Strain identifier

BacDive ID: 136605

Type strain: No

Species: Photobacterium damselae

Strain Designation: C-8

Strain history: CIP <- 1995, T. Fujii, Science Univ. of Tokyo, Tokyo, Japan, Photobacterium histaminum: strain C-8 <- R. Yoguchi

NCBI tax ID(s): 38293 (species)

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General

@ref: 36062

BacDive-ID: 136605

keywords: 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped

description: Photobacterium damselae C-8 is a facultative anaerobe, Gram-negative, motile bacterium of the family Vibrionaceae.

NCBI tax id

  • NCBI tax id: 38293
  • Matching level: species

strain history

@refhistory
67770T. Fujii C-8.
36062CIP <- 1995, T. Fujii, Science Univ. of Tokyo, Tokyo, Japan, Photobacterium histaminum: strain C-8 <- R. Yoguchi

doi: 10.13145/bacdive136605.20240510.9

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
  • full scientific name: Photobacterium damselae corrig. (Love et al. 1982) Smith et al. 1991

  • synonyms

    @refsynonym
    20215Vibrio damsela
    20215Vibrio damselae
    20215Photobacterium histaminum
    20215Photobacterium damsela
    20215Listonella damsela
    20215Listonella damselae

@ref: 36062

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium damselae

strain designation: C-8

type strain: no

Morphology

cell morphology

  • @ref: 36062
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36062Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
36062CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
36062positivegrowth25
67770positivegrowth25
36062positivegrowth15-37
36062nogrowth5
36062nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 36062
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
36062NaClpositivegrowth2-8 %
36062NaClnogrowth0 %
36062NaClnogrowth10 %

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
36062citrate-carbon source16947
36062esculin-hydrolysis4853
36062glucose+fermentation17234
36062lactose-fermentation17716
36062nitrate+reduction17632
36062nitrite-reduction16301
36062sodium thiosulfate-builds gas from132112
36062glucose+degradation17234
36062nitrate+respiration17632

metabolite production

  • @ref: 36062
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3606215688acetoin-
3606217234glucose+

enzymes

@refvalueactivityec
36062oxidase+
36062beta-galactosidase-3.2.1.23
36062alcohol dehydrogenase-1.1.1.1
36062gelatinase-
36062amylase+
36062DNase+
36062caseinase-3.4.21.50
36062catalase+1.11.1.6
36062tween esterase-
36062gamma-glutamyltransferase-2.3.2.2
36062lecithinase+
36062lipase+
36062lysine decarboxylase-4.1.1.18
36062ornithine decarboxylase-4.1.1.17
36062phenylalanine ammonia-lyase-4.3.1.24
36062protease-
36062tryptophan deaminase-
36062urease+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
36062-+++-+----++-----+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
36062+---+----++++--------+----++---+---+-------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
36062+++++----++----+---+-----------+-----------------+-----------------------------++-----+--+---------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typehost speciesisolation date
36062KonagawaJapanJPNAsia
67770Skin of a labracoglossid fish (Labracoglassa argentiventris)Labracoglassa argentiventris
36062KanagawaJapanJPNAsiaLabracoglossid fish, skin1987

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: AB032014
  • Sequence Identity:
  • Total samples: 6454
  • soil counts: 214
  • aquatic counts: 3204
  • animal counts: 2991
  • plant counts: 45

Safety information

risk assessment

  • @ref: 36062
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Photobacterium histaminum gene for 16S rRNA, partial sequenceAB0320141550nuccore85581
67770Photobacterium damselae subsp. damselae gene for 16S rRNAD253081472nuccore85581

GC content

  • @ref: 67770
  • GC-content: 41.6
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 36062

culture collection no.: CIP 104414, JCM 8968, ATCC 51805, CECT 4996, CGMCC 1.3753, NCIMB 13351

literature

  • topic: Phylogeny
  • Pubmed-ID: 10843080
  • title: Photobacterium histaminum Okuzumi et al. 1994 is a later subjective synonym of Photobacterium damselae subsp. damselae (Love et al. 1981) Smith et al. 1991.
  • authors: Kimura B, Hokimoto S, Takahashi H, Fujii T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-3-1339
  • year: 2000
  • mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Genes, rRNA, Histamine/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Photobacterium/*classification/*genetics/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Terminology as Topic
  • topic2: Metabolism

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
36062Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104414Collection of Institut Pasteur (CIP 104414)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/