Strain identifier

BacDive ID: 17106

Type strain: Yes

Species: Tsukamurella pseudospumae

Strain Designation: N1176

Strain history: IFM 10600 <-- DSM 44118 <-- M. Goodfellow N1176.

NCBI tax ID(s): 239498 (species)

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General

@ref: 11413

BacDive-ID: 17106

DSM-Number: 44118

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

description: Tsukamurella pseudospumae N1176 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from foam on the surface of aeration tanks in an activated-sludge-treatment plant.

NCBI tax id

  • NCBI tax id: 239498
  • Matching level: species

strain history

@refhistory
11413<- M. Goodfellow, N 1176
67770IFM 10600 <-- DSM 44118 <-- M. Goodfellow N1176.

doi: 10.13145/bacdive17106.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Tsukamurellaceae
  • genus: Tsukamurella
  • species: Tsukamurella pseudospumae
  • full scientific name: Tsukamurella pseudospumae Nam et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Tsukamurella sunchonensis

@ref: 11413

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Tsukamurellaceae

genus: Tsukamurella

species: Tsukamurella pseudospumae

full scientific name: Tsukamurella pseudospumae Nam et al. 2004 emend. Teng et al. 2016

strain designation: N1176

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30099positiverod-shapedno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19629Red orange10-14 daysISP 2
19629Yellow orange10-14 daysISP 3
19629Yellow orange10-14 daysISP 4
19629Yellow orange10-14 daysISP 5
19629Yellow orange10-14 daysISP 6
19629Yellow orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19629noISP 2
19629noISP 3
19629noISP 4
19629noISP 5
19629noISP 6
19629noISP 7

pigmentation

  • @ref: 30099
  • production: yes

multimedia

  • @ref: 11413
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44118.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11413TRYPTICASE 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
11413BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
11413GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19629ISP 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
19629ISP 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:
19629ISP 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
19629ISP 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
19629ISP 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
19629ISP 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

culture temp

@refgrowthtypetemperaturerange
11413positivegrowth28mesophilic
19629positiveoptimum28mesophilic
30099positivegrowth10-37
30099positiveoptimum23.5psychrophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30099
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30099no
69481no91
69480no99.926

observation

  • @ref: 67770
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1962917234glucose+
1962922599arabinose-
1962917992sucrose+
1962918222xylose-
1962917268myo-inositol-
1962929864mannitol-
1962928757fructose+
1962926546rhamnose-
1962916634raffinose-
1962962968cellulose-
3009922599arabinose+carbon source
3009918403L-arabitol+carbon source
3009922653asparagine+carbon source
3009917057cellobiose+carbon source
3009916947citrate+carbon source
3009928757fructose+carbon source
3009928260galactose+carbon source
3009917234glucose+carbon source
3009917306maltose+carbon source
3009937684mannose+carbon source
3009950048phenylethylamine+carbon source
3009915361pyruvate+carbon source
3009926546rhamnose+carbon source
3009933942ribose+carbon source
3009917822serine+carbon source
3009917992sucrose+carbon source
3009927082trehalose+carbon source
3009953426tween 80+carbon source
300994853esculin+hydrolysis
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
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
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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-fucosidase-3.2.1.51

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSACNITControlGLURIBXYLMANMALLACGLYG
19629+-+--+-++--
11413--+--+-++--+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19629+++-+++--+----++-+-
11413++/-+/--+----+----++----

Isolation, sampling and environmental information

isolation

@refsample typecontinentcountryorigin.country
11413foam on the surface of aeration tanks in an activated-sludge-treatment plantEurope
67770Activated sludge foam from Stoke Bardolph Water Reclamation Works near NottinghamEuropeUnited KingdomGBR

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Water treatment plant
#Environmental#Aquatic#Foam

taxonmaps

  • @ref: 69479
  • File name: preview.99_3845.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1974;97_2373;98_2929;99_3845&stattab=map
  • Last taxonomy: Tsukamurella
  • 16S sequence: AY238513
  • Sequence Identity:
  • Total samples: 12359
  • soil counts: 3431
  • aquatic counts: 2978
  • animal counts: 5160
  • plant counts: 790

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114131Risk group (German classification)
196291Risk group (German classification)

Sequence information

16S sequences

  • @ref: 11413
  • description: Tsukamurella pseudospumae strain N1176 16S ribosomal RNA gene, complete sequence
  • accession: AY238513
  • length: 1510
  • database: ena
  • NCBI tax ID: 239498

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tsukamurella sunchonensis strain JCM 13375105579.6wgspatric239498
66792Tsukamurella sunchonensis JCM 133752667527863draftimg239498
67770Tsukamurella pseudospumae JCM 13375GCA_001575205contigncbi239498

GC content

@refGC-contentmethod
1141370.5sequence analysis
6777070.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
motileno92.783yes
flagellatedno97.372yes
gram-positiveyes90.366no
anaerobicno99.55yes
aerobicyes91.694no
halophileno94.277no
spore-formingno79.527yes
thermophileno99.553yes
glucose-utilyes91.378yes
glucose-fermentno89.847yes

External links

@ref: 11413

culture collection no.: DSM 44118, CIP 108828, JCM 13375, NCIMB 13963, NRRL B-24668, IFM 10600

straininfo link

  • @ref: 86107
  • straininfo: 50498

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280293Tsukamurella pseudospumae sp. nov., a novel actinomycete isolated from activated sludge foam.Nam SW, Kim W, Chun J, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.02939-02004Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Sewage/*microbiologyEnzymology
Phylogeny26530900Tsukamurella hongkongensis sp. nov. and Tsukamurella sinensis sp. nov., isolated from patients with keratitis, catheter-related bacteraemia and conjunctivitis.Teng JLL, Tang Y, Wong SSY, Ngan AHY, Huang Y, Tsang CC, Choi GKY, Lau SKP, Woo PCYInt J Syst Evol Microbiol10.1099/ijsem.0.0007332015Actinomycetales/*classification/genetics/isolation & purification, Adult, Bacteremia/*microbiology, Bacterial Typing Techniques, Base Composition, Catheters, Indwelling/microbiology, Conjunctiva/microbiology, Conjunctivitis/*microbiology, Cornea/microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hong Kong, Humans, Keratitis/*microbiology, Male, Middle Aged, Molecular Sequence Data, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
11413Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44118)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44118
19629Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44118.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
30099Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2645528776041
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
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86107Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50498.1StrainInfo: A central database for resolving microbial strain identifiers