Amnibacterium kyonggiense (DSM 24782, JCM 16463, KEMC 51201-037)

Name: Amnibacterium kyonggiense (DSM 24782, JCM 16463, KEMC 51201-037)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7508

Type strain

Strain Designation KSL51201-037

Culture col. no. DSM 24782 JCM 16463 KEMC 51201-037 KSL51201-037 NBRC 109360 1 more

NCBI tax ID(s) 595671

Special Collections DSMZ JCM Wink compendium Literature strains

History DSMZ <- JCM <- S.-S. Lee; Graduate School of Kyonggi University; KSL51201-037 JCM <-- S.-S. Lee KSL51201-037.

Links

Amnibacterium kyonggiense KSL51201-037 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Anyang stream.

Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401682

JCM 16463,DSM 24782

@ref 20215

Last LPSN update 2026-05-29 08:26:40

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Amnibacterium

Species Amnibacterium kyonggiense

Full scientific name Amnibacterium kyonggiense Kim and Lee 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29690	positive	0.275 µm	0.175 µm	rod-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
21380	Lemon yellow (1012)	10-14 days	ISP 2
21380	n.d.	10-14 days	ISP 3
21380	none	10-14 days	ISP 4
21380	none	10-14 days	ISP 5
21380	none	10-14 days	ISP 7
21380	none	10-14 days	Suter with tyrosine
21380	none	10-14 days	Suter without tyrosine

Multicellular morphology

@ref	Forms multicellular complex	Medium name
21380		ISP 2
21380		ISP 3
21380		ISP 4
21380		ISP 5
21380		ISP 7
21380		Suter with tyrosine
21380		Suter without tyrosine

Pigmentation

29690

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17770	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
21380	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21380	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21380	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21380	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21380	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21380	Suter with tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21380	Suter without tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)
17770	positive	growth	28
29690	positive	growth	10-37
29690	positive	optimum	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH
29690	positive	optimum	6
29690	positive	growth	5.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29690	aerobe
125439	obligate aerobe	99.586

Spore formation

@ref	Spore formation	Confidence
125439		91.737

Halophily

@ref	Salt	Growth	Tested relation	Concentration
21380	NaCl	positive	growth	0 %
29690	NaCl	positive	growth	0-2 %

Observation

@ref	Observation
29690	aggregates in clumps
67770	quinones: MK-11, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
21380	22599 ChEBI	arabinose	-
21380	62968 ChEBI	cellulose	-
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
29690	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
21380	28757 ChEBI	fructose	-
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
21380	17234 ChEBI	glucose	-
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
21380	37684 ChEBI	mannose	-
21380	17268 ChEBI	myo-inositol	-
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
21380	16634 ChEBI	raffinose	-
21380	26546 ChEBI	rhamnose	-
21380	17992 ChEBI	sucrose	-
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
21380	18222 ChEBI	xylose	-

Enzymes

@ref	Value	Activity	Ec
29690	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
29690	alpha-galactosidase	+	3.2.1.22
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
29690	catalase	+	1.11.1.6
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
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
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
21380	-	-	-	-	-	-	-	-	+	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

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
21380	not determinedn.d.	+/-	+	+	-	+	+/-	+/-	-	-	+	+	+	-	-	+/-	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
17770	Anyang stream	Republic of Korea	KOR	Asia
67770	Anyang stream	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17770	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	ASM436455v1 assembly for Amnibacterium kyonggiense DSM 24782	contig	GCA_004364555	595671.3	2734482167	595671	75.91
124043	ASM3953229v1 assembly for Amnibacterium kyonggiense JCM 16463	contig	GCA_039532295			595671	70.14

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17770	Amnibacterium kyonggiense 16S ribosomal RNA gene, partial sequence	FJ527819	1459		595671

GC content

@ref	GC-content (mol%)	Method
17770	72.7	high performance liquid chromatography (HPLC)
29690	72.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM436455v1 assembly for Amnibacterium kyonggiense DSM 24782
BV-BRC: 595671.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.59	no
125439	gram_stain	BacteriaNetⓘ	positive	79.80	no
125439	motility	BacteriaNetⓘ	yes	41.20	no
125439	spore_formation	BacteriaNetⓘ	no	91.74	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amnibacterium kyonggiense strain DSM 24782
PATRIC: 595671.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.24	yes
125438	anaerobic	anaerobicⓘ	no	96.59	yes
125438	spore-forming	spore-formingⓘ	no	76.64	no
125438	aerobic	aerobicⓘ	yes	82.61	yes
125438	thermophilic	thermophileⓘ	no	97.51	no
125438	flagellated	motile2+ⓘ	no	82.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Naasia lichenicola sp. nov., an actinobacterium isolated from lichen.	Jiang LQ, Zhang K, Li GD, Wang XY, Shi SB, Li QY, An DF, Lang L, Wang LS, Jiang CL, Jiang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.003865	2020
Phylogeny	Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail.	Kim I, Chhetri G, Kim J, Seo T	Antonie Van Leeuwenhoek	10.1007/s10482-019-01302-7	2019
Phylogeny	Amnibacterium flavum sp. nov., a novel endophytic actinobacterium isolated from bark of Nerium indicum Mill.	Tuo L, Yan XR, Li FN, Yang C, An MB, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003156	2018
Phylogeny	Amnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum.	Li FN, Tuo L, Lee SM, Jin T, Liao S, Li W, Yan X, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002676	2018
Phylogeny	Amnibacterium soli sp. nov., an actinobacterium isolated from grass soil.	Jin L, Lee HG, Kim HS, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijs.0.052506-0	2013
Phylogeny	Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air.	Weon HY, Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Suzuki KI, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.046599-0	2012
Phylogeny	Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae.	Kim SJ, Lee SS	Int J Syst Evol Microbiol	10.1099/ijs.0.018788-0	2010

References

#17770	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24782
#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 )
#21380	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#26075	IJSEM 155 2011 ( DOI 10.1099/ijs.0.018788-0 , PubMed 20173001 )
#29690	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 #26075
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Amnibacterium kyonggiense (DSM 24782, JCM 16463, KEMC 51201-037)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004364555

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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