Amycolatopsis regifaucium (DSM 45072, NCIMB 14277, GY080)

Name: Amycolatopsis regifaucium (DSM 45072, NCIMB 14277, GY080)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13264

Type strain

Strain Designation GY080

Culture col. no. DSM 45072 NCIMB 14277 GY080 JCM 15588

NCBI tax ID(s) 546365

Special Collections DSMZ JCM Wink compendium Literature strains

History DSMZ <- M. Goodfellow; GY080 <- G. Y. A. Tan JCM <-- NCIMB 14277 <-- R. Brown <-- G. Y. A. Tan GY080.

Links

Amycolatopsis regifaucium GY080 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

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

Name and taxonomic classification

SI-ID 403617

JCM 15588,NCIMB 14277,DSM 45072

@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 regifaucium

Full scientific name Amycolatopsis regifaucium Tan et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32107	positive	rod-shaped
125438			90
125439	positive		90.552

Colony morphology

@ref	Colony color	Incubation period	Medium used
19909	Siganl yellow	10-14 days	ISP 2
19909	Ivory	10-14 days	ISP 3
19909	Light ivory	10-14 days	ISP 4
19909	Beige	10-14 days	ISP 5
19909	Sand yellow	10-14 days	ISP 6
19909	Sand yellow	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19909		ISP 2
19909		ISP 3
19909		ISP 4
19909		ISP 5
19909		ISP 6
19909		ISP 7

Pigmentation

32107

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12315	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
12315	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19909	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
19909	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:
19909	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
19909	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
19909	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
19909	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

Culture temp

@ref	Growth	Type	Temperature (°C)
12315	positive	growth	28
19909	positive	optimum	28
32107	positive	growth	28-37
32107	positive	optimum	32.5
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32107	positive	optimum	7
32107	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32107	aerobe
125438	aerobe	91.198
125439	obligate aerobe	97.73

Spore formation

32107

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32107	NaCl	positive	optimum	5 %

Observation

@ref	Observation
32107	aggregates in chains
67770	quinones: MK-9(H₄), MK-9(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
19909	22599 ChEBI	arabinose	+
32107	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
32107	17057 ChEBI	cellobiose	+	carbon source
19909	62968 ChEBI	cellulose	-
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
32107	23652 ChEBI	dextrin	+	carbon source
32107	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
19909	28757 ChEBI	fructose	+
32107	28260 ChEBI	galactose	+	carbon source
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
19909	17234 ChEBI	glucose	+
32107	17234 ChEBI	glucose	+	carbon source
32107	17754 ChEBI	glycerol	+	carbon source
32107	28087 ChEBI	glycogen	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
32107	18403 ChEBI	L-arabitol	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
32107	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
19909	29864 ChEBI	mannitol	+
32107	29864 ChEBI	mannitol	+	carbon source
19909	17268 ChEBI	myo-inositol	+
32107	17268 ChEBI	myo-inositol	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
32107	17632 ChEBI	nitrate	+	reduction
19909	16634 ChEBI	raffinose	-
19909	26546 ChEBI	rhamnose	-
32107	33942 ChEBI	ribose	+	carbon source
19909	17992 ChEBI	sucrose	-
32107	17992 ChEBI	sucrose	+	carbon source
32107	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
32107	17151 ChEBI	xylitol	+	carbon source
19909	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
32107	16136 ChEBI	hydrogen sulfide
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
32107	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68369	urease	-	3.5.1.5	from API 20NE

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
19909	not determinedn.d.	+	+	+	+	+	+	-	+	+	+	+	+	+	-	+	+	+	+	-
12315	-	-	+/-	+/-	-	+	-	-	-	+/-	-	+	-	-	-	-	-	+	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
12315	+/-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

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
12315	soil	Kings Canyon	Australia	AUS	Australia and Oceania
67770	Arid Australian soil

Taxonmaps

69479

Global distribution of 16S sequence AY129760 (>99% sequence identity) for Amycolatopsis from Microbeatlas

Aquatic Samples	14
Soil Samples	213
Animal Samples	67
Plant Samples	25
Total Samples	319

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12315	1	Risk group (German classification) According to TRBA 466
19909	1	Risk group (German 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	IMG-taxon 2634166327 annotated assembly for Amycolatopsis regifaucium DSM 45072	contig	GCA_900113515	546365.11	2634166327	546365	69.35
67770	ASM161393v1 assembly for Amycolatopsis regifaucium GY080	scaffold	GCA_001613935	546365.8	2744054546	546365	68.55
67770	ASM155812v2 assembly for Amycolatopsis regifaucium GY080	scaffold	GCA_001558125	546365.7	2728369078	546365	66.33

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12315	Amycolatopsis regifaucium strain GY080 16S ribosomal RNA gene, partial sequence	AY129760	1470		546365

GC content

@ref	GC-content (mol%)	Method
67770	68.5	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2634166327 annotated assembly for Amycolatopsis regifaucium DSM 45072
NCBI: GCA_900113515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.73	no
125439	gram_stain	BacteriaNetⓘ	positive	90.55	no
125439	spore_formation	BacteriaNetⓘ	yes	47.67	no
125439	motility	BacteriaNetⓘ	no	85.09	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis regifaucium strain DSM 45072
PATRIC: 546365.11

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.54	no
125438	anaerobic	anaerobicⓘ	no	97.90	yes
125438	spore-forming	spore-formingⓘ	yes	84.85	yes
125438	aerobic	aerobicⓘ	yes	91.20	no
125438	thermophilic	thermophileⓘ	no	96.48	yes
125438	flagellated	motile2+ⓘ	no	90.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins.	Tan GYA, Robinson S, Lacey E, Brown R, Kim W, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijs.0.64974-0	2007

References

#12315	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45072
#19909	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 )
#28352	IJSEM 2562 2007 ( DOI 10.1099/ijs.0.64974-0 , PubMed 17978218 )
#32107	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 #28352
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#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 regifaucium (DSM 45072, NCIMB 14277, GY080)

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

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900113515

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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