Strain identifier

BacDive ID: 8514

Type strain: Yes

Species: Mycobacterium tokaiense

Strain Designation: 47503

Strain history: CIP <- 2000, JCM <- M. Tsukamura: strain 47503

NCBI tax ID(s): 39695 (species)

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

@ref: 11944

BacDive-ID: 8514

DSM-Number: 44635

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

description: Mycobacterium tokaiense 47503 is an obligate aerobe, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 39695
  • Matching level: species

strain history

@refhistory
11944<- T. Kudo, JCM <- M. Tsukamura; 47503
67770M. Tsukamura 47503.
123557CIP <- 2000, JCM <- M. Tsukamura: strain 47503

doi: 10.13145/bacdive8514.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium tokaiense
  • full scientific name: Mycobacterium tokaiense (ex Tsukamura 1973) Tsukamura 1981
  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium tokaiense

@ref: 11944

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium tokaiense

full scientific name: Mycobacterium tokaiense (ex Tsukamura 1973) Tsukamura 1981

strain designation: 47503

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.352
69480100positive
123557norod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19872Dahlia yellow10-14 days5006
19872Dahlia yellow10-14 daysMB7H10
19872Dahlia yellow10-14 daysMB7H11

multicellular morphology

@refforms multicellular complexmedium name
19872noISP 2
19872noISP 3
19872noISP 4
19872noISP 5
19872noISP 6
19872noISP 7

multimedia

  • @ref: 11944
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44635.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11944MIDDLEBROOK 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
19872MB7H10yesName: Middlebrook 7H10 (MB7H10) Broth Base Composition: amount in percent Middlebrook 7H10 Agar 1.9% Glycerol 0.5% OADC-Enrichment in ml (NL5633) 10ml Comments: Add broth base and glycerol to ddh2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
19872MB7H11yesName: Middlebrook 7H11 (MB7H11) Broth Base Composition: Middlebrook 7H11 Agar 2% Glycerol 0.5% OADC-Enrichment 10ml Comments: Add broth base and glycerol to ddH2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-Stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
198725006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
36359MEDIUM 55 - for Mycobacteriumyes
123557CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19872positiveoptimum37mesophilic
11944positivegrowth37mesophilic
36359positivegrowth37mesophilic
67770positivegrowth37mesophilic
123557positivegrowth22-30
123557nogrowth10psychrophilic
123557nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123557
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no90
69480no99.005

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
123557606565hippurate-hydrolysis
12355717632nitrate-reduction
12355716301nitrite-reduction
12355717632nitrate-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

metabolite production

  • @ref: 123557
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
68379pyrazinamidase+3.5.1.B15
123557oxidase-
123557beta-galactosidase-3.2.1.23
123557catalase+1.11.1.6
123557gamma-glutamyltransferase-2.3.2.2
123557urease+3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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
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
19872-++/-+-----+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19872++++++---+----++---
123557-++-+++++++---+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11944soilTokai districtJapanJPNAsia
67770SoilTokai districtJapanJPNAsia
123557Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119441Risk group (German classification)
198721Risk group (German classification)
1235571Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium tokaiense 16S ribosomal RNA gene, partial sequenceAF4805901451ena39695
20218Mycobacterium tokaiense strain CIP 106807 16S ribosomal RNA gene, partial sequenceAF547972540ena39695

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium tokaiense JCM 6373GCA_010725885completencbi39695
66792Mycolicibacterium tokaiense strain JCM 637339695.9completepatric39695
66792Mycolicibacterium tokaiense strain NCTC1082139695.6wgspatric39695
66792Mycolicibacterium tokaiense NCTC 108212869196048draftimg39695
67770Mycolicibacterium tokaiense NCTC10821GCA_900453365contigncbi39695
66792Mycolicibacterium tokaiense DSM 44635GCA_025821705contigncbi39695

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno89.023no
flagellatedno97.53no
gram-positiveyes90.24no
anaerobicno99.4no
aerobicyes89.032no
halophileno85.297no
spore-formingno82.847no
glucose-utilyes87.491no
thermophileno99.556no
glucose-fermentno89.948yes

External links

@ref: 11944

culture collection no.: DSM 44635, ATCC 27282, CIP 106807, JCM 6373, NCTC 10821, CCUG 42430

straininfo link

  • @ref: 77904
  • straininfo: 46657

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16912859Physiological, biochemical, and genetic characterization of an alicyclic amine-degrading Mycobacterium sp. strain THO100 isolated from a morpholine-containing culture of activated sewage sludge.Kim YH, Kang I, Bergeron H, Lau PC, Engesser KH, Kim SJArch Microbiol10.1007/s00203-006-0157-x2006Amines/*metabolism, Biodegradation, Environmental, Genes, Bacterial/genetics, Germany, *Industrial Microbiology, Morpholines/*metabolism, Multigene Family, Mycobacterium/classification/isolation & purification/*physiology, Phylogeny, Piperidines/metabolism, Pyrrolidines/metabolism, Sequence Homology, Sewage/chemistry/*microbiology, Species Specificity, *Waste Disposal, FluidMetabolism
Phylogeny27499106Mycobacterium oryzae sp. nov., a scotochromogenic, rapidly growing species is able to infect human macrophage cell line.Ramaprasad EVV, Rizvi A, Banerjee S, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijsem.0.0013862016Bacterial Typing Techniques, Base Composition, Cell Line, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Humans, India, Macrophages/*microbiology, Mycobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Oryza, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyPathogenicity
Phylogeny34878372Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov., two new rapidly growing mycobacterial species.Cheng Y, Lei W, Wang X, Tian Z, Liu H, Yang J, Lu S, Lai XH, Pu J, Huang Y, Zhang S, Yang C, Lian X, Bai Y, Wan K, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0050192021Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Feces/microbiology, Mycobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TibetTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11944Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44635)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44635
19872Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44635.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
36359Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18979
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
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
77904Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46657.1StrainInfo: A central database for resolving microbial strain identifiers
123557Curators of the CIPCollection of Institut Pasteur (CIP 106807)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106807