Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades

Anaerobe

Volumn 28, Issue , 2014, Pages 182-198

  Gupta, Radhey S ^a   Sethi, Mohit ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Conserved signature indels; Fusobacteriaceae; Fusobacterium; Leptotrichiaceae; Molecular signatures; Phylogenetic trees

Indexed keywords

BACTERIAL RNA; INTERNAL TRANSCRIBED SPACER; RNA 16S; BACTERIAL DNA; BACTERIAL PROTEIN; GENETIC MARKER;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; CLADISTICS; CONTROLLED STUDY; FUSOBACTERIA; FUSOBACTERIACEAE; GENE SEQUENCE; GENETIC MARKER; GENETIC VARIABILITY; GENOME ANALYSIS; LEPTOTRICHIACEAE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE HOMOLOGY; SPECIES COMPARISON; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; GENETICS; MOLECULAR GENETICS; MULTILOCUS SEQUENCE TYPING; PHYLOGENY;

BACTERIAL PROTEINS; CLUSTER ANALYSIS; DNA, BACTERIAL; FUSOBACTERIA; GENETIC MARKERS; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 84903899062     PISSN: 10759964     EISSN: 10958274     Source Type: Journal    
DOI: 10.1016/j.anaerobe.2014.06.007     Document Type: Article

References (81)

1. Adeolu M., Gupta R.S. Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov. Antonie Van Leeuwenhoek 2013, 104:1-24.
2. Ahmod N.Z., Gupta R.S., Shah H.N. Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B.anthracis from the B.cereus group. JMicrobiol Meth 2011, 87:278-285.
3. Ajawatanawong P., Baldauf S.L. Evolution of protein indels in plants, animals and fungi. BMC Evol Biol 2013, 13:140.
4. Bhandari V., Ahmod N.Z., Shah H.N., Gupta R.S. Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus. Int J Syst Evol Microbiol 2013, 63:2712-2726.
5. Bhandari V., Naushad H.S., Gupta R.S. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution. Front Cell Infect Microbiol 2012, 2:98.
6. Bolstad A.I., Jensen H.B., Bakken V. Taxonomy, biology, and periodontal aspects of Fusobacterium nucleatum. Clin Microbiol Rev 1996, 9:55-71.
7. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17:540-552.
8. Ciccarelli F.D., Doerks T., von Mering C., Creevey C.J., Snel B., Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311:1283-1287.
9. Citron D.M. Update on the taxonomy and clinical aspects of the genus Fusobacterium. Clin Infect Dis 2002, 35:S22-S27.
10. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., et al. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009, 37:D141-D145.
11. Conrads G., Claros M.C., Citron D.M., Tyrrell K.L., Merriam V., Goldstein E.J.C. 16S-23S rDNA internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium. Int J Syst Evol Microbiol 2002, 52:493-499.
12. Dewhirst F.E., Chen T., Izard J., Paster B.J., Tanner A.C., Yu W.H., et al. The human oral microbiome. JBacteriol 2010, 192:5002-5017.
13. Duncan M.J. Genomics of oral bacteria. Crit Rev Oral Biol Med 2003, 14:175-187.
14. Dzink J.L., Sheenan M.T., Socransky S.S. Proposal of three subspecies of Fusobacterium nucleatum Knorr 1922: Fusobacterium nucleatum subsp. nucleatum subsp. nov., comb. nov.; Fusobacterium nucleatum subsp. polymorphum subsp. nov., nom. rev., comb. nov.; and Fusobacterium nucleatum subsp. vincentii subsp. nov., nom. rev., comb. nov. Int J Syst Bacteriol 1990, 40:74-78.
15. Edwards K.J., Gharbia S.E. Genus I. Leptotrichia Trevisan 1879, 138AL. Bergey's manual of systematic bacteriology 2010, 766-769. Springer, New York. N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster, N.L. Ward (Eds.).
16. Finegold S.M. Anaerobic bacteria in human disease 1977, Academic Press, New York.
17. Flügge C. Die mikroorganismen Leipzig 1886, [Germany. Ref Type: Generic].
18. Gao B., Gupta R.S. Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Microbiol 2005, 55:2401-2412.
19. Gao B., Gupta R.S. Microbial systematics in the post-genomics era. Antonie Van Leeuwenhoek 2012, 101:45-54.
20. Gao B., Gupta R.S. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 2012, 76:66-112.
21. Garrity G.M., Holt J.G. The road map to the manual. Bergey's manual of systematic bacteriology 2001, 119-166. Springer-Verlag, Berlin. D.R. Boone, R.W. Castenholz (Eds.).
22. George W.L., Kirby B.D., Sutter V.L., Citron D.M., Finegold S.M. Gram-negative anaerobic bacilli: their role in infection and patterns of susceptibility to antimicrobial agents. II. Little-known Fusobacterium species and miscellaneous genera. Rev Infect Dis 1981, 3:599-626.
23. Gharbia S.E., Shah H.N. Identification of Fusobacterium species by the electrophoretic migration of glutamate dehydrogenase and 2-oxoglutarate reductase in relation to their DNA base composition and peptidoglycan dibasic amino acids. JMed Microbiol 1990, 33:183-188.
24. Gharbia S.E., Shah H.N. Fusobacterium nucleatum subsp. fusiforme subsp. nov. and Fusobacterium nucleatum subsp. animalis subsp. nov. as additional subspecies within Fusobacterium nucleatum. Int J Syst Bacteriol 1992, 42:296-298.
25. Gharbia S.E., Shah H.N., Bernard K. Minutes: International Committee on systematics of Prokaryotessubcommittee on the taxonomy of gram-negative anaerobic rods minutes of the open meeting, 1-2 February 2011, Health Protection Agency, Colindale, London, UK. Int J Syst Evol Microbiol 2012, 62:467-471.
26. Gharbia S.E., Shah H.N., Edwards K.J. Genus I. Fusobacterium Knorr 1922, 4AL. Bergey's manual of systematic bacteriology 2010, 748-758. Springer, New York. N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster, N.L. Ward (Eds.).
27. Gogarten J.P., Doolittle W.F., Lawrence J.G. Prokaryotic evolution in light of gene transfer. Mol Biol Evol 2002, 19:2226-2238.
28. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007, 57:81-91.
29. Griffiths E., Petrich A., Gupta R.S. Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification. Microbiology 2005, 151:2647-2657.
30. Gupta R.S., Bhandari V. Phylogeny and molecular signatures for the phylum thermotogae and its subgroups. Antonie Van Leeuwenhoek 2011, 100:1-34.
31. Gupta R.S. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 1998, 62:1435-1491.
32. Gupta R.S. Applications of conserved indels for understanding microbial phylogeny. Molecular phylogeny of microorganisms 2010, 135-150. Caister Academic Press, Norfolk, U.K. A. Oren, R.T. Papke (Eds.).
33. Gupta R.S. Identification of conserved indels that are useful for classification and evolutionary studies. Bacterial taxonomy, methods in microbiology 2014, vol. 41. Elsevier, London. M. Goodfellow, I.C. Sutcliffe, J. Chun (Eds.).
34. Gupta R.S., Gao B. Recent advances in understanding microbial systematics. Microbial population genetics 2010, 1-14. Caister Academic Press, Norfolk, U.K. J. Xu (Ed.).
35. Gupta R.S., Griffiths E. Critical issues in bacterial phylogeny. Theor Popul Biol 2002, 61:423-434.
36. Haggar F.A., Boushey R.P. Colorectal cancer epidemiology: incidence, mortality, survival, and risk factors. Clin Colon Rectal Surg 2009, 22:191-197.
37. Harmon-Smith M., Celia L., Chertkov O., Lapidus A., Copeland A., Rio Del, et al. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T). Stand Genomic Sci 2010, 2:220.
38. Harris N.M. Bacillus mortiferus (nov. spec.). JExp Med 1901, 6:519-547.
39. Hofstad T. The genus Fusobacterium. prokaryotes 2006, 7:1016-1027.
40. Ivanova N., Gronow S., Lapidus A., Copeland A., Del Rio T.G., et al. Complete genome sequence of Leptotrichia buccalis type strain (C-1013-bT). Stand Genomic Sci 2009, 1:126.
41. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci CABIOS 1992, 8:275-282.
42. Jousimies-Somer H., Summanen P. Recent taxonomic changes and terminology update of clinically significant anaerobic gram-negative bacteria (excluding spirochetes). Clin Infect Dis 2002, 35:S17-S21.
43. Kapatral V., Anderson I., Ivanova N., Reznik G., Los T., Lykidis A., et al. Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. JBacteriol 2002, 184:2005-2018.
44. Kapatral V., Ivanova N., Anderson I., Reznik G., Bhattacharyya A., Gardner W.L., et al. Genome analysis of F.nucleatum sub spp vincentii and its comparison with the genome of F.nucleatum ATCC 25586. Genome Res 2003, 13:1180-1189.
45. Karkos P.D., Asrani S., Karkos C.D., Leong S.C., Theochari E.G., Alexopoulou T.D., et al. Lemierre's syndrome: a systematic review. Laryngoscope 2009, 119:1552-1559.
46. Kimura M. Asimple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. JMol Evol 1980, 16:111-120.
47. Knorr M. Uber die fusospirillare Symbiose, die gattung Fusobacterium (K.B. Lehmann) und Spirillum SPUTIGENUM. zugleich ein beitrag zur bakteriologie der Mundhohle. II. Mitteilung. die gattung Fusobacterium. Zentralbl Bakteriol Parasitenkd Infekt Hyg Abt I 1922, 89:4-22.
48. Konstantinidis K.T., Tiedje J.M. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005, 102:2567-2572.
49. Kostic A.D., Gevers D., Pedamallu C.S., Michaud M., Duke F., Earl A.M., et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 2012, 22:292-298.
50. Kumar S., Nei M., Dudley J., Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008, 9:299-306.
51. Kuppalli K., Livorsi D., Talati N.J., Osborn M. Lemierre's syndrome due to Fusobacterium necrophorum. Lancet Infect Dis 2012, 12:808-815.
52. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., et al. clustal W and clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
53. Ludwig W., Klenk H.-P. Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systamatics. Bergey's manual of systematic bacteriology 2005, 49-65. Springer-Verlag, Berlin. D.J. Brenner, N.R. Krieg, J.T. Staley, G.M. Garrity (Eds.).
54. Mira A., Pushker R., Legault B.A., Moreira D., Rodriguez-Valera F. Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evol Biol 2004, 4:50.
55. Moore W.E.C., Holdeman L.V. Anaerobic gram-negative non-sporeforming rods. Outline of clinical methods in anaerobic bacteriology 1969, Virginia Polytechnic Institute Anaerobe Laboratory, Blacksburg, Virginia. Cato, Cummins, Holdeman, Johnson, Moore, Smibert (Eds.).
56. Nolan M., Gronow S., Lapidus A., Ivanova N., Copeland A., Lucas S., et al. Complete genome sequence of Streptobacillus moniliformis type strain (9901T). Stand Genomic Sci 2009, 1:300.
57. Park S.N., Kong S.W., Park M.S., Lee J.W., Cho E., Lim Y.K., et al. Draft genome sequence of Fusobacterium nucleatum subsp. fusiforme ATCC 51190T. JBacteriol 2012, 194:5445-5446.
58. Ribeiro F.J., Przybylski D., Yin S., Sharpe T., Gnerre S., Abouelleil A., et al. Finished bacterial genomes from shotgun sequence data. Genome Res 2012, 22:2270-2277.
59. Richter M., Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009, 106:19126-19131.
60. Rokas A., Holland P.W. Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 2000, 15:454-459.
61. Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
62. Schink B., Janssen P.H., Brune A. Genus II. Ilyobacter Stieb and Schink 1985, 375VP. Bergey's manual of systematic bacteriology 2010, 759-761. (Effective publication: Steib and Schink 1984, 145), Springer, New York. N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster, N.L. Ward (Eds.).
63. Schoeffler A.J., May A.P., Berger J.M. Adomain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Res 2010, 38:7830-7844.
64. Segata N., Bornigen D., Morgan X.C., Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013, 4:2304.
65. Shah H.N., Olsen I., Bernard K., Finegold S.M., Gharbia S.E., Gupta R.S. Approaches to the study of the systematics of anaerobic, Gram-negative, non-spore-forming rods: current status and perspectives. Anaerobe 2009, 15:179-194.
66. Sikorski J., Chertkov O., Lapidus A., Nolan M., Lucas S., Rio Del, et al. Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1). Stand Genomic Sci 2010, 3:304-314.
67. Singh B., Gupta R.S. Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. Mol Genet Genomics 2009, 281:361-373.
68. Skerman V.B.D., McGowan V., Sneath P.H.A. Approved lists of bacterial names. Int J Syst Bacteriol 1980, 30:225-420.
69. Staley J.T., Whitman W.B. Family I. Fusobacteriaceae fam.nov. Bergey's manual of systematic bacteriology 2010, 747. Springer, New York. N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster, N.L. Ward (Eds.).
70. Staley J.T., Whitman W.B. Family II. Leptotrichiaceae fam.nov. Bergey's manual of systematic bacteriology 2010, 766. Springer, New York. N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster, N.L. Ward (Eds.).
71. Staley J.T., Whitman W.B. Phylum XIX. Fusobacteria; Garrity and Holt 2001, 140. Bergey's manual of systematic bacteriology 2010, 747. Springer, New York. N.R. Krieg, J.T. Staley, D.R. Brown, B.P. Hedlund, B.J. Paster, N.L. Ward (Eds.).
72. Staley J.T., Whitman W.B. Fusobacteria phyl. nov. In validation of the publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2012, 62:1-4. List No. 143.
73. Staley J.T., Whitman W.B. Fusobacteriaceae fam. nov. In validation of the publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2012, 62:1-4. List No. 143.
74. Staley J.T., Whitman W.B. Leptotrichiaceae fam. nov. In validation of the publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2012, 62:1-4. List No. 143.
75. Trevisan V. Prime linee d'introduzione allo studio dei Batterj italiani. Rend R Ist Lomb Sci Ser II 1879, 12:133-151.
76. Whelan S., Goldman N. Ageneral empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18:691-699.
77. Wu D., Hugenholtz P., Mavromatis K., Pukall R., Dalin E., Ivanova N.N., et al. Aphylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009, 462:1056-1060.
78. Yarza P., Ludwig W., Euzeby J., Amann R., Schleifer K.H., Glockner F.O., et al. Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010, 33:291-299.
79. Yarza P., Ludwig W., Euzeby J., Amann R., Schleifer K.H., Glockner F.O., et al. Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010, 33:291-299.
80. Yarza P., Ludwig W., Euzeby J., Amann R., Schleifer K.H., Glockner F.O., et al. Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010, 33:291-299.
81. Yarza P., Ludwig W., Euzeby J., Amann R., Schleifer K.H., Glockner F.O., et al. Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010, 33:291-299.