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type strain genome server  (DSMZ)


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    Structured Review

    DSMZ type strain genome server
    (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server <t>(TYGS),</t> places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.
    Type Strain Genome Server, supplied by DSMZ, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/type strain genome server/product/DSMZ
    Average 90 stars, based on 1 article reviews
    type strain genome server - by Bioz Stars, 2026-05
    90/100 stars

    Images

    1) Product Images from "Exposure to third generation cephalosporin induces L-form transition in Shigella sonnei , potentially acting as a bacterial reservoir for persistent infection"

    Article Title: Exposure to third generation cephalosporin induces L-form transition in Shigella sonnei , potentially acting as a bacterial reservoir for persistent infection

    Journal: bioRxiv

    doi: 10.1101/2025.07.17.665312

    (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server (TYGS), places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.
    Figure Legend Snippet: (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server (TYGS), places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.

    Techniques Used: Functional Assay



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    (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server <t>(TYGS),</t> places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.
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    (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server <t>(TYGS),</t> places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.
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    (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server <t>(TYGS),</t> places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.
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    (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server <t>(TYGS),</t> places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.
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    (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server <t>(TYGS),</t> places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.
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    https://www.bioz.com/result/type (strain) genome server/product/DSMZ
    Average 90 stars, based on 1 article reviews
    type (strain) genome server - by Bioz Stars, 2026-05
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    Image Search Results


    (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server (TYGS), places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.

    Journal: bioRxiv

    Article Title: Exposure to third generation cephalosporin induces L-form transition in Shigella sonnei , potentially acting as a bacterial reservoir for persistent infection

    doi: 10.1101/2025.07.17.665312

    Figure Lengend Snippet: (A) Circular map of the 4.57 Mb chromosome of S. sonnei HK8. The concentric rings, from the outside in, represent: (1-2) COG functional categories and coding sequences (CDS) on the positive strand; (3) RNA genes; (4-5) CDS and COG categories on the negative strand; (6) GC content relative to the mean; and (7) GC skew [(G-C)/(G+C)]. (B) Whole-genome phylogenomic tree illustrating the evolutionary position of S. sonnei HK8. The analysis, performed using the Type Strain Genome Server (TYGS), places HK8 (highlighted in red) directly adjacent to the Shigella sonnei ATCC 29930 type strain, confirming its species identity. The tree scale indicates the evolutionary distance. (C) Bar chart showing the absolute counts of putative virulence-associated genes in the HK8 genome, categorized by confidence level. The analysis identified a large number of genes with homology to “Potential Non-secreted Virulence factors” and a substantial fraction classified as “Unknown.” Genes with stronger evidence were categorized as “Non-secreted Virulence factors,” “Secreted Virulence factors,” and “Potential Secreted Virulence factors,” providing a quantitative overview of the isolate’s pathogenic potential.

    Article Snippet: For comprehensive genome-based phylogenomic analysis and strain-level classification, the assembled genome was submitted to the Type Strain Genome Server (TYGS) ( https://tygs.dsmz.de/ ).

    Techniques: Functional Assay