Strain identifier

BacDive ID: 17099

Type strain: Yes

Species: Tsukamurella inchonensis

Strain Designation: D-771

Strain history: CIP <- 1996, A.F. Yassin, Bonn Univ., Germany: strain IMMIB D-771

NCBI tax ID(s): 42777 (species)

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General

@ref: 11467

BacDive-ID: 17099

DSM-Number: 44067

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

description: Tsukamurella inchonensis D-771 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from blood culture of a patient, who ingested HCl.

NCBI tax id

  • NCBI tax id: 42777
  • Matching level: species

strain history

@refhistory
11467<- A. F. Yassin; D-771 <- H. J. Lee;
67770DSM 44067 <-- A. F. Yassin IMMIB D-771 <-- H. J. Lee.
120074CIP <- 1996, A.F. Yassin, Bonn Univ., Germany: strain IMMIB D-771

doi: 10.13145/bacdive17099.20230509.8.1

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 inchonensis
  • full scientific name: Tsukamurella inchonensis Yassin et al. 1995

@ref: 11467

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Tsukamurellaceae

genus: Tsukamurella

species: Tsukamurella inchonensis

full scientific name: Tsukamurella inchonensis Yassin et al. 1995

strain designation: D-771

type strain: yes

Morphology

cell morphology

  • @ref: 120074
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19624Beige10-14 daysISP 2
19624Beige10-14 daysISP 3
19624Beige10-14 daysISP 4
19624Beige10-14 daysISP 5
19624Beige10-14 daysISP 6
19624Beige10-14 daysISP 7
120074

multimedia

  • @ref: 11467
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44067.jpg
  • caption: Medium 215 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11467BHI 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
11467TRYPTICASE 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
11467MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
19624ISP 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
19624ISP 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:
19624ISP 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
19624ISP 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
19624ISP 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
19624ISP 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
39097MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
120074CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
11467positivegrowth28mesophilic
39097positivegrowth37mesophilic
67770positivegrowth37mesophilic
120074positivegrowth15-41
120074nogrowth10psychrophilic
120074nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120074
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
19624NaClpositivemaximum7.5 %
120074NaClpositivegrowth0-10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12007416947citrate-carbon source
1200744853esculin+hydrolysis
120074606565hippurate-hydrolysis
12007417632nitrate-reduction
12007416301nitrite-reduction
12007417632nitrate-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: 120074
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12007435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12007415688acetoin-
12007417234glucose-

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
120074oxidase-
120074beta-galactosidase+3.2.1.23
120074alcohol dehydrogenase-1.1.1.1
120074gelatinase-
120074amylase+
120074DNase+
120074caseinase-3.4.21.50
120074catalase+1.11.1.6
120074tween esterase+
120074gamma-glutamyltransferase-2.3.2.2
120074lecithinase-
120074lipase-
120074lysine decarboxylase-4.1.1.18
120074ornithine decarboxylase-4.1.1.17
120074phenylalanine ammonia-lyase-4.3.1.24
120074protease-
120074tryptophan deaminase-
120074urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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
19624--++-++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19624+++++++--++-+-++---
120074+++-+----+--+-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19624---------+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120074+++++--+--+------++---+--++-----+++++----+------+++--+--+--+++-----------+-+--+++---+-+-+++++++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11467blood culture of a patient, who ingested HCl
67770Blood culture of a patient who ingested hydrochloric acidInchonRepublic of KoreaKORAsia
120074Human, BloodIncheonRepublic of KoreaKORAsia1993

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#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: X85955
  • 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
114672Risk group (German classification)
196242Risk group (German classification)
1200741Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Tsukamurella inchonensis clone F7 16S ribosomal RNA gene, partial sequenceAY262285502ena42777
20218Tsukamurella inchonensis 16S rRNA gene, strain IMMIB D-771TX859551490ena42777
11467Tsukamurella inchonensis strain ATCC700082 16S ribosomal RNA gene, complete sequenceAF2832811512ena42777

GC content

  • @ref: 67770
  • GC-content: 72
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 11467

culture collection no.: DSM 44067, ATCC 700082, JCM 10110, CCUG 35731, CIP 104790, IFM 0808, KCTC 9866, PCM 2577, IMMIB D-771

straininfo link

  • @ref: 86099
  • straininfo: 46212

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8590680Tsukamurella inchonensis sp. nov.Yassin AF, Rainey FA, Brzezinka H, Burghardt J, Lee HJ, Schaal KPInt J Syst Bacteriol10.1099/00207713-45-3-5221995Actinomycetales/chemistry/*classification/genetics/metabolism, Actinomycetales Infections/microbiology, Amino Acids/metabolism, Antibiotics, Antitubercular/pharmacology, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry, DNA, Ribosomal/genetics, Enzymes/metabolism, Humans, Molecular Sequence Data, Mycolic Acids/chemistry, Phylogeny, Polysorbates/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Temperature, Vitamin K/analysis/chemistryMetabolism
Phylogeny8934902Tsukamurella pulmonis sp. nov.Yassin AF, Rainey FA, Brzezinka H, Burghardt J, Rifai M, Seifert P, Feldmann K, Schaal KPInt J Syst Bacteriol10.1099/00207713-46-2-4291996Aged, Aged, 80 and over, Bacterial Proteins/analysis, Base Sequence, Cytosine/analysis, DNA, Bacterial/analysis, Female, Guanine/analysis, Humans, Lipids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Mycobacterium/*classification/genetics/ultrastructure, Mycobacterium Infections/*microbiology, Phylogeny, Pneumonia/microbiology, RNA, Ribosomal, 16S/analysisPathogenicity
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
Enzymology15533305Identification of a cation-specific channel (TipA) in the cell wall of the gram-positive mycolata Tsukamurella inchonensis: the gene of the channel-forming protein is identical to mspA of Mycobacterium smegmatis and mppA of Mycobacterium phlei.Dorner U, Maier E, Benz RBiochim Biophys Acta10.1016/j.bbamem.2004.09.0012004Actinomycetales/*chemistry/genetics, Base Sequence, Cloning, Molecular, Evolution, Molecular, Ion Channels/analysis/*genetics/isolation & purification, Mycobacterium phlei, Mycobacterium smegmatis, Sequence Homology, Nucleic AcidPhylogeny
Phylogeny27257031Tsukamurella serpentis sp. nov., isolated from the oral cavity of Chinese cobras (Naja atra).Tang Y, Teng JLL, Cheung CLW, Ngan AHY, Huang Y, Wong SSY, Yip EKT, Ng KHL, Que TL, Lau SKP, Woo PCYInt J Syst Evol Microbiol10.1099/ijsem.0.0011872016Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Elapidae/*microbiology, Fatty Acids/chemistry, Hong Kong, Mouth/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11467Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44067)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44067
19624Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44067.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
39097Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16737
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
86099Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46212.1StrainInfo: A central database for resolving microbial strain identifiers
120074Curators of the CIPCollection of Institut Pasteur (CIP 104790)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104790