Strain identifier

BacDive ID: 14183

Type strain: Yes

Species: Sphingobium chungbukense

Strain Designation: DJ77

Strain history: CIP <- 2002, JCM, Sphingomonas chungbukensis <- 2001, KCTC <- S.J. Jim: strain DJ77

NCBI tax ID(s): 56193 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6541

BacDive-ID: 14183

DSM-Number: 16638

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

description: Sphingobium chungbukense DJ77 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from contaminated sediment.

NCBI tax id

  • NCBI tax id: 56193
  • Matching level: species

strain history

@refhistory
6541<- KCTC <- Y.-C. Kim; DJ77
67770KCTC 2955 <-- S.-J. Kim DJ77.
67771<- YC Kim, DJ77
118266CIP <- 2002, JCM, Sphingomonas chungbukensis <- 2001, KCTC <- S.J. Jim: strain DJ77

doi: 10.13145/bacdive14183.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingobium
  • species: Sphingobium chungbukense
  • full scientific name: Sphingobium chungbukense (Kim et al. 2000) Pal et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Sphingomonas chungbukensis

@ref: 6541

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium chungbukense

full scientific name: Sphingobium chungbukense (Kim et al. 2000) Pal et al. 2005

strain designation: DJ77

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771negative
118266negativerod-shapedno

pigmentation

  • @ref: 118266
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6541MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)yeshttps://mediadive.dsmz.de/medium/457Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
6541CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
34204MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118266CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6541positivegrowth28mesophilic
34204positivegrowth30mesophilic
59715positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth28mesophilic
118266positivegrowth25-41
118266nogrowth5psychrophilic
118266nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59715aerobe
67771aerobe
118266obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
118266NaClpositivegrowth0 %
118266NaClnogrowth2 %
118266NaClnogrowth4 %
118266NaClnogrowth6 %
118266NaClnogrowth8 %
118266NaClnogrowth10 %

observation

@refobservation
67770quinones: Q-10
67771quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11826616947citrate-carbon source
1182664853esculin-hydrolysis
11826617632nitrate-reduction
11826616301nitrite-reduction
11826617632nitrate-respiration

metabolite production

  • @ref: 118266
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118266oxidase+
118266beta-galactosidase-3.2.1.23
118266alcohol dehydrogenase-1.1.1.1
118266gelatinase-
118266amylase-
118266DNase+
118266caseinase-3.4.21.50
118266catalase+1.11.1.6
118266tween esterase-
118266lecithinase-
118266lipase-
118266lysine decarboxylase-4.1.1.18
118266ornithine decarboxylase-4.1.1.17
118266protease-
118266tryptophan deaminase-
118266urease-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
118266-+++-++--+++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118266+-+-+----++---------++--------------------------------+-----+-++--++--------------------++++++--++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6541contaminated sedimentnear TaejonRepublic of KoreaKORAsia
67770Chemically contaminated freshwater sedimentTaejonRepublic of KoreaKORAsia
67771From sedimentRepublic of KoreaKORAsia
118266Environment, Chemically contaminated fresh water sedimentChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6010.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_32;97_33;98_4460;99_6010&stattab=map
  • Last taxonomy: Sphingobium chungbukense subclade
  • 16S sequence: AF159257
  • Sequence Identity:
  • Total samples: 722
  • soil counts: 198
  • aquatic counts: 373
  • animal counts: 43
  • plant counts: 108

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65411Risk group (German classification)
1182661Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6541
  • description: Sphingomonas chungbukensis strain DJ77 16S ribosomal RNA gene, complete sequence
  • accession: AF159257
  • length: 1502
  • database: ena
  • NCBI tax ID: 56193

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobium chungbukense DJ77GCA_001005725contigncbi56193
66792Sphingobium chungbukense DJ772636415887draftimg56193

GC content

@refGC-contentmethod
654163
6777063thermal denaturation, midpoint method (Tm)
6777163.0

External links

@ref: 6541

culture collection no.: DSM 16638, CIP 107741, IMSNU 11152, KCTC 2955, CCUG 52897, JCM 11454

straininfo link

  • @ref: 83346
  • straininfo: 100958

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10939671Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov.Kim SJ, Chun J, Bae KS, Kim YCInt J Syst Evol Microbiol10.1099/00207713-50-4-16412000Base Composition, Benzoquinones, DNA, Bacterial/chemistry/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Sphingomonas/chemistry/*classification/genetics, Stearic Acids/analysisGenetics
Phylogeny16166696Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.Pal R, Bala S, Dadhwal M, Kumar M, Dhingra G, Prakash O, Prabagaran SR, Shivaji S, Cullum J, Holliger C, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.63201-02005Bacterial Proteins/*genetics/metabolism, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/enzymology/genetics/physiology, Sphingomonas/*classification/enzymology/genetics/physiologyMetabolism
Phylogeny17673949Degradation of diphenyl phthalate by Sphingomonas chungbukensis.Kim DS, Um HJ, Lim ES, Min J, Kim YHBiotechnol Lett10.1007/s10529-007-9497-02007Biodegradation, Environmental, Industrial Waste/*prevention & control, Phthalic Acids/isolation & purification/*metabolism, Polycyclic Aromatic Hydrocarbons/isolation & purification/*metabolism, Sewage/*microbiology, Species Specificity, Sphingomonas/*classification/*metabolismMetabolism
Metabolism18795366Biodegradation of a phthalate plasticizer, di-isononyl phthalate (DINP), by Sphingobium chungbukense.Park JM, Jeon M, Lim ES, Um HJ, Kim YC, Min J, Kim YHCurr Microbiol10.1007/s00284-008-9232-72008Biodegradation, Environmental, Environmental Pollutants/chemistry/*metabolism, Phthalic Acids/chemistry/*metabolism, Plasticizers/chemistry/*metabolism, Sphingomonadaceae/*metabolism

Reference

@idauthorscataloguedoi/urltitle
6541Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16638)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16638
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
34204Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5210
59715Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52897)https://www.ccug.se/strain?id=52897
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
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
83346Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100958.1StrainInfo: A central database for resolving microbial strain identifiers
118266Curators of the CIPCollection of Institut Pasteur (CIP 107741)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107741