Amycolatopsis echigonensis (DSM 45165, CCTCC AB 206020, CIP 109735)

Name: Amycolatopsis echigonensis (DSM 45165, CCTCC AB 206020, CIP 109735)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13266

Type strain

Strain Designation LC11

Culture col. no. DSM 45165 CCTCC AB 206020 CIP 109735 IAM 15388 JCM 21832 1 more

NCBI tax ID(s) 2576905

Special Collections DSMZ JCM CIP Literature strains

Links

Amycolatopsis echigonensis LC11 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from filtration substrate made from volcanic soil.

Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 309426

DSM 45165,IAM 15388,JCM 21832,CIP 109735

@ref 20215

Last LPSN update 2025-12-16 09:50:03

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis echigonensis

Full scientific name Amycolatopsis echigonensis Ding et al. 2007

Synonyms (1)

Amycolatopsis niigatensis

BacDive ID	Other strains from **Amycolatopsis echigonensis** (1)	Type strain
13265	A. echigonensis LC2, DSM 45164, CCTCC AB 206019, CIP 109736, ... (type strain)

Morphology

Cell morphology

@ref	Gram stain	Motility	Confidence
32003	positive
125439	positive		99

Multimedia

@ref:	15470
multimedia content:	DSM_45165.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45165.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15470	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15470	positive	growth	28	mesophilic
32003	positive	growth	5.0-45
32003	positive	optimum	30	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32003	positive	optimum	9
32003	positive	growth	6.0-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32003	aerobe
125439	obligate aerobe	98.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32003	NaCl	positive	growth	3.0-7.0 %
32003	NaCl	positive	optimum	5 %

Observation

67770

Observationquinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
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
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
32003	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
32003	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
32003	26546 ChEBI	rhamnose	+	carbon source
32003	15963 ChEBI	ribitol	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
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
32003	acid phosphatase	+	3.1.3.2
32003	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
68382	alpha-mannosidase	+	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
32003	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
32003	gelatinase	+
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
32003	pyrazinamidase	+	3.5.1.B15
68382	trypsin	-	3.4.21.4	from API zym
32003	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

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
15470	-	+	-	+/-	-	+	-	-	-	-	+/-	+/-	-	-	-	-	+/-	+	+	-

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
15470	not determinedn.d.	-	-	-	-	+	-	+/-	+	+	+	+	+	+/-	+	-	+/-	+	+	+/-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Volcanic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15470	filtration substrate made from volcanic soil	Niigata	Japan	JPN	Asia
67770	Filtration substrate made from volcanic soil	Niigata	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB248537 (>99% sequence identity) for Amycolatopsis from Microbeatlas

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15470	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	ASM284661v1 assembly for Amycolatopsis echigonensis DSM 45165	contig	GCA_002846615	369932.4	2627854290	369932	63.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15470	Amycolatopsis niigatensis gene for 16S rRNA, partial sequence	AB248537	1472		369932

GC content

@ref	GC-content (mol%)	Method
15470	72.4
67770	72.4	high performance liquid chromatography (HPLC)
67770	69.5	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Amycolatopsis niigatensis DSM 45165
NCBI: GCA_002846615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	80.60	no
125439	motility	BacteriaNetⓘ	no	87.70	no
125439	gram_stain	BacteriaNetⓘ	positive	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis niigatensis strain DSM 45165
PATRIC: 369932.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.80	yes
125438	anaerobic	anaerobicⓘ	no	95.92	yes
125438	spore-forming	spore-formingⓘ	yes	77.90	no
125438	aerobic	aerobicⓘ	yes	89.97	yes
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	89.10	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
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

#15470	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45165
#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)
#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 echigonensis (DSM 45165, CCTCC AB 206020, CIP 109735)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

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_002846615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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