Strain identifier

BacDive ID: 10620

Type strain: Yes

Species: Jongsikchunia kroppenstedtii

Strain Designation: NP8-5

Strain history: CIP <- 2009, DSMZ <- K. K. Kim, KCTC, Korea: strain NP8-5

NCBI tax ID(s): 468556 (strain), 1121721 (species)

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General

@ref: 12380

BacDive-ID: 10620

DSM-Number: 45133

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

description: Jongsikchunia kroppenstedtii NP8-5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from polluted stream.

NCBI tax id

NCBI tax idMatching level
468556strain
1121721species

strain history

@refhistory
12380<- K. K. Kim; NP8-5
67770KCTC 19360 <-- K. K. Kim NP8-5.
67771<- KK Kim, KRIBB
120504CIP <- 2009, DSMZ <- K. K. Kim, KCTC, Korea: strain NP8-5

doi: 10.13145/bacdive10620.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Gordoniaceae
  • genus: Jongsikchunia
  • species: Jongsikchunia kroppenstedtii
  • full scientific name: Jongsikchunia kroppenstedtii (Kim et al. 2009) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Gordonia kroppenstedtii

@ref: 12380

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Jongsikchunia

species: Jongsikchunia kroppenstedtii

full scientific name: Jongsikchunia kroppenstedtii (Kim et al. 2009) Nouioui et al. 2018

strain designation: NP8-5

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29065positiverod-shapedno
67771positive
69480no97.802
69480positive100
120504positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20169Cream (9001)10-14 daysISP 2
20169Grey white (9002)10-14 daysISP 3
20169Grey white (9002)10-14 daysISP 4
20169Grey white (9002)10-14 daysISP 5
20169Light ivory (1015)10-14 daysISP 6
2016910-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20169noISP 2
20169noISP 3
20169noISP 4
20169noISP 5
20169noISP 6
20169noISP 7

multimedia

  • @ref: 12380
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45133.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12380TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20169ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20169ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20169ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20169ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20169ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20169ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37898MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120504CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
120504CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12380positivegrowth28mesophilic
20169positiveoptimum28mesophilic
29065positivegrowth10-30
29065positiveoptimum25-30mesophilic
37898positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
29065positivegrowth06-09alkaliphile
29065positiveoptimum06-07

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29065aerobe
67771aerobe
120504obligate aerobe

spore formation

@refspore formationconfidence
29065no
69480no99.971

halophily

@refsaltgrowthtested relationconcentration
29065NaClpositivegrowth1-6.5 %
29065NaClpositiveoptimum<10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2016917234glucose+
2016922599arabinose+/-
2016917992sucrose+/-
2016918222xylose+/-
2016917268myo-inositol+/-
2016929864mannitol+/-
2016928757fructose+/-
2016926546rhamnose+/-
2016916634raffinose-
2016962968cellulose-
2906516449alanine+carbon source
2906527689decanoate+carbon source
2906528260galactose+carbon source
2906525017leucine+carbon source
2906517268myo-inositol+carbon source
2906533942ribose+carbon source
2906517822serine+carbon source
2906530031succinate+carbon source
2906517992sucrose+carbon source
290654853esculin+hydrolysis
12050417632nitrate-reduction
12050416301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 120504
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29065catalase+1.11.1.6
29065urease+3.5.1.5
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
120504oxidase-
120504catalase+1.11.1.6
120504urease+3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20169---+--+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20169+++++----++-+-++---
120504-++-+----++-+-++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12380polluted streamGumiRepublic of KoreaKORAsia
67770Sediment of a polluted streamGumiRepublic of KoreaKORAsia
67771From sewageGwangam Stream, GumiRepublic of KoreaKORAsia
120504Environment, Stream, pollutedGumiRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic#River (Creek)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123801Risk group (German classification)
1205041Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12380
  • description: Gordonia sp. NP8-5 partial 16S rRNA gene, strain NP8-5
  • accession: AM883151
  • length: 1463
  • database: ena
  • NCBI tax ID: 468556

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia kroppenstedtii DSM 45133468556.3wgspatric468556
66792Jongsikchunia kroppenstedtii DSM 451332519899672draftimg468556
67770Jongsikchunia kroppenstedtii DSM 45133 NP8-5GCA_000380485contigncbi468556

GC content

@refGC-contentmethod
1238068.5high performance liquid chromatography (HPLC)
2906568.5
6777067.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
gram-positiveyes90.377no
anaerobicno99.609no
halophileno91.853no
spore-formingno86.633yes
glucose-utilyes88.599yes
aerobicyes94.531yes
flagellatedno98.368yes
thermophileno99.103yes
motileno96.349yes
glucose-fermentno91.465yes

External links

@ref: 12380

culture collection no.: DSM 45133, CIP 110031, KCTC 19360, JCM 16948

straininfo link

  • @ref: 79892
  • straininfo: 364135

literature

  • topic: Phylogeny
  • Pubmed-ID: 19567568
  • title: Gordonia kroppenstedtii sp. nov., a phenol-degrading actinomycete isolated from a polluted stream.
  • authors: Kim KK, Lee KC, Klenk HP, Oh HM, Lee JS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.005322-0
  • year: 2009
  • mesh: Actinobacteria/*classification/genetics/isolation & purification/*metabolism, Aerobiosis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Korea, Locomotion, Molecular Sequence Data, Phenol/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, *Water Pollution, Chemical
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12380Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45133)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45133
20169Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45133.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
29065Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2549528776041
37898Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7843
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
79892Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364135.1StrainInfo: A central database for resolving microbial strain identifiers
120504Curators of the CIPCollection of Institut Pasteur (CIP 110031)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110031