Strain identifier

BacDive ID: 17100

Type strain: Yes

Species: Tsukamurella pulmonis

Strain history: CIP <- 1996, A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB D-1321

NCBI tax ID(s): 47312 (species)

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

@ref: 11519

BacDive-ID: 17100

DSM-Number: 44142

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

description: Tsukamurella pulmonis DSM 44142 is an aerobe, mesophilic bacterium that was isolated from sputum of an 92 year old woman with lung tuberculosis.

NCBI tax id

  • NCBI tax id: 47312
  • Matching level: species

strain history

@refhistory
11519<- A. F. Yassin, IMMIB; IMMIB D-1321
67770DSM 44142 <-- A. F. Yassin IMMIB D-1321.
122050CIP <- 1996, A.F. Yassin, Bonn Univ., Bonn, Germany: strain IMMIB D-1321

doi: 10.13145/bacdive17100.20230509.8.1

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 pulmonis
  • full scientific name: Tsukamurella pulmonis Yassin et al. 1996
  • synonyms

    • @ref: 20215
    • synonym: Tsukamurella spongiae

@ref: 11519

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Tsukamurellaceae

genus: Tsukamurella

species: Tsukamurella pulmonis

full scientific name: Tsukamurella pulmonis Yassin et al. 1996 emend. Teng et al. 2016

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.659
69480100positive
122050nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20005Pastel yellow (1034)10-14 daysISP 2
20005Pastel yellow (1034)10-14 daysISP 3
20005Pastel yellow (1034)10-14 daysISP 4
20005Pastel yellow (1034)10-14 daysISP 5
20005Pastel yellow (1034)10-14 daysISP 6
20005Pastel yellow (1034)10-14 daysISP 7
529452-3 days
122050

multicellular morphology

@refforms multicellular complexmedium name
20005noISP 2
20005noISP 3
20005noISP 4
20005noISP 5
20005noISP 6
20005noISP 7

multimedia

  • @ref: 11519
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44142.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11519TRYPTICASE 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
20005ISP 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
20005ISP 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:
20005ISP 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
20005ISP 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
20005ISP 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
20005ISP 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
42108MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
11519COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
122050CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
11519positivegrowth28mesophilic
42108positivegrowth30mesophilic
52945positivegrowth37mesophilic
67770positivegrowth28mesophilic
122050positivegrowth15-41
122050nogrowth10psychrophilic
122050nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
52945aerobe
122050obligate aerobe

spore formation

@refspore formationconfidence
69481no93
69480no99.969

halophily

@refsaltgrowthtested relationconcentration
20005NaClpositivemaximum7.5 %
122050NaClpositivegrowth0-8 %
122050NaClnogrowth10 %

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
12205016947citrate+carbon source
1220504853esculin+hydrolysis
122050606565hippurate-hydrolysis
12205017632nitrate-reduction
12205016301nitrite-reduction
12205017632nitrate-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: 122050
  • 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
12205035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12205015688acetoin-
12205017234glucose-

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
122050oxidase-
122050beta-galactosidase+3.2.1.23
122050alcohol dehydrogenase-1.1.1.1
122050gelatinase-
122050amylase-
122050DNase+
122050caseinase-3.4.21.50
122050catalase+1.11.1.6
122050tween esterase+
122050gamma-glutamyltransferase-2.3.2.2
122050lecithinase-
122050lipase-
122050lysine decarboxylase-4.1.1.18
122050ornithine decarboxylase-4.1.1.17
122050phenylalanine ammonia-lyase-4.3.1.24
122050protease-
122050tryptophan deaminase-
122050urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
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-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20005---+--+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20005++++++++-++---++-+-
122050+++-+----+----++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20005-+++--+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122050+++----+----------+-----+-+----+-+-++-------------+--+-----++----+------++-+-+++----+-+-+-+++++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
11519sputum of an 92 year old woman with lung tuberculosisMunich, GautingGermanyDEUEurope48.066811.3537
52945Human sputum,92-yr-old woman w/ lung tuberculosis
67770Sputum of a 92-year-old woman who suffered from pulmonary tuberculosis
122050Human, SputumGautingGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Infection#Disease#Tuberculosis
#Host#Human#Female
#Host Body-Site#Oral cavity and airways#Lung
#Host Body Product#Fluids#Sputum

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: X92981
  • 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
115192Risk group (German classification)
200052German classification
1220501Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Tsukamurella pulmonis strain DSM 44142 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536514442ena47312
20218Tsukamurella pulmonis strain DSM 44142 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536515442ena47312
20218Tsukamurella pulmonis strain DSM 44142 note copy 3 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536516442ena47312
20218Tsukamurella pulmonis strain DSM 44142 note copy 4 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536517442ena47312
11519Tsukamurella pulmonis 16S rRNA gene, strain IMMIB D-1321TX929811460ena47312

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tsukamurella pulmonis strain CCUG 3573247312.10wgspatric47312
66792Tsukamurella pulmonis strain DSM 4414247312.12wgspatric47312
66792Tsukamurella pulmonis strain NCTC1323047312.13wgspatric47312
66792Tsukamurella pulmonis CCUG 357322700989555draftimg47312
66792Tsukamurella pulmonis DSM 441422634166370draftimg47312
66792Tsukamurella pulmonis NCTC 132302835265895draftimg47312
67770Tsukamurella pulmonis DSM 44142GCA_900103175contigncbi47312
67770Tsukamurella pulmonis CCUG 35732GCA_001575165contigncbi47312
67770Tsukamurella pulmonis NCTC13230GCA_900460155contigncbi47312

GC content

@refGC-contentmethod
1151970.4sequence analysis
6777070.4genome sequence analysis
6777069.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
gram-positiveyes88.947no
anaerobicno99.648yes
halophileno93.117no
spore-formingno87.421no
glucose-utilyes91.678no
aerobicyes92.927yes
flagellatedno97.404no
thermophileno99.247yes
motileno92.909no
glucose-fermentno89.883yes

External links

@ref: 11519

culture collection no.: DSM 44142, CCUG 35732, JCM 10111, IMMIB D-1321, ATCC 700081, CIP 104791, IFM 0809, KCTC 9963, NCTC 13230, PCM 2578

straininfo link

  • @ref: 86100
  • straininfo: 43761

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny19262077[A case of catheter-related bacteremia of Tsukamurella pulmonis].Shim HE, Sung H, Baek SM, Namgung S, Kim MN, Kim YG, Lee GHKorean J Lab Med10.3343/kjlm.2009.29.1.412009Actinomycetales/classification/genetics/isolation & purification, Actinomycetales Infections/diagnosis/*microbiology/therapy, Adult, Bacteremia/*diagnosis/microbiology/therapy, Bone Marrow Transplantation, Catheter-Related Infections/*microbiology, Humans, Leukemia, Myeloid, Acute/therapy, Male, Phylogeny, RNA, Ribosomal, 16S/geneticsPathogenicity
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/urltitlejournalpubmed
11519Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44142)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44142
20005Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44142.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
42108Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16738
52945Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35732)https://www.ccug.se/strain?id=35732
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
86100Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43761.1StrainInfo: A central database for resolving microbial strain identifiers
122050Curators of the CIPCollection of Institut Pasteur (CIP 104791)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104791