Dietzia kunjamensis subsp. schimae (DSM 45139, CCTCC AA 207015, JCM 16003)

Name: Dietzia kunjamensis subsp. schimae (DSM 45139, CCTCC AA 207015, JCM 16003)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4261

Type strain

Culture col. no. DSM 45139 CCTCC AA 207015 JCM 16003 YIM 65001

NCBI tax ID(s) 498198

Special Collections DSMZ JCM Wink compendium Literature strains

History <- S.-K. Tang; YIM 65001 <- J. Li DSM 45139 <-- S.-K. Tang YIM 65001 <-- J. Li.

Links

Dietzia kunjamensis subsp. schimae DSM 45139 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from surface-sterilized stem sample of Schima sp..

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

Name and taxonomic classification

SI-ID 360130

DSM 45139,JCM 16003,LMG 28487

@ref 20215

Last LPSN update 2026-02-09 11:18:41

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Dietziaceae

Genus Dietzia

Species Dietzia kunjamensis subsp. schimae

Full scientific name Dietzia kunjamensis subsp. schimae (Li et al. 2008) Nouioui et al. 2018

Synonyms (1)

Dietzia schimae

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31198	positive	rod-shaped
125439	positive		98.5
125438			93.1
125438	positive		90.417

Colony morphology

@ref	Colony color	Incubation period	Medium used
20170	Pastel orange (2003)	10-14 days	ISP 2
20170		10-14 days	ISP 3
20170		10-14 days	ISP 4
20170		10-14 days	ISP 5
20170		10-14 days	ISP 6
20170	Pastel orange (2003)	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20170		ISP 2
20170		ISP 3
20170		IPS 4
20170		ISP 5
20170		ISP 6
20170		ISP 7

Pigmentation

31198

Productionyes

Multimedia

@ref:	12383
multimedia content:	DSM_45139.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45139.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12383	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
12383	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
20170	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
20170	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:
20170	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
20170	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
20170	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
20170	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

Culture temp

@ref	Growth	Type	Temperature (°C)
12383	positive	growth	28
20170	positive	optimum	28
31198	positive	growth	10-45
31198	positive	optimum	28
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31198	positive	optimum	7
31198	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31198	aerobe
125439	obligate aerobe	93.8

Spore formation

31198

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31198	NaCl	positive	growth	0-15 %
31198	NaCl	positive	optimum	0-15 %

Observation

@ref	Observation
31198	aggregates in chains
67770	quinones: MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31198	17057 ChEBI	cellobiose	+	carbon source
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
31198	28757 ChEBI	fructose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31198	17234 ChEBI	glucose	+	carbon source
31198	17754 ChEBI	glycerol	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
31198	17716 ChEBI	lactose	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
31198	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
31198	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
31198	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
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
68382	alkaline phosphatase	+	3.1.3.1	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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
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
31198	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68369	gelatinase	-		from API 20NE
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
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
68369	urease	-	3.5.1.5	from API 20NE
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
20170	-	-	-	+	-	-	+	-	-	-	-	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
20170	not determinedn.d.	+	+	+	-	+	-	-	-	-	+	-	-	-	-	+	+	-	-	-
12383	-	+	+/-	+	+/-	+	-	-	-	-	+/-	+/-	-	-	-	+	-	-	-	-

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
12383	+	-	-	-	-	+/-	-	-	-	-	+/-	-	-	-	-	-	+/-	-	+/-	+/-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Stem (Branch)
#Host Body-Site	#Plant	#Sterilized plant part

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
12383	surface-sterilized stem sample of Schima sp.	Schima	Yunnan	China	CHN	Asia
67770	Surface-sterilized stem of Schima sp. from Yunnan Province	Schima		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence HQ259254 (>99% sequence identity) for Dietzia from Microbeatlas

Aquatic Samples	2957
Soil Samples	1292
Animal Samples	6479
Plant Samples	280
Total Samples	11008

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12383	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
66792	IMG-taxon 2724679793 annotated assembly for Dietzia kunjamensis subsp. schimae DSM 45139	contig	GCA_900182685	498198.3	2724679793	498198	75.64
124043	ASM3953156v1 assembly for Dietzia kunjamensis subsp. schimae JCM 16003	scaffold	GCA_039531565			498198	71.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Dietzia schimae culture-collection DSM:45139 16S ribosomal RNA gene, partial sequence	HQ259254	1439		498198
12383	Dietzia schimae strain YIM 65001 16S ribosomal RNA gene, partial sequence	EU375845	1515		498198

GC content

@ref	GC-content (mol%)	Method
12383	71.9
67770	70.5	genome sequence analysis
67770	71.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dietzia kunjamensis subsp. schimae DSM 45139
NCBI: GCA_900182685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	66.80	no
125439	motility	BacteriaNetⓘ	no	73.20	no
125439	gram_stain	BacteriaNetⓘ	positive	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dietzia schimae strain DSM 45139
PATRIC: 498198.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.42	yes
125438	anaerobic	anaerobicⓘ	no	96.62	no
125438	spore-forming	spore-formingⓘ	no	68.98	yes
125438	aerobic	aerobicⓘ	yes	88.20	yes
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	no	93.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
Phylogeny	Dietzia schimae sp. nov. and Dietzia cercidiphylli sp. nov., from surface-sterilized plant tissues.	Li J, Zhao GZ, Zhang YQ, Klenk HP, Pukall R, Qin S, Xu LH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/000919-0	2008

References

#12383	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45139
#20170	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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#27525	IJSEM 2549 2008 ( DOI 10.1099/ijs.0.2008/000919-0 , PubMed 18984691 )
#31198	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 #27525
#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 .
#68379	Automatically annotated from API Coryne .
#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 .
#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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Dietzia kunjamensis subsp. schimae (DSM 45139, CCTCC AA 207015, JCM 16003)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API coryne

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_900182685

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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