Strain identifier

BacDive ID: 17235

Type strain: Yes

Species: Photobacterium kishitanii

Strain Designation: pjapo.1.1

Strain history: <- P. V. Dunlap, University of Michigan

NCBI tax ID(s): 318456 (species)

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General

@ref: 8405

BacDive-ID: 17235

DSM-Number: 19954

keywords: genome sequence, 16S sequence, Bacteria, psychrophilic

description: Photobacterium kishitanii pjapo.1.1 is a psychrophilic bacterium that was isolated from Light organ of Physiculus japonicus.

NCBI tax id

  • NCBI tax id: 318456
  • Matching level: species

strain history

  • @ref: 8405
  • history: <- P. V. Dunlap, University of Michigan

doi: 10.13145/bacdive17235.20230509.8.1

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: 8405

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: pjapo.1.1

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 8405
  • name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514c
  • composition: Name: 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

culture temp

  • @ref: 8405
  • growth: positive
  • type: growth
  • temperature: 22
  • range: psychrophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836916899D-mannitol-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8405+-++----+-+-+++------
8405+-++----------+------

Isolation, sampling and environmental information

isolation

  • @ref: 8405
  • sample type: Light organ of Physiculus japonicus
  • host species: Physiculus japonicus
  • geographic location: Manzuru, Sagami Bay, Honshu
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2
#Host#Fishes
#Host Body-Site#Organ

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: AY341439
  • Sequence Identity:
  • Total samples: 5263
  • soil counts: 73
  • aquatic counts: 2884
  • animal counts: 2251
  • plant counts: 55

Safety information

risk assessment

  • @ref: 8405
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8405
  • description: Photobacterium kishitanii strain pjapo.1.1 16S ribosomal RNA gene, partial sequence
  • accession: AY341439
  • length: 1461
  • database: ena
  • NCBI tax ID: 318456

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium kishitanii pjapo.1.1GCA_003025975contigncbi318456
66792Photobacterium kishitanii pjapo.1.12876224593draftimg318456

External links

@ref: 8405

culture collection no.: DSM 19954, ATCC BAA 1194, LMG 23890

straininfo link

  • @ref: 86234
  • straininfo: 298267

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766874Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes.Ast JC, Cleenwerck I, Engelbeen K, Urbanczyk H, Thompson FL, De Vos P, Dunlap PVInt J Syst Evol Microbiol10.1099/ijs.0.65153-02007Animal Structures/microbiology, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Catalase/biosynthesis, Chromosomes, Bacterial, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Circular, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fishes/*microbiology/physiology, Flagella, Genes, rRNA, Locomotion/physiology, Luminescence, Luminescent Proteins/*biosynthesis, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Nucleic Acid Hybridization, Oxidoreductases/biosynthesis, Photobacterium/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Skin/microbiology, *SymbiosisGenetics
Phylogeny24951451Photobacterium piscicola sp. nov., isolated from marine fish and spoiled packed cod.Figge MJ, Cleenwerck I, van Uijen A, De Vos P, Huys G, Robertson LSyst Appl Microbiol10.1016/j.syapm.2014.05.0032014Amplified Fragment Length Polymorphism Analysis, Animals, Aquatic Organisms/microbiology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Food Microbiology, Gadiformes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Photobacterium/*classification/genetics/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology
Phylogeny27154455Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater.Huang Z, Dong C, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0011422016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/chemistry, Phospholipids/chemistry, *Phylogeny, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Salinity, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, Vibrionaceae/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitle
8405Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19954)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19954
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
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)
68369Automatically annotated from API 20NE
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
86234Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID298267.1StrainInfo: A central database for resolving microbial strain identifiers