Name: Amycolatopsis coloradensis DSM 44225
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13229

Type strain:

Species: Amycolatopsis coloradensis

Culture col. no.: DSM 44225, ATCC 53629, IFO 15804, NBRC 15804, NRRL 3218, JCM 9869, IMSNU 22096, KCTC 9818, NBIMCC 1779, NCIMB 13017, VKM Ac-1732

Strain history: NRRL 3218 <-- Lederle Labs.; AV-290.

NCBI tax ID(s): 76021 (species)

SI-ID 43380

ATCC 53629, DSM 44225, IFO 15804, NRRL 3218, JCM 9869, NCIMB 13017, VKM Ac-1732, KCTC 9818, NBRC 15804, NBIMCC 1779

Special Collections

Section

Amycolatopsis coloradensis DSM 44225 is a spore-forming bacterium that builds an aerial mycelium and was isolated from soil.

spore-forming
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Amycolatopsis*
	Species	**Amycolatopsis coloradensis**
	Full Scientific Name (LPSN)	Amycolatopsis coloradensis Labeda 1995

Information on morphological and physiological properties Morphology

[Ref.: #19637]	Colony color	Dahlia yellow
[Ref.: #19637]	Incubation period	10-14 days
[Ref.: #19637]	Cultivation medium used	ISP 2

[Ref.: #19637]	Colony color	Ivory
[Ref.: #19637]	Incubation period	10-14 days
[Ref.: #19637]	Cultivation medium used	ISP 3

[Ref.: #19637]	Colony color	Ochre brown
[Ref.: #19637]	Incubation period	10-14 days
[Ref.: #19637]	Cultivation medium used	ISP 4

[Ref.: #19637]	Colony color	Pastel yellow
[Ref.: #19637]	Incubation period	10-14 days
[Ref.: #19637]	Cultivation medium used	ISP 5

[Ref.: #19637]	Colony color	Ochre brown
[Ref.: #19637]	Incubation period	10-14 days
[Ref.: #19637]	Cultivation medium used	ISP 6

[Ref.: #19637]	Colony color	Pastel yellow
[Ref.: #19637]	Incubation period	10-14 days
[Ref.: #19637]	Cultivation medium used	ISP 7

[Ref.: #19637]	Multicellular complex forming ability	yes
[Ref.: #19637]	Multicellular complex name	Aerial Mycelium
[Ref.: #19637]	Multicellular complex color	Oyster white
[Ref.: #19637]	Medium Name (multicellularity)	ISP 2

[Ref.: #19637]	Multicellular complex forming ability	yes
[Ref.: #19637]	Multicellular complex name	Aerial Mycelium
[Ref.: #19637]	Multicellular complex color	Oyster white
[Ref.: #19637]	Medium Name (multicellularity)	ISP 3

[Ref.: #19637]	Multicellular complex forming ability	no
[Ref.: #19637]	Medium Name (multicellularity)	ISP 4

[Ref.: #19637]	Multicellular complex forming ability	no
[Ref.: #19637]	Medium Name (multicellularity)	ISP 5

[Ref.: #19637]	Multicellular complex forming ability	no
[Ref.: #19637]	Medium Name (multicellularity)	ISP 6

[Ref.: #19637]	Multicellular complex forming ability	no
[Ref.: #19637]	Medium Name (multicellularity)	ISP 7

Information on culture and growth conditions Culture and growth conditions

[Ref.: #11609]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #11609]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #19637]

Culture medium

ISP 2

[Ref.: #19637]

Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #19637]

Culture medium

ISP 3

[Ref.: #19637]

Culture medium growth

[Ref.: #19637]

Culture medium composition

expand / minimize

[Ref.: #19637]

Culture medium

ISP 4

[Ref.: #19637]

Culture medium growth

[Ref.: #19637]

Culture medium composition

expand / minimize

[Ref.: #19637]

Culture medium

ISP 5

[Ref.: #19637]

Culture medium growth

[Ref.: #19637]

Culture medium composition

expand / minimize

[Ref.: #19637]

Culture medium

ISP 6

[Ref.: #19637]

Culture medium growth

[Ref.: #19637]

Culture medium composition

expand / minimize

[Ref.: #19637]

Culture medium

ISP 7

[Ref.: #19637]

Culture medium growth

[Ref.: #19637]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #11609]			growth	28 °C
[Ref.: #67770]			growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Oxygen tolerance

aerobe Confidence in %90.568

[Ref.: #69481]

Ability of spore formation

yes Confidence in %97

[Ref.: #11609]	Name of produced compound	avoparcin
[Ref.: #11609]	Name of produced compound	teicoplanin
[Ref.: #19637]	Name of produced compound	Avoparcin

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #19637]		NaCl		maximum	5	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-9(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #19637]	arabinose ChEBI	-
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19637]	cellulose ChEBI	-
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #19637]	fructose ChEBI	+
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19637]	glucose ChEBI	+
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #19637]	mannitol ChEBI	-
[Ref.: #19637]	myo-inositol ChEBI	+
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #19637]	raffinose ChEBI	-
[Ref.: #19637]	rhamnose ChEBI	-
[Ref.: #19637]	sucrose ChEBI	-
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
[Ref.: #19637]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #67770]	avoparcin	yes
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	-	3.2.1.23	* from API 20E, API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68368]	gelatinase	+		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #68368]	lysine decarboxylase	+	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68368]	ornithine decarboxylase	+	4.1.1.17	* from API 20E
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	+	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #19637]	476	-	+	+	+	+	-	+	-	-	-	+	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:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #19637]	464	not determinedn.d.	+	-	+	+	+	-	-	+	+	+	-	-	-	-	-	-	+	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #11609]	Sample type/isolated from	soil
[Ref.: #11609]	Geographic location (country and/or sea, region)	Colorado
[Ref.: #11609]	Country	USA
[Ref.: #11609]	Country ISO 3 Code	USA
[Ref.: #11609]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	CO
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF051341 (>99% sequence identity) for Amycolatopsis from Microbeatlas

Aquatic Samples	3
Soil Samples	92
Animal Samples	11
Plant Samples
Total Samples	106

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #11609]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #19637]	Biosafety level	1	Risk group (German classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Amycolatopsis coloradensis 16S rRNA gene, strain DSM 44225T	AJ421142	1483	GenBank ENA	76021 tax ID	*
[Ref.: #20218]	Amycolatopsis coloradensis partial 16S rRNA gene, strain MSNU 22096T	AJ293753	1488	GenBank ENA	76021 tax ID	*
[Ref.: #20218]	Amycolatopsis coloradensis 16S ribosomal RNA gene, partial sequence	AF051341	1445	GenBank ENA	76021 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amycolatopsis coloradensis DSM 44225	GCA_001953865	scaffold	GenBank ENA	76021 tax ID
[Ref.: #66792]	Amycolatopsis coloradensis strain DSM 44225	76021.8	wgs	PATRIC	76021 tax ID	*
[Ref.: #66792]	Amycolatopsis coloradensis DSM 44225	2854982711	draft	JGI IMG/M	76021 tax ID	*

[Ref.: #11609]	GC-content	66 mol%
[Ref.: #67770]	GC-content	68.4 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Amycolatopsis coloradensis DSM 44225 NCBI: GCA_001953865.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	97	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amycolatopsis coloradensis strain DSM 44225 PATRIC: 76021.8
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	89.152	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.429	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	90.568	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	83.207	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	88	no

Availability in culture collections External links

[Ref.: #11609]

Culture collection no.

DSM 44225, ATCC 53629, IFO 15804, NBRC 15804, NRRL 3218, JCM 9869, IMSNU 22096, KCTC 9818, NBIMCC 1779, NCIMB 13017, VKM Ac-1732

[Ref.: #82434]

SI-ID 43380

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis thailandensis sp. nov., a poly(L-lactic acid)-degrading actinomycete, isolated from soil.	Chomchoei A, Pathom-Aree W, Yokota A, Kanongnuch C, Lumyong S	Int J Syst Evol Microbiol	10.1099/ijs.0.023564-0	2010	*
Metabolism	Heterologous expression of glycopeptide resistance vanHAX gene clusters from soil bacteria in Enterococcus faecalis.	Hasman H, Aarestrup FM, Dalsgaard A, Guardabassi L	J Antimicrob Chemother	10.1093/jac/dkl033	2006	*

References

#11609

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44225

#19637

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 )

#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;

#68368

Automatically annotated from API 20E .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82434

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID43380.1 )

* These data were automatically processed and therefore are not curated

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Amycolatopsis coloradensis DSM 44225

Amycolatopsis coloradensis strain DSM 44225

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