article.php?larub=152&titre=16s-yourself).
57. Eggerth AH, Gagnon BH. The Bacteroides of Human Feces. J Bacteriol 1933; 25:389-413. PubMed
58. Shah HN. 1992. The genus Bacteroides and re-lated taxa. In The Prokaryotes, 2nd edn, pp. 3593-3607. Edited by Balows A, Truper HG,Dworkin M, Harder M & Schleifer KH. New York: Springer.
59. Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y. Bacteroides intestinalis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2006; 56:151-154. PubMed http://dx.doi.org/10.1099/ijs.0.63914-0
60. Robert C, Chassard C, Lawson PA, Bernalier-Donadille A. Bacteroides cellulosilyticus sp. nov., a cellulolytic bacterium from the human gut microbial community. Int J Syst Evol Microbiol 2007; 57:1516-1520. PubMed http://dx.doi.org/10.1099/ijs.0.64998-0
61. Johnson JL. Taxonomy of the Bacteroides I. De-oxyribonucleic acid homologies among Bacteroides fragilis and other saccharolytic Bacteroides species. Int J Syst Evol Microbiol 1978; 28:245-256.
62. Cato EP, Johnson JL. Reinstatement of species rank for Bacteroides fragilis, B. ovatus, B. distasonis, B. thetaiotaomicron, and B. vulgatus: Designation of Neotype Strains for Bacteroides fragilis (Veillon and Zuber) Castellani and Chalmers and Bacteroides thetaiotaomicron (Distaso) Castellani and Chalmers. Int J Syst Bacteriol 1976; 26:230-237. http://dx.doi.org/10.1099/00207713-26-2-230
63. Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 2003; 299:2074-2076. PubMed http://dx.doi.org/10.1126/science.1080029
64. Lan PT, Sakamoto M, Sakata S, Benno Y. Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum. Int J Syst Evol Microbiol 2006; 56:2853-2859. Pub-Med http://dx.doi.org/10.1099/ijs.0.64517-0
65. Benno Y, Watabe J, Mitsuoka T. Bacteroides pyogenes sp. nov., Bacteroides suis sp. nov., and Bacteroides helcogenes sp. nov., New Spe-cies from Abscesses and Feces of Pigs. Syst Appl Microbio 1983; l4:396-407.
66. Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, et al. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). Stand Genomic Sci 2011; 4:45-53. PubMed http://dx.doi.org/10.4056/sigs.1513795
67. Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y. Bacteroides finegoldii sp. nov., iso-lated from human faeces. Int J Syst Evol Microbiol 2006; 56:931-935. PubMed http://dx.doi.org/10.1099/ijs.0.64084-0
68. Seng P, Drancourt M, Gouriet F, La SB, Fournier PE, Rolain JM, 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
69. Prodigal. http://prodigal.ornl.gov/
70. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Ac-ids Res 2012; 40:D48-D53. PubMed http://dx.doi.org/10.1093/nar/gkr1202
71. 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. PubMed http://dx.doi.org/10.1093/nar/25.5.0955
72. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100-3108. Pub-Med http://dx.doi.org/10.1093/nar/gkm160
73. 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
74. 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
75. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39:W347-W352. PubMed http://dx.doi.org/10.1093/nar/gkr485
76. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: rapid an-notations using subsystems technology. BMC Genomics 2008; 9:75. PubMed http://dx.doi.org/10.1186/1471-2164-9-75
77. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: se-quence visualization and annotation. Bioinfor-matics 2000; 16:944-945. PubMed http://dx.doi.org/10.1093/bioinformatics/16.10.944
78. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear inter-active genome visualization. Bioinformatics 2009; 25:119-120. PubMed http://dx.doi.org/10.1093/bioinformatics/btn578
79. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved ge-nomic sequence with rearrangements. Genome Res 2004; 14:1394-1403. PubMed http://dx.doi.org/10.1101/gr.2289704
80. Lechner M, Findeib S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124. PubMed http://dx.doi.org/10.1186/1471-2105-12-124