Strain identifier

BacDive ID: 11151

Type strain: Yes

Species: Nocardioides hungaricus

Strain Designation: 1RaM5-12, RaM5-12

Strain history: DSM 21673 <-- E. M. Tóth RaM5-12 (=1RaM5-12).

NCBI tax ID(s): 520089 (species)

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General

@ref: 15878

BacDive-ID: 11151

DSM-Number: 21673

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

description: Nocardioides hungaricus 1RaM5-12 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from drinking water network.

NCBI tax id

  • NCBI tax id: 520089
  • Matching level: species

strain history

@refhistory
15878<- E. M. Tóth, Eötvös Loránd Univ. Budapest, Hungary; RaM5-12 <- J. Makk
67770DSM 21673 <-- E. M. Tóth RaM5-12 (=1RaM5-12).

doi: 10.13145/bacdive11151.20230509.8.1

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 hungaricus
  • full scientific name: Nocardioides hungaricus Tóth et al. 2011

@ref: 15878

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides hungaricus

full scientific name: Nocardioides hungaricus Tóth et al. 2011

strain designation: 1RaM5-12, RaM5-12

type strain: yes

Morphology

cell morphology

  • @ref: 29860
  • gram stain: positive
  • cell length: 1.25 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
21355Sand yellow (1002)10-14 daysISP 2
21355Light ivory (1015)10-14 daysISP 3
2135510-14 daysISP 4
2135510-14 daysISP 5
2135510-14 daysISP 7
2135510-14 dayssuter with tyrosine
2135510-14 dayssuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21355noISP 2
21355noISP 3
21355noISP 4
21355noISP 5
21355noISP 7
21355noSuter with tyrosine
21355noSuter without tyrosine

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15878R2A 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
15878TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
21355ISP 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
21355ISP 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:
21355ISP 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
21355ISP 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
21355ISP 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
21355suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21355suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
15878positivegrowth28mesophilic
29860positivegrowth20-37
29860positiveoptimum24psychrophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29860positivegrowth05-09alkaliphile
29860positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29860
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29860
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
21355NaClpositivegrowth0 %
29860NaClpositivegrowth0-2.5 %

murein

  • @ref: 15878
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2135517234glucose-
2135522599arabinose-
2135517992sucrose-
2135518222xylose-
2135517268myo-inositol-
2135537684mannose-
2135528757fructose-
2135526546rhamnose-
2135516634raffinose-
2135562968cellulose+
2986053426tween 80+carbon source
298604853esculin+hydrolysis
2986017632nitrate+reduction
6837917632nitrate-reduction
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
29860acid phosphatase+3.1.3.2
29860alkaline phosphatase+3.1.3.1
29860catalase+1.11.1.6
29860gelatinase+
68379gelatinase-
68379urease-3.5.1.5
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21355--++--+-+/-----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21355++++/-++/----++-+-++--+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15878drinking water networkBudapestHungaryHUNEurope
67770Drinking water supply system of BudapestHungaryHUNEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_151092.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_57325;97_74139;98_99810;99_151092&stattab=map
  • Last taxonomy: Nocardioides hungaricus subclade
  • 16S sequence: AM981198
  • Sequence Identity:
  • Total samples: 876
  • soil counts: 560
  • aquatic counts: 85
  • animal counts: 121
  • plant counts: 110

Safety information

risk assessment

  • @ref: 15878
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15878
  • description: Nocardioides hungaricus partial 16S rRNA gene, type strain 1RaM5-12T
  • accession: AM981198
  • length: 1462
  • database: ena
  • NCBI tax ID: 520089

GC content

@refGC-contentmethod
1587871.4high performance liquid chromatography (HPLC)
2986071.4

External links

@ref: 15878

culture collection no.: DSM 21673, JCM 19558, NCAIM 02330, NCAIM B.02330

straininfo link

  • @ref: 80400
  • straininfo: 396761

literature

  • topic: Phylogeny
  • Pubmed-ID: 20382790
  • title: Nocardioides hungaricus sp. nov., isolated from a drinking water supply system.
  • authors: Toth EM, Keki Z, Makk J, Homonnay ZG, Marialigeti K, Schumann P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022939-0
  • year: 2010
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid, Fatty Acids, Hungary, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2, *Water Microbiology, Water Supply
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15878Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21673)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21673
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
21355Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21673.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29860Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2623428776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
80400Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396761.1StrainInfo: A central database for resolving microbial strain identifiers