Strain identifier

BacDive ID: 11120

Type strain: Yes

Species: Nocardioides insulae

Strain Designation: DS-51

Strain history: CIP <- 2007, DSMZ <- J.H. Yoon, KRIBB, Taejon, Korea: strain DS-51

NCBI tax ID(s): 1122610 (strain), 394734 (species)

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General

@ref: 7280

BacDive-ID: 11120

DSM-Number: 17944

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

description: Nocardioides insulae DS-51 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
394734species
1122610strain

strain history

@refhistory
7280<- J.-H. Yoon; DS-51
67770KCTC 19180 <-- J.-H. Yoon DS-51.
67771<- JH Yoon, KRIBB
120139CIP <- 2007, DSMZ <- J.H. Yoon, KRIBB, Taejon, Korea: strain DS-51

doi: 10.13145/bacdive11120.20230509.8.1

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 insulae
  • full scientific name: Nocardioides insulae Yoon et al. 2007

@ref: 7280

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides insulae

full scientific name: Nocardioides insulae Yoon et al. 2007

strain designation: DS-51

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31895positive3.65 µm0.8 µmrod-shapedno
67771positive
69480no94.952
69480positive100
120139positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18409Lemon yellow (1012)10-14 daysISP 2
18409Beige (1001)10-14 daysISP 3
18409Beige (1001)10-14 daysISP 4
18409Beige (1001)10-14 daysISP 5
18409Lemon yellow (1012)10-14 daysISP 6
18409Lemon yellow (1012)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18409noISP 2
18409noISP 3
18409noISP 4
18409noISP 5
18409noISP 6
18409noISP 7

pigmentation

  • @ref: 31895
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7280TRYPTICASE 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
18409ISP 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
18409ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18409ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18409ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18409ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18409ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
33314MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120139CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7280positivegrowth28mesophilic
18409positiveoptimum28mesophilic
31895positivegrowth10-34
31895positiveoptimum30mesophilic
33314positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31895positivegrowth6.5-8
31895positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31895aerobe
67771aerobe
120139obligate aerobe

spore formation

  • @ref: 31895
  • spore formation: no

halophily

  • @ref: 31895
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0-3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3189530089acetate+carbon source
3189517057cellobiose+carbon source
3189528260galactose+carbon source
3189517234glucose+carbon source
3189529987glutamate+carbon source
3189525115malate+carbon source
3189517306maltose+carbon source
3189537684mannose+carbon source
3189515361pyruvate+carbon source
3189517814salicin+carbon source
3189527082trehalose+carbon source
3189518222xylose+carbon source
3189517632nitrate+reduction
12013917632nitrate+reduction
12013916301nitrite-reduction
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

metabolite production

  • @ref: 120139
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31895alkaline phosphatase+3.1.3.1
31895cytochrome oxidase+1.9.3.1
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
120139oxidase+
120139catalase+1.11.1.6
120139urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
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
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
18409-+++--+--++------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18409+++-+--+-++---+----
120139+++------++---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7280soilDokdoRepublic of KoreaKORAsia
67770Soil
67771From soilDokdoRepublic of KoreaKORAsia
120139Environment, SoilDokdo islandRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72801Risk group (German classification)
184091German classification
1201391Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7280
  • description: Nocardioides insulae strain DS-51 16S ribosomal RNA gene, partial sequence
  • accession: DQ786794
  • length: 1484
  • database: ena
  • NCBI tax ID: 394734

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides insulae DSM 179441122610.3wgspatric1122610
66792Nocardioides insulae DSM 179442524614651draftimg1122610
67770Nocardioides insulae DSM 17944GCA_000422825scaffoldncbi1122610

GC content

@refGC-contentmethod
728071.1
6777071.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno80no
motileno97.236yes
flagellatedno98.799no
gram-positiveyes94.233no
anaerobicno99.099no
aerobicyes94.991yes
halophileno77.304no
spore-formingno81.438yes
glucose-utilyes90.445yes
thermophileno98.465yes
glucose-fermentno94.061yes

External links

@ref: 7280

culture collection no.: DSM 17944, CIP 109626, KCTC 19180, JCM 15308

straininfo link

  • @ref: 80369
  • straininfo: 297274

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220455Nocardioides insulae sp. nov., isolated from soil.Yoon JH, Kang SJ, Lee CH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64612-02007Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny18676470Nocardioides fonticola sp. nov., a novel actinomycete isolated from spring water.Chou JH, Cho NT, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65810-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, TaiwanGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7280Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17944)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17944
18409Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17944.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
31895Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2815428776041
33314Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7390
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
68379Automatically annotated from API Coryne
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)
80369Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297274.1StrainInfo: A central database for resolving microbial strain identifiers
120139Curators of the CIPCollection of Institut Pasteur (CIP 109626)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109626