Strain identifier

BacDive ID: 17230

Type strain: Yes

Species: Photobacterium profundum

Strain Designation: DSJ4, DSJ14

Strain history: CIP <- 1999, JCM <- Y. Nogi: strain DSJ4

NCBI tax ID(s): 74109 (species)

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General

@ref: 15552

BacDive-ID: 17230

DSM-Number: 21095

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

description: Photobacterium profundum DSJ4 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from deep-sea sediment at 5100 m depth.

NCBI tax id

  • NCBI tax id: 74109
  • Matching level: species

strain history

@refhistory
15552<- JCM <- Y. Nogi, Japan Marine Sci Technol Center Yokosuka; DS14
67770Y. Nogi DSJ4.
121959CIP <- 1999, JCM <- Y. Nogi: strain DSJ4

doi: 10.13145/bacdive17230.20230509.8.1

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 profundum
  • full scientific name: Photobacterium profundum Nogi et al. 1998

@ref: 15552

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium profundum

full scientific name: Photobacterium profundum Nogi et al. 1998

strain designation: DSJ4, DSJ14

type strain: yes

Morphology

cell morphology

  • @ref: 121959
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15552BACTO 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
41484Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121959CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
15552positivegrowth10psychrophilic
41484positivegrowth10psychrophilic
67770positivegrowth10psychrophilic
121959positivegrowth5-15psychrophilic
121959nogrowth22psychrophilic
121959nogrowth30mesophilic
121959nogrowth37mesophilic
121959nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121959
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
121959NaClpositivegrowth2-4 %
121959NaClnogrowth0 %
121959NaClnogrowth6 %
121959NaClnogrowth8 %
121959NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

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
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose-builds acid from17992
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
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
121959esculin-hydrolysis4853
121959nitrate+reduction17632
121959nitrite+reduction16301
121959glucose+degradation17234

metabolite production

  • @ref: 121959
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12195915688acetoin-
12195917234glucose-

enzymes

@refvalueactivityec
121959oxidase+
121959beta-galactosidase-3.2.1.23
121959alcohol dehydrogenase-1.1.1.1
121959gelatinase+/-
121959amylase-
121959caseinase+3.4.21.50
121959catalase+1.11.1.6
121959tween esterase+
121959gamma-glutamyltransferase-2.3.2.2
121959lecithinase+
121959lipase-
121959lysine decarboxylase-4.1.1.18
121959ornithine decarboxylase-4.1.1.17
121959phenylalanine ammonia-lyase-4.3.1.24
121959protease+
121959tryptophan deaminase-
121959urease-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
121959-+++-------+-----+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121959+/---------+/-+/-+/-+/----+/-+/----+/------+/--+/--+/----+/-+/-------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121959++-++----++--------------------+-+---------------+---------+-------------------++------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
15552deep-sea sediment at 5100 m depthRyukyu Trench, Japanese Exclusive Economic ZoneJapanJPNAsia24.25126.783
67770Deep sea sediment
121959Environment, Deep sea sedimentThe Ryukyu Trench at a depth of 5110 m, Philippine Sea in the Pacific OceanPhilippinesPHLAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4540.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_318;97_2402;98_2969;99_4540&stattab=map
  • Last taxonomy: Photobacterium profundum subclade
  • 16S sequence: D21226
  • Sequence Identity:
  • Total samples: 197
  • soil counts: 1
  • aquatic counts: 145
  • animal counts: 49
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
155521Risk group (German classification)
1219591Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15552
  • description: Photobacterium profundum gene for 16S rRNA, partial sequence, strain: DSJ4
  • accession: D21226
  • length: 1519
  • database: ena
  • NCBI tax ID: 74109

GC content

  • @ref: 67770
  • GC-content: 42
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 15552

culture collection no.: DSM 21095, CIP 106289, JCM 10084, KCTC 12378

straininfo link

  • @ref: 86229
  • straininfo: 13209

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9676237Photobacterium profundum sp. nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment.Nogi Y, Masui N, Kato CExtremophiles10.1007/s0079200500361998Base Composition, DNA, Bacterial/chemistry, Fatty Acids/analysis, Photobacterium/*classification/isolation & purification/*physiology, *Phylogeny, Pressure, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Vibrionaceae/classificationEnzymology
Phylogeny15653897Photobacterium lipolyticum sp. nov., a bacterium with lipolytic activity isolated from the Yellow Sea in Korea.Yoon JH, Lee JK, Kim YO, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63215-02005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/microbiology, Korea, Lipase/*metabolism, Molecular Sequence Data, Phenotype, Photobacterium/*classification/enzymology/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Pathogenicity16227349Vibrionaceae as a possible source of Qnr-like quinolone resistance determinants.Poirel L, Liard A, Rodriguez-Martinez JM, Nordmann PJ Antimicrob Chemother10.1093/jac/dki3712005Amino Acid Sequence, Anti-Bacterial Agents/*pharmacology, Bacterial Proteins/chemistry/genetics, DNA, Bacterial/chemistry/genetics, Drug Resistance, Bacterial/*genetics, Escherichia coli/drug effects/genetics, *Gene Transfer, Horizontal, *Genes, Bacterial, Microbial Sensitivity Tests, Molecular Sequence Data, Photobacterium/drug effects/genetics, Polymerase Chain Reaction, Quinolones/*pharmacology, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Vibrio parahaemolyticus/drug effects/genetics, Vibrio vulnificus/drug effects/genetics, Vibrionaceae/*drug effects/*geneticsGenetics

Reference

@idauthorscataloguedoi/urltitle
15552Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21095)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21095
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
41484Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18403
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86229Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13209.1StrainInfo: A central database for resolving microbial strain identifiers
121959Curators of the CIPCollection of Institut Pasteur (CIP 106289)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106289