Strain identifier

BacDive ID: 7480

Type strain: Yes

Species: Pseudoclavibacter chungangensis

Strain history: <- CCUG <- W. Kim, Chung-Ang Univ., Seoul, Republic of Korea

NCBI tax ID(s): 587635 (species)

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

@ref: 17389

BacDive-ID: 7480

DSM-Number: 23821

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

description: Pseudoclavibacter chungangensis DSM 23821 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from wastewater,activated sludge.

NCBI tax id

  • NCBI tax id: 587635
  • Matching level: species

strain history

  • @ref: 17389
  • history: <- CCUG <- W. Kim, Chung-Ang Univ., Seoul, Republic of Korea

doi: 10.13145/bacdive7480.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Pseudoclavibacter
  • species: Pseudoclavibacter chungangensis
  • full scientific name: Pseudoclavibacter chungangensis Cho et al. 2010

@ref: 17389

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Pseudoclavibacter

species: Pseudoclavibacter chungangensis

full scientific name: Pseudoclavibacter chungangensis Cho et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29545positive1.3-1.7 µm0.1-0.2 µmrod-shapedno
69480no92.748
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21373Corn yellow (1006)10-14 daysISP 2
616082 days

multicellular morphology

@refforms multicellular complexmedium name
21373noISP 2
21373noISP 4
21373noISP 5

pigmentation

  • @ref: 29545
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17389R2A 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
21373ISP 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

culture temp

@refgrowthtypetemperaturerange
17389positivegrowth28mesophilic
29545positivegrowth04-50
29545positiveoptimum30mesophilic
61608positivegrowth30-37mesophilic

culture pH

@refabilitytypepHPH range
29545positivegrowth03-11alkaliphile
29545positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29545aerobe
61608aerobe

spore formation

@refspore formationconfidence
29545no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
21373NaClpositivemaximum5 %
29545NaClpositivegrowth0-15 %
29545NaClpositiveoptimum5 %

observation

  • @ref: 29545
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2137317234glucose-
2137322599arabinose-
2137317992sucrose-
2137318222xylose+
2137317268myo-inositol+
2137337684mannose-
2137328757fructose-
2137326546rhamnose-
2137316634raffinose-
2137362968cellulose+
2954528757fructose+carbon source
2954517754glycerol+carbon source
2954529864mannitol+carbon source
2954516634raffinose+carbon source
2954517992sucrose+carbon source
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29545catalase+1.11.1.6
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
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

API coryne

@refNITPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACGLYG
21373-----------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21373+/-+/-+/--++++/-+/----------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
17389wastewater,activated sludgeCheonanRepublic of KoreaKORAsia
61608Wastewater,activated sludgeCheonanRepublic of KoreaKORAsia2005-07-13

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_141538.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_459;97_27937;98_94053;99_141538&stattab=map
  • Last taxonomy: Pseudoclavibacter chungangensis subclade
  • 16S sequence: FJ514934
  • Sequence Identity:
  • Total samples: 480
  • soil counts: 111
  • aquatic counts: 108
  • animal counts: 190
  • plant counts: 71

Safety information

risk assessment

  • @ref: 17389
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17389
  • description: Pseudoclavibacter chungangensis strain CAU 59 16S ribosomal RNA gene, partial sequence
  • accession: FJ514934
  • length: 1424
  • database: ena
  • NCBI tax ID: 587635

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoclavibacter chungangensis DSM 23821GCA_013410545contigncbi587635
66792Pseudoclavibacter chungangensis DSM 23821GCA_008831135scaffoldncbi587635
66792Pseudoclavibacter chungangensis strain DSM 23821587635.3wgspatric587635
66792Pseudoclavibacter chungangensis strain DSM 23821587635.4wgspatric587635
66792Pseudoclavibacter chungangensis DSM 238212857404025draftimg587635

GC content

  • @ref: 17389
  • GC-content: 66.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.725yes
flagellatedno97.231yes
gram-positiveyes90.911yes
anaerobicno99.468yes
aerobicyes93.808yes
halophileno86.211no
spore-formingno91.796yes
thermophileno99.53yes
glucose-utilyes77.231yes
glucose-fermentno87.802yes

External links

@ref: 17389

culture collection no.: DSM 23821, CCUG 58142, KCTC 22691, CAU 59

straininfo link

  • @ref: 76925
  • straininfo: 406880

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19734288Pseudoclavibacter chungangensis sp. nov., isolated from activated sludge.Cho SL, Jung MY, Park MH, Chang YH, Yoon JH, Myung SC, Kim WInt J Syst Evol Microbiol10.1099/ijs.0.015552-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Base Composition, Base Sequence, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiologyGenetics
Phylogeny26311346Pseudoclavibacter terrae sp. nov. isolated from rhizosphere soil of Ophiopogon japonicus.Du J, Singh H, Yang JE, Shik Yin C, Kook M, Yu H, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0005602015Actinomycetales/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Ophiopogon/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny26739161Pseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis.Li YQ, Li L, Fu YS, Cui ZQ, Duan YQ, Salam N, Guo JW, Chen W, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0008762016

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17389Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23821)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23821
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
21373Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM23821.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29545Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2594128776041
61608Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58142)https://www.ccug.se/strain?id=58142
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)
68379Automatically annotated from API Coryne
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
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
76925Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406880.1StrainInfo: A central database for resolving microbial strain identifiers