Amycolatopsis japonica (DSM 44213, MG 417-CF 17, NRRL B-24138)

Name: Amycolatopsis japonica (DSM 44213, MG 417-CF 17, NRRL B-24138)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13231

Type strain

Strain Designation MG 417-CF 17

Culture col. no. DSM 44213 MG 417-CF 17 NRRL B-24138 KCTC 9817 CIP 106801 1 more

NCBI tax ID(s) 208439

Special Collections DSMZ JCM KCTC CIP Wink compendium

Links

Amycolatopsis japonica MG 417-CF 17 is an obligate aerobe, mesophilic, Gram-positive prokaryote that builds an aerial mycelium.

Gram-positive rod-shaped obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 50525

CIP 106801,JCM 10140,DSM 44213,KCTC 9817,NRRL B-24138

@ref 20215

Last LPSN update 2025-12-16 09:50:02

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis japonica

Full scientific name Amycolatopsis japonica corrig. Goodfellow et al. 1997

Synonyms (1)

Amycolatopsis japonicum

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
120312	positive	rod-shaped
125439	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
19636	Saffron yellow	10-14 days	ISP 2
19636		10-14 days	ISP 3
19636		10-14 days	ISP 4
19636		10-14 days	ISP 5
19636	Saffron yellow	10-14 days	ISP 6
19636	Saffron yellow	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19636	Aerial Mycelium	White	ISP 2
19636	Aerial Mycelium	White	ISP 3
19636	Aerial Mycelium		ISP 4
19636	Aerial Mycelium	White	ISP 5
19636			ISP 6
19636	Aerial Mycelium	White	ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11600	BENNETT'S AGAR (DSMZ Medium 548)	Medium recipe at MediaDive	Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water
19636	ISP 2		Name: 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
19636	ISP 3		Name: 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:
19636	ISP 4		Name: 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
19636	ISP 5		Name: 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
19636	ISP 6		Name: 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
19636	ISP 7		Name: 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
35992	MEDIUM 128 - for Nocardia brevicatena, Nocardia flavorosea subsp. fusca and Streptomyces ambofaciens		Distilled water make up to (1000.000 ml);Maltose (10.000 g);Agar (20.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
120312	CIP Medium 129	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11600	positive	growth	28	mesophilic
19636	positive	optimum	28	mesophilic
35992	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
120312	positive	growth	10-45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
120312	obligate aerobe
125439	obligate aerobe

Compound production

@ref	Compound
11600	catalase
11600	lipolytic enzymes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19636	NaCl	positive	maximum	2.5 %
120312	NaCl	positive	growth	0-6 %
120312	NaCl		growth	8 %
120312	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
19636	22599 ChEBI	arabinose	+
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
19636	62968 ChEBI	cellulose	-
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
120312	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
19636	28757 ChEBI	fructose	+
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
19636	17234 ChEBI	glucose	+
120312	606565 ChEBI	hippurate	+	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
19636	29864 ChEBI	mannitol	+
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
19636	17268 ChEBI	myo-inositol	+
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
120312	17632 ChEBI	nitrate	-	reduction
120312	17632 ChEBI	nitrate	-	respiration
120312	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
19636	16634 ChEBI	raffinose	+
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
19636	26546 ChEBI	rhamnose	-
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
19636	17992 ChEBI	sucrose	-
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
19636	18222 ChEBI	xylose	-

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
120312	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
67770		Ethylenediamine-N,N'-disuccinic acid (EDDS)
68368	16136 ChEBI	hydrogen sulfide	from API 20E
120312	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
120312	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	+	from API 20E
120312	17234 ChEBI	glucose
68368	35581 ChEBI	indole		from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120312	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
120312	amylase	-
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
120312	beta-galactosidase	+	3.2.1.23
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
120312	caseinase	+	3.4.21.50
120312	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
120312	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120312	gamma-glutamyltransferase	+	2.3.2.2
120312	gelatinase	+
68368	gelatinase	+		from API 20E
120312	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
120312	lipase	-
120312	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120312	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
120312	oxidase	+
120312	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
120312	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
120312	tween esterase	+
120312	urease	+	3.5.1.5
68368	urease	+	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
19636	+	+	+	+	+	-	+	-	-	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	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
19636	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+
120312	-	+	+	+	-	+	-	+	+	+	+	+	-	-	-	-	+	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
120312	not determinedn.d.	+/-	+/-	-	-	-	-	-	+/-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	+	-	+/-	-	-	-	-	-	-	-	-	+/-	+/-	-	-	-	-	-	-	+/-	-	-	+/-	-	-

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11600	1	Risk group (German classification) According to TRBA 466
19636	1	Risk group (German classification) According to TRBA 466
120312	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
67770	ASM73292v1 assembly for Amycolatopsis japonica MG417-CF17	complete	GCA_000732925	208439.3	2585427649	208439	98.32

Genome browser: GCA_000732925

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11600	Amycolatopsis japonica 16S rRNA gene, type strain DSM 44213T	AJ508236	1485		208439
67770	Amycolatopsis.sp (MG 417) 16S rRNA gene	X77959	1471		37632

GC content

@ref	GC-content (mol%)
11600	69.5
67770	68.89

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Amycolatopsis japonica MG417-CF17, DSM 44213
IMG: 2585427649

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	67.00	no
125439	motility	BacteriaNetⓘ	no	83.10	no
125439	gram_stain	BacteriaNetⓘ	positive	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis japonica strain MG417-CF17 (=DSM 44213)
PATRIC: 208439.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.56	no
125438	anaerobic	anaerobicⓘ	no	96.87	yes
125438	spore-forming	spore-formingⓘ	yes	81.15	no
125438	aerobic	aerobicⓘ	yes	89.39	yes
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Investigation of Vitamin D₂ and Vitamin D₃ Hydroxylation by Kutzneria albida.	Schmitz LM, Kinner A, Althoff K, Rosenthal K, Lutz S.	Chembiochem	10.1002/cbic.202100027	2021
Genetics	Genetics and Genomics of the Genus Amycolatopsis.	Kumari R, Singh P, Lal R.	Indian J Microbiol	10.1007/s12088-016-0590-8	2016
Metabolism	Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development.	Kuhl M, Ruckert C, Glaser L, Beganovic S, Luzhetskyy A, Kalinowski J, Wittmann C	Biotechnol Bioeng	10.1002/bit.27818	2021
Genetics	Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17(T) (=DSM 44213T) producing (S,S)-N,N'-ethylenediaminedisuccinic acid.	Stegmann E, Albersmeier A, Spohn M, Gert H, Weber T, Wohlleben W, Kalinowski J, Ruckert C	J Biotechnol	10.1016/j.jbiotec.2014.08.034	2014

References

#11600	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44213
#19636	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 )
#35992	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#120312	Collection of Institut Pasteur ; Curators of the CIP; CIP 106801
#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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Amycolatopsis japonica (DSM 44213, MG 417-CF 17, NRRL B-24138)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

API 50CHac

Isolation, sampling and environmental information

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000732925

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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