Name: Amycolatopsis niigatensis LC11
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13266

Type strain:

Species: Amycolatopsis niigatensis

Strain Designation: LC11

Culture col. no.: DSM 45165, CCTCC AB 206020, CIP 109735, IAM 15388, JCM 21832

Strain history: IAM 15388 <-- L. Ding LC11.

NCBI tax ID(s): 369932 (species)

SI-ID 309426

IAM 15388, JCM 21832, CIP 109735

Special Collections

Section

Amycolatopsis niigatensis LC11 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from filtration substrate made from volcanic soil.

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

Information on morphological and physiological properties Morphology

[Ref.: #32003]	Gram stain	positive

[Ref.: #32003]	Motility	no

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

		Temperature
[Ref.: #15470]	growth	28 °C
[Ref.: #32003]	growth	5.0-45 °C
[Ref.: #32003]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

	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.: #69481]

Ability of spore formation

yes Confidence in %100

	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.: #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]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #32003]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #32003]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #32003]	rhamnose ChEBI	+	carbon source
[Ref.: #32003]	ribitol ChEBI	+	carbon source
[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.: #32003]	acid phosphatase	+	3.1.3.2
[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.: #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.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32003]	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.: #32003]	gelatinase	+
[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.: #32003]	pyrazinamidase	+	3.5.1.B15
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #32003]	urease	+	3.5.1.5
[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.: #15470]	25331	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.: #15470]	14334	-	+	-	+/-	-	+	-	-	-	-	+/-	+/-	-	-	-	-	+/-	+	+	-

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

[Ref.: #15470]	Sample type/isolated from	filtration substrate made from volcanic soil
[Ref.: #15470]	Geographic location (country and/or sea, region)	Niigata
[Ref.: #15470]	Country	Japan
[Ref.: #15470]	Country ISO 3 Code	JPN
[Ref.: #15470]	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
* 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 AB248537 (>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.: #15470]

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.: #15470]	Amycolatopsis niigatensis gene for 16S rRNA, partial sequence	AB248537	1472	GenBank ENA	369932 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amycolatopsis niigatensis DSM 45165	GCA_002846615	contig	GenBank ENA	369932 tax ID
[Ref.: #66792]	Amycolatopsis niigatensis strain DSM 45165	369932.4	wgs	PATRIC	369932 tax ID	*
[Ref.: #66792]	Amycolatopsis niigatensis DSM 45165	2627854290	draft	JGI IMG/M	369932 tax ID	*

[Ref.: #15470]	GC-content	72.4 mol%
[Ref.: #67770]	GC-content	72.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	69.5 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 niigatensis strain DSM 45165 PATRIC: 369932.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Amycolatopsis niigatensis strain DSM 45165 PATRIC: 369932.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	86.803	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.921	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	77.897	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	89.97	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	89.1	yes

Availability in culture collections External links

[Ref.: #15470]

Culture collection no.

DSM 45165, CCTCC AB 206020, CIP 109735, IAM 15388, JCM 21832

[Ref.: #82470]

SI-ID 309426

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)

#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 .

#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 )

#82470

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-ID309426.1 )

#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 niigatensis strain DSM 45165

Amycolatopsis niigatensis strain DSM 45165

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