Strain identifier

BacDive ID: 11145

Type strain: Yes

Species: Nocardioides caeni

Strain Designation: MN8

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 574700 (species)

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General

@ref: 16724

BacDive-ID: 11145

DSM-Number: 23134

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

description: Nocardioides caeni MN8 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sludge of domestic wastewater.

NCBI tax id

  • NCBI tax id: 574700
  • Matching level: species

strain history

@refhistory
16724<- KCTC <- J. H. Yoon, KRIBB
67770CCUG 57506 <-- J.-H. Yoon MN8.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive11145.20250331.9.3

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 caeni
  • full scientific name: Nocardioides caeni Yoon et al. 2009

@ref: 16724

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides caeni

full scientific name: Nocardioides caeni Yoon et al. 2009

strain designation: MN8

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29281positive1.6 µm0.5 µmrod-shapedno
67771positive
125439positive99.6

colony morphology

@refcolony colorincubation periodmedium used
19803Sand yellow10-14 daysISP 2
613527 days

multicellular morphology

  • @ref: 19803
  • forms multicellular complex: no
  • medium name: ISP 2

pigmentation

  • @ref: 29281
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16724R2A 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
19803ISP 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
16724TRYPTICASE 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

@refgrowthtypetemperature
16724positivegrowth28
19803positiveoptimum28
29281positivegrowth10-35
29281positiveoptimum30
61352positivegrowth30
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepHPH range
29281positivegrowth6-9.5alkaliphile
29281positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29281aerobe
61352aerobe
67771aerobe
125439obligate aerobe98.9

spore formation

  • @ref: 29281
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29281NaClpositivegrowth0-1 %
29281NaClpositiveoptimum0.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2928122599arabinose+carbon source
2928117057cellobiose+carbon source
2928126546rhamnose+carbon source
2928153424tween 20+carbon source
2928153423tween 40+carbon source
2928153425tween 60+carbon source
2928153426tween 80+carbon source
292814853esculin+hydrolysis
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin-hydrolysis
6837917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2928116136hydrogen sulfideyes
2928135581indoleyes

metabolite tests

  • @ref: 29281
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29281cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
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
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alkaline phosphatase+3.1.3.1
68382alpha-mannosidase-3.2.1.24
68382trypsin-3.4.21.4
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19803--++--+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19803+++++++--++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16724sludge of domestic wastewaterDaejeonRepublic of KoreaKORAsia
61352Sludge of a domestic wastewaterTaejonRepublic of KoreaKORAsia2006-01-01
67770Sludge of domestic wastewaterRepublic of KoreaKORAsia
67771From wastewaterDaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Wastewater
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_88256.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_452;97_518;98_2479;99_88256&stattab=map
  • Last taxonomy: Nocardioides caeni
  • 16S sequence: FJ423551
  • Sequence Identity:
  • Total samples: 24
  • soil counts: 14
  • aquatic counts: 3
  • animal counts: 7

Safety information

risk assessment

  • @ref: 16724
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16724
  • description: Nocardioides sp. MN8 16S ribosomal RNA gene, partial sequence
  • accession: FJ423551
  • length: 1474
  • database: nuccore
  • NCBI tax ID: 574700

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides caeni strain DSM 23134574700.3wgspatric574700
67770Nocardioides caeni DSM 23134GCA_004912195scaffoldncbi574700

GC content

@refGC-contentmethod
1672471.5high performance liquid chromatography (HPLC)
2928171.5

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes87.092yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.472yes
125438spore-formingspore-formingAbility to form endo- or exosporesno60.439yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.589yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.107no
125438motile2+flagellatedAbility to perform flagellated movementno62no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno66.8
125439BacteriaNetmotilityAbility to perform movementno67.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.9

External links

@ref: 16724

culture collection no.: DSM 23134, CCUG 57506, KCTC 19600, JCM 19119

straininfo link

  • @ref: 80394
  • straininfo: 397370

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16724Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23134)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23134
19803Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM23134.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
29281Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2569728776041
61352Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57506)https://www.ccug.se/strain?id=57506
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
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
80394Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397370.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1