Defining natural species of bacteria: Clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Tang, Le ^a,b,c   Li, Yang ^a   Deng, Xia ^a   Johnston, Randal N ^d   Liu, Gui Rong ^a,b,c   Liu, Shu Lin ^a,b,c,e  

^a Genomics Research Center   (China)

^b HMU UCFM Centre for Infection and Genomics   (China)

^c HARBIN MEDICAL UNIVERSITY   (China)

^d Departments of Oncology   (Canada)

^e UNIVERSITY OF CALGARY   (Canada)

Author keywords

Genetic boundary; Natural species; Salmonella

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; DNA RECOMBINATION; GENE CLUSTER; GENE SEQUENCE; GENE STRUCTURE; GENETIC BOUNDARY; GENETIC DISTANCE; GENETIC LINE; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SALMONELLA; STAPHYLOCOCCUS; YERSINIA;

BACTERIA; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOMICS; NUCLEOTIDES; PHYLOGENY; RECOMBINATION, GENETIC;

SALMONELLA; YERSINIA;

EID: 84880183950     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-489     Document Type: Article

References (33)

1. Kauffmann F, Edwards PR. A revised, simplified Kauffmann-White schema. Acta Pathol Microbiol Scand 1957, 41(3):242-246.
2. Le Minor L, Popoff MY. Designation of Salmonella enterica sp. nov., nom. rev., as the type and only species of the genus Salmonella. Int J Syst Bacteriol 1987, 37:465-468.
3. Popoff MY, Le Minor LE. Genus XXXIII. Salmonella. Bergey's Mannual of Systematic Bacteriology 2005, 764-799. Springer, Brenner DJ, Krieg NR, Stanley JT, 2.
4. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kampfer P, Maiden MC, Nesme X, Rossello-Mora R, Swings J, Truper HG, et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002, 52(Pt 3):1043-1047.
5. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rDNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994, 44:846-849.
6. Liu SL, Hessel A, Sanderson KE. The XbaI-BlnI-CeuI genomic cleavage map of Salmonella typhimurium LT2 determined by double digestion, end labelling, and pulsed-field gel electrophoresis. J Bacteriol 1993, 175(13):4104-4120. 204840, 8320226.
7. Liu SL, Sanderson KE. Genomic cleavage map of Salmonella typhi Ty2. J Bacteriol 1995, 177(17):5099-5107. 177289, 7665489.
8. Liu SL, Schryvers AB, Sanderson KE, Johnston RN. Bacterial phylogenetic clusters revealed by genome structure. J Bacteriol 1999, 181(21):6747-6755. 94140, 10542177.
9. Zahrt TC, Mora GC, Maloy S. Inactivation of mismatch repair overcomes the barrier to transduction between Salmonella typhimurium and Salmonella typhi. J Bacteriol 1994, 176(5):1527-1529. 205224, 8113197.
10. Liu WQ, Feng Y, Wang Y, Zou QH, Chen F, Guo JT, Peng YH, Jin Y, Li YG, Hu SN, et al. Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi. PLoS One 2009, 4(2):e4510. 10.1371/journal.pone.0004510, 2640428, 19229335.
11. Feng Y, Liu S-L. Pathogenic Salmonella. Omics, Microbial Modeling, and Technologies for Food-borne Pathogens 2011, 43-68. Lancaster, Pennsylvania, USA: DEStech Publications, Inc, Yan X, Juneja V, Fratamico PM, Smith J.
12. Feng Y, Liu W-Q, Sanderson KE, Liu S-L. Comparison of Salmonella genomes. Salmonella from genome to function 2011, 49-67. Norfolk: Caister Academic Press, Porwollik S.
13. Tang L, Liu SL. The 3Cs provide a novel concept of bacterial species: messages from the genome as illustrated by Salmonella. Antonie Van Leeuwenhoek 2012, 101(1):67-72. 10.1007/s10482-011-9680-0, 22113699.
14. Crosa JH, Brenner DJ, Ewing WH, Falkow S. Molecular relationships among the Salmonelleae. J Bacteriol 1973, 115(1):307-315. 246244, 4717519.
15. Le Minor L, et al. Genus III. Salmonella. Bergey's Manual of Systematic Bacteriology 1984, 427-458. Baltimore: Williams & Wilkins.
16. McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, et al. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 2001, 413(6858):852-856. 10.1038/35101614, 11677609.
17. Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 2001, 413(6858):848-852. 10.1038/35101607, 11677608.
18. Parry CM, Hien TT, Dougan G, White NJ, Farrar JJ. Typhoid fever. N Engl J Med 2002, 347(22):1770-1782. 10.1056/NEJMra020201, 12456854.
19. Liu SL, Hessel A, Sanderson KE. Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci U S A 1993, 90(14):6874-6878. 10.1073/pnas.90.14.6874, 47035, 8341713.
20. Liu SL, Hessel A, Cheng HY, Sanderson KE. The XbaI-BlnI-CeuI genomic cleavage map of Salmonella paratyphi B. J Bacteriol 1994, 176(4):1014-1024. 205152, 8106312.
21. Liu SL, Sanderson KE. I-CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium. J Bacteriol 1995, 177(11):3355-3357. 177035, 7768842.
22. Liu SL, Sanderson KE. The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnG. J Bacteriol 1995, 177(22):6585-6592. 177512, 7592437.
23. Feng Y, Xu HF, Li QH, Zhang SY, Wang CX, Zhu DL, Cao FL, Li YG, Johnston RN, Zhou J, et al. Complete genome sequence of Salmonella enterica serovar pullorum RKS5078. J Bacteriol 2012, 194(3):744. 10.1128/JB.06507-11, 3264078, 22247537.
24. Feng Y, Johnston RN, Liu GR, Liu SL. Genomic comparison between Salmonella Gallinarum and Pullorum: differential pseudogene formation under common host restriction. PLoS One 2013, 8(3):e59427. 10.1371/journal.pone.0059427, 3598799, 23555032.
25. Liu SL. Physical mapping of Salmonella genomes. Methods Mol Biol 2007, 394:39-58. 10.1007/978-1-59745-512-1_3, 18363230.
26. Liu SL, Sanderson KE. A physical map of the Salmonella typhimurium LT2 genome made by using XbaI analysis. J Bacteriol 1992, 174(5):1662-1672. 206564, 1311300.
27. Liu GR, Rahn A, Liu WQ, Sanderson KE, Johnston RN, Liu SL. The evolving genome of Salmonella enterica serovar Pullorum. J Bacteriol 2002, 184(10):2626-2633. 10.1128/JB.184.10.2626-2633.2002, 135040, 11976291.
28. Thomson NR, Clayton DJ, Windhorst D, Vernikos G, Davidson S, Churcher C, Quail MA, Stevens M, Jones MA, Watson M, et al. Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res 2008, 18(10):1624-1637. 10.1101/gr.077404.108, 2556274, 18583645.
29. McClelland M, Jones R, Patel Y, Nelson M. Restriction endonucleases for pulsed field mapping of bacterial genomes. Nucleic Acids Res 1987, 15(15):5985-6005. 10.1093/nar/15.15.5985, 306063, 2819819.
30. Chen F, Liu WQ, Eisenstark A, Johnston RN, Liu GR, Liu SL. Multiple genetic switches spontaneously modulating bacterial mutability. BMC Evol Biol 2010, 10:277. 10.1186/1471-2148-10-277, 2955026, 20836863.
31. Chen F, Liu WQ, Liu ZH, Zou QH, Wang Y, Li YG, Zhou J, Eisenstark A, Johnston RN, Liu GR, et al. mutL as a genetic switch of bacterial mutability: turned on or off through repeat copy number changes. FEMS Microbiol Lett 2010, 312(2):126-132. 10.1111/j.1574-6968.2010.02107.x, 20874753.
32. Gong J, Liu WQ, Liu GR, Chen F, Li JQ, Xu GM, Wang L, Johnston RN, Eisenstark A, Liu SL. Spontaneous conversion between mutL and 6 bpDeltamutL in Salmonella typhimurium LT7: association with genome diversification and possible roles in bacterial adaptation. Genomics 2007, 90(4):542-549. 10.1016/j.ygeno.2007.06.009, 17689047.
33. Liu SL, Hessel A, Sanderson KE. The XbaI-BlnI-CeuI genomic cleavage map of Salmonella enteritidis shows an inversion relative to Salmonella typhimurium LT2. Mol Microbiol 1993, 10(3):655-664. 10.1111/j.1365-2958.1993.tb00937.x, 7968542.