Dietzia cercidiphylli (DSM 45140, CCTCC AA 207016, JCM 16002)

Name: Dietzia cercidiphylli (DSM 45140, CCTCC AA 207016, JCM 16002)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4260

Type strain

Culture col. no. DSM 45140 CCTCC AA 207016 JCM 16002 YIM 65002

NCBI tax ID(s) 498199

Special Collections DSMZ JCM Wink compendium Literature strains

History <- S.-K. Tang; YIM 65002 <- J. Li DSM 45140 <-- S.-K. Tang YIM 65002 <-- J. Li.

Links

Dietzia cercidiphylli DSM 45140 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from surface sterilized root sample of Cercidiphyllum japonicum.

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

Name and taxonomic classification

SI-ID 407580

JCM 16002,DSM 45140

@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 cercidiphylli

Full scientific name Dietzia cercidiphylli Li et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
31198	positive	rod-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
19716	Pure orange	10-14 days	ISP 2
19716		10-14 days	ISP 3
19716		10-14 days	ISP 4
19716		10-14 days	ISP 5
19716		10-14 days	ISP 6
19716	Pure orange	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19716		ISP 2
19716		ISP 3
19716		ISP 4
19716		ISP 5
19716		ISP 6
19716		ISP 7

Pigmentation

31198

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12384	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
19716	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
19716	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:
19716	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
19716	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
19716	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
19716	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)	Range
12384	positive	growth	28	mesophilic
19716	positive	optimum	28	mesophilic
31198	positive	growth	10-37
31198	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

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

Physiology and metabolism

Oxygen tolerance

31198

Oxygen toleranceaerobe

Spore formation

31198

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31198	NaCl	positive	growth	0-10 %
31198	NaCl	positive	optimum	0-10 %

Observation

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31198	22599 ChEBI	arabinose	+	carbon source
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
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
31198	28757 ChEBI	fructose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
31198	17234 ChEBI	glucose	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
31198	17716 ChEBI	lactose	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
31198	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
31198	37684 ChEBI	mannose	+	carbon source
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
31198	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
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
31198	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	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
31198	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
19716	-	-	-	+	-	-	+	-	-	-	-	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
19716	not determinedn.d.	+	+	+	-	+	-	-	-	-	+	-	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
12384	surface sterilized root sample of Cercidiphyllum japonicum	Cercidiphyllum japonicum	Yunnan Province	China	CHN	Asia
67770	Surface-sterilized root of Cercidiphyllum japonicum from Yunnan Province	Cercidiphyllum japonicum		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence HQ259255 (>99% sequence identity) for Dietzia from Microbeatlas

Aquatic Samples	1379
Soil Samples	321
Animal Samples	3158
Plant Samples	158
Total Samples	5016

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12384	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953154v1 assembly for Dietzia cercidiphylli JCM 16002	scaffold	GCA_039531545	498199	66.76

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Dietzia cercidiphylli culture-collection DSM:45140 16S ribosomal RNA gene, partial sequence	HQ259255	1439	498199
12384	Dietzia cercidiphylli strain YIM 65002 16S ribosomal RNA gene, partial sequence	EU375846	1456	498199
124043	Dietzia cercidiphylli strain YIM 65002 16S ribosomal RNA gene, partial sequence.	MW111212	649	498199

GC content

@ref	GC-content (mol%)	Method
12384	72.6
67770	72.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis.	Dahal RH, Kim S, Kim YK, Kim ES, Kim J.	Front Microbiol	10.3389/fmicb.2023.1174832	2023
Metabolism	Phylogenetic diversity and biological activity of actinobacteria isolated from the Chukchi Shelf marine sediments in the Arctic Ocean.	Yuan M, Yu Y, Li HR, Dong N, Zhang XH.	Mar Drugs	10.3390/md12031281	2014
	Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems.	Fretin M, Martin B, Rifa E, Isabelle VM, Pomies D, Ferlay A, Montel MC, Delbes C.	Sci Rep	10.1038/s41598-017-18447-y	2018
Metabolism	Bacteria in crude oil survived autoclaving and stimulated differentially by exogenous bacteria.	Gong XC, Liu ZS, Guo P, Chi CQ, Chen J, Wang XB, Tang YQ, Wu XL, Liu CZ.	PLoS One	10.1371/journal.pone.0040842	2012
Phylogeny	Dietzia aurantiaca sp. nov., isolated from a human clinical specimen.	Kampfer P, Falsen E, Frischmann A, Busse HJ.	Int J Syst Evol Microbiol	10.1099/ijs.0.032557-0	2012
Phylogeny	Dietzia aerolata sp. nov., isolated from the air of a duck barn, and emended description of the genus Dietzia Rainey et al. 1995.	Kampfer P, Langer S, Martin E, Jackel U, Busse HJ.	Int J Syst Evol Microbiol	10.1099/ijs.0.012807-0	2010
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

#12384	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45140
#19716	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
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 cercidiphylli (DSM 45140, CCTCC AA 207016, JCM 16002)

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

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039531545

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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