Name: Amycolatopsis methanolica 239
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 165740

Type strain:

Species: Amycolatopsis methanolica

Strain Designation: 239

Culture col. no.: JCM 8087, DSM 44096, IFO 15065, IMSNU 20055, KCTC 9411, NBRC 15065, NCCB 80032, NCIMB 11946, NRRL B-24139, DSM 113301, LMD 80.32, NCIB 11946

Strain history: <- T. Iino, JCM; JCM 8087 <- NCMB; NCIMB 11946 <- LMD 80.32

NCBI tax ID(s): 1068978 (strain), 1814 (species)

SI-ID 88626

DSM 44096, IFO 15065, JCM 8087, NCIB 11946, NRRL B-24139, NCIMB 11946, LMD 80.32, KCTC 9298, KCTC 9411, NBRC 15065, NCCB 80032, DSM 113301

Other strains from Amycolatopsis methanolica

A. methanolica ST033316(HKI),

Section

Amycolatopsis methanolica 239 is a mesophilic bacterium that was isolated from soil.

mesophilic
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 methanolica**
	Full Scientific Name (LPSN)	Amycolatopsis methanolica De Boer et al. 1990

Information on culture and growth conditions Culture and growth conditions

[Ref.: #68696]

Culture medium

ISP2 MEDIUM (DSMZ Medium 987)

[Ref.: #68696]

Culture medium growth

[Ref.: #68696]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #67770]			growth	28 °C
[Ref.: #68696]			growth	28 °C

[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #68696]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-9(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* 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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from 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.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #67770]	25264	-	-	-	-	-	+/-	+	+/-	+	+/-	+/-	+/-	+	+/-	+	-	+	+	+/-	+	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.: #67770]	14308	-	+/-	-	+/-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #68696]	Sample type/isolated from	soil
[Ref.: #68696]	Geographic location (country and/or sea, region)	country of origin unknown
* marker position based on {}

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

[Ref.: #68696]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #67770]	Amycolatopsis methanolica partial 16S rRNA	X54274	1343	ENA	1068978 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amycolatopsis methanolica 239	GCA_000371885	contig	GenBank	1068978 tax ID
[Ref.: #67770]	Amycolatopsis methanolica 239	GCA_000739085	complete	GenBank	1068978 tax ID
[Ref.: #66792]	Amycolatopsis methanolica 239, DSM 44096	2517572242	draft	JGI IMG/M	1068978 tax ID	*
[Ref.: #66792]	Amycolatopsis methanolica 239	1068978.7	complete	PATRIC	1068978 tax ID	*
[Ref.: #66792]	Amycolatopsis methanolica 239	1068978.3	wgs	PATRIC	1068978 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amycolatopsis methanolica 239 239 NCBI: GCA_000739085.1
[Ref.: #69480]	motile	no	91.429	no
[Ref.: #69480]	flagellated	no	97.341	no
[Ref.: #69480]	gram-positive	yes	92.928	no
[Ref.: #69480]	anaerobic	no	99.241	no
[Ref.: #69480]	aerobic	yes	91.582	no
[Ref.: #69480]	halophile	no	81.605	no
[Ref.: #69480]	spore-forming	yes	91.16	no
[Ref.: #69480]	glucose-util	yes	89.571	yes
[Ref.: #69480]	thermophile	no	96.105	yes
[Ref.: #69480]	glucose-ferment	no	93.243	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 8087, DSM 44096, IFO 15065, IMSNU 20055, KCTC 9411, NBRC 15065, NCCB 80032, NCIMB 11946, NRRL B-24139, DSM 113301, LMD 80.32, NCIB 11946

[Ref.: #114568]

SI-ID 88626

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L.	Miao Q, Qin S, Bian GK, Yuan B, Xing K, Zhang YJ, Li Q, Tang SK, Li WJ, Jiang JH	Antonie Van Leeuwenhoek	10.1007/s10482-011-9588-8	2011	*
Enzymology	A second molybdoprotein aldehyde dehydrogenase from Amycolatopsis methanolica NCIB 11946.	Kim SW, Luykx DM, de Vries S, Duine JA	Arch Biochem Biophys	10.1006/abbi.1996.0001	1996	*
Phylogeny	Amycolatopsis methanolica sp. nov., a facultatively methylotrophic actinomycete.	de Boer L, Dijkhuizen L, Grobben G, Goodfellow M, Stackebrandt E, Parlett JH, Whitehead D, Witt D	Int J Syst Bacteriol	10.1099/00207713-40-2-194	1990	*

References

#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 )

#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;

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#68696

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 113301

#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) .

#114568

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-ID88626.1 )

* These data were automatically processed and therefore are not curated

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Amycolatopsis methanolica 239 239

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