Strain identifier

BacDive ID: 133929

Type strain: Yes

Species: Nocardioides daeguensis

Strain Designation: 2C1-5

Strain history: <- MJ Lee, H-Plus Eco, Korea

NCBI tax ID(s): 908359 (species)

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General

@ref: 30899

BacDive-ID: 133929

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

description: Nocardioides daeguensis 2C1-5 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from wastewater.

NCBI tax id

  • NCBI tax id: 908359
  • Matching level: species

strain history

@refhistory
67770S.-T. Lee 2C1-5.
67771<- MJ Lee, H-Plus Eco, Korea

doi: 10.13145/bacdive133929.20230509.8.1

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 daeguensis
  • full scientific name: Nocardioides daeguensis Cui et al. 2013

@ref: 30899

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides daeguensis

strain designation: 2C1-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30899positive0.95 µm0.6 µmrod-shapedno
67771rod-shaped
67771positive

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30899positivegrowth25-42
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
30899positivegrowth5.5-8.0
30899positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30899aerobe
67771aerobe

spore formation

  • @ref: 30899
  • spore formation: no

halophily

  • @ref: 30899
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

@refobservation
67770quinones: MK-8(H4)
67771quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30899370543-hydroxybutyrate+carbon source
3089930089acetate+carbon source
3089924265gluconate+carbon source
3089917234glucose+carbon source
3089928087glycogen+carbon source
3089925115malate+carbon source
30899506227N-acetylglucosamine+carbon source
3089918401phenylacetate+carbon source
3089926271proline+carbon source
3089917272propionate+carbon source
3089917992sucrose+carbon source
3089931011valerate+carbon source
3089917632nitrate+reduction

enzymes

  • @ref: 30899
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
30899wastewater
67770Activated sludge of an industrial wastewater treatmentDaeguRepublic of KoreaKORAsia
67771Republic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_74145.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_452;97_518;98_2479;99_74145&stattab=map
  • Last taxonomy: Nocardioides daeguensis
  • 16S sequence: HQ246164
  • Sequence Identity:
  • Total samples: 475
  • soil counts: 363
  • aquatic counts: 41
  • animal counts: 30
  • plant counts: 41

Sequence information

16S sequences

  • @ref: 30899
  • description: Nocardioides daeguensis strain 2C1-5 16S ribosomal RNA gene, partial sequence
  • accession: HQ246164
  • length: 1383
  • database: nuccore
  • NCBI tax ID: 908359

Genome sequences

  • @ref: 66792
  • description: Nocardioides daeguensis 2C1-5
  • accession: GCA_019192965
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 908359

GC content

@refGC-contentmethod
3089974.9
6777074.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno95.625yes
gram-positiveyes91.753no
anaerobicno98.581yes
aerobicyes90.55yes
halophileno97.846no
spore-formingno79.059no
motileno80.95yes
thermophileno97.464no
glucose-utilyes83.747no
glucose-fermentno89.315no

External links

@ref: 30899

culture collection no.: JCM 17460, KCTC 19799

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23645020Nocardioides daeguensis sp. nov., a nitrate-reducing bacterium isolated from activated sludge of an industrial wastewater treatment plant.Cui Y, Woo SG, Lee J, Sinha S, Kang MS, Jin L, Kim KK, Park J, Lee M, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.047043-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/analysis, Waste Water/microbiologyGenetics
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
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

@idauthorstitledoi/urlID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
30899Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172722928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/