Jongsikchunia kroppenstedtii (DSM 45133, CIP 110031, KCTC 19360)

Name: Jongsikchunia kroppenstedtii (DSM 45133, CIP 110031, KCTC 19360)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10620

Type strain

Strain Designation NP8-5

Culture col. no. DSM 45133 CIP 110031 KCTC 19360 NP8-5 JCM 16948

NCBI tax ID(s) 468556 1121721

Special Collections DSMZ JCM KCTC CIP Wink compendium Literature strains

History <- K. K. Kim; NP8-5 KCTC 19360 <-- K. K. Kim NP8-5. <- KK Kim, KRIBB CIP <- 2009, DSMZ <- K. K. Kim, KCTC, Korea: strain NP8-5

Links

Jongsikchunia kroppenstedtii NP8-5 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from polluted stream.

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

Name and taxonomic classification

SI-ID 364135

DSM 45133,KCTC 19360,JCM 16948,CIP 110031

@ref 20215

Last LPSN update 2026-02-09 11:20:18

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Gordoniaceae

Genus Jongsikchunia

Species Jongsikchunia kroppenstedtii

Full scientific name Jongsikchunia kroppenstedtii (Kim et al. 2009) Nouioui et al. 2018

Synonyms (1)

Gordonia kroppenstedtii

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
29065	positive	rod-shaped
67771	positive
120504	positive	rod-shaped
125438			91.5
125438	positive		92.759

Colony morphology

@ref	Colony color	Incubation period	Medium used
20169	Cream (9001)	10-14 days	ISP 2
20169	Grey white (9002)	10-14 days	ISP 3
20169	Grey white (9002)	10-14 days	ISP 4
20169	Grey white (9002)	10-14 days	ISP 5
20169	Light ivory (1015)	10-14 days	ISP 6
20169		10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20169		ISP 2
20169		ISP 3
20169		ISP 4
20169		ISP 5
20169		ISP 6
20169		ISP 7

Multimedia

@ref:	12380
multimedia content:	DSM_45133.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45133.jpg
caption:	Medium 535 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12380	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20169	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
20169	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:
20169	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
20169	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
20169	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20169	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
37898	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120504	CIP Medium 6	Medium recipe at CIP
120504	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
12380	positive	growth	28
20169	positive	optimum	28
29065	positive	growth	10-30
29065	positive	optimum	25-30
37898	positive	growth	30
67770	positive	growth	28
67771	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
29065	positive	optimum	06-07
29065	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29065	aerobe
67771	aerobe
120504	obligate aerobe
125438	aerobe	90.892
125439	obligate aerobe	99.4

Spore formation

29065

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29065	NaCl	positive	growth	1-6.5 %
29065	NaCl	positive	optimum	<10 %

Observation

67770

Observationquinones: MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29065	16449 ChEBI	alanine	+	carbon source
20169	22599 ChEBI	arabinose	+/-
20169	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
29065	27689 ChEBI	decanoate	+	carbon source
29065	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
20169	28757 ChEBI	fructose	+/-
29065	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
20169	17234 ChEBI	glucose	+
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
29065	25017 ChEBI	leucine	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
20169	29864 ChEBI	mannitol	+/-
20169	17268 ChEBI	myo-inositol	+/-
29065	17268 ChEBI	myo-inositol	+	carbon source
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
120504	17632 ChEBI	nitrate	-	reduction
120504	16301 ChEBI	nitrite	-	reduction
20169	16634 ChEBI	raffinose	-
20169	26546 ChEBI	rhamnose	+/-
29065	33942 ChEBI	ribose	+	carbon source
29065	17822 ChEBI	serine	+	carbon source
29065	30031 ChEBI	succinate	+	carbon source
20169	17992 ChEBI	sucrose	+/-
29065	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
20169	18222 ChEBI	xylose	+/-

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120504	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
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
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	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
29065	catalase	+	1.11.1.6
120504	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
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	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
120504	oxidase	-
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
29065	urease	+	3.5.1.5
120504	urease	+	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

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
20169	-	-	-	+	-	-	+	-	-	-	-	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
20169	not determinedn.d.	+	+	+	+	+	-	-	-	-	+	+	-	+	-	+	+	-	-	-
120504	-	-	+	+	-	+	-	-	-	-	+	+	-	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12380	polluted stream	Gumi	Republic of Korea	KOR	Asia
67770	Sediment of a polluted stream	Gumi	Republic of Korea	KOR	Asia
67771	From sewage	Gwangam Stream, Gumi	Republic of Korea	KOR	Asia
120504	Environment, Stream, polluted	Gumi	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12380	1	Risk group (German classification) According to TRBA 466
120504	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM5203815v1 assembly for Jongsikchunia kroppenstedtii DSM 45133	scaffold	GCA_052038155			1121721	71.86
67770	ASM38048v1 assembly for Jongsikchunia kroppenstedtii DSM 45133 NP8-5	contig	GCA_000380485	468556.3	2519899672	468556	68.99

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12380	Gordonia sp. NP8-5 partial 16S rRNA gene, strain NP8-5	AM883151	1463		468556

GC content

@ref	GC-content (mol%)	Method
12380	68.5	high performance liquid chromatography (HPLC)
29065	68.5
67770	67.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Jongsikchunia kroppenstedtii DSM 45133 NP8-5
NCBI: GCA_000380485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	88.20	no
125439	motility	BacteriaNetⓘ	yes	51.30	no
125439	gram_stain	BacteriaNetⓘ	positive	70.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gordonia kroppenstedtii DSM 45133
PATRIC: 468556.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.76	yes
125438	anaerobic	anaerobicⓘ	no	97.55	yes
125438	spore-forming	spore-formingⓘ	no	64.58	yes
125438	aerobic	aerobicⓘ	yes	90.89	yes
125438	thermophilic	thermophileⓘ	no	96.00	no
125438	flagellated	motile2+ⓘ	no	91.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome Analysis Identifies a Novel Type III Secretion System (T3SS) Category in Vibrio Species.	Zakaria D, Matsuda S, Iida T, Hayashi T, Arita M.	Microorganisms	10.3390/microorganisms11020290	2023
	The Small RNA NcS25 Regulates Biological Amine-Transporting Outer Membrane Porin BCAL3473 in Burkholderia cenocepacia.	Sass AM, Coenye T.	mSphere	10.1128/msphere.00083-23	2023
	Antagonistic Properties of Some Halophilic Thermoactinomycetes Isolated from Superficial Sediment of a Solar Saltern and Production of Cyclic Antimicrobial Peptides by the Novel Isolate Paludifilum halophilum.	Frikha Dammak D, Zarai Z, Najah S, Abdennabi R, Belbahri L, Rateb ME, Mejdoub H, Maalej S.	Biomed Res Int	10.1155/2017/1205258	2017
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Genetics	Genomic and taxonomic characterization of Niallia pakistanensis sp. nov. NCCP-28^T: a novel antibiotic-resistant and heavy-metal-tolerant bacterium isolated from the legume rhizosphere in Pakistan.	Manzoor S, Abbas S, Zulfiqar S, Wu D, Wang HC, Li WJ, Arshad M, Ahmed I.	Antonie Van Leeuwenhoek	10.1007/s10482-025-02132-6	2025
Phylogeny	Kroppenstedtia guangzhouensis sp. nov., a thermoactinomycete isolated from soil.	Yang G, Qin D, Wu C, Yuan Y, Zhou S, Cai Y.	Int J Syst Evol Microbiol	10.1099/ijs.0.051011-0	2013
Phylogeny	Gordonia kroppenstedtii sp. nov., a phenol-degrading actinomycete isolated from a polluted stream.	Kim KK, Lee KC, Klenk HP, Oh HM, Lee JS	Int J Syst Evol Microbiol	10.1099/ijs.0.005322-0	2009

References

#12380	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45133
#20169	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#25495	IJSEM 1992 2009 ( DOI 10.1099/ijs.0.005322-0 , PubMed 19567568 )
#29065	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 #25495
#37898	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#120504	Collection of Institut Pasteur ; Curators of the CIP; CIP 110031
#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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Jongsikchunia kroppenstedtii (DSM 45133, CIP 110031, KCTC 19360)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

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_052038155

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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