Mycobacterium tokaiense (DSM 44635, ATCC 27282, CIP 106807)

Name: Mycobacterium tokaiense (DSM 44635, ATCC 27282, CIP 106807)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8514

Type strain

Strain Designation 47503

Culture col. no. DSM 44635 ATCC 27282 CIP 106807 JCM 6373 NCTC 10821 2 more

NCBI tax ID(s) 39695

Special Collections DSMZ CCUG JCM CIP Wink compendium

History DSMZ <- T. Kudo, JCM <- M. Tsukamura; 47503 JCM <-- M. Tsukamura 47503. CIP <- 2000, JCM <- M. Tsukamura: strain 47503

Links

Mycobacterium tokaiense 47503 is an obligate aerobe, rod-shaped bacterium that was isolated from soil.

rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 46657

CT2025-00084,ATCC 27282,NCTC 10821,CIP 106807,JCM 6373,DSM 44635,CCUG 42430,CNCTC 7299

@ref 20215

Last LPSN update 2026-05-29 08:26:53

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 (1)

Mycolicibacterium tokaiense

Morphology

Cell morphology

@ref	Cell shape	Motility	Gram stain	Confidence
123557	rod-shaped
125439			positive	95.927

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		ISP 2
19872		ISP 3
19872		ISP 4
19872		ISP 5
19872		ISP 6
19872		ISP 7

Multimedia

@ref:	11944
multimedia content:	DSM_44635.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44635.jpg
caption:	Medium 645 37°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11944	MIDDLEBROOK MEDIUM (DSMZ Medium 645)	Medium recipe at MediaDive	Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
19872	MB7H10		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		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		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
123557	CIP Medium 55	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11944	positive	growth	37
19872	positive	optimum	37
36359	positive	growth	37
67770	positive	growth	37
123557	positive	growth	22-30
123557	negative	growth	10
123557	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
123557	obligate aerobe
125438	aerobe	91.556
125439	obligate aerobe	99.241

Observation

67770

Observationquinones: MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
123557	606565 ChEBI	hippurate	-	hydrolysis
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
123557	17632 ChEBI	nitrate	-	reduction
123557	17632 ChEBI	nitrate	-	respiration
123557	16301 ChEBI	nitrite	-	reduction
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123557	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
123557	beta-galactosidase	-	3.2.1.23
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
123557	catalase	+	1.11.1.6
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
123557	gamma-glutamyltransferase	-	2.3.2.2
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
123557	oxidase	-
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
123557	urease	+	3.5.1.5
68379	urease	+	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
19872	-	+	+/-	+	-	-	-	-	-	+	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
19872	not determinedn.d.	+	+	+	+	+	+	-	-	-	+	-	-	-	-	+	+	-	-	-
123557	-	-	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11944	soil	Tokai district	Japan	JPN	Asia
67770	Soil	Tokai district	Japan	JPN	Asia
123557	Environment, Soil

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11944	1	Risk group (German classification) According to TRBA 466
19872	1	Risk group (German classification) According to TRBA 466
123557	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1072588v1 assembly for Mycolicibacterium tokaiense JCM 6373	complete	GCA_010725885	39695.9	8112662825	39695	95.43
67770	52601_E01 assembly for Mycolicibacterium tokaiense NCTC10821	contig	GCA_900453365	39695.6	2869196048	39695	73.49
66792	ASM2582170v1 assembly for Mycolicibacterium tokaiense DSM 44635	contig	GCA_025821705	39695.12	8113863833	39695	68.17

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Mycobacterium tokaiense 16S ribosomal RNA gene, partial sequence	AF480590	1451		39695
20218	Mycobacterium tokaiense strain CIP 106807 16S ribosomal RNA gene, partial sequence	AF547972	540		39695

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1072588v1 assembly for Mycolicibacterium tokaiense JCM 6373
BV-BRC: 39695.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.24	no
125439	gram_stain	BacteriaNetⓘ	positive	95.93	no
125439	motility	BacteriaNetⓘ	no	88.16	no
125439	spore_formation	BacteriaNetⓘ	no	73.24	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycolicibacterium tokaiense JCM 6373
NCBI: GCA_010725885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.96	no
125438	anaerobic	anaerobicⓘ	no	97.73	yes
125438	aerobic	aerobicⓘ	yes	91.56	no
125438	spore-forming	spore-formingⓘ	no	65.07	no
125438	thermophilic	thermophileⓘ	no	96.67	yes
125438	flagellated	motile2+ⓘ	no	87.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.	Gupta RS, Lo B, Son J.	Front Microbiol	10.3389/fmicb.2018.00067	2018
	In Vitro Activity of the Sudapyridine (WX-081) against Non-Tuberculous Mycobacteria Isolated in Beijing, China.	Zhu R, Shang Y, Chen S, Xiao H, Ren R, Wang F, Xue Y, Li L, Li Y, Chu N, Huang H.	Microbiol Spectr	10.1128/spectrum.01372-22	2022
	In Vitro Antimicrobial Activities of Tigecycline, Eravacycline, Omadacycline, and Sarecycline against Rapidly Growing Mycobacteria.	Zhang T, Du J, Dong L, Wang F, Zhao L, Jia J, Wang C, Cheng M, Yu X, Huang H.	Microbiol Spectr	10.1128/spectrum.03238-22	2023
	In vitro and intracellular inhibitory activities of nosiheptide against Mycobacterium abscessus.	Zhu R, Yu X, Zhang T, Kong Y, Wang F, Jia J, Xue Y, Huang H.	Front Microbiol	10.3389/fmicb.2022.926361	2022
Pathogenicity	In Vitro Activities of Bedaquiline and Delamanid against Nontuberculous Mycobacteria Isolated in Beijing, China.	Yu X, Gao X, Li C, Luo J, Wen S, Zhang T, Ma Y, Dong L, Wang F, Huang H.	Antimicrob Agents Chemother	10.1128/aac.00031-19	2019
Pathogenicity	Dual-probe assay for rapid detection of drug-resistant Mycobacterium tuberculosis by real-time PCR.	Wada T, Maeda S, Tamaru A, Imai S, Hase A, Kobayashi K.	J Clin Microbiol	10.1128/jcm.42.11.5277-5285.2004	2004
Phylogeny	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
Phylogeny	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
Phylogeny	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

References

#11944	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44635
#19872	Wink, J.: 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.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#36359	; Curators of the CIP;
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#123557	Collection of Institut Pasteur ; Curators of the CIP; CIP 106807
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Mycobacterium tokaiense (DSM 44635, ATCC 27282, CIP 106807)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_010725885

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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