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EcoSal Plus

Domain 6:

Evolution and Genomics

The "Cryptic"

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  • Author: Seth T. Walk1
  • Editor: David A. Rasko2
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717; 2: University of Maryland, School of Medicine, Baltimore, MD
  • Received 11 February 2015 Accepted 17 June 2015 Published 30 July 2015
  • Address correspondence to Seth T. Walk, seth.walk@montana.edu
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  • Abstract:

    In 2009, five monophyletic clades were described and referred to as “cryptic” based on the inability to distinguish them from representative isolates using diagnostic biochemical reactions. Since this original publication, a number of studies have explored the genomic, transcriptomic, and phenotypic diversity of cryptic clade isolates to better understand their phylogenetic, physiological, and ecological distinctiveness with respect to previously named species. This chapter reviews the original discovery of the cryptic clades, discusses available evidence that some are environmentally adapted, and evaluates current support for taxonomic designations of these microorganisms. The importance of these clades to clinical research, epidemiology, population genetics, and microbial speciation is also discussed.

  • Citation: Walk S. 2015. The "Cryptic" , EcoSal Plus 2015; doi:10.1128/ecosalplus.ESP-0002-2015

Key Concept Ranking

Shiga Toxin 2
0.56578946
Multilocus Sequence Typing
0.42669186
0.56578946

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/content/journal/ecosalplus/10.1128/ecosalplus.ESP-0002-2015
2015-07-30
2017-10-21

Abstract:

In 2009, five monophyletic clades were described and referred to as “cryptic” based on the inability to distinguish them from representative isolates using diagnostic biochemical reactions. Since this original publication, a number of studies have explored the genomic, transcriptomic, and phenotypic diversity of cryptic clade isolates to better understand their phylogenetic, physiological, and ecological distinctiveness with respect to previously named species. This chapter reviews the original discovery of the cryptic clades, discusses available evidence that some are environmentally adapted, and evaluates current support for taxonomic designations of these microorganisms. The importance of these clades to clinical research, epidemiology, population genetics, and microbial speciation is also discussed.

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Figures

Image of Figure 1
Figure 1

This neighbor-joining dendrogram was generated based on the Kimura-2 parameter as implemented in MEGA6 ( 45 ) with support for nodes based on 1,000 bootstrap replications. doi:10.1128/ecosalplus.ESP-0002-2015.f1

Citation: Walk S. 2015. The "Cryptic" , EcoSal Plus 2015; doi:10.1128/ecosalplus.ESP-0002-2015
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Image of Figure 2
Figure 2

To date, clade I isolates have been isolated from cases of human disease and found to carry virulence factors that define pathotypes, including ETEC and STEC. Representative strains referred to in the text are shown. CG, clonal group. doi:10.1128/ecosalplus.ESP-0002-2015.f2

Citation: Walk S. 2015. The "Cryptic" , EcoSal Plus 2015; doi:10.1128/ecosalplus.ESP-0002-2015
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Image of Figure 3
Figure 3

This is a time tree as implemented in MEGA6 ( 45 ) based on the Kimura-2 parameter. The scale bar displays the relative divergence times of each node. A name has not been proposed for subspecies VII. Representative isolates belonging to subspecies VII share the same biotype as subspecies ( 42 , 43 ). doi:10.1128/ecosalplus.ESP-0002-2015.f3

Citation: Walk S. 2015. The "Cryptic" , EcoSal Plus 2015; doi:10.1128/ecosalplus.ESP-0002-2015
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Figure 4

Between-genome comparisons mentioned in the text are indicated by colored symbols. Dotted lines represent ANI and dDDH cutoff values for bacterial species. Genome identification numbers can be found in Supplemental Table 1. doi:10.1128/ecosalplus.ESP-0002-2015.f4

Citation: Walk S. 2015. The "Cryptic" , EcoSal Plus 2015; doi:10.1128/ecosalplus.ESP-0002-2015
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Tables

Generic image for table
Table 1

The numbers of variable nucleotide sites among 22 MLST loci for pairwise group comparisons of , cryptic clades, , and isolates

Citation: Walk S. 2015. The "Cryptic" , EcoSal Plus 2015; doi:10.1128/ecosalplus.ESP-0002-2015
Generic image for table
Table 2

dDDH values (%) for representative genomes of previously named subspecies

Citation: Walk S. 2015. The "Cryptic" , EcoSal Plus 2015; doi:10.1128/ecosalplus.ESP-0002-2015

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