Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov

Standards in Genomic Sciences

Volumn 9, Issue 3, 2015, Pages 1031-1045

  Keita, Mamadou Bhoye ^a   Padhmananabhan, Roshan ^a   Caputo, Aurélia ^a   Robert, Catherine ^a   Delaporte, Eric ^b   Raoult, Didier ^a,c   Fournier, Pierre Edouard ^a   Bittar, Fadi ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

^b INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^c KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Culturomics; Genome; Paenibacillus gorillae; Taxonomo genomics

Indexed keywords

RIBOSOME RNA; RNA 16S; TRANSFER RNA;

AMINO ACID METABOLISM; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIUM IDENTIFICATION; BIOSYNTHESIS; DNA BASE COMPOSITION; ENERGY CONVERSION; GENE SEQUENCE; GENETIC VARIABILITY; MAXIMUM LIKELIHOOD METHOD; METABOLITE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PAENIBACILLUS; PHENOTYPE; POLYMERASE CHAIN REACTION; TRANSMISSION ELECTRON MICROSCOPY;

EID: 84954115435     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.4056/sigs.5189179     Document Type: Article

References (53)

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. Dubourg G, Lagier JC, Armougom F, Robert C, Hamad I, Brouqui P, Raoult D. 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. PubMed http://dx.doi.org/10.1007/s10096-012-1787-3
3. Pfleiderer A, Lagier JC, Armougom F, Robert C, Vialettes B, Raoult D. Culturomics identified 11 new bacterial species from a single anorexia ner-vosa stool sample. Eur J Clin Microbiol Infect Dis 2013; 32:1471-1481. PubMed http://dx.doi.org/10.1007/s10096-013-1900-2
4. Ash C, Priest FG, Collins MD. Molecular identifi-cation of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 1993; 64:253-260. PubMed http://dx.doi.org/10.1007/BF00873085
5. Judicial Commission of the International Committee on Systematics of Prokaryotes. The type species of the genus Paenibacillus Ash et al. 1994 is Paenibacillus polymyxa. Opinion 77. Int J Syst Evol Microbiol 2005; 55:513. PubMed http://dx.doi.org/10.1099/ijs.0.63546-0
6. Abstract for the genus Paenibacillus. NamesforLife, LLC. Retrieved Novembre 1, 2013.
7. 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
8. Glaeser SP, Falsen E, Busse HJ, Kämpfer P. Paenibacillus vulneris sp. nov., isolated from a necrotic wound. Int J Syst Evol Microbiol 2013; 63:777-782. PubMed http://dx.doi.org/10.1099/ijs.0.041210-0
9. Anikpeh YF, Keller P, Bloemberg GV, Grünenfelder J, Zinkernagel AS. Spacecraft bacte-rium, Paenibacillus pasadenensis, causing wound infection in humans. BMJ Case Rep 2010.
10. Rieg S, Martin Bauer T, Peyerl-Hoffmann G, Held J, Ritter W, Wagner D, Kern WV, Serr A. Paenibacillus larvae bacteremia in injection drug users. Emerg Infect Dis 2010; 16:487-489. PubMed http://dx.doi.org/10.3201/eid1603.091457
11. Ouyang J, Pei Z, Lutwick L, Dalal S, Yang L, Cassai N, Sandhu K, Hanna B, Wieczorek RL, Bluth M, Pincus MR. Case report: Paenibacillus thiaminolyticus: a new cause of human infection, inducing bacteremia in a patient on hemodialysis. Ann Clin Lab Sci 2008; 38:393-400. PubMed
12. Teng JL, Woo PC, Leung KW, Lau SK, Wong MK, Yuen KY. Pseudobacteraemia in a patient with neutropenic fever caused by a novel paenibacillus species: Paenibacillus hongkongensis sp. nov. Mol Pathol 2003; 56:29-35. PubMed http://dx.doi.org/10.1136/mp.56.1.29
13. Ferrand J, Hadou T, Selton-Suty C, Goehringer F, Sadoul N, Alauzet C, Lozniewski A. Cardiac De-vice-Related Endocarditis Caused by Paenibacillus glucanolyticus. J Clin Microbiol 2013; 51:3439-3442. PubMed http://dx.doi.org/10.1128/JCM.00864-13
14. Keita MB, Diene S, Robert C, Raoult D, Fournier PE, Bittar F. Non-contiguous finished genome se-quence and description of Bacillus massiliogorillae sp. nov. Stand Genomic Sci 2013; 9:93-105. PubMed http://dx.doi.org/10.4056/sigs.4388124
15. 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
16. 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
17. 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
18. 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
19. 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
20. Hugon P, Ramasamy D, Lagier JC, Rivet R, Couderc C, Raoult D, Fournier PE. Non contigu-ous-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
21. Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE. Non contiguous-finished genome se-quence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae. Stand Genomic Sci 2013; 8:336-351. PubMed http://dx.doi.org/10.4056/sigs.3567059
22. 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 Micrococcinae. Stand Genomic Sci 2013; 8:318-335. PubMed http://dx.doi.org/10.4056/sigs.3476977
23. Mishra AK, Hugon P, Lagier JC, Nguyen TT, Couderc C, Raoult D, Fournier PE. Non contigu-ous-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. PubMed http://dx.doi.org/10.4056/sigs.3426906
24. Ramasamy D, Lagier JC, Gorlas A, Raoult D, Fournier PE. Non contiguous-finished genome se-quence and description of Bacillus massiliosenegalensis sp. nov. Stand Genomic Sci 2013; 8:264-278. PubMed http://dx.doi.org/10.4056/sigs.3496989
25. Hugon P, Mishra AK, Lagier JC, Nguyen TT, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and de-scription of Brevibacillus massiliensis sp. nov. Stand Genomic Sci 2013; 8:1-14. PubMed http://dx.doi.org/10.4056/sigs.3466975
26. Sentausa E, Fournier PE. Advantages and limita-tions of genomics in prokaryotic taxonomy. Clin Microbiol Infect 2013. PubMed http://dx.doi.org/10.1111/1469-0691.12181
27. 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
28. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archae, Bacteria, and Eukarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
29. 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
30. 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.
31. 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.
32. Ludwig W, Schleifer KH, Whitman WB. 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 Systemat-ic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 19-20.
33. 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
34. 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
35. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692
36. De Vos P, Ludwig W, Schleifer KH, Whitman WB. Family IV. Paenibacillaceae fam. nov. In Bergey's Manual of Systematic Bacteriology, 2nd Edition, vol 3 (The Firmicutes), Springer; New York, 2009, p. 269.
37. Validation List no. 51. Validation of the publica-tion of new names and new combinations previ-ously effectively published outside the IJSB. Int J Syst Bacteriol 1994; 44:852. http://dx.doi.org/10.1099/00207713-44-4-852
38. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K. Transfer of Bacillus alginolyticus,Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the ge-nus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 1997; 47:289-298. PubMed http://dx.doi.org/10.1099/00207713-47-2-289
39. Behrendt U, Schumann P, Stieglmeier M, Pukall R, Augustin J, Spröer C, Schwendner P, Moissl-Eichinger C, Ulrich A. Characterization of hetero-trophic nitrifying bacteria with respiratory am-monification and denitrification activity - De-scription of Paenibacillus uliginis sp. nov., an in-habitant of fen peat soil and Paenibacillus purispatii sp. nov., isolated from a spacecraft as-sembly clean room. Syst Appl Microbiol 2010; 33:328-336. PubMed http://dx.doi.org/10.1016/j.syapm.2010.07.004
40. 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
41. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011; 28:2731-2739. PubMed http://dx.doi.org/10.1093/molbev/msr121
42. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol To-day 2006; 33:152-155.
43. Kim DS, Bae CY, Jeon JJ, Chun SJ, Oh HW, Hong SG, Baek KS, Moon EY, Bae KS. Paenibacillus elgii sp. nov., with broad antimicrobial activity. Int J Syst Evol Microbiol 2004; 54:2031-2035. PubMed http://dx.doi.org/10.1099/ijs.0.02414-0
44. Ueda J, Yamamoto S, Kurosawa N. Paenibacillus thermoaerophilus sp. nov., a moderately thermophilic bacterium isolated from compost. Int J Syst Evol Microbiol 2013; 63:3330-3335. PubMed http://dx.doi.org/10.1099/ijs.0.048090-0
45. Lee FL, Kuo HP, Tai CJ, Yokota A, Lo CC. Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan. Int J Syst Evol Microbiol 2007; 57:1351-1354. PubMed http://dx.doi.org/10.1099/ijs.0.64764-0
46. Roux V, Raoult D. Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures. Int J Syst Evol Microbiol 2004; 54:1049-1054. PubMed http://dx.doi.org/10.1099/ijs.0.02954-0
47. Takebe F, Hirota K, Nodasaka Y, Yumoto I. Brevibacillus nitrificans sp. nov., a nitrifying bac-terium isolated from a microbiological agent for enhancing microbial digestion in sewage treat-ment tanks. Int J Syst Evol Microbiol 2012; 62:2121-2126. PubMed http://dx.doi.org/10.1099/ijs.0.032342-0
48. 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
49. Prodigal. http://prodigal.ornl.gov
50. GenBank database. http://www.ncbi.nlm.nih.gov/genbank
51. Lowe TM, Eddy SR. t-RNAscan-SE: a program for improved detection of transfer RNA gene in ge-nomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed http://dx.doi.org/10.1093/nar/25.5.0955
52. 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
53. Lechner M, Findeib S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinfor-matics 2011; 12:124. PubMed http://dx.doi.org/10.1186/1471-2105-12-124