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Microbiology Society logo Microbiology

Volume 166, Issue 3

‘Community evolution’ – laboratory strains and pedigrees in the age of genomics Open Access

Abstract

Molecular microbiologists depend heavily on laboratory strains of bacteria, which are ubiquitous across the community of research groups working on a common organism. However, this presumes that strains present in different laboratories are in fact identical. Work on a culture of preserved from 1916 provoked us to consider recent studies, which have used both classical genetics and next-generation sequencing to study the heterogeneity of laboratory strains. Here, we review and discuss mutations and phenotypic variation in supposedlyisogenic reference strains of and , and we propose that by virtue of the dissemination of laboratory strains across the world, a large ‘community evolution’ experiment is currently ongoing.

  • Received:
  • Accepted:
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© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2020-01-20
2025-03-23
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References

  1. Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR et al. International Code of Nomenclature of Bacteria: Bacteriological Code Washington, DC: ASM Press; 1990 Revision
     [Google Scholar]
  2. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 2014; 12:e1001920 [View Article][PubMed]
     [Google Scholar]
  3. Hobman JL, Penn CW, Pallen MJ. Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?. Mol Microbiol 2007; 64:881–885 [View Article][PubMed]
     [Google Scholar]
  4. Dorman MJ, Kane L, Domman D, Turnbull JD, Cormie C et al. The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One. Proc Biol Sci 2019; 286:20182025 [View Article][PubMed]
     [Google Scholar]
  5. Gardner AD, Venkatraman KV. The antigens of the cholera group of vibrios. J Hyg 1935; 35:262–282 [View Article][PubMed]
     [Google Scholar]
  6. Colwell RR. Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 1970; 104:410–433[PubMed]
     [Google Scholar]
  7. Davis GH, Park RW. A taxonomic study of certain bacteria currently classified as Vibrio species. J Gen Microbiol 1962; 27:101–119 [View Article][PubMed]
     [Google Scholar]
  8. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae . Nature 2000; 406:477–483 [View Article][PubMed]
     [Google Scholar]
  9. Val M-E, Marbouty M, de Lemos Martins F, Kennedy SP, Kemble H et al. A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae . Sci Adv 2016; 2:e1501914 [View Article][PubMed]
     [Google Scholar]
  10. Matthey N, Drebes Dörr NC, Blokesch M. Long-read-based genome sequences of pandemic and environmental Vibrio cholerae strains. Microbiol Resour Announc 2018; 7: [View Article][PubMed]
     [Google Scholar]
  11. Kemter FS, Messerschmidt SJ, Schallopp N, Sobetzko P, Lang E et al. Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae . PLoS Genet 2018; 14:e1007251 [View Article][PubMed]
     [Google Scholar]
  12. Allué-Guardia A, Echazarreta M, Koenig SSK, Klose KE, Eppinger M. Closed genome sequence of Vibrio cholerae O1 El Tor Inaba strain A1552. Genome Announc 2018; 6:e00098–18 [View Article][PubMed]
     [Google Scholar]
  13. Stutzmann S, Blokesch M. Circulation of a quorum-sensing-impaired variant of Vibrio cholerae strain C6706 masks important phenotypes. mSphere 2016; 1: [View Article][PubMed]
     [Google Scholar]
  14. Meibom KL, Blokesch M, Dolganov NA, Wu C-Y, Schoolnik GK. Chitin induces natural competence in Vibrio cholerae . Science 2005; 310:1824–1827 [View Article][PubMed]
     [Google Scholar]
  15. Blokesch M. A quorum sensing-mediated switch contributes to natural transformation of Vibrio cholerae . Mob Genet Elements 2012; 2:224–227 [View Article][PubMed]
     [Google Scholar]
  16. Marvig RL, Blokesch M. Natural transformation of Vibrio cholerae as a tool--optimizing the procedure. BMC Microbiol 2010; 10:155 [View Article][PubMed]
     [Google Scholar]
  17. Lo Scrudato M, Blokesch M. The regulatory network of natural competence and transformation of Vibrio cholerae . PLoS Genet 2012; 8:e1002778 [View Article][PubMed]
     [Google Scholar]
  18. Lo Scrudato M, Blokesch M. A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable. Nucleic Acids Res 2013; 41:3644–3658 [View Article][PubMed]
     [Google Scholar]
  19. Suckow G, Seitz P, Blokesch M. Quorum sensing contributes to natural transformation of Vibrio cholerae in a species-specific manner. J Bacteriol 2011; 193:4914–4924 [View Article][PubMed]
     [Google Scholar]
  20. Blokesch M, Schoolnik GK. The extracellular nuclease Dns and its role in natural transformation of Vibrio cholerae . J Bacteriol 2008; 190:7232–7240 [View Article][PubMed]
     [Google Scholar]
  21. Zhu J, Miller MB, Vance RE, Dziejman M, Bassler BL et al. Quorum-sensing regulators control virulence gene expression in Vibrio cholerae . Proc Natl Acad Sci U S A 2002; 99:3129–3134 [View Article][PubMed]
     [Google Scholar]
  22. Joelsson A, Liu Z, Zhu J. Genetic and phenotypic diversity of quorum-sensing systems in clinical and environmental isolates of Vibrio cholerae . Infect Immun 2006; 74:1141–1147 [View Article][PubMed]
     [Google Scholar]
  23. Paul K, Ghosh A, Sengupta N, Chowdhury R. Competitive growth advantage of nontoxigenic mutants in the stationary phase in archival cultures of pathogenic Vibrio cholerae strains. Infect Immun 2004; 72:5478–5482 [View Article][PubMed]
     [Google Scholar]
  24. Kimbrough JH, Stabb EV. Antisocial luxO Mutants provide a stationary-phase survival advantage in Vibrio fischeri ES114. J Bacteriol 2016; 198:673–687 [View Article]
     [Google Scholar]
  25. Jung SA, Chapman CA, Ng W-L. Quadruple quorum-sensing inputs control Vibrio cholerae virulence and maintain system robustness. PLoS Pathog 2015; 11:e1004837 [View Article][PubMed]
     [Google Scholar]
  26. Kovacikova G, Skorupski K. Regulation of virulence gene expression in Vibrio cholerae by quorum sensing: HapR functions at the aphA promoter. Mol Microbiol 2002; 46:1135–1147 [View Article][PubMed]
     [Google Scholar]
  27. Bachmann BJ. Derivations and genotypes of some mutant derivatives of Escherichia coli K-12. In: Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology . ASM Press 1996
     [Google Scholar]
  28. Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K et al. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2006; 2:2006.0007 [View Article][PubMed]
     [Google Scholar]
  29. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006; 2:2006.0008 [View Article][PubMed]
     [Google Scholar]
  30. Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 2000; 97:6640–6645 [View Article][PubMed]
     [Google Scholar]
  31. Guyer MS, Reed RR, Steitz JA, Low KB. Identification of a sex-factor-affinity site in E. coli as gamma delta. Cold Spring Harb Symp Quant Biol 1981; 45 Pt 1:135–140 [View Article][PubMed]
     [Google Scholar]
  32. Bachmann BJ. Pedigrees of some mutant strains of Escherichia coli K-12. Bacteriol Rev 1972; 36:525–557[PubMed]
     [Google Scholar]
  33. Grenier F, Matteau D, Baby V, Rodrigue S. Complete genome sequence of Escherichia coli BW25113. Genome Announc 2014; 2:e01038-14 [View Article][PubMed]
     [Google Scholar]
  34. Berlyn MB, Letovsky S. Genome-related datasets within the E. coli genetic stock center database. Nucleic Acids Res 1992; 20:6143–6151 [View Article][PubMed]
     [Google Scholar]
  35. Faure D, Frederick R, Włoch D, Portier P, Blot M et al. Genomic changes arising in long-term stab cultures of Escherichia coli . J Bacteriol 2004; 186:6437–6442 [View Article][PubMed]
     [Google Scholar]
  36. Barratt RW, Tatum EL. A simplified method of lyophilizing microorganisms. Science 1950; 112:122–123 [View Article][PubMed]
     [Google Scholar]
  37. Desroches M, Royer G, Roche D, Mercier-Darty M, Vallenet D et al. The odyssey of the ancestral Escherich strain through culture collections: an example of allopatric diversification. mSphere 2018; 3:e00553–17 [View Article][PubMed]
     [Google Scholar]
  38. Dunne KA, Chaudhuri RR, Rossiter AE, Beriotto I, Browning DF et al. Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain. Microb Genom 2017; 3:mgen000106 [View Article][PubMed]
     [Google Scholar]
  39. Méric G, Hitchings MD, Pascoe B, Sheppard SK. From Escherich to the Escherichia coli genome. Lancet Infect Dis 2016; 16:634–636 [View Article][PubMed]
     [Google Scholar]
  40. Khetrapal V, Mehershahi KS, Chen SL. Complete genome sequence of the original Escherichia coli isolate, strain NCTC86. Genome Announc 2017; 5:e00243–17 [View Article][PubMed]
     [Google Scholar]
  41. Pascoe B, Williams LK, Calland JK, Meric G, Hitchings MD et al. Domestication of Campylobacter jejuni NCTC 11168. Microb Genom 2019; 5: [View Article][PubMed]
     [Google Scholar]
  42. Liu B, Eydallin G, Maharjan RP, Feng L, Wang L et al. Natural Escherichia coli isolates rapidly acquire genetic changes upon laboratory domestication. Microbiology 2017; 163:22–30 [View Article][PubMed]
     [Google Scholar]
  43. Bleibtreu A, Clermont O, Darlu P, Glodt J, Branger C et al. The rpoS gene is predominantly inactivated during laboratory storage and undergoes source-sink evolution in Escherichia coli species. J Bacteriol 2014; 196:4276–4284 [View Article][PubMed]
     [Google Scholar]
  44. Spira B, de Almeida Toledo R, Maharjan RP, Ferenci T. The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example. BMC Microbiol 2011; 11:248 [View Article][PubMed]
     [Google Scholar]
  45. Zambrano MM, Siegele DA, Almirón M, Tormo A, Kolter R. Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 1993; 259:1757–1760 [View Article][PubMed]
     [Google Scholar]
  46. Wilmes-Riesenberg MR, Foster JW, Curtiss R. An altered rpoS allele contributes to the avirulence of Salmonella typhimurium LT2. Infect Immun 1997; 65:203–210[PubMed]
     [Google Scholar]
  47. Blount ZD, Borland CZ, Lenski RE. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli . Proc Natl Acad Sci U S A 2008; 105:7899–7906 [View Article][PubMed]
     [Google Scholar]
  48. Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. The dynamics of molecular evolution over 60,000 generations. Nature 2017; 551:45–50 [View Article][PubMed]
     [Google Scholar]
  49. Boundy-Mills K, Hess M, Bennett AR, Ryan M, Kang S et al. The United States culture collection network (USCCN): enhancing microbial genomics research through living microbe culture collections. Appl Environ Microbiol 2015; 81:5671–5674 [View Article][PubMed]
     [Google Scholar]
  50. Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE et al. Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Sci Transl Med 2017; 9:eaak9745 [View Article][PubMed]
     [Google Scholar]
/content/journal/micro/10.1099/mic.0.000869
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‘Community evolution’ – laboratory strains and pedigrees in the age of genomics
Microbiology 166, 233 (2020); https://doi.org/10.1099/mic.0.000869
/content/journal/micro/10.1099/mic.0.000869
/content/journal/micro/10.1099/mic.0.000869
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