Strain identifier

BacDive ID: 11155

Type strain: Yes

Species: Nocardioides daejeonensis

Strain Designation: MJ31

Strain history: M. K. Kim MJ31.

NCBI tax ID(s): 1046556 (species)

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General

@ref: 17996

BacDive-ID: 11155

DSM-Number: 25320

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

description: Nocardioides daejeonensis MJ31 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sludge sample of a sewage disposal plant.

NCBI tax id

  • NCBI tax id: 1046556
  • Matching level: species

strain history

@refhistory
17996<- KCTC; KCTC 19772
67770M. K. Kim MJ31.

doi: 10.13145/bacdive11155.20230509.8.1

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 daejeonensis
  • full scientific name: Nocardioides daejeonensis Woo et al. 2012

@ref: 17996

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides daejeonensis

full scientific name: Nocardioides daejeonensis Woo et al. 2012

strain designation: MJ31

type strain: yes

Morphology

cell morphology

  • @ref: 30315
  • gram stain: positive
  • cell length: 0.8-2 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colormedium used
69321Beige (1001)ISP 2
69321Beige (1001)ISP 6
69321Beige (1001)suter with tyrosine
69321Ivory (1014)suter without tyrosine
69321Light ivory (1015)ISP 7
69321Oyster white (1013)ISP 3
69321Oyster white (1013)ISP 4
69321Oyster white (1013), ivory (1014)ISP 5

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69321noAerial myceliumISP 2
69321noAerial myceliumISP 3
69321noAerial myceliumISP 4
69321noAerial myceliumISP 5
69321noAerial myceliumISP 6
69321noAerial myceliumISP 7
69321noAerial myceliumsuter with tyrosine
69321noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
30315yes
69321noMelanin
69321nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69321DSM_25320_image5.jpeg(ISP6, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69321DSM_25320_image6.jpeg(ISP6, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17996R2A 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
17996TRYPTICASE 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
17996TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
17996positivegrowth28mesophilic
30315positivegrowth15-37
30315positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30315positivegrowth5.5-9alkaliphile
30315positiveoptimum7.5-8

Physiology and metabolism

oxygen tolerance

  • @ref: 30315
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30315NaClpositivegrowth0-10 %
30315NaClpositiveoptimum2 %
69321NaClpositivegrowth0-5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6932122599arabinose+growth
30315168082-dehydro-D-gluconate+carbon source
30315161933-hydroxybenzoate+carbon source
30315178794-hydroxybenzoate+carbon source
3031522599arabinose+carbon source
3031527689decanoate+carbon source
3031516947citrate+carbon source
3031524996lactate+carbon source
3031515792malonate+carbon source
3031517306maltose+carbon source
3031526546rhamnose+carbon source
3031517822serine+carbon source
303154853esculin+hydrolysis
3031517632nitrate+reduction
6932162968cellulose-growth
6932128757fructose+growth
6932117234glucose+growth
6932117268inositol+growth
6932137684mannose+growth
6932116634raffinose+growth
6932126546rhamnose+growth
6932117992sucrose+growth
6932118222xylose+growth
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

enzymes

@refvalueactivityec
30315acid phosphatase+3.1.3.2
30315alkaline phosphatase+3.1.3.1
30315catalase+1.11.1.6
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
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
69321+--+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69321++++/-+++/-+/--++-+/---+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17996sludge sample of a sewage disposal plantDaejeonRepublic of KoreaKORAsia
67770Sludge at the Daejeon sewage-disposal plantRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Water treatment plant
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_67823.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1270;97_36144;98_46741;99_67823&stattab=map
  • Last taxonomy: Nocardioides daejeonensis
  • 16S sequence: JF937066
  • Sequence Identity:
  • Total samples: 274
  • soil counts: 53
  • aquatic counts: 37
  • animal counts: 170
  • plant counts: 14

Safety information

risk assessment

  • @ref: 17996
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17996
  • description: Nocardioides daejeonensis strain MJ31 16S ribosomal RNA gene, partial sequence
  • accession: JF937066
  • length: 1468
  • database: ena
  • NCBI tax ID: 1046556

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides daejeonensis MJ312866264325draftimg1046556
67770Nocardioides daejeonensis MJ31GCA_003194585contigncbi1046556

GC content

@refGC-contentmethod
1799671.2high performance liquid chromatography (HPLC)
3031571.2

External links

@ref: 17996

culture collection no.: DSM 25320, JCM 16922, KCTC 19772

straininfo link

  • @ref: 80404
  • straininfo: 398561

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21742819Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.Woo SG, Srinivasan S, Yang J, Jung YA, Kim MK, Lee MInt J Syst Evol Microbiol10.1099/ijs.0.033308-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Denitrification, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analysisGenetics
Phylogeny25805631Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla).Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH, Shen FT, Lai WA, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.0002062015Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Seafood/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny25893957Nocardioides solisilvae sp. nov., isolated from a forest soil.Sultanpuram VR, Mothe T, Mohammed FAntonie Van Leeuwenhoek10.1007/s10482-015-0455-x2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Forests, India, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny27170166Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan.Amin A, Ahmed I, Habib N, Abbas S, Xiao M, Hozzein WN, Li WJAntonie Van Leeuwenhoek10.1007/s10482-016-0711-82016Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Aerobiosis, Bacterial Typing Techniques, Diaminopimelic Acid/analysis, Fatty Acids/metabolism, Hot Springs/*microbiology, Nucleic Acid Hybridization, Pakistan, Phenotype, Phospholipids/metabolism, Phylogeny, Sequence Analysis, DNA, Sodium Chloride/metabolism, Water MicrobiologyMetabolism
Phylogeny27411814Nocardioides gilvus sp. nov., isolated from Namtso Lake.Zhang HX, Wang K, Xu ZX, Chen GJ, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-016-0735-02016Actinomycetales/classification/*isolation & purification, Base Composition, DNA, Bacterial, Lakes/*microbiology, Molecular Typing, PhylogenyEnzymology
Phylogeny30362934Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces.Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Zhang G, Huang Y, Zhu W, Wu X, Liang H, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0030762018Actinomycetales/*classification/genetics/isolation & purification, Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sheep, TibetTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17996Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25320)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25320
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
30315Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2665628776041
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69321Wink, J.https://cdn.dsmz.de/wink/DSM%2025320.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
80404Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398561.1StrainInfo: A central database for resolving microbial strain identifiers