Strain identifier

BacDive ID: 17234

Type strain: Yes

Species: Photobacterium lutimaris

Strain Designation: DF-42

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 388278 (species)

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General

@ref: 15943

BacDive-ID: 17234

DSM-Number: 21778

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

description: Photobacterium lutimaris DF-42 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 388278
  • Matching level: species

strain history

@refhistory
15943<- KCTC <- J. H. Yoon, KRIBB
67770J.-H. Yoon DF-42.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive17234.20230509.8.1

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 lutimaris
  • full scientific name: Photobacterium lutimaris Jung et al. 2007

@ref: 15943

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium lutimaris

full scientific name: Photobacterium lutimaris Jung et al. 2007

strain designation: DF-42

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31877negative1.8 µm1.1 µmovoid-shapedyes
67771negative

pigmentation

  • @ref: 31877
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15943
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
15943positivegrowth28mesophilic
31877positivegrowth04-41
31877positiveoptimum27.5mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31877positivegrowth5.0-8.5alkaliphile
31877positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31877anaerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
31877NaClpositivegrowth0.1-6 %
31877NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3187717057cellobiose+carbon source
3187716947citrate+carbon source
3187728757fructose+carbon source
3187717234glucose+carbon source
3187725115malate+carbon source
3187717268myo-inositol+carbon source
3187715361pyruvate+carbon source
3187733942ribose+carbon source
3187717814salicin+carbon source
3187730031succinate+carbon source
3187753424tween 20+carbon source
3187753423tween 40+carbon source
3187753425tween 60+carbon source
3187753426tween 80+carbon source
3187718222xylose+carbon source
318774853esculin+hydrolysis

enzymes

@refvalueactivityec
31877acid phosphatase+3.1.3.2
31877alkaline phosphatase+3.1.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15943tidal flat sedimentSaemankumRepublic of KoreaKORAsia
67770Tidal flat sediment at SaemankunRepublic of KoreaKORAsia
67771From gaetbulRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

Safety information

risk assessment

  • @ref: 15943
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15943
  • description: Photobacterium lutimaris strain DF-42 16S ribosomal RNA gene, partial sequence
  • accession: DQ534014
  • length: 1508
  • database: ena
  • NCBI tax ID: 388278

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium lutimaris strain CECT 7642388278.4wgspatric388278
66792Photobacterium lutimaris strain JCM 13586388278.3wgspatric388278
66792Photobacterium lutimaris JCM 135862858373912draftimg388278
66792Photobacterium lutimaris CECT 76422770939603draftimg388278
67770Photobacterium lutimaris JCM 13586GCA_003025555contigncbi388278
67770Photobacterium lutimaris CECT 7642GCA_004363665scaffoldncbi388278

GC content

@refGC-contentmethod
1594348.3high performance liquid chromatography (HPLC)
3187748.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.924no
anaerobicno96.087no
halophileno62.52no
spore-formingno93.982no
glucose-utilyes89.886no
aerobicyes80.328no
motileyes89.772no
flagellatedyes84.097no
thermophileno99.642yes
glucose-fermentyes88.309no

External links

@ref: 15943

culture collection no.: DSM 21778, JCM 13586, KCTC 12723, CAIM 1851, CECT 7642, CIP 109547, LMG 25278

straininfo link

  • @ref: 86233
  • straininfo: 297306

literature

  • topic: Phylogeny
  • Pubmed-ID: 17267974
  • title: Photobacterium lutimaris sp. nov., isolated from a tidal flat sediment in Korea.
  • authors: Jung SY, Jung YT, Oh TK, Yoon JH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64580-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Carbohydrate Metabolism, Fatty Acids/analysis/chemistry, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Photobacterium/*classification/cytology/*isolation & purification/physiology, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Sodium Chloride, Soil Microbiology, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15943Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21778)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21778
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
31877Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2813728776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
86233Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297306.1StrainInfo: A central database for resolving microbial strain identifiers