Strain identifier

BacDive ID: 17229

Type strain: Yes

Species: Photobacterium damselae subsp. piscicida

Strain Designation: K-1

Strain history: CIP <- 1995, NCIMB <- R. Kusuda: strain K-1, Pasteurella piscicida

NCBI tax ID(s): 38294 (subspecies)

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General

@ref: 16539

BacDive-ID: 17229

DSM-Number: 22834

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped, animal pathogen

description: Photobacterium damselae subsp. piscicida K-1 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from yellowtail with pseudotuberculosis.

NCBI tax id

  • NCBI tax id: 38294
  • Matching level: subspecies

strain history

@refhistory
16539<- NCIMB <- R. Kusuda <- ?
118853CIP <- 1995, NCIMB <- R. Kusuda: strain K-1, Pasteurella piscicida

doi: 10.13145/bacdive17229.20230509.8.1

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 damselae subsp. piscicida
  • full scientific name: Photobacterium damselae subsp. piscicida corrig. (ex Janssen and Surgalla 1968) Gauthier et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Photobacterium damsela subsp. piscicida

@ref: 16539

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium damselae subsp. piscicida

full scientific name: Photobacterium damselae subsp. piscicida (ex Janssen and Surgalla 1968) Gauthier et al. 1995

strain designation: K-1

type strain: yes

Morphology

cell morphology

  • @ref: 118853
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16539BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 NaHCO3 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
16539BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
35165Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118853CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
16539positivegrowth25mesophilic
35165positivegrowth25mesophilic
52772positivegrowth22psychrophilic
118853positivegrowth10-30
118853nogrowth5psychrophilic
118853nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118853
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
118853NaClpositivegrowth2-6 %
118853NaClnogrowth0 %
118853NaClnogrowth8 %
118853NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11885317632nitrate-reduction
11885316301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11885335581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
11885315688acetoin-

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
118853oxidase+
118853beta-galactosidase+/-3.2.1.23
118853alcohol dehydrogenase+1.1.1.1
118853gelatinase-
118853amylase-
118853caseinase-3.4.21.50
118853catalase+1.11.1.6
118853gamma-glutamyltransferase+2.3.2.2
118853lecithinase+
118853lipase-
118853lysine decarboxylase-4.1.1.18
118853ornithine decarboxylase-4.1.1.17
118853urease-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

fatty acid profile

  • @reffatty acidpercentageECL
    52772C12:06.512
    52772C14:01114
    52772C15:00.515
    52772C16:020.216
    52772C18:00.418
    52772C12:0 3OH5.613.455
    52772C12:0 ALDE ?0.310.915
    52772C13:0 ISO 2OH2.413.814
    52772C14:0 3OH/C16:1 ISO I5.415.485
    52772C16:1 ω5c0.315.908
    52772C16:1 ω7c40.615.819
    52772C18:1 ω7c /12t/9t5.617.824
    52772Unidentified0.218.557
    52772unknown 11.7980.311.798
    52772unknown 12.4860.812.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    52772C12:05.612
    52772C14:08.614
    52772C15:00.315
    52772C16:023.516
    52772C18:00.418
    52772C12:0 3OH6.113.455
    52772C12:0 ALDE ?0.310.915
    52772C13:0 ISO 2OH1.413.814
    52772C14:0 3OH/C16:1 ISO I5.815.485
    52772C16:1 ω7c38.515.819
    52772C16:1 ω9c0.515.774
    52772C18:1 ω7c /12t/9t7.917.824
    52772Unidentified0.213.241
    52772unknown 12.4860.712.486
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118853-+++-+----+------+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16539--++-+------+-------+
16539--++----------------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
16539yellowtail (Seriola queradiata) with pseudotuberculosisSeriola quinqueradiataJapanJPNAsia
52772Yellowtail,Seriola queradiata,w/pseudotuberculosis
118853Yellowtail, spleenJapanJPNAsiaKashiwajima, Otsuki1970

isolation source categories

  • Cat1: #Host
  • Cat2: #Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_1769.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_1002;97_1168;98_1396;99_1769&stattab=map
  • Last taxonomy: Photobacterium damselae subclade
  • 16S sequence: X78105
  • Sequence Identity:
  • Total samples: 6454
  • soil counts: 214
  • aquatic counts: 3204
  • animal counts: 2991
  • plant counts: 45

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
16539yes1Risk group (German classification)
1188531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16539
  • description: P.damsela (NCIMB 2058) 16S rRNA gene
  • accession: X78105
  • length: 1434
  • database: ena
  • NCBI tax ID: 38293

External links

@ref: 16539

culture collection no.: DSM 22834, ATCC 51736, CIP 104404, KCTC 12268, LMG 21869, NCIMB 2058, CCUG 35502

straininfo link

  • @ref: 86228
  • straininfo: 43150

literature

  • topic: Phylogeny
  • Pubmed-ID: 29464363
  • title: Corallibacterium pacifica gen. nov., sp. nov., a Novel Bacterium of the Family Vibrionaceae Isolated from Hard Coral.
  • authors: Hettiarachchi SA, Lee SJ, Lee Y, Kwon YK, Kwon KK, Yang SH, Jo E, Kang DH, Oh C
  • journal: Curr Microbiol
  • DOI: 10.1007/s00284-018-1455-7
  • year: 2018
  • mesh: Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Micronesia, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Vibrionaceae/classification/genetics/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
16539Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22834)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22834
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
35165Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16308
52772Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35502)https://www.ccug.se/strain?id=35502
68369Automatically annotated from API 20NE
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
86228Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43150.1StrainInfo: A central database for resolving microbial strain identifiers
118853Curators of the CIPCollection of Institut Pasteur (CIP 104404)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104404