Strain identifier

BacDive ID: 135721

Type strain: No

Species: Shigella dysenteriae

Strain Designation: 588

Strain history: CIP <- 1958, Huet: strain 588

NCBI tax ID(s): 622 (species)

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General

@ref: 34902

BacDive-ID: 135721

keywords: genome sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Shigella dysenteriae 588 is a facultative anaerobe, mesophilic, Gram-negative bacterium of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 622
  • Matching level: species

strain history

@refhistory
349021958, Huet: strain 588
34902CIP <- 1958, Huet: strain 588

doi: 10.13145/bacdive135721.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Shigella
  • species: Shigella dysenteriae
  • full scientific name: Shigella dysenteriae (Shiga 1897) Castellani and Chalmers 1919 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacillus dysentericus

@ref: 34902

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Enterobacteriaceae

genus: Shigella

species: Shigella dysenteriae

strain designation: 588

type strain: no

Morphology

cell morphology

  • @ref: 34902
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34902MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
34902CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
34902positivegrowth30mesophilic
34902positivegrowth30-41
34902nogrowth5psychrophilic
34902nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 34902
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
34902mannitol-fermentation29864
34902citrate-carbon source16947
34902glucose+fermentation17234
34902lactose-fermentation17716
34902nitrate+reduction17632
34902nitrite-reduction16301
34902malonate-assimilation15792
34902sodium thiosulfate-builds gas from132112
34902glucose+degradation17234

antibiotic resistance

  • @ref: 34902
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 34902
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3490215688acetoin-
3490217234glucose+

enzymes

@refvalueactivityec
34902oxidase-
34902beta-galactosidase+3.2.1.23
34902alcohol dehydrogenase-1.1.1.1
34902gelatinase-
34902catalase+1.11.1.6
34902lysine decarboxylase-4.1.1.18
34902ornithine decarboxylase-4.1.1.17
34902phenylalanine ammonia-lyase-4.3.1.24
34902tryptophan deaminase-
34902urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
34902-+---+--+-++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
34902+/---------++++--------+---------+--------------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
34902+++++--------------------------+-----------------+---------++--------------+---++-----+--+---------

Isolation, sampling and environmental information

isolation

  • @ref: 34902
  • geographic location: Tunis
  • country: Tunisia
  • origin.country: TUN
  • continent: Africa

Safety information

risk assessment

  • @ref: 34902
  • biosafety level: 3
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Shigella dysenteriae strain CIP58.1
  • accession: 622.146
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 622

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.093no
anaerobicno94.726no
halophileno91.584no
spore-formingno94.234no
glucose-utilyes91.238no
thermophileno98.981yes
flagellatedno83.291no
aerobicyes76.654no
motileyes67.534no
glucose-fermentyes92.458no

External links

@ref: 34902

culture collection no.: CIP 58.1

straininfo link

  • @ref: 93019
  • straininfo: 70121

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
34902Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2058.1Collection of Institut Pasteur (CIP 58.1)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
93019Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID70121.1