Strain identifier

BacDive ID: 17101

Type strain: Yes

Species: Tsukamurella tyrosinosolvens

Strain history: CIP <- 2000, DSMZ <- A.F. Yassin: strain IMMIB D-1397

NCBI tax ID(s): 57704 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11496

BacDive-ID: 17101

DSM-Number: 44234

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

description: Tsukamurella tyrosinosolvens DSM 44234 is an aerobe, mesophilic bacterium that was isolated from clinical material; blood culture of a patient with cardiac pacemaker implants.

NCBI tax id

  • NCBI tax id: 57704
  • Matching level: species

strain history

@refhistory
11496<- A. F. Yassin, IMMIB D-1397
67770DSM 44234 <-- A. F. Yassin IMMIB D-1397.
123704CIP <- 2000, DSMZ <- A.F. Yassin: strain IMMIB D-1397

doi: 10.13145/bacdive17101.20230509.8.1

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 tyrosinosolvens
  • full scientific name: Tsukamurella tyrosinosolvens Yassin et al. 1997
  • synonyms

    • @ref: 20215
    • synonym: Tsukamurella carboxydivorans

@ref: 11496

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Tsukamurellaceae

genus: Tsukamurella

species: Tsukamurella tyrosinosolvens

full scientific name: Tsukamurella tyrosinosolvens Yassin et al. 1997 emend. Teng et al. 2016

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.183
69480100positive
123704nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
20028Sand yellow (1002)10-14 daysISP 2
20028Beige (1001)10-14 daysISP 3
2002810-14 daysISP 4
20028Beige (1001)10-14 daysISP 5
20028Sand yellow (1002)10-14 daysISP 6
20028Beige (1001)10-14 daysISP 7
1237041

multicellular morphology

@refforms multicellular complexmedium name
20028noISP 2
20028noISP 3
20028noISP 4
20028noISP 5
20028noISP 6
20028noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11496TRYPTICASE 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
20028ISP 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
20028ISP 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:
20028ISP 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
20028ISP 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
20028ISP 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
20028ISP 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
42109MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123704CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11496positivegrowth28mesophilic
20028positiveoptimum28mesophilic
42109positivegrowth30mesophilic
54294positivegrowth30-37mesophilic
67770positivegrowth28mesophilic
123704positivegrowth15-37
123704nogrowth10psychrophilic
123704nogrowth41thermophilic
123704nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54294aerobe
123704obligate aerobe

spore formation

@refspore formationconfidence
69481no91
69480no99.964

halophily

@refsaltgrowthtested relationconcentration
20028NaClpositivemaximum7.5 %
123704NaClpositivegrowth0-8 %
123704NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-8, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2002817234glucose+
2002822599arabinose-
2002817992sucrose+
2002818222xylose-
2002817268myo-inositol+
2002829864mannitol+
2002828757fructose+
2002826546rhamnose-
2002816634raffinose-
2002862968cellulose-
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12370416947citrate-carbon source
1237044853esculin+hydrolysis
123704606565hippurate-hydrolysis
12370417632nitrate-reduction
12370416301nitrite-reduction
12370417632nitrate-respiration
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

antibiotic resistance

  • @ref: 123704
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12370435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12370415688acetoin-
12370417234glucose-

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
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
123704oxidase-
123704beta-galactosidase+3.2.1.23
123704alcohol dehydrogenase-1.1.1.1
123704gelatinase-
123704amylase-
123704DNase-
123704caseinase-3.4.21.50
123704catalase+1.11.1.6
123704tween esterase+
123704gamma-glutamyltransferase+2.3.2.2
123704lecithinase-
123704lipase-
123704lysine decarboxylase-4.1.1.18
123704ornithine decarboxylase-4.1.1.17
123704phenylalanine ammonia-lyase-4.3.1.24
123704tryptophan deaminase-
123704urease-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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20028--++-++-++---------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123704-+++++----++---++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
20028-++++-+-------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123704+++++--+--+-----------+-+++-----+++++----+-------++--+--+--+++-----+----+--+-+-++---+-+-+++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11496clinical material; blood culture of a patient with cardiac pacemaker implantsBochumGermanyDEUEurope
54294Human blood
67770Blood culture from a 62-year-old woman who had cardiac pacemaker implants
123704Human, Blood

isolation source categories

Cat1Cat2Cat3
#Infection#Medical environment#Clinic
#Infection#Patient#Blood culture

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: Y12246
  • 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
114962Risk group (German classification)
200282German classification
1237041Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Tsukamurella tyrosinosolvens strain DSM 44234 16S ribosomal RNA, complete sequenceAY2385141512ena57704
67770Tsukamurella tyrosinosolvens 16S rRNA gene, isolate D-1397Y122461460ena57704

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tsukamurella tyrosinosolvens NCTC13231GCA_900637875completencbi57704
66792Tsukamurella tyrosinosolvens strain CCUG 3849957704.13wgspatric57704
66792Tsukamurella tyrosinosolvens strain DSM 4423457704.16wgspatric57704
66792Tsukamurella tyrosinosolvens strain NCTC1323157704.19completepatric57704
66792Tsukamurella tyrosinosolvens DSM 442342639762617draftimg57704
66792Tsukamurella tyrosinosolvens CCUG 384992667527978draftimg57704
67770Tsukamurella tyrosinosolvens DSM 44234GCA_900104775contigncbi57704
67770Tsukamurella tyrosinosolvens CCUG 38499GCA_001575155contigncbi57704

GC content

@refGC-contentmethod
1149671.2sequence analysis
6777071.2genome sequence analysis
6777073.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
flagellatedno97.39no
gram-positiveyes87.682no
anaerobicno99.616no
aerobicyes92.573no
halophileno93.569no
spore-formingno86.839no
thermophileno98.978yes
glucose-utilyes92.297no
motileno92.944no
glucose-fermentno90.552yes

External links

@ref: 11496

culture collection no.: DSM 44234, CCUG 38499, CIP 106771, JCM 10112, IMMIB D-1397, IFM 0810, KCTC 19177, KCTC 9965, NCTC 13231, PCM 2579

straininfo link

  • @ref: 86101
  • straininfo: 50526

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9226890Tsukamurella tyrosinosolvens sp. nov.Yassin AF, Rainey FA, Burghardt J, Brzezinka H, Schmitt S, Seifert P, Zimmermann O, Mauch H, Gierth D, Lux I, Schaal KPInt J Syst Bacteriol10.1099/00207713-47-3-6071997Actinomycetales/*classification/*genetics/ultrastructure, Actinomycetales Infections/*microbiology, Bacterial Proteins/analysis, Blood/microbiology, Chromatography, Thin Layer, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Humans, Lipids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, PhylogenyPathogenicity
Phylogeny19502350Tsukamurella carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete.Park SW, Kim SM, Park ST, Kim YMInt J Syst Evol Microbiol10.1099/ijs.0.005959-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbon Monoxide/*metabolism, DNA, Bacterial/analysis, Fatty Acids/analysis, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19734289Tsukamurella soli sp. nov., isolated from soil.Weon HY, Yoo SH, Anandham R, Schumann P, Kroppenstedt RM, Kwon SW, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.014852-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Base Composition, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11496Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44234)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44234
20028Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44234.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
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
42109Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18938
54294Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38499)https://www.ccug.se/strain?id=38499
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/
68368Automatically annotated from API 20E
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
86101Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50526.1StrainInfo: A central database for resolving microbial strain identifiers
123704Curators of the CIPCollection of Institut Pasteur (CIP 106771)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106771