Strain identifier

BacDive ID: 5174

Type strain: Yes

Species: Shigella boydii

Strain Designation: P288

Strain history: CIP <- 1982, ATCC <- NCTC, Shigella paradysenteriae <- J. Boyd: strain P288

NCBI tax ID(s): 621 (species)

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General

@ref: 3205

BacDive-ID: 5174

DSM-Number: 7532

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Shigella boydii P288 is an aerobe, mesophilic, Gram-negative bacterium of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 621
  • Matching level: species

strain history

@refhistory
3205<- ATCC <- NCTC <- AMC (Shigella paradysenteriae) <- J. Boyd; P288
116980CIP <- 1982, ATCC <- NCTC, Shigella paradysenteriae <- J. Boyd: strain P288

doi: 10.13145/bacdive5174.20230509.8.1

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 boydii
  • full scientific name: Shigella boydii Ewing 1949 (Approved Lists 1980)

@ref: 3205

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Shigella

species: Shigella boydii

full scientific name: Shigella boydii Ewing 1949

strain designation: P288

type strain: yes

Morphology

cell morphology

  • @ref: 116980
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 116980

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3205CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
40739MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116980CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3205positivegrowth37mesophilic
40739positivegrowth30mesophilic
58445positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58445aerobe
116980obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11698017632nitrate+reduction
11698016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836835581indoleno
6836816136hydrogen sulfideno
11698035581indoleno

metabolite tests

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
116980oxidase-
116980alcohol dehydrogenase-1.1.1.1
116980catalase+1.11.1.6
116980lysine decarboxylase-4.1.1.18
116980ornithine decarboxylase-4.1.1.17
116980urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116980-++--++---+----+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
3205---------+-++------+-
3205-----------++------+/--

Isolation, sampling and environmental information

isolation

  • @ref: 3205
  • country: India
  • origin.country: IND
  • continent: Asia

taxonmaps

  • @ref: 69479
  • File name: preview.99_8.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_7;99_8&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: HF558388
  • Sequence Identity:
  • Total samples: 97630
  • soil counts: 2111
  • aquatic counts: 5613
  • animal counts: 88071
  • plant counts: 1835

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32052Risk group (German classification)
1169802Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Shigella boydii partial 16S rRNA gene, strain P288
  • accession: HF558388
  • length: 1515
  • database: ena
  • NCBI tax ID: 621

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shigella boydii NCTC12985GCA_900457095contigncbi621
66792Shigella boydii ATCC 8700GCA_002946735completencbi621
66792Shigella boydii strain ATCC 8700621.213completepatric621
66792Shigella boydii strain DMB SH130621.253wgspatric621
66792Shigella boydii strain FDAARGOS_1139621.337completepatric621
66792Shigella boydii strain NCTC12985621.296wgspatric621
66792Shigella boydii ATCC 87002850761752completeimg621
66792Shigella boydii ATCC 8700GCA_003572535contigncbi621

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno58.115no
gram-positiveno98.599no
anaerobicno95.575yes
aerobicyes77.823no
halophileno91.67no
spore-formingno94.548no
glucose-utilyes92.847no
thermophileno98.526yes
motileyes87.301no
glucose-fermentyes91.674yes

External links

@ref: 3205

culture collection no.: DSM 7532, ATCC 8700, CCUG 49022, CIP 82.50, NCTC 12985

straininfo link

  • @ref: 74666
  • straininfo: 34992

literature

Pubmed-IDtitleauthorsjournalyearmeshtopictopic2
17063774Determination of the profile of fatty acids of 4 species of Shigella spp by chromatography of gases.Robles Valderrama E, Hurtado Bocanegra MD, Gonzalez Arreaga ME, Ramirez Garcia P, Duran Diaz A, Ayala Patino R, Martinez Perez MERev Latinoam Microbiol2002Chromatography, Gas, Fatty Acids/*analysis, Shigella/*chemistry
19553175Evaluation of antibacterial activity, phenol and flavonoid contents of Thespesia populnea flower extracts.Saravanakumar A, Venkateshwaran K, Vanitha J, Ganesh M, Vasudevan M, Sivakumar TPak J Pharm Sci2009Alkaloids/isolation & purification/pharmacology, Anthraquinones/isolation & purification/pharmacology, Anti-Bacterial Agents/chemistry/*pharmacology, Bacteria/*drug effects, Chromatography, High Pressure Liquid, Flavonoids/isolation & purification/*pharmacology, Flowers/*chemistry, Glycosides/isolation & purification/pharmacology, Malvaceae/*chemistry, Microbial Sensitivity Tests, Phenols/isolation & purification/*pharmacology, Plant Extracts/chemistry/pharmacology, Tannins/isolation & purification/pharmacologyEnzymologyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3205Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7532)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7532
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40739Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11322
58445Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49022)https://www.ccug.se/strain?id=49022
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
74666Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID34992.1StrainInfo: A central database for resolving microbial strain identifiers
116980Curators of the CIPCollection of Institut Pasteur (CIP 82.50)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.50