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

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 Vibrio cholerae 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 V. cholerae and Escherichia coli , and we propose that by virtue of the dissemination of laboratory strains across the world, a large ‘community evolution’ experiment is currently ongoing.

• Publication year

  2020

• Venue

  Microbiology

• Publication date

  2020-01-20

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1099/mic.0.000869PMID 31958052PMCID 7376263
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Domestication of Campylobacter jejuni NCTC 11168

  2019cited by this paper
• The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One

  2019cited by this paper
• Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae

  2018influential reference
• The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification

  2018cited by this paper
• Long-Read-Based Genome Sequences of Pandemic and Environmental Vibrio cholerae Strains

  2018cited by this paper
• Closed Genome Sequence of Vibrio cholerae O1 El Tor Inaba Strain A1552

  2018cited by this paper
• Complete Genome Sequence of the Original Escherichia coli Isolate, Strain NCTC86

  2017cited by this paper
• The Dynamics of Molecular Evolution Over 60,000 Generations

  2017cited by this paper
• Natural Escherichia coli isolates rapidly acquire genetic changes upon laboratory domestication.

  2017cited by this paper
• Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community

  2017cited by this paper
• Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain

  2017cited by this paper
• A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae

  2016cited by this paper
• Circulation of a Quorum-Sensing-Impaired Variant of Vibrio cholerae Strain C6706 Masks Important Phenotypes

  2016influential reference
• From Escherich to the Escherichia coli genome.

  2016cited by this paper
• The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

  2015cited by this paper
• Antisocial luxO Mutants Provide a Stationary-Phase Survival Advantage in Vibrio fischeri ES114

  2015cited by this paper
• Quadruple Quorum-Sensing Inputs Control Vibrio cholerae Virulence and Maintain System Robustness

  2015influential reference
• The rpoS Gene Is Predominantly Inactivated during Laboratory Storage and Undergoes Source-Sink Evolution in Escherichia coli Species

  2014cited by this paper
• Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

  2014cited by this paper
• Complete Genome Sequence of Escherichia coli BW25113

  2014cited by this paper
• A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable

  2013cited by this paper
• The Regulatory Network of Natural Competence and Transformation of Vibrio cholerae

  2012cited by this paper
• A quorum sensing-mediated switch contributes to natural transformation of Vibrio cholerae

  2012cited by this paper
• The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example

  2011cited by this paper
• Quorum Sensing Contributes to Natural Transformation of Vibrio cholerae in a Species-Specific Manner

  2011cited by this paper
• Natural transformation of Vibrio cholerae as a tool - Optimizing the procedure

  2010cited by this paper
• Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

  2008cited by this paper
• The Extracellular Nuclease Dns and Its Role in Natural Transformation of Vibrio cholerae

  2008influential reference
• Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?

  2007cited by this paper
• Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110

  2006cited by this paper
• Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

  2006cited by this paper
• Genetic and Phenotypic Diversity of Quorum-Sensing Systems in Clinical and Environmental Isolates of Vibrio cholerae

  2006cited by this paper
• Chitin Induces Natural Competence in Vibrio cholerae

  2005cited by this paper
• Competitive Growth Advantage of Nontoxigenic Mutants in the Stationary Phase in Archival Cultures of Pathogenic Vibrio cholerae Strains

  2004influential reference
• Genomic Changes Arising in Long-Term Stab Cultures of Escherichia coli

  2004cited by this paper
• Quorum-sensing regulators control virulence gene expression in Vibrio cholerae

  2002cited by this paper
• Regulation of virulence gene expression in Vibrio cholerae by quorum sensing: HapR functions at the aphA promoter

  2002cited by this paper
• DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae

  2000influential reference
• One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

  2000cited by this paper
• An altered rpoS allele contributes to the avirulence of Salmonella typhimurium LT2

  1997cited by this paper
• Microbial competition: Escherichia coli mutants that take over stationary phase cultures.

  1993cited by this paper
• Genome-related datasets within the E. coli Genetic Stock Center database.

  1992cited by this paper
• Derivations and genotypes of some mutant derivatives of Escherichia coli K12

  1987influential reference
• Identification of a sex-factor-affinity site in E. coli as gamma delta.

  1981influential reference
• International Code of Nomenclature of Bacteria. Bacteriological Code

  1977cited by this paper
• Pedigrees of some mutant strains of Escherichia coli K-12.

  1972influential reference
• Polyphasic Taxonomy of the Genus Vibrio: Numerical Taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and Related Vibrio Species

  1970cited by this paper
• A taxonomic study of certain bacteria currently classified as Vibrio species.

  1962cited by this paper
• A simplified method of lyophilizing microorganisms.

  1950cited by this paper
• The Antigens of the Cholera Group of Vibrios

  1935cited by this paper

• History shapes regulatory and evolutionary responses to tigecycline in strains of Acinetobacter baumannii from the pre- and post-antibiotic eras

  2025cites this paper
• History shapes regulatory and evolutionary responses to tigecycline in two reference strains of Acinetobacter baumannii

  2025cites this paper
• ‘Wild Type’

  2024cites this paper
• The ATCC genome portal: 3,938 authenticated microbial reference genomes

  2024cites this paper
• Structural Differences between the Genomes of Deinococcus radiodurans Strains from Different Laboratories

  2024cites this paper
• A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life

  2024cites this paper
• Uncharacterized and lineage-specific accessory genes within the Proteus mirabilis pan-genome landscape

  2023cites this paper
• Genotypic and phenotypic characterization of a Salmonella Typhimurium strain resistant to pulsed electric fields.

  2023cites this paper
• Dynamic changes in thymic sub-populations during acute and long-term infections with virulent and virulence-attenuated Salmonella Typhimurium strains in C57BL/6 and autoimmune-prone lpr mice.

  2023cites this paper
• Vibrio cholerae O37: one of the exceptions that prove the rule

  2023cites this paper
• Genome diversity of domesticated Acinetobacter baumannii ATCC 19606T strains

  2022cites this paper
• Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence.

  2021cites this paper
• Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies

  2021cites this paper