Strain identifier

BacDive ID: 14259

Type strain: Yes

Species: Sphingomonas japonica

Strain Designation: KC7

Strain history: CIP <- 2012, JCM <- 2008, N. Tanaka: strain KC7

NCBI tax ID(s): 511662 (species)

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

@ref: 16495

BacDive-ID: 14259

DSM-Number: 22753

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Sphingomonas japonica KC7 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine crustacean specimen Paralithodes camtschatica.

NCBI tax id

  • NCBI tax id: 511662
  • Matching level: species

strain history

@refhistory
16495<- L. A. Romanenko, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia; KMM 3038 <- N. Tanaka; KC7
67770N. Tanaka KC7.
120316CIP <- 2012, JCM <- 2008, N. Tanaka: strain KC7

doi: 10.13145/bacdive14259.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas japonica
  • full scientific name: Sphingomonas japonica Romanenko et al. 2009

@ref: 16495

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas japonica

full scientific name: Sphingomonas japonica Romanenko et al. 2009 emend. Feng et al. 2017

strain designation: KC7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28989negative1.65 µm0.7 µmrod-shapedyes
69480negative99.986
120316negativerod-shapedyes

pigmentation

  • @ref: 28989
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16495BACTO 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
36629Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120316CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
16495positivegrowth28mesophilic
28989positivegrowth04-37
28989positiveoptimum26.5mesophilic
36629positivegrowth25mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 28989
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.99

observation

  • @ref: 28989
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2898925115malate+carbon source
2898953426tween 80+carbon source
289894853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2898916136hydrogen sulfideyes
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
28989acid phosphatase+3.1.3.2
28989alkaline phosphatase+3.1.3.1
28989catalase+1.11.1.6
28989gelatinase+
28989cytochrome oxidase+1.9.3.1
68369cytochrome oxidase-1.9.3.1
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16495-----+-+++---+-------
16495-----+++-------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16495marine crustacean specimen Paralithodes camtschaticaParalithodes camtschaticaSea of Japan, Peter the Great BayRussiaRUSAsia
67770Paralithodes camtschatica collected from Peter the Great BayParalithodes camtschaticaSea of JapanRussiaRUS
120316Paralithodes camtschatica collected from Peter the Great BaySea of JapanRussian FederationRUSEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Arthropoda#Crustacea

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
164951Risk group (German classification)
1203161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16495
  • description: Sphingomonas japonica gene for 16S rRNA, partial sequence, strain: KC7
  • accession: AB428568
  • length: 1480
  • database: ena
  • NCBI tax ID: 511662

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas japonica strain DSM 22753511662.4wgspatric511662
66792Sphingomonas japonica DSM 227532828348002draftimg511662
67770Sphingomonas japonica DSM 22753GCA_011762085contigncbi511662

GC content

  • @ref: 16495
  • GC-content: 66.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveno97.126yes
anaerobicno99.434yes
halophileno89.519no
spore-formingno95.999no
glucose-utilyes82.842no
aerobicyes96.524yes
thermophileno96.814yes
flagellatedno87.287no
motileyes77.713yes
glucose-fermentno92.468yes

External links

@ref: 16495

culture collection no.: DSM 22753, JCM 15438, KMM 3038, NRIC 0738, CIP 110395

straininfo link

  • @ref: 83418
  • straininfo: 362852

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406815Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica.Romanenko LA, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.003285-02009Animals, Anomura/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny28691655Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead-zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica.Feng GD, Yang SZ, Xiong X, Li HP, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0019052017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, ZincTranscriptome
Phylogeny36173732Sphingomonas baiyangensis sp. nov., isolated from water in Baiyang Lake.Wei DW, Yang Y, Zeng Y, Wang C, Feng JInt J Syst Evol Microbiol10.1099/ijsem.0.0053262022Bacterial Typing Techniques, Base Composition, Cardiolipins, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Glycosphingolipids, Lakes/microbiology, Nucleotides, Phosphatidylcholines, Phosphatidylethanolamines, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, *Sphingomonas, WaterTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16495Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22753)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22753
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
28989Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2542228776041
36629Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8250
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/
68369Automatically annotated from API 20NE
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83418Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362852.1StrainInfo: A central database for resolving microbial strain identifiers
120316Curators of the CIPCollection of Institut Pasteur (CIP 110395)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110395