Strain identifier

BacDive ID: 17233

Type strain: Yes

Species: Photobacterium ganghwense

Strain Designation: FR1311

Strain history: <- J Chun, Seoul National Univ.

NCBI tax ID(s): 320778 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16632

BacDive-ID: 17233

DSM-Number: 22954

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

description: Photobacterium ganghwense FR1311 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 320778
  • Matching level: species

strain history

@refhistory
16632<- KCTC <- J. Chun, Seoul Natl. Univ., Republic of Korea
67770J. Chun FR1311.
67771<- J Chun, Seoul National Univ.

doi: 10.13145/bacdive17233.20230509.8.1

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 ganghwense
  • full scientific name: Photobacterium ganghwense Park et al. 2006

@ref: 16632

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium ganghwense

full scientific name: Photobacterium ganghwense Park et al. 2006

strain designation: FR1311

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31562negative1.3-2 µm0.8-1.2 µmovoid-shapedyes
67771negative

pigmentation

  • @ref: 31562
  • production: yes

multimedia

  • @ref: 16632
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_22954.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 16632
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16632positivegrowth28mesophilic
31562positivegrowth10-45
31562positiveoptimum35mesophilic
67770positivegrowth25mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31562positivegrowth05-11alkaliphile
31562positiveoptimum08-09

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31562facultative anaerobe
67771aerobe

spore formation

  • @ref: 31562
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31562NaClpositivegrowth01-07 %
31562NaClpositiveoptimum2 %

observation

@refobservation
31562aggregates in chains
67770quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3156217128adipate+carbon source
3156227689decanoate+carbon source
3156216947citrate+carbon source
3156224265gluconate+carbon source
3156217234glucose+carbon source
3156225115malate+carbon source
3156229864mannitol+carbon source
3156237684mannose+carbon source
31562506227N-acetylglucosamine+carbon source
3156218401phenylacetate+carbon source

enzymes

@refvalueactivityec
31562catalase+1.11.1.6
31562cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
16632sea waterGanghwa Island (37°35'39.1'' N 126°27'24.5'' E)Republic of KoreaKORAsia37.5942126.457
67770SeawaterGanghwa IslandRepublic of KoreaKORAsia
67771From seawaterKangwhaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_5078.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_2475;97_3023;98_3791;99_5078&stattab=map
  • Last taxonomy: Photobacterium ganghwense subclade
  • 16S sequence: AY960847
  • Sequence Identity:
  • Total samples: 382
  • soil counts: 44
  • aquatic counts: 241
  • animal counts: 93
  • plant counts: 4

Safety information

risk assessment

  • @ref: 16632
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16632
  • description: Photobacterium ganghwense strain FR1311 16S ribosomal RNA gene, partial sequence
  • accession: AY960847
  • length: 1474
  • database: ena
  • NCBI tax ID: 320778

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium ganghwense JCM 12487GCA_003025595contigncbi320778
66792Photobacterium ganghwense DSM 22954GCA_001029455contigncbi320778
66792Photobacterium ganghwense strain DSM 22954320778.3wgspatric320778
66792Photobacterium ganghwense strain JCM 12487320778.6wgspatric320778
66792Photobacterium ganghwense DSM 229542713896764draftimg320778
66792Photobacterium ganghwense JCM 124872868869919draftimg320778

GC content

@refGC-contentmethod
1663244.0
3156244
6777044thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.794yes
anaerobicno96.561yes
halophileno63.888no
spore-formingno93.663yes
glucose-utilyes93.161yes
motileyes91.498yes
flagellatedyes91.303no
thermophileno99.744yes
aerobicyes73.358no
glucose-fermentyes85.378no

External links

@ref: 16632

culture collection no.: DSM 22954, IMSNU 60287, JCM 12487, KCTC 12328, CIP 109254, DSM 22358, NCIMB 14495

straininfo link

  • @ref: 86232
  • straininfo: 232818

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585687Photobacterium ganghwense sp. nov., a halophilic bacterium isolated from sea water.Park YD, Baik KS, Seong CN, Bae KS, Kim S, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.63811-02006DNA, Bacterial/analysis, Fatty Acids/analysis, Molecular Sequence Data, Photobacterium/*classification/enzymology/genetics/*isolation & purification, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sodium Chloride/metabolismGenetics
Pathogenicity28659560Environmental Impact of Tributyltin-Resistant Marine Bacteria in the Indigenous Microbial Population of Tributyltin-Polluted Surface Sediments.Mimura H, Yagi M, Yoshida KBiocontrol Sci10.4265/bio.22.892017DNA, Ribosomal, *Drug Resistance, Microbial, Geologic Sediments/*microbiology, Photobacterium/*drug effects/growth & development, Trialkyltin Compounds/*pharmacology, Water Microbiology, Water Pollutants, Chemical/pharmacology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16632Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22954)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22954
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
31562Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2785228776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
86232Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232818.1StrainInfo: A central database for resolving microbial strain identifiers