Amycolatopsis samaneae (DSM 45649, BCC 35842, NBRC 106095)

Name: Amycolatopsis samaneae (DSM 45649, BCC 35842, NBRC 106095)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13273

Type strain

Culture col. no. DSM 45649 BCC 35842 NBRC 106095 TISTR 1919 RM 287 1 more

NCBI tax ID(s) 664691

Special Collections DSMZ JCM Wink compendium Literature strains

History DSMZ <- C Suriyachadkun, BCC; BCC 35842 <- R. Mingma JCM <-- BCC 35842 <-- K. Duangmal RM287.

Links

Amycolatopsis samaneae DSM 45649 is an aerobe, spore-forming, Gram-positive bacterium that builds an aerial mycelium and was isolated from roots of Samanea saman.

spore-forming Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 403813

NBRC 106095,JCM 17934,DSM 45649

@ref 20215

Last LPSN update 2026-05-29 08:28:00

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis samaneae

Full scientific name Amycolatopsis samaneae Duangmal et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Motility	Confidence
29853	positive
125439	positive		94.388

Colony morphology

@ref	Colony color	Incubation period	Medium used
21390	Maize yellow (1006)	10-14 days	ISP 2
21390	Sand yellow (1002)	10-14 days	ISP 3
21390	Traffic yellow (1023)	10-14 days	ISP 4
21390	Traffic yellow (1023)	10-14 days	ISP 5
21390	Sun yellow (1037)	10-14 days	ISP 7
21390	Ochre yellow (1024)	10-14 days	Suter with tyrosine
21390	Golden yellow (1004)	10-14 days	Suter without tyrosine

Multicellular morphology

@ref	Complex name	Complex color	Medium name
21390	Aerial Mycelium	Oyster white (1013)	ISP 2
21390	Aerial Mycelium	Cream (9001)	ISP 3
21390	Aerial Mycelium	Cream (9001)	ISP 4
21390	Aerial Mycelium	Light ivory (1015)	ISP 5
21390	Aerial Mycelium	Grey white (9002)	ISP 7
21390	Aerial Mycelium	Oyster white (1013)	Suter with tyrosine
21390	Aerial Mycelium	Golden yellow (1004)	Suter without tyrosine

Pigmentation

29853

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17974	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
21390	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
21390	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:
21390	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
21390	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
21390	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
21390	Suter with tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21390	Suter without tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)
17974	positive	growth	28
29853	positive	growth	16-40
29853	positive	optimum	29.5
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
29853	positive	optimum	8
29853	positive	growth	05-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29853	aerobe
125439	obligate aerobe	98.641

Spore formation

29853

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
21390	NaCl	positive	maximum	5 %
29853	NaCl	positive	growth	0-10 %
29853	NaCl	positive	optimum	5 %

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
21390	22599 ChEBI	arabinose	-
21390	62968 ChEBI	cellulose	-
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
29853	4853 ChEBI	esculin	+	hydrolysis
21390	28757 ChEBI	fructose	+
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
21390	17234 ChEBI	glucose	+
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
21390	37684 ChEBI	mannose	+
21390	17268 ChEBI	myo-inositol	+
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
21390	16634 ChEBI	raffinose	-
21390	26546 ChEBI	rhamnose	-
21390	17992 ChEBI	sucrose	-
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
21390	18222 ChEBI	xylose	-

Enzymes

@ref	Value	Activity	Ec
29853	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
29853	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
29853	catalase	+	1.11.1.6
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
29853	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
21390	-	+	+	+	-	-	+	+	-	+	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.
17974	-	-	+	+	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	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
21390	not determinedn.d.	+	+	+	-	+	+	+/-	-	+	+	+	-	-	-	+	+	+	-	-
17974	-	+	+/-	-	-	+	+	+/-	-	+	+	+	-	-	-	+/-	+	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
17974	roots of Samanea saman		Bangkok, Kasetsart University	Thailand	THA	Asia
67770	Roots of Samanea saman (Jacq.) Merr. from Kasetsart Univ.	Samanea saman	Bangkok	Thailand	THA	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17974	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3954197v1 assembly for Amycolatopsis samaneae JCM 17934	scaffold	GCA_039541975	664691	65.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17974	Amycolatopsis samaneae strain RM287 16S ribosomal RNA gene, partial sequence	GQ381310	1417		664691

GC content

@ref	GC-content (mol%)	Method
17974	71.7
67770	71.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3954197v1 assembly for Amycolatopsis samaneae JCM 17934
NCBI: GCA_039541975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.64	no
125439	gram_stain	BacteriaNetⓘ	positive	94.39	no
125439	spore_formation	BacteriaNetⓘ	yes	63.52	no
125439	motility	BacteriaNetⓘ	no	85.09	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis ponsaeliensis sp. nov., a novel endophytic actinobacterium isolated from the root nodules of Alnus glutinosa.	Thompson RM, Fox EM, Koutsidis G, Del Carmen Montero-Calasanz M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006810	2025
Phylogeny	Amycolatopsis samaneae sp. nov., isolated from roots of Samanea saman (Jacq.) Merr.	Duangmal K, Mingma R, Pathom-Aree W, Thamchaipenet A, Inahashi Y, Matsumoto A, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.022699-0	2010

References

#17974	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45649
#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 )
#21390	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#26227	IJSEM 951 2011 ( DOI 10.1099/ijs.0.022699-0 , PubMed 20511469 )
#29853	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26227
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 samaneae (DSM 45649, BCC 35842, NBRC 106095)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

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_039541975

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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