Nocardioides ginkgobilobae (DSM 100492, KCTC 39594, SYP-A7303)

Name: Nocardioides ginkgobilobae (DSM 100492, KCTC 39594, SYP-A7303)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132516

Type strain

Strain Designation SYP-A7303

Culture col. no. DSM 100492 KCTC 39594 SYP-A7303 JCM 30556

NCBI tax ID(s) 1630595

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- Y. Zhang, Shenyang Pharmaceutical Univ., China; SYP-A7303 <- H. Xu JCM <-- Y.-X. Zhang; Shenyang Pharm. Univ., China; SYP-A7303.

Links

Nocardioides ginkgobilobae SYP-A7303 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root of Ginkgo biloba L..

Gram-positive rod-shaped colony-forming aerobe 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407567

KCTC 39594,JCM 30556,DSM 100492

@ref 20215

Last LPSN update 2026-05-29 08:37:52

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides ginkgobilobae

Full scientific name Nocardioides ginkgobilobae Xu et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43657	positive	1.7-2.6 µm	0.7 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43657	1-2 mm	Yellow	circular	3 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43657	Reasoner's 2A agar (R2A)
24305	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

Culture temp

@ref	Growth	Type	Temperature (°C)
24305	positive	growth	28
43657	positive	growth	21-42
43657	positive	optimum	28
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
43657	positive	optimum	7
43657	positive	growth	4-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

43657

Oxygen toleranceaerobe

Spore formation

43657

Spore formationno

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
43657		NaCl	positive	growth	0-6 %(w/v)
43657	non-halophilic	NaCl	positive	optimum	0 %(w/v)

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43657	16651 ChEBI	(S)-lactate	-	carbon source
43657	64552 ChEBI	2-hydroxybutyrate	-	carbon source
43657	16763 ChEBI	2-oxobutanoate	-	carbon source
43657	30916 ChEBI	2-oxoglutarate	-	carbon source
43657	37054 ChEBI	3-hydroxybutyrate	-	carbon source
43657	73918 ChEBI	3-O-methyl-D-glucose	-	carbon source
43657	30089 ChEBI	acetate	+	carbon source
43657	13705 ChEBI	acetoacetate	+	carbon source
43657	17925 ChEBI	alpha-D-glucose	+	carbon source
43657	36219 ChEBI	alpha-lactose	-	carbon source
43657	73706 ChEBI	bromosuccinate	-	carbon source
43657	17057 ChEBI	cellobiose	+	carbon source
43657	62968 ChEBI	cellulose	-	hydrolysis
43657	18333 ChEBI	D-arabitol	+	carbon source
43657	29990 ChEBI	D-aspartate	-	carbon source
43657	15824 ChEBI	D-fructose	-	carbon source
43657	78697 ChEBI	D-fructose 6-phosphate	-	carbon source
43657	28847 ChEBI	D-fucose	-	carbon source
43657	12936 ChEBI	D-galactose	-	carbon source
43657	18024 ChEBI	D-galacturonic acid	+/-	carbon source
43657	8391 ChEBI	D-gluconate	+	carbon source
43657	17634 ChEBI	D-glucose	+	carbon source
43657	14314 ChEBI	D-glucose 6-phosphate	+	carbon source
43657	15588 ChEBI	D-malate	-	carbon source
43657	16899 ChEBI	D-mannitol	-	carbon source
43657	16024 ChEBI	D-mannose	-	carbon source
43657	23652 ChEBI	dextrin	+	carbon source
43657	4853 ChEBI	esculin	+	hydrolysis
43657	16537 ChEBI	galactarate	-	carbon source
43657	5291 ChEBI	gelatin	-	hydrolysis
43657	5291 ChEBI	gelatin	+	carbon source
43657	24265 ChEBI	gluconate	-	carbon source
43657	17234 ChEBI	glucose	-	fermentation
43657	32323 ChEBI	glucuronamide	-	carbon source
43657	17754 ChEBI	glycerol	+	carbon source
43657	17596 ChEBI	inosine	-	carbon source
43657	16977 ChEBI	L-alanine	-	carbon source
43657	16467 ChEBI	L-arginine	-	carbon source
43657	29991 ChEBI	L-aspartate	+	carbon source
43657	18287 ChEBI	L-fucose	-	carbon source
43657	29985 ChEBI	L-glutamate	+	carbon source
43657	15971 ChEBI	L-histidine	-	carbon source
43657	15589 ChEBI	L-malate	-	carbon source
43657	18183 ChEBI	L-pyroglutamic acid	-	carbon source
43657	62345 ChEBI	L-rhamnose	-	carbon source
43657	17115 ChEBI	L-serine	-	carbon source
43657	17306 ChEBI	maltose	+	carbon source
43657	17268 ChEBI	myo-inositol	+	carbon source
43657	17632 ChEBI	nitrate	+	reduction
43657	17309 ChEBI	pectin	+	carbon source
43657	17272 ChEBI	propionate	+	carbon source
43657	26490 ChEBI	quinate	-	carbon source
43657	17814 ChEBI	salicin	+	carbon source
43657	28017 ChEBI	starch	-	hydrolysis
43657	17992 ChEBI	sucrose	+	carbon source
43657	27082 ChEBI	trehalose	+	carbon source
43657	32528 ChEBI	turanose	+	carbon source
43657	53424 ChEBI	tween 20	-	hydrolysis
43657	53423 ChEBI	tween 40	-	hydrolysis
43657	53425 ChEBI	tween 60	+	hydrolysis
43657	53426 ChEBI	tween 80	+	hydrolysis
43657	16199 ChEBI	urea	+	degradation

Antibiotic resistance

@ref	ChEBI	Metabolite
43657		1 % sodium lactate
43657	16523	d-serine
43657	71321	fusidate
43657	32735	guanidinium chloride
43657	6472	lincomycin
43657	48607	lithium chloride
43657	50694	minocycline
43657	75273	niaproof
43657	75248	potassium tellurite
43657	29673	rifamycin sv
43657	75229	sodium bromate
43657	75198	tetrazolium blue
43657	75193	tetrazolium violet
43657	45735	troleandomycin
43657	28001	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43657	16136 ChEBI	hydrogen sulfide
43657	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43657	acid phosphatase	+	3.1.3.2
43657	alkaline phosphatase	+	3.1.3.1
43657	alpha-galactosidase	-	3.2.1.22
43657	alpha-glucosidase	+	3.2.1.20
43657	alpha-mannosidase	-	3.2.1.24
43657	arginine dihydrolase	-	3.5.3.6
43657	beta-D-fucosidase	-	3.2.1.38
43657	beta-galactosidase	+	3.2.1.23
43657	beta-glucosidase	+	3.2.1.21
43657	beta-glucuronidase	-	3.2.1.31
43657	catalase	-	1.11.1.6
43657	chymotrypsin	-	3.4.4.5
43657	cystine arylamidase	+	3.4.11.3
43657	cytochrome oxidase	-	1.9.3.1
43657	esterase (C 4)	+
43657	esterase Lipase (C 8)	+
43657	gelatinase	-
43657	lipase (C 14)	+
43657	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43657	trypsin	+	3.4.21.4
43657	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Sterilized plant part
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24305	surface-sterilized root of Ginkgo biloba L.	Ginkgo biloba	Liaoning Province, Dandong (40° 41' 31.2'' N 124° 33' 46.1'' E)	China	CHN	Asia	40.692	124.563 40.692/124.563
43657	a root of Ginkgo biloba L. collected from Dandong	Ginkgo biloba	Dandong, Liaoning province	China	CHN	Asia	40.692	124.562 40.692/124.562
67770	Root of Ginkgo biloba L.	Ginkgo biloba

Taxonmaps

69479

Global distribution of 16S sequence KP128917 (>99% sequence identity) for Nocardioides ginkgobilobae subclade from Microbeatlas

Aquatic Samples	893
Soil Samples	422
Animal Samples	1147
Plant Samples	118
Total Samples	2580

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24305	1	Risk group (German classification)

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24305	Nocardioides sp. SYP-A7303 16S ribosomal RNA gene, partial sequence	KP128917	1552		1630595

GC content

@ref	GC-content (mol%)	Method
43657	72	high performance liquid chromatography (HPLC)
24305	72.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides eburneus sp. nov., isolated from commercial soil.	Kang MS, Yu JY, Kim YH, Dong K, Srinivasan S, Lee SS.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006743	2025
	Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza.	Chen X, Zheng Z, Li F, Ma X, Chen F, Chen M, Tuo L.	Syst Appl Microbiol	10.1016/j.syapm.2022.126391	2023
Phylogeny	Nocardioides mangrovi sp. nov., a novel endophytic actinobacterium isolated from root of Kandelia candel.	Chen MS, Chen F, Chen XH, Zheng ZQ, Ma X, Tuo L	Int J Syst Evol Microbiol	10.1099/ijsem.0.005295	2022
Phylogeny	Nocardioides agrisoli sp. nov., isolated from farmland soil.	Wang X, Jiang WK, Cui MD, Yang ZG, Yu X, Hu G, Zhang H, Hong Q	Int J Syst Evol Microbiol	10.1099/ijsem.0.002158	2017
Phylogeny	Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L.	Xu H, Zhang S, Cheng J, Asem MD, Zhang MY, Manikprabhu D, Zhang TY, Wu YY, Li WJ, Zhang YX	Int J Syst Evol Microbiol	10.1099/ijsem.0.000983	2016

References

#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 )
#24305	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100492
#43657	Huan Xu, Sheng Zhang, Juan Cheng, Mipeshwaree Devi Asem, Meng-Yue Zhang, Deene Manikprabhu, Tian-Yuan Zhang, Ying-Ying Wu, Wen-Jun Li, Yi-Xuan Zhang: Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L.. IJSEM 66: 2013 - 2018 2016 ( DOI 10.1099/ijsem.0.000983 , PubMed 26902329 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Nocardioides ginkgobilobae (DSM 100492, KCTC 39594, SYP-A7303)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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