Strain identifier

BacDive ID: 14253

Type strain: Yes

Species: Sphingomonas kaistensis

Strain Designation: PB56

Strain history: CIP <- 2012, DSMZ <- M.K. Kim, Daejeon, South Korea: strain PB56

NCBI tax ID(s): 298708 (species)

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General

@ref: 6631

BacDive-ID: 14253

DSM-Number: 16846

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

description: Sphingomonas kaistensis PB56 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 298708
  • Matching level: species

strain history

@refhistory
6631<- M. K. Kim, Daejeon, South Korea; PB56
67771<- ST Lee, KAIST
120371CIP <- 2012, DSMZ <- M.K. Kim, Daejeon, South Korea: strain PB56

doi: 10.13145/bacdive14253.20230509.8.1

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 kaistensis
  • full scientific name: Sphingomonas kaistensis Kim et al. 2007

@ref: 6631

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas kaistensis

full scientific name: Sphingomonas kaistensis Kim et al. 2007

strain designation: PB56

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31876negative1.1 µm0.7 µmrod-shapedno
67771negative
69480negative99.924
120371negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6631R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
36261MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
120371CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
6631positivegrowth30mesophilic
31876positiveoptimum27.5mesophilic
36261positivegrowth25mesophilic
67771positivegrowth30mesophilic
6631positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31876aerobe
67771aerobe

spore formation

@refspore formationconfidence
31876no
69481no99
69480no99.971

observation

  • @ref: 67771
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31876178794-hydroxybenzoate+carbon source
3187617128adipate+carbon source
3187624265gluconate+carbon source
3187617234glucose+carbon source
3187617306maltose+carbon source
3187629864mannitol+carbon source
3187637684mannose+carbon source
31876506227N-acetylglucosamine+carbon source
3187626546rhamnose+carbon source
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
31876catalase+1.11.1.6
31876cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6631-----+-------+---+--+/-
6631-----+--+----+--++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6631soilDaejeon CityRepublic of KoreaKORAsia
67771From sediment, small pond in KAISTDaejeonRepublic of KoreaKORAsia
120371Environment, SoilRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66311Risk group (German classification)
1203711Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31876
  • description: Sphingomonas kaistensis strain PB56 16S ribosomal RNA gene, partial sequence
  • accession: AY769083
  • length: 1421
  • database: nuccore
  • NCBI tax ID: 298708

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas kaistensis DSM 16846GCA_011927725contigncbi298708
66792Sphingomonas kaistensis strain DSM 16846298708.4wgspatric298708
66792Sphingomonas kaistensis DSM 168462829822250draftimg298708

GC content

@refGC-content
3187669.9
6777164.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveno96.641yes
anaerobicno98.436yes
halophileno92.184no
spore-formingno96.163yes
glucose-utilyes82.385yes
flagellatedno96.281yes
aerobicyes87.343no
thermophileno96.089no
motileno79.893yes
glucose-fermentno90.458no

External links

@ref: 6631

culture collection no.: DSM 16846, CIP 110410, KCTC 12334

straininfo link

  • @ref: 83412
  • straininfo: 232821

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625188Sphingomonas kaistensis sp. nov., a novel alphaproteobacterium containing pufLM genes.Kim MK, Schubert K, Im WT, Kim KH, Lee ST, Overmann JInt J Syst Evol Microbiol10.1099/ijs.0.64579-02007Bacterial Proteins/analysis/*genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Light-Harvesting Protein Complexes/*genetics, Molecular Sequence Data, Photosynthetic Reaction Center Complex Proteins/*genetics, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingomonas/chemistry/*classification/*genetics/isolation & purificationGenetics
Phylogeny25985832Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond.Kim JH, Kim SH, Kim KH, Lee PCInt J Syst Evol Microbiol10.1099/ijs.0.0003372015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycosides/biosynthesis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, *Ponds, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Xanthophylls/biosynthesisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6631Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16846)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16846
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
31876Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2813628776041
36261Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8266
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
83412Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232821.1StrainInfo: A central database for resolving microbial strain identifiers
120371Curators of the CIPCollection of Institut Pasteur (CIP 110410)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110410