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The Phylogeny of

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  • Authors: Richard T. Okinaka1, Paul Keim2
  • Editors: Patrick Eichenberger3, Adam Driks4
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    Affiliations: 1: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073; 2: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073; 3: New York University, New York, NY; 4: Loyola University Medical Center, Maywood, IL
    • Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
  • Received 17 October 2012 Accepted 15 December 2015 Published 12 February 2016
  • Richard Okinaka, [email protected]
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  • Abstract:

    The three main species of the , , , and , were recognized and established by the early 1900s because they each exhibited distinct phenotypic traits. isolates and their parasporal crystal proteins have long been established as a natural pesticide and insect pathogen. , the etiological agent for anthrax, was used by Robert Koch in the 19th century as a model to develop the germ theory of disease, and , a common soil organism, is also an occasional opportunistic pathogen of humans. In addition to these three historical species designations, are three less-recognized and -understood species: , , and . All of these “species” combined comprise the group. Despite these apparently clear phenotypic definitions, early molecular approaches to separate the first three by various DNA hybridization and 16S/23S ribosomal sequence analyses led to some “confusion” because there were limited differences to differentiate between these species. These and other results have led to frequent suggestions that a taxonomic change was warranted to reclassify this group to a single species. But the pathogenic properties of and the biopesticide applications of appear to “have outweighed pure taxonomic considerations” and the separate species categories are still being maintained. represents a classic example of a now common bacterial species taxonomic quandary.

  • Citation: Okinaka R, Keim P. 2016. The Phylogeny of . Microbiol Spectrum 4(1):TBS-0012-2012. doi:10.1128/microbiolspec.TBS-0012-2012.

References

1. Aronso n AI. 1993. Insecticidal toxins, p 953–963. In Sonenshein AL, Hoch JA, Losick R (ed), Bacillus subtilis and Other Gram-Positive Bacteria. American Society for Microbiology, Washington, DC.
2. Turnbull PCB. 2002. Introduction: anthrax history, disease and ecology, p 1–19. In Koehler TM (ed), Anthrax, vol 271. Springer-Verlag, Berlin, Germany.
3. Drobniewski FA. 1993. Bacillus cereus and related species. Clin Microbiol Rev 6:324–338. [PubMed]
4. Granum PE, Lund T. 1997. Bacillus cereus and its food poisoning toxins. FEMS Microbiol Lett 157:223–228. [PubMed][CrossRef]
5. Helgason E, Caugant DA, Olsen I, Kolstø AB. 2000. Genetic structure of population of Bacillus cereus and B. thuringiensis isolates associated with periodontitis and other human infections. J Clin Microbiol 38:1615–1622. [PubMed]
6. Priest FG. 1993. Systematics and ecology of bacillus, p 3–33. In Sonenshien A, Hoch JA, Losick R (ed), Bacillus subtilis and Other Gram-Positive Bacteria. American Society for Microbiology, Washington, DC. [CrossRef]
7. Helgason E, Okstad OA, Caugant DA, Johansen HA, Fouet A, Mock M, Hegna I, Kolstø AB. 2000. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis–one species on the basis of genetic evidence. Appl Environ Microbiol 66:2627–2630. [PubMed][CrossRef]
8. Schnepf E, Crickmore N, Van Rie J, Lereclus D, Baum J, Feitelson J, Zeigler DR, Dean DH. 1998. Bacillus thuringiensis and its pesticidal crystal proteins. Microbiol Mol Biol Rev 62:775–806. [PubMed]
9. Didelot X, Barker M, Falush D, Priest FG. 2009. Evolution of pathogenicity in the Bacillus cereus group. Syst Appl Microbiol 32:81–90. [PubMed][CrossRef]
10. Staley JT. 2006. The bacterial species dilemma and the genomic-phylogenetic species concept. Philos Trans R Soc Lond B Biol Sci 361:1899–1909. [PubMed][CrossRef]
11. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. [PubMed][CrossRef]
12. Keim P, Kalif A, Schupp J, Hill K, Travis SE, Richmond K, Adair DM, Hugh-Jones M, Kuske CR, Jackson P. 1997. Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. J Bacteriol 179:818–824. [PubMed]
13. Ticknor LO, Kolstø AB, Hill KK, Keim P, Laker MT, Tonks M, Jackson PJ. 2001. Fluorescent amplified fragment length polymorphism analysis of Norwegian Bacillus cereus and Bacillus thuringiensis soil isolates. Appl Environ Microbiol 67:4863–4873. [PubMed][CrossRef]
14. Hill KK, Ticknor LO, Okinaka RT, Asay M, Blair H, Bliss KA, Laker M, Pardington PE, Richardson AP, Tonks M, Beecher DJ, Kemp JD, Kolstø AB, Wong AC, Keim P, Jackson PJ. 2004. Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates. Appl Environ Microbiol 70:1068–1080. [PubMed][CrossRef]
15. Helgason E, Tourasse NJ, Meisal R, Caugant DA, Kolstø AB. 2004. Multilocus sequence typing scheme for bacteria of the Bacillus cereus group. Appl Environ Microbiol 70:191–201. [PubMed][CrossRef]
16. Priest FG, Barker M, Baillie LW, Holmes EC, Maiden MC. 2004. Population structure and evolution of the Bacillus cereus group. J Bacteriol 186:7959–7970. [PubMed][CrossRef]
17. Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ, Hugh-Jones ME. 2000. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 182:2928–2936. [PubMed][CrossRef]
18. Hoffmaster AR, Hill KK, Gee JE, Marston CK, De BK, Popovic T, Sue D, Wilkins PP, Avashia SB, Drumgoole R, Helma CH, Ticknor LO, Okinaka RT, Jackson PJ. 2006. Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes. J Clin Microbiol 44:3352–3360. [PubMed][CrossRef]
19. Klee SR, Brzuszkiewicz EB, Nattermann H, Brüggemann H, Dupke S, Wollherr A, Franz T, Pauli G, Appel B, Liebl W, Couacy-Hymann E, Boesch C, Meyer FD, Leendertz FH, Ellerbrok H, Gottschalk G, Grunow R, Liesegang H. 2010. The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids. PLoS One 5:e10986. doi:10.1371/journal.pone.0010986. [PubMed][CrossRef]
20. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145. [PubMed][CrossRef]
21. Ko KS, Kim JW, Kim JM, Kim W, Chung SI, Kim IJ, Kook YH. 2004. Population structure of the Bacillus cereus group as determined by sequence analysis of six housekeeping genes and the plcR gene. Infect Immun 72:5253–5261. [PubMed][CrossRef]
22. Cardazzo B, Negrisolo E, Carraro L, Alberghini L, Patarnello T, Giaccone V. 2008. Multiple-locus sequence typing and analysis of toxin genes in Bacillus cereus food-borne isolates. Appl Environ Microbiol 74:850–860. [PubMed][CrossRef]
23. Olsen JS, Skogan G, Fykse EM, Rawlinson EL, Tomaso H, Granum PE, Blatny JM. 2007. Genetic distribution of 295 Bacillus cereus group members based on adk-screening in combination with MLST (Multilocus Sequence Typing) used for validating a primer targeting a chromosomal locus in B. anthracis. J Microbiol Methods 71:265–274. [PubMed][CrossRef]
24. Sorokin A, Candelon B, Guilloux K, Galleron N, Wackerow-Kouzova N, Ehrlich SD, Bourguet D, Sanchis V. 2006. Multiple-locus sequence typing analysis of Bacillus cereus and Bacillus thuringiensis reveals separate clustering and a distinct population structure of psychrotrophic strains. Appl Environ Microbiol 72:1569–1578. [PubMed][CrossRef]
25. Tourasse NJ, Helgason E, Økstad OA, Hegna IK, Kolstø AB. 2006. The Bacillus cereus group: novel aspects of population structure and genome dynamics. J Appl Microbiol 101:579–593. [PubMed][CrossRef]
26. Guinebretière MH, Thompson FL, Sorokin A, Normand P, Dawyndt P, Ehling-Schulz M, Svensson B, Sanchis V, Nguyen-The C, Heyndrickx M, De Vos P. 2008. Ecological diversification in the Bacillus cereus group. Environ Microbiol 10:851–865. [PubMed][CrossRef]
27. Tourasse NJ, Helgason E, Klevan A, Sylvestre P, Moya M, Haustant M, Økstad OA, Fouet A, Mock M, Kolstø AB. 2011. Extended and global phylogenetic view of the Bacillus cereus group population by combination of MLST, AFLP, and MLEE genotyping data. Food Microbiol 28:236–244. [PubMed][CrossRef]
28. Maughan H, Van der Auwera G. 2011. Bacillus taxonomy in the genomic era finds phenotypes to be essential though often misleading. Infect Genet Evol 11:789–797. [PubMed][CrossRef]
29. Helgason E, Caugant DA, Lecadet MM, Chen Y, Mahillon J, Lövgren A, Hegna I, Kvaløy K, Kolstø AB. 1998. Genetic diversity of Bacillus cereus/B. thuringiensis isolates from natural sources. Curr Microbiol 37:80–87. [PubMed][CrossRef]
30. Friedberg EC, Walker GC, Siede W, Schultz RA, Ellenberger T. 2006. DNA Repair and Mutagenesis, 2nd ed. ASM Press, Washington, DC.
31. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG. 2004. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 186:1518–1530. [PubMed][CrossRef]
32. Jolley KA, Wilson DJ, Kriz P, McVean G, Maiden MC. 2005. The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis. Mol Biol Evol 22:562–569. [PubMed][CrossRef]
33. Spratt BG, Hanage WP, Li B, Aanensen DM, Feil EJ. 2004. Displaying the relatedness among isolates of bacterial species – the eBURST approach. FEMS Microbiol Lett 241:129–134. [PubMed][CrossRef]
34. Didelot X, Falush D. 2007. Inference of bacterial microevolution using multilocus sequence data. Genetics 175:1251–1266. [PubMed][CrossRef]
35. Didelot X, Maiden MC. 2010. Impact of recombination on bacterial evolution. Trends Microbiol 18:315–322. [PubMed][CrossRef]
36. Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, Iida T, Takami H, Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, Shinagawa H. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 8:11–22. [PubMed][CrossRef]
37. Lawrence JG, Ochman H. 1998. Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95:9413–9417. [PubMed][CrossRef]
38. Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J. 2008. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–6893. [PubMed][CrossRef]
39. Welch RA, Burland V, Plunkett G III, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99:17020–17024. [PubMed][CrossRef]
40. 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, Margarit y Ros I, 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 L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O’Connor KJ, 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. [PubMed][CrossRef]
41. Tettelin H, Riley D, Cattuto C, Medini D. 2008. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 11:472–477. [PubMed][CrossRef]
42. Zwick ME, Joseph SJ, Didelot X, Chen PE, Bishop-Lilly KA, Stewart AC, Willner K, Nolan N, Lentz S, Thomason MK, Sozhamannan S, Mateczun AJ, Du L, Read TD. 2012. Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis. Genome Res 22:1512–1524. [PubMed][CrossRef]
43. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–876. [PubMed][CrossRef]
44. Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM, Rasko DA. 2009. The complete genome sequence of Bacillus anthracis Ames “Ancestor”. J Bacteriol 191:445–446. [PubMed][CrossRef]
45. Lapierre P, Gogarten JP. 2009. Estimating the size of the bacterial pan-genome. Trends Genet 25:107–110. [PubMed][CrossRef]
46. Vos M, Didelot X. 2009. A comparison of homologous recombination rates in bacteria and archaea. ISME J 3:199–208. [PubMed][CrossRef]
47. Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H, Tuanyok A, Price EP, Glass MB, Leadem B, Beckstrom-Sternberg JS, Allan GJ, Foster JT, Wagner DM, Okinaka RT, Sim SH, Pearson O, Wu Z, Chang J, Kaul R, Hoffmaster AR, Brettin TS, Robison RA, Mayo M, Gee JE, Tan P, Currie BJ, Keim P. 2009. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 7:78. doi:10.1186/1741-7007-7-78. [PubMed][CrossRef]
48. Ash C, Collins MD. 1992. Comparative analysis of 23S ribosomal RNA gene sequences of Bacillus anthracis and emetic Bacillus cereus determined by PCR-direct sequencing. FEMS Microbiol Lett 73:75–80. [PubMed][CrossRef]
49. Ash C, Farrow JA, Dorsch M, Stackebrandt E, Collins MD. 1991. Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int J Syst Bacteriol 41:343–346. [PubMed][CrossRef]
50. Lawrence JG. 2005. Common themes in the genome strategies of pathogens. Curr Opin Genet Dev 15:584–588. [PubMed][CrossRef]
51. Ochman H, Davalos LM. 2006. The nature and dynamics of bacterial genomes. Science 311:1730–1733. [PubMed][CrossRef]
52. Andersson SG, Zomorodipour A, Andersson JO, Sicheritz-Pontén T, Alsmark UC, Podowski RM, Näslund AK, Eriksson AS, Winkler HH, Kurland CG. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133–140. [PubMed][CrossRef]
53. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honoré N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG. 2001. Massive gene decay in the leprosy bacillus. Nature 409:1007–1011. [PubMed][CrossRef]
54. Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O’Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848–852. [PubMed][CrossRef]
55. Toby IT, Widmer J, Dyer DW. 2014. Divergence of protein-coding capacity and regulation in the B. cereus sensu lato group. BMC Bioinformatics 15(Suppl 11) :S8. doi:10.1186/1471-2105-15-S11-S8. [CrossRef]
56. Agaisse H, Gominet M, Okstad OA, Kolstø AB, Lereclus D. 1999. PlcR is a pleiotropic regulator of extracellular virulence factor gene expression in Bacillus thuringiensis. Mol Microbiol 32:1043–1053. [PubMed][CrossRef]
57. Ross CL, Thomason KS, Koehler TM. 2009. An extracytoplasmic function sigma factor controls beta-lactamase gene expression in Bacillus anthracis and other Bacillus cereus group species. J Bacteriol 191:6683–6693. [PubMed][CrossRef]
58. Gould SJ. 1977. This view of life: the return of hopeful monsters. Nat Hist 86:22–30.
59. Keim PS, Wagner DM. 2009. Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases. Nat Rev Microbiol 7:813–821. [PubMed][CrossRef]
60. Lapidus A, Goltsman E, Auger S, Galleron N, Ségurens B, Dossat C, Land ML, Broussolle V, Brillard J, Guinebretiere MH, Sanchis V, Nguen-The C, Lereclus D, Richardson P, Wincker P, Weissenbach J, Ehrlich SD, Sorokin A. 2008. Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity. Chem Biol Interact 171:236–249. [PubMed][CrossRef]
61. Papazisi L, Rasko DA, Ratayake S, Bock GR, Remortel BG, Appalla L, Liu J, Dracheva T, Braisted JC, Shallome S, Jarrahi B, Snesrud E, Ahn S, Sun Q, Rilstone J, Okstad OA, Kolsto A-B, Fleischmann RD, Peterson SN. 2011. Investigating the genome diversity of B. cereus and evolutionary aspects of B. anthracis emergence. Genomics 98:26–39. [PubMed][CrossRef]
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2016-02-12
2021-04-14

Abstract:

The three main species of the , , , and , were recognized and established by the early 1900s because they each exhibited distinct phenotypic traits. isolates and their parasporal crystal proteins have long been established as a natural pesticide and insect pathogen. , the etiological agent for anthrax, was used by Robert Koch in the 19th century as a model to develop the germ theory of disease, and , a common soil organism, is also an occasional opportunistic pathogen of humans. In addition to these three historical species designations, are three less-recognized and -understood species: , , and . All of these “species” combined comprise the group. Despite these apparently clear phenotypic definitions, early molecular approaches to separate the first three by various DNA hybridization and 16S/23S ribosomal sequence analyses led to some “confusion” because there were limited differences to differentiate between these species. These and other results have led to frequent suggestions that a taxonomic change was warranted to reclassify this group to a single species. But the pathogenic properties of and the biopesticide applications of appear to “have outweighed pure taxonomic considerations” and the separate species categories are still being maintained. represents a classic example of a now common bacterial species taxonomic quandary.

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The Phylogeny of
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Citation: Okinaka R, Keim P. 2016. The phylogeny of . microbiolspec 4(1): doi:10.1128/microbiolspec.TBS-0012-2012
/content/microbiolspec/10.1128/microbiolspec.TBS-0012-2012.fig1
FIGURE 1
AFLP-based phylogenetic tree of . This is a schematic representation redrawn from Hill et al. ( 12 ) of 332 isolates. While 10 distinct branches were identified, they formed three main clusters labeled as 1, 2, and 3 to correspond to subgroups identified by Priest et al. ( 15 ) to maintain consistency between AFLP and MLST trees based on the positions of known matching isolates in both trees.
microbiolspec/4/1/TBS-0012-2012-fig1_thmb.gif
microbiolspec/4/1/TBS-0012-2012-fig1.gif
Image of FIGURE 1

Click to view

FIGURE 1

AFLP-based phylogenetic tree of . This is a schematic representation redrawn from Hill et al. ( 12 ) of 332 isolates. While 10 distinct branches were identified, they formed three main clusters labeled as 1, 2, and 3 to correspond to subgroups identified by Priest et al. ( 15 ) to maintain consistency between AFLP and MLST trees based on the positions of known matching isolates in both trees.

Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
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/content/microbiolspec/10.1128/microbiolspec.TBS-0012-2012.fig2
FIGURE 2
An example of homologous recombination identified in MLST profiles. (A) The diversity of an original MLST subclade (Sotto) based on seven MLST fragments ( 15 ). The same branch is shown, but is now dissected by ClonalFrame ( 33 ) and separated into six consistent fragments (B) and a second inconsistent fragment () (C) to show that the fragment has two sequence types, 55 and 49, that had experienced recombination events with two other distinct clades.
microbiolspec/4/1/TBS-0012-2012-fig2_thmb.gif
microbiolspec/4/1/TBS-0012-2012-fig2.gif
Image of FIGURE 2

Click to view

FIGURE 2

An example of homologous recombination identified in MLST profiles. (A) The diversity of an original MLST subclade (Sotto) based on seven MLST fragments ( 15 ). The same branch is shown, but is now dissected by ClonalFrame ( 33 ) and separated into six consistent fragments (B) and a second inconsistent fragment () (C) to show that the fragment has two sequence types, 55 and 49, that had experienced recombination events with two other distinct clades.

Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
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/content/microbiolspec/10.1128/microbiolspec.TBS-0012-2012.fig3
FIGURE 3
A graph of the distribution of gene families across genomes redrawn from Zwick et al. ( 41 ). This figure is based on the definition of the extended core as genes encoding proteins present in 49 or more genomes and accessory genes as those present in <6 genomes. The class between these extremes defined the character gene set.
microbiolspec/4/1/TBS-0012-2012-fig3_thmb.gif
microbiolspec/4/1/TBS-0012-2012-fig3.gif
Image of FIGURE 3

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FIGURE 3

A graph of the distribution of gene families across genomes redrawn from Zwick et al. ( 41 ). This figure is based on the definition of the extended core as genes encoding proteins present in 49 or more genomes and accessory genes as those present in <6 genomes. The class between these extremes defined the character gene set.

Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
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FIGURE 4
Whole-genome phylogeny of . This tree was redrawn based on data sets of concatenated, conserved protein sequences by using a neighbor-joining algorithm ( 41 ). Note that the relative distribution of the isolates based on a conserved whole-genome phylogeny is essentially the same as those observed in numerous MLST and AFLP studies and separated into three major clades.
microbiolspec/4/1/TBS-0012-2012-fig4_thmb.gif
microbiolspec/4/1/TBS-0012-2012-fig4.gif
Image of FIGURE 4

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FIGURE 4

Whole-genome phylogeny of . This tree was redrawn based on data sets of concatenated, conserved protein sequences by using a neighbor-joining algorithm ( 41 ). Note that the relative distribution of the isolates based on a conserved whole-genome phylogeny is essentially the same as those observed in numerous MLST and AFLP studies and separated into three major clades.

Source: microbiolspec February 2016 vol. 4 no. 1 doi:10.1128/microbiolspec.TBS-0012-2012
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