Amycolatopsis vancoresmycina (DSM 44592, JCM 12675, NRRL B-24208)

Name: Amycolatopsis vancoresmycina (DSM 44592, JCM 12675, NRRL B-24208)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13256

Type strain

Strain Designation ST101170

Culture col. no. DSM 44592 JCM 12675 NRRL B-24208 ST101170

NCBI tax ID(s) 1292037 208444

Special Collections DSMZ JCM Wink compendium

History <- J. Wink; ST101170 DSM 44592 <-- J. Wink ST 101170.

Links

Amycolatopsis vancoresmycina ST101170 is a bacterium that builds an aerial mycelium and produces antibiotic compounds.

antibiotic compound production genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 97666

DSM 44592,NRRL B-24208,JCM 12675

@ref 20215

Last LPSN update 2026-02-09 11:21:05

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis vancoresmycina

Full scientific name Amycolatopsis vancoresmycina Wink et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.8

Colony morphology

@ref	Colony color	Incubation period	Medium used
19679	Saffron yellow	10-14 days	ISP 2
19679	Maize yellow	10-14 days	ISP 3
19679	Maize yellow	10-14 days	ISP 4
19679	Maize yellow	10-14 days	ISP 5
19679	Brown beige	10-14 days	ISP 6
19679	Maize yellow	10-14 days	ISP 7

Multicellular morphology

@ref	Complex name	Complex color	Medium name
19679	Aerial Mycelium	White	ISP 2
19679	Aerial Mycelium	White	ISP 3
19679	Aerial Mycelium	White	ISP 4
19679			ISP 5
19679			ISP 6
19679	Aerial Mycelium		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11907	CZAPEK PEPTONE AGAR (DSMZ Medium 83)	Medium recipe at MediaDive	Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
19679	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
19679	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:
19679	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
19679	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
19679	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
19679	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)
11907	positive	growth	28
19679	positive	optimum	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.8

Compound production

@ref	Compound
11907	vancoresmycin
19679	Vancoresmycin

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
19679	22599 ChEBI	arabinose	+
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
19679	62968 ChEBI	cellulose	+
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
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
19679	28757 ChEBI	fructose	+
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
19679	17234 ChEBI	glucose	+
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
19679	29864 ChEBI	mannitol	+
19679	17268 ChEBI	myo-inositol	+
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
19679	16634 ChEBI	raffinose	+
19679	26546 ChEBI	rhamnose	+
19679	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
19679	18222 ChEBI	xylose	-

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E
67770		vancoresmycin

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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	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
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
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
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	+		from API Coryne
68368	gelatinase	+		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	+		from API zym
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
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
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	+	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68379	urease	+	3.5.1.5	from API Coryne
68368	urease	+	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

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
19679	+	+	+	+	+	-	+	-	-	-	+	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 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
19679	-	-	-	+	-	-	-	+	+	+	+	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
19679	not determinedn.d.	+	-	+	+	+	+	+	+	+	+	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
11907	indian soil
67770	Soil	India	IND	Asia

Taxonmaps

69479

Global distribution of 16S sequence AJ508240 (>99% sequence identity) for Amycolatopsis from Microbeatlas

Aquatic Samples	20
Soil Samples	1065
Animal Samples	41
Plant Samples	104
Total Samples	1230

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11907	1	Risk group (German classification) According to TRBA 466
19679	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	ASM71678v1 assembly for Amycolatopsis vancoresmycina NRRL B-24208	contig	GCA_000716785	208444.4	2772190728	208444	62.58
67770	Whole genome assembly for Amycolatopsis vancoresmycina DSM 44592	contig	GCA_000388135	1292037.4	2545824680	1292037

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11907	Amycolatopsis vancoresmycetica 16S rRNA gene, type strain DSM 44592T	AJ508240	1478		208444

GC content

@ref	GC-content (mol%)	Method
67770	72	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Amycolatopsis vancoresmycina DSM 44592
NCBI: GCA_000388135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	81.20	no
125439	motility	BacteriaNetⓘ	no	85.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis vancoresmycina DSM 44592
PATRIC: 1292037.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.28	no
125438	anaerobic	anaerobicⓘ	no	94.07	no
125438	spore-forming	spore-formingⓘ	yes	72.70	no
125438	aerobic	aerobicⓘ	yes	80.66	no
125438	thermophilic	thermophileⓘ	no	97.99	yes
125438	flagellated	motile2+ⓘ	no	86.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Discovery, isolation, heterologous expression and mode-of-action studies of the antibiotic polyketide tatiomicin from Amycolatopsis sp. DEM30355.	Kepplinger B, Mardiana L, Cowell J, Morton-Laing S, Dashti Y, Wills C, Marrs ECL, Perry JD, Gray J, Goodfellow M, Errington J, Probert MR, Clegg W, Bogaerts J, Herrebout W, Allenby NEE, Hall MJ.	Sci Rep	10.1038/s41598-022-18726-3	2022
Genetics	Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity.	Campillo-Brocal JC, Chacon-Verdu MD, Lucas-Elio P, Sanchez-Amat A.	BMC Genomics	10.1186/s12864-015-1455-y	2015
Metabolism	Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria.	Peng T, Lin J, Xu YZ, Zhang Y.	ISME J	10.1038/ismej.2015.246	2016
Metabolism	Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism.	Boukouvala S, Kontomina E, Olbasalis I, Patriarcheas D, Tzimotoudis D, Arvaniti K, Manolias A, Tsatiri MA, Basdani D, Zekkas S.	Sci Rep	10.1038/s41598-024-65342-4	2024
	A Semisynthetic Kanglemycin Shows In Vivo Efficacy against High-Burden Rifampicin Resistant Pathogens.	Peek J, Xu J, Wang H, Suryavanshi S, Zimmerman M, Russo R, Park S, Perlin DS, Brady SF.	ACS Infect Dis	10.1021/acsinfecdis.0c00223	2020
Enzymology	Genome-based analysis of non-ribosomal peptide synthetase and type-I polyketide synthase gene clusters in all type strains of the genus Herbidospora.	Komaki H, Ichikawa N, Oguchi A, Hamada M, Tamura T, Fujita N.	BMC Res Notes	10.1186/s13104-015-1526-9	2015
Pathogenicity	Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.	Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF.	Nat Commun	10.1038/s41467-018-06587-2	2018
Genetics	Genome sequencing and annotation of Amycolatopsis vancoresmycina strain DSM 44592(T).	Kaur N, Kumar S, Mayilraj S	Genom Data	10.1016/j.gdata.2013.10.006	2013
Phylogeny	Amycolatopsis melonis sp. nov., a novel protease-producing and cellulose-degrading actinobacterium isolated from soil.	Xu Y, Zhao X, Jin J, Zhang R, Zhou C, Wang Z, Yao S, Wang X, Xiang W, Song J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006559	2024
Phylogeny	Amycolatopsis silviterrae sp. nov., isolated from forest soil.	Jamjan W, Suriyachadkun C, Tanasupawat S, Sakai K, Tashiro Y, Okugawa Y, Tongpim S	Int J Syst Evol Microbiol	10.1099/ijsem.0.002687	2018
Phylogeny	Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil.	Souza WR, Silva RE, Goodfellow M, Busarakam K, Figueiro FS, Ferreira D, Rodrigues-Filho E, Moraes LAB, Zucchi TD	Int J Syst Evol Microbiol	10.1099/ijs.0.000176	2015
Phylogeny	Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils.	Zucchi TD, Bonda AN, Frank S, Kim BY, Kshetrimayum JD, Goodfellow M	Antonie Van Leeuwenhoek	10.1007/s10482-012-9716-0	2012
Phylogeny	Three new antibiotic producing species of the genus Amycolatopsis, Amycolatopsis balhimycina sp. nov., A. tolypomycina sp. nov., A. vancoresmycina sp. nov., and description of Amycolatopsis keratiniphila subsp. keratiniphila subsp. nov. and A. keratiniphila subsp. nogabecina subsp. nov.	Wink JM, Kroppenstedt RM, Ganguli BN, Nadkarni SR, Schumann P, Seibert G, Stackebrandt E	Syst Appl Microbiol	10.1078/072320203322337290	2003

References

#11907	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44592
#19679	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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68379	Automatically annotated from API Coryne .
#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 vancoresmycina (DSM 44592, JCM 12675, NRRL B-24208)

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

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000716785

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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