Strain identifier

BacDive ID: 11124

Type strain: Yes

Species: Nocardioides kongjuensis

Strain Designation: A2-4

Strain history: CIP <- 2006, JCM <- 2004, KRIBB

NCBI tax ID(s): 349522 (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: 7874

BacDive-ID: 11124

DSM-Number: 19082

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

description: Nocardioides kongjuensis A2-4 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 349522
  • Matching level: species

strain history

@refhistory
7874<- JCM <- J.-H. Yoon, A2-4
67770J.-H. Yoon A2-4.
67771<- JH Yoon, KRIBB
120460CIP <- 2006, JCM <- 2004, KRIBB

doi: 10.13145/bacdive11124.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides kongjuensis
  • full scientific name: Nocardioides kongjuensis Yoon et al. 2006

@ref: 7874

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides kongjuensis

full scientific name: Nocardioides kongjuensis Yoon et al. 2006

strain designation: A2-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31722positive0.8-3 µm0.4-0.7 µmovoid-shapedno
67771positive
69480positive100
120460positiverod-shapedno

pigmentation

  • @ref: 31722
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7874TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
36074Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
7874BACTO 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
120460CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120460CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7874positivegrowth28mesophilic
31722positivegrowth10-40
31722positiveoptimum30mesophilic
36074positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31722positivegrowth5.5-8
31722positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31722aerobe
67771aerobe
120460obligate aerobe

spore formation

@refspore formationconfidence
31722no
69480no99.587

halophily

  • @ref: 31722
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

@refobservation
31722aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3172225115malate+carbon source
3172237684mannose+carbon source
3172215361pyruvate+carbon source
3172227082trehalose+carbon source
12046017632nitrate-reduction
12046016301nitrite-reduction

metabolite production

  • @ref: 120460
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31722cytochrome oxidase+1.9.3.1
120460oxidase-
120460catalase+1.11.1.6
120460urease-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
120460-+-+-+--+-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7874soilKongjuRepublic of KoreaKORAsia
67770SoilKongjuRepublic of KoreaKORAsia
67771From SoilKongjuRepublic of KoreaKORAsia
120460Environment, SoilKongjuRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78741Risk group (German classification)
1204601Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7874
  • description: Nocardioides kongjuensis strain A2-4 16S ribosomal RNA gene, partial sequence
  • accession: DQ218275
  • length: 1475
  • database: ena
  • NCBI tax ID: 349522

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides kongjuensis strain DSM 19082349522.3wgspatric349522
66792Nocardioides kongjuensis DSM 190822844818640draftimg349522
67770Nocardioides kongjuensis DSM 19082GCA_013409625contigncbi349522

GC content

@refGC-contentmethod
787472.1
6777072.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno65no
gram-positiveyes87.352no
anaerobicno98.333yes
halophileno96.437no
spore-formingno80.608no
glucose-utilyes87.503no
motileno74.155yes
flagellatedno93.167yes
thermophileno98.879yes
aerobicyes91.626yes
glucose-fermentno89.732no

External links

@ref: 7874

culture collection no.: DSM 19082, CIP 109335, JCM 12609, KCTC 19054, BCRC 16836, KCTC 9995

straininfo link

  • @ref: 80373
  • straininfo: 232305

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902008Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium.Yoon JH, Lee JK, Jung SY, Kim JA, Kim HK, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64120-02006Actinobacteria/chemistry/*classification/genetics/isolation & purification, Base Composition, Fatty Acids/analysis, Korea, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, Vitamin K 2/analysisGenetics
Phylogeny19625430Nocardioides humi sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Kim MK, Srinivasan S, Park MJ, Sathiyaraj G, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.008821-02009Actinomycetales/classification/enzymology/genetics/*isolation & purification, Bacterial Proteins/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, *Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, beta-Glucosidase/*metabolismMetabolism
Phylogeny19628618Nocardioides caeni sp. nov., isolated from wastewater.Yoon JH, Kang SJ, Park S, Kim W, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.010124-02009Actinomycetales/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, *Water MicrobiologyMetabolism
Phylogeny19651712Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field.Cho CH, Lee JS, An DS, Whon TW, Kim SGInt J Syst Evol Microbiol10.1099/ijs.0.012690-02009Actinomycetales/*classification/genetics/physiology, Base Composition, Base Sequence, DNA, Bacterial/chemistry, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny20833879Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil.Lee DW, Lee SY, Yoon JH, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.022715-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Apiaceae/*microbiology, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, *Soil MicrobiologyMetabolism
Phylogeny26530636Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil.Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0007302015Actinomycetales/*classification/genetics/isolation & purification, Agriculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26802009Nocardioides flava sp. nov., isolated from rhizosphere of poppy plant, Republic of Korea.Singh H, Yin CSArch Microbiol10.1007/s00203-015-1178-02016Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/metabolism, Fatty Acids/chemistry, Papaver/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species SpecificityEnzymology
Phylogeny29683418Nocardioides pelophilus sp. nov., isolated from freshwater mud.Yan ZF, Lin P, Li CT, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0027762018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fresh Water, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31535960Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil.Liu SW, Xue CM, Li FN, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0037182020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35714383Nocardioides carbamazepini sp. nov., an ibuprofen degrader isolated from a biofilm bacterial community enriched on carbamazepine.Benedek T, Papai M, Gharieb K, Bedics A, Tancsics A, Toth E, Daood H, Maroti G, Wirth R, Menashe O, Boka K, Kriszt BSyst Appl Microbiol10.1016/j.syapm.2022.1263392022*Actinomycetales, Bacterial Typing Techniques, Base Composition, Biofilms, Carbamazepine, DNA, Bacterial/genetics, Fatty Acids/analysis, Ibuprofen, *Nocardioides, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7874Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19082)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19082
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
31722Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2799828776041
36074Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7065
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
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)
80373Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232305.1StrainInfo: A central database for resolving microbial strain identifiers
120460Curators of the CIPCollection of Institut Pasteur (CIP 109335)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109335