Strain identifier

BacDive ID: 17220

Type strain: No

Species: Photobacterium kishitanii

Strain Designation: I

Strain history: CIP <- 1994, M. Gauthier, INSERM, Nice, France, Photobacterium phosphoreum <- CCM <- NCIB <- R. Spencer <- D.L. Georgala: strain I

NCBI tax ID(s): 318456 (species)

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General

@ref: 990

BacDive-ID: 17220

DSM-Number: 2167

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, toxin production

description: Photobacterium kishitanii I is a facultative anaerobe, mesophilic, Gram-negative bacterium that produces toxins.

NCBI tax id

  • NCBI tax id: 318456
  • Matching level: species

strain history

@refhistory
990<- CCM <- NCMB <- R. Spencer <- D.L. Georgala, I
120446CIP <- 1994, M. Gauthier, INSERM, Nice, France, Photobacterium phosphoreum <- CCM <- NCIB <- R. Spencer <- D.L. Georgala: strain I

doi: 10.13145/bacdive17220.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Photobacterium
  • species: Photobacterium kishitanii
  • full scientific name: Photobacterium kishitanii Ast et al. 2007

@ref: 990

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium kishitanii

full scientific name: Photobacterium kishitanii Ast et al. 2007

strain designation: I

type strain: no

Morphology

cell morphology

  • @ref: 120446
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
990REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)yeshttps://mediadive.dsmz.de/medium/514cName: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
38493Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120446CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
990positivegrowth25mesophilic
38493positivegrowth25mesophilic
120446positivegrowth5-22psychrophilic
120446nogrowth30mesophilic
120446nogrowth37mesophilic
120446nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120446
  • oxygen tolerance: facultative anaerobe

compound production

  • @ref: 990
  • compound: tetrodotoxin

halophily

@refsaltgrowthtested relationconcentration
120446NaClpositivegrowth2-8 %
120446NaClnogrowth0 %
120446NaClnogrowth10 %

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
68371glycerol-builds acid from17754
120446esculin-hydrolysis4853
120446nitrate+reduction17632
120446nitrite-reduction16301

metabolite production

  • @ref: 120446
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12044615688acetoin-
12044617234glucose-

enzymes

@refvalueactivityec
120446oxidase-
120446beta-galactosidase-3.2.1.23
120446alcohol dehydrogenase-1.1.1.1
120446gelatinase-
120446amylase-
120446DNase-
120446caseinase-3.4.21.50
120446catalase+1.11.1.6
120446tween esterase-
120446gamma-glutamyltransferase-2.3.2.2
120446lecithinase+
120446lipase-
120446lysine decarboxylase-4.1.1.18
120446ornithine decarboxylase-4.1.1.17
120446phenylalanine ammonia-lyase-4.3.1.24
120446protease+
120446tryptophan deaminase-
120446urease-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
120446-+++-+----++-----++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120446-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
38493Cape TownSouth AfricaZAFAfrica
990South AfricaZAFAfricaskin of Merluccius capensis
120446Cape TownSouth AfricaZAFAfricaAnimal, Fish, hake, Merluccius capensis

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Organ#Skin, Nail, Hair
#Host#Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_518.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_318;97_354;98_399;99_518&stattab=map
  • Last taxonomy: Photobacterium
  • 16S sequence: AY341438
  • Sequence Identity:
  • Total samples: 5263
  • soil counts: 73
  • aquatic counts: 2884
  • animal counts: 2251
  • plant counts: 55

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
9901Risk group (German classification)
1204461Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Photobacterium kishitanii strain NCMB 844 16S ribosomal RNA gene, partial sequence
  • accession: AY341438
  • length: 1467
  • database: ena
  • NCBI tax ID: 318456

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium kishitanii strain GCSL-P48318456.9wgspatric318456
66792Photobacterium kishitanii DSM 21672905565123draftimg318456
66792Photobacterium kishitanii DSM 2167GCA_001676215contigncbi318456

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.778no
anaerobicno97.792no
halophileno54.721no
spore-formingno95.157no
glucose-utilyes93.587no
motileyes90.5no
flagellatedyes73.621no
aerobicyes75.887no
thermophileno99.393yes
glucose-fermentyes85.193no

External links

@ref: 990

culture collection no.: DSM 2167, CCM 2348, LMG 23895, NCMB 844, CIP 104260, NCIMB 844

straininfo link

  • @ref: 86219
  • straininfo: 3836

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
990Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2167)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2167
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
38493Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16149
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)
68371Automatically annotated from API 50CH acid
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
86219Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3836.1StrainInfo: A central database for resolving microbial strain identifiers
120446Curators of the CIPCollection of Institut Pasteur (CIP 104260)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104260