Erratum: A call to arms for systematists: Revitalising the purpose and practises underpinning the description of novel microbial taxa (Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology (2012) 101:13 DOI 10.1007/s10482-011-9664-0);A call to arms for systematists: Revitalising the purpose and practises underpinning the description of novel microbial taxa

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 101, Issue 1, 2012, Pages 13-20

  Sutcliffe, Iain C ^a   Trujillo, Martha E ^b   Goodfellow, Michael ^c  

^a NORTHUMBRIA UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF SALAMANCA   (Spain)

^c NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Bacterial species; Chemotaxonomy; Microbial diversity; Phylogeny; Systematics; Taxonomy

Indexed keywords

16S RRNA GENE; BACTERIAL GENOME; BACTERIAL STRAIN; CHEMOTAXONOMY; CONFERENCE PAPER; DNA BASE COMPOSITION; DNA DNA HYBRIDIZATION; GENE SEQUENCE; GENOME ANALYSIS; GENOMICS; MICROBIAL DIVERSITY; MOLECULAR PHYLOGENY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROKARYOTE; RNA GENE; TAXONOMY; THIN LAYER CHROMATOGRAPHY;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84856214874     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-012-9801-4     Document Type: Erratum

References (52)

1. Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nature Rev Microbiol 6:431-440 (Pubitemid 351696437)
2. Adékambi T, Butler RW,Hanrahan F, Delcher AL, Drancourt M, Shinnick TM(2011) Core gene set as the basis of multilocus sequence analysis of the subclass Actinobacteridae. PLOS One 6:e14792
3. Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone S-A, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N (2004) Submission of microarray data to public repositories. PLOS Biol 2:e317
4. Butler-Wu SM, Sengupta DJ, Kittichotirat W, Matsen FA III, Bumgarner RE (2011) Genome sequence of a novel species, Propionibacterium humerusii. J Bacteriol 193:3678
5. Chun J, Lee J-H, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259-2261 (Pubitemid 350031697)
6. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly evolved tree of life. Science 311:1283-1287 (Pubitemid 43334717)
7. Coeyne T, Gevers D, van de Peer Y, Vandamme P, Swings J (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29:147-167 (Pubitemid 40432465)
8. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis 37:D141-D145
9. Cowan ST (1965) Principles and practise of bacterial taxonomy- a forward look. J Gen Microbiol 39:143-158
10. Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Nat Acad Sci USA 99:10494-10499
11. Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P, Hirsch PR, Vogel TM (2011) Acessing the soil metagenome for studies of microbial diversity. Appl Env Microbiol 77:1315-1324
12. Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11:R107
13. Dykhuizen DE (1998) Santa Rosalia revisited: why are there so mnay species of bacteria? Antonie van Leeuwenhoek 73:25-33 (Pubitemid 28209896)
14. Felis GE, Dellaglio F (2007) On species descriptions based on a single strain: proposal to introduce the status species proponenda (sp. pr.). Int J Syst Evol Microbiol 57: 2185-2187 (Pubitemid 47497168)
15. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch- Mizrachi I, Klenk H-P, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone S-A, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J (2011) The genomics standards consortium. PLOS Biol 9:e1001088
16. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Re-evaluating prokaryotic species. Nature Rev Microbiol 3:733-739 (Pubitemid 41195089)
17. Gilbert JA, Meyer F, Antonoploulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Kostantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R (2010) Meeting report. The terabase metagenomics workshop and the vision of an earth microbiome project. Stand in Genom Sci 3:243-248
18. Goodfellow M, Fiedler H-P (2010) A guide to successful bio prospecting: informed by actinobacterial systematics. Antonie van Leeuwenhoek 98:119-142
19. Gupta RS, Shami A (2011) Molecular signatures for the Crenarchaeota and the Thaumarchaeota. Antonie van Leeuwenhoek 99:133-157
20. Gupta RS, Vaibhav B (2011) Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups. Antonie van Leeuwenhoek 100:1-34
21. Hanage WP, Frase C, Spratt BG (2006) Sequences, sequence clusters and bacterial species. Phil Trans R Soc B 361: 1917-1927 (Pubitemid 44787027)
22. Jensen P (2010) Linking species concepts to natural product discovery in the post-genomic era. J Ind Microbiol Biotechnol 37:219-224
23. Klenk H-P, Göker G (2010) En route to a genome-based classification of archaea and bacteria. Syst Appl Microbiol 33:175-182
24. Konstantinidis KT, Tiedje JM (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 10:504-509 (Pubitemid 350052687)
25. Lagesen K, Ussery DW, Wassenaar TM (2010) Genome update: the 1000th genome-a cautionary tale. Microbiology 156: 603-608
26. Lefébure T, Stanhope MJ (2007) Evolution of the core and pangenome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8:R71
27. Maiden MCM (2006) Multilocus sequence typing of bacteria. Ann Rev Microbiol 60:561-588
28. Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relamn DA, Quake SR (2007) Dissecting biological 'dark matter' with singlecell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Nat Acad Sci USA 104:11889-11894 (Pubitemid 47185600)
29. Mira A, Martín-Cuadrado AB, D'auria G, Rodríguez-Valera F (2010) The bacterial pan-genome: a new paradigm in microbiology. Int Microbiol 13:45-57
30. Murray RGE, Stackebrandt E (1995) Taxonomic note: implementation of the provisional status Candidatus for incompletely described prokaryotes. Int J Syst Bacteriol 45:186-187
31. Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73:565-576
32. Pérez-Núñez D, Briandet R, David B, Gautier C, Renault P, Hallet B, Hols P, Carballido-López R, Guédon E (2011) A new morphogenesis pathway in bacteria: unbalanced activity of cell wall synthesis machineries leads to coccusto- rod transition and filamentation in ovococci. Mol Microbiol 79:759-771
33. Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188-7196
34. Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Ann Rev Microbiol 57:369-394 (Pubitemid 37392948)
35. Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39-67 (Pubitemid 32057196)
36. Schleifer KH (2009) Classification of bacteria and archaea: past, present and future. Syst Appl Microbiol 32:533-542
37. Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U (2011) Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 5: 61-70
38. Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30:225-420 (Pubitemid 10114719)
39. Sneath PHA (1995) 30 years of numerical taxonomy. System Biol 44:281-298
40. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152-155
41. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J System Evol Microbiol 52:1043-1047 (Pubitemid 34591239)
42. Staley JT (2010) Comprehending microbial diversity: the fourth goal of microbial taxonomy. Bulletin of BISMiS 1. http:// www.bergeys.org/ bismisbulletintoc.html
43. Sutcliffe IC (2010) A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 18:464-470
44. Taylor CF, Paton NW, Lilley KS, Binz P-A, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJR, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR III, Hermjakob H (2007) The minimum information about a proteomics experiment (MIAPE). Nature Biotech 25:887-893 (Pubitemid 47236919)
45. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, DeBoy RT, Davidsen TM, Mora M, Scarselli M, Ros IMY, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou LW, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJB, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'. Proc Natl Acad Sci USA 102:13950-13955 (Pubitemid 41377684)
46. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterisation of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60: 249-266
47. Trujillo ME (2011) Taxonomic subcommittees and minimal standards for the description of prokaryotes. Microbiology Australia 32:64-66
48. Turner KME, Feil EJ (2007) The secret life of the multilocus sequence type. Int J Antimicrob Agents 29:129-135 (Pubitemid 46073677)
49. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Mol Biol Rev 60:407-438 (Pubitemid 26170913)
50. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463-464
51. Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng J-F (2010) One bacterial cell, one complete genome. PLOS One 5:e10314
52. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng J-F, Lucas S, Kerfeld C, Lang E, Gronow S,Chain P,Bruce D,Rubin EM, Kyrpides NC, Klenk H-P, Eisen JA (2009) A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462:1056-1060