Strain identifier

BacDive ID: 17093

Type strain: Yes

Species: Tsukamurella spumae

Strain Designation: N1171, N 1171

Strain history: CIP <- 2003, NCIMB <- M. Goodfellow, Newcastle Univ., Newcastle upon Tyne, UK: strain N 1171

NCBI tax ID(s): 44753 (species)

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General

@ref: 11408

BacDive-ID: 17093

DSM-Number: 44113

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, human pathogen

description: Tsukamurella spumae N1171 is an aerobe, mesophilic human pathogen that was isolated from foam on the surface of aeration tanks in an activated-sludge sewage-treatment plant.

NCBI tax id

  • NCBI tax id: 44753
  • Matching level: species

strain history

@refhistory
11408<- M. Goodfellow, N 1171
67770NCIMB 13947 <-- M. Goodfellow N1171.
123275CIP <- 2003, NCIMB <- M. Goodfellow, Newcastle Univ., Newcastle upon Tyne, UK: strain N 1171

doi: 10.13145/bacdive17093.20230509.8.1

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 spumae
  • full scientific name: Tsukamurella spumae Nam et al. 2003

@ref: 11408

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Tsukamurellaceae

genus: Tsukamurella

species: Tsukamurella spumae

full scientific name: Tsukamurella spumae Nam et al. 2003

strain designation: N1171, N 1171

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.998
69480100positive
123275nopositiverod-shaped

colony morphology

@refincubation period
583143 days
123275

multimedia

@refmultimedia contentintellectual property rightscaption
11408https://www.dsmz.de/microorganisms/photos/DSM_44113-1.jpg© Leibniz-Institut DSMZ
11408https://www.dsmz.de/microorganisms/photos/DSM_44113-2.jpg© Leibniz-Institut DSMZ
11408https://www.dsmz.de/microorganisms/photos/DSM_44113.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11408GYM 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
32903MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
123275CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11408positivegrowth28mesophilic
32903positivegrowth30mesophilic
58314positivegrowth30mesophilic
67770positivegrowth28mesophilic
123275positivegrowth15-37
123275nogrowth10psychrophilic
123275nogrowth41thermophilic
123275nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58314aerobe
123275obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.993

halophily

@refsaltgrowthtested relationconcentration
123275NaClpositivegrowth0-2 %
123275NaClnogrowth4 %
123275NaClnogrowth6 %
123275NaClnogrowth8 %
123275NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12327516947citrate-carbon source
1232754853esculin-hydrolysis
123275606565hippurate-hydrolysis
12327517632nitrate-reduction
12327516301nitrite-reduction
12327517632nitrate-respiration

antibiotic resistance

  • @ref: 123275
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123275
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12327515688acetoin-
12327517234glucose-

enzymes

@refvalueactivityec
123275oxidase-
123275beta-galactosidase-3.2.1.23
123275alcohol dehydrogenase-1.1.1.1
123275gelatinase-
123275amylase-
123275DNase-
123275caseinase-3.4.21.50
123275catalase+1.11.1.6
123275tween esterase-
123275gamma-glutamyltransferase+2.3.2.2
123275lecithinase-
123275lipase-
123275lysine decarboxylase-4.1.1.18
123275ornithine decarboxylase-4.1.1.17
123275phenylalanine ammonia-lyase-4.3.1.24
123275protease-
123275tryptophan deaminase-
123275urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
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
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123275-+++++----++---+--+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123275++++---+--+-----------+--++-----+++++----+-------+---------+-+++-+----+-++-+---++-----+-+++++++-+--

Isolation, sampling and environmental information

isolation

@refsample typecontinentgeographic locationcountryorigin.country
11408foam on the surface of aeration tanks in an activated-sludge sewage-treatment plantEurope
58314Sludge,foam on the surface of aeration tanksEuropeEnglandUnited KingdomGBR
67770Activated sludge foamEuropenear NottinghamUnited KingdomGBR
123275Environment, Foam on the surface of aeration tanks, activated-sludgeEuropeUnited KingdomGBR

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Container (Reservoir)
#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: Z37150
  • Sequence Identity:
  • Total samples: 12359
  • soil counts: 3431
  • aquatic counts: 2978
  • animal counts: 5160
  • plant counts: 790

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11408yes, in single cases1Risk group (German classification)
1232751Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Tsukamurella spumae strain DSM 44113 16S ribosomal RNA gene, partial sequenceKF4103671366ena44753
11408T.spumae gene for 16S ribosomal RNAZ371501474ena44753

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tsukamurella spumae strain DSM 4411344753.4wgspatric44753
67770Tsukamurella spumae DSM 44113GCA_012396015contigncbi44753

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno71no
gram-positiveyes89.87no
anaerobicno99.646no
halophileno95.213no
spore-formingno81.889no
glucose-utilyes91.766no
aerobicyes90.551yes
flagellatedno97.599no
thermophileno99.289yes
motileno93.305no
glucose-fermentno87.225no

External links

@ref: 11408

culture collection no.: DSM 44113, NCIMB 13947, CCUG 48751, JCM 12608, CIP 108213, IFM 10523

straininfo link

  • @ref: 86093
  • straininfo: 50493

literature

  • topic: Phylogeny
  • Pubmed-ID: 14529179
  • title: Tsukamurella spumae sp. nov., a novel actinomycete associated with foaming in activated sludge plants.
  • authors: Nam SW, Chun J, Kim S, Kim W, Zakrzewska-Czerwinska J, Goodfellow M
  • journal: Syst Appl Microbiol
  • DOI: 10.1078/072320203322497392
  • year: 2003
  • mesh: Actinomycetales/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Base Sequence, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/chemistry/genetics, Ribotyping, Sewage/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11408Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44113)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44113
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32903Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5811
58314Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48751)https://www.ccug.se/strain?id=48751
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/
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)
86093Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50493.1StrainInfo: A central database for resolving microbial strain identifiers
123275Curators of the CIPCollection of Institut Pasteur (CIP 108213)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108213