Strain identifier
BacDive ID: 8514
Type strain:
Species: Mycobacterium tokaiense
Strain Designation: 47503
Strain history: CIP <- 2000, JCM <- M. Tsukamura: strain 47503
NCBI tax ID(s): 39695 (species)
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
@ref | history |
---|---|
11944 | <- T. Kudo, JCM <- M. Tsukamura; 47503 |
67770 | M. Tsukamura 47503. |
123557 | CIP <- 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 92.352 | ||
69480 | 100 | positive | ||
123557 | no | rod-shaped |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19872 | Dahlia yellow | 10-14 days | 5006 |
19872 | Dahlia yellow | 10-14 days | MB7H10 |
19872 | Dahlia yellow | 10-14 days | MB7H11 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19872 | no | ISP 2 |
19872 | no | ISP 3 |
19872 | no | ISP 4 |
19872 | no | ISP 5 |
19872 | no | ISP 6 |
19872 | no | ISP 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
@ref | name | growth | link | composition |
---|---|---|---|---|
11944 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
19872 | MB7H10 | yes | Name: 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 | |
19872 | MB7H11 | yes | Name: 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 | |
19872 | 5006 | yes | Medium: 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 | |
36359 | MEDIUM 55 - for Mycobacterium | yes | ||
123557 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19872 | positive | optimum | 37 | mesophilic |
11944 | positive | growth | 37 | mesophilic |
36359 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
123557 | positive | growth | 22-30 | |
123557 | no | growth | 10 | psychrophilic |
123557 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 123557
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 90 |
69480 | no | 99.005 |
observation
- @ref: 67770
- observation: quinones: MK-9(H2)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
123557 | 606565 | hippurate | - | hydrolysis |
123557 | 17632 | nitrate | - | reduction |
123557 | 16301 | nitrite | - | reduction |
123557 | 17632 | nitrate | - | respiration |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
- @ref: 123557
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | gelatinase | - | |
68379 | urease | + | 3.5.1.5 |
68379 | beta-glucosidase | - | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | - | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
123557 | oxidase | - | |
123557 | beta-galactosidase | - | 3.2.1.23 |
123557 | catalase | + | 1.11.1.6 |
123557 | gamma-glutamyltransferase | - | 2.3.2.2 |
123557 | urease | + | 3.5.1.5 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19872 | - | + | +/- | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19872 | + | + | + | + | + | + | - | - | - | + | - | - | - | - | + | + | - | - | - | |
123557 | - | + | + | - | + | + | + | + | + | + | + | - | - | - | + | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
11944 | soil | Tokai district | Japan | JPN | Asia |
67770 | Soil | Tokai district | Japan | JPN | Asia |
123557 | Environment, Soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11944 | 1 | Risk group (German classification) |
19872 | 1 | Risk group (German classification) |
123557 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium tokaiense 16S ribosomal RNA gene, partial sequence | AF480590 | 1451 | ena | 39695 |
20218 | Mycobacterium tokaiense strain CIP 106807 16S ribosomal RNA gene, partial sequence | AF547972 | 540 | ena | 39695 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycolicibacterium tokaiense JCM 6373 | GCA_010725885 | complete | ncbi | 39695 |
66792 | Mycolicibacterium tokaiense strain JCM 6373 | 39695.9 | complete | patric | 39695 |
66792 | Mycolicibacterium tokaiense strain NCTC10821 | 39695.6 | wgs | patric | 39695 |
66792 | Mycolicibacterium tokaiense NCTC 10821 | 2869196048 | draft | img | 39695 |
67770 | Mycolicibacterium tokaiense NCTC10821 | GCA_900453365 | contig | ncbi | 39695 |
66792 | Mycolicibacterium tokaiense DSM 44635 | GCA_025821705 | contig | ncbi | 39695 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 90 | no |
motile | no | 89.023 | no |
flagellated | no | 97.53 | no |
gram-positive | yes | 90.24 | no |
anaerobic | no | 99.4 | no |
aerobic | yes | 89.032 | no |
halophile | no | 85.297 | no |
spore-forming | no | 82.847 | no |
glucose-util | yes | 87.491 | no |
thermophile | no | 99.556 | no |
glucose-ferment | no | 89.948 | yes |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16912859 | Physiological, 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 SJ | Arch Microbiol | 10.1007/s00203-006-0157-x | 2006 | Amines/*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, Fluid | Metabolism |
Phylogeny | 27499106 | Mycobacterium 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 CV | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001386 | 2016 | Bacterial 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 Microbiology | Pathogenicity |
Phylogeny | 34878372 | Mycolicibacterium 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 J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005019 | 2021 | Animals, 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, Tibet | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11944 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44635) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44635 | |||
19872 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44635.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
36359 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18979 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
77904 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46657.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123557 | Curators of the CIP | Collection of Institut Pasteur (CIP 106807) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106807 |