Name: Amycolatopsis echigonensis LC2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13265

Type strain:

Species: Amycolatopsis echigonensis

Strain Designation: LC2

Culture col. no.: DSM 45164, CCTCC AB 206019, CIP 109736, IAM 15387, JCM 21831

Strain history: CIP <- 2007, JCM <- 2007, IAM <- L. Ding, Tokyo Univ., Tokyo, Japan: strain LC2

NCBI tax ID(s): 369930 (species)

SI-ID 309425

IAM 15387, JCM 21831, CIP 109736

Section

Amycolatopsis echigonensis LC2 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from filtration substrate made from volcanic soil.

Gram-positive
aerobe
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 echigonensis**
	Full Scientific Name (LPSN)	Amycolatopsis echigonensis Ding et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32003]	Gram stain	positive
[Ref.: #118993]	Gram stain	positive

[Ref.: #32003]	Motility	no
[Ref.: #118993]	Motility	no

[Ref.: #118993]	Cell shape	rod-shaped

Multimedia content

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Caption:

Medium 65 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #37659]

Culture medium

MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum

[Ref.: #37659]

Culture medium growth

[Ref.: #37659]

Culture medium composition

expand / minimize

[Ref.: #118993]

Culture medium

CIP Medium 116

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15469]	growth	28 °C
[Ref.: #32003]	growth	5.0-45 °C
[Ref.: #32003]	optimum	30 °C
[Ref.: #37659]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #15469]	Temperature range	mesophilic
[Ref.: #32003]	Temperature range	mesophilic
[Ref.: #37659]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32003]			optimum	9
[Ref.: #32003]			growth	6.0-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32003]	Oxygen tolerance	aerobe
[Ref.: #118993]	Oxygen tolerance	obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32003]		NaCl		growth	3.0-7.0	%
[Ref.: #32003]		NaCl		optimum	5	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32003]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32003]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32003]	lactate ChEBI	+	carbon source
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32003]	myo-inositol ChEBI	+	carbon source
[Ref.: #32003]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32003]	nitrate ChEBI	+	reduction
[Ref.: #118993]	nitrate ChEBI	-	reduction
[Ref.: #118993]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32003]	rhamnose ChEBI	+	carbon source
[Ref.: #32003]	ribitol ChEBI	+	carbon source
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32003]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118993]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #32003]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32003]	alkaline phosphatase	+	3.1.3.1
[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.: #32003]	alpha-galactosidase	+	3.2.1.22
[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.: #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.: #32003]	catalase	+	1.11.1.6
[Ref.: #118993]	catalase	+	1.11.1.6
[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.: #32003]	gelatinase	+
[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.: #118993]	oxidase	-
[Ref.: #32003]	pyrazinamidase	+	3.5.1.B15
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #32003]	urease	+	3.5.1.5
[Ref.: #118993]	urease	+	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #118993]	11645	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.: #118993]	12073	-	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-

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

[Ref.: #15469]	Sample type/isolated from	filtration substrate made from volcanic soil
[Ref.: #15469]	Geographic location (country and/or sea, region)	Niigata
[Ref.: #15469]	Country	Japan
[Ref.: #15469]	Country ISO 3 Code	JPN
[Ref.: #15469]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Filtration substrate made from volcanic soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Niigata
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #118993]	Sample type/isolated from	Environment, Substrate, volcanic soil
[Ref.: #118993]	Geographic location (country and/or sea, region)	Niigata
[Ref.: #118993]	Country	Japan
[Ref.: #118993]	Country ISO 3 Code	JPN
[Ref.: #118993]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Volcanic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB248535 (>99% sequence identity) for Amycolatopsis from Microbeatlas

Aquatic Samples	1
Soil Samples	53
Animal Samples	16
Plant Samples	4
Total Samples	74

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

[Ref.: #15469]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118993]	Biosafety level	1	Risk group (French 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.: #15469]	Amycolatopsis echigonensis gene for 16S rRNA, partial sequence	AB248535	1473	ENA	369930 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amycolatopsis echigonensis JCM 21831	GCA_014174495	contig	GenBank	369930 tax ID
[Ref.: #66792]	Amycolatopsis echigonensis strain JCM 21831	369930.3	wgs	PATRIC	369930 tax ID	*

[Ref.: #15469]	GC-content	72.7 mol%
[Ref.: #67770]	GC-content	72.7 mol%	high performance liquid chromatography (HPLC)

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 echigonensis strain JCM 21831 PATRIC: 369930.3
[Ref.: #69480]	gram-positive	yes	88.641	no
[Ref.: #69480]	anaerobic	no	99.332	no
[Ref.: #69480]	halophile	no	90.331	no
[Ref.: #69480]	spore-forming	yes	91.225	no
[Ref.: #69480]	glucose-util	yes	87.115	yes
[Ref.: #69480]	aerobic	yes	91.119	no
[Ref.: #69480]	motile	no	94.155	no
[Ref.: #69480]	flagellated	no	97.927	yes
[Ref.: #69480]	thermophile	no	98.573	no
[Ref.: #69480]	glucose-ferment	no	92.702	no

Availability in culture collections External links

[Ref.: #15469]

Culture collection no.

DSM 45164, CCTCC AB 206019, CIP 109736, IAM 15387, JCM 21831

[Ref.: #82469]

SI-ID 309425

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl.	Tedsree N, Tanasupawat S, Sritularak B, Kuncharoen N, Likhitwitayawuid K	Int J Syst Evol Microbiol	10.1099/ijsem.0.004902	2021	*
Phylogeny	Amycolatopsis echigonensis sp. nov. and Amycolatopsis niigatensis sp. nov., novel actinomycetes isolated from a filtration substrate.	Ding L, Hirose T, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64791-0	2007	*

References

#15469

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45164

#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 )

#32003

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 #28257 (see below)

#37659 ; Curators of the CIP;

#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;

#68371

Automatically annotated from API 50CH acid .

#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) .

#82469

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-ID309425.1 )

#118993 Collection of Institut Pasteur ; Curators of the CIP; CIP 109736

#28257

IJSEM 1747 2007 ( DOI 10.1099/ijs.0.64791-0 , PubMed 17684249 )

* These data were automatically processed and therefore are not curated

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Amycolatopsis echigonensis strain JCM 21831

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