Rhodococcus erythropolis (DSM 45222, CGMCC 1.6580, KCTC 19205)

Name: Rhodococcus erythropolis (DSM 45222, CGMCC 1.6580, KCTC 19205)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11046

Type strain

Strain Designation djl-6

Culture col. no. DSM 45222 CGMCC 1.6580 KCTC 19205 djl-6 CCM 8451 1 more

NCBI tax ID(s) 1303681 334542

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- CGMCC; CGMCC 1.6580 JCM <-- CGMCC 1.6580 <-- J.-L. Xu et al. djl-6.

Links

Rhodococcus erythropolis djl-6 is an aerobe, Gram-positive, ovoid-shaped bacterium that was isolated from carbendazim-contaminated soil sample from a vegetable field.

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

Name and taxonomic classification

SI-ID 404329

KCTC 19205,JCM 15477,NCIM 5452,DSM 45222

@ref 20215

Last LPSN update 2026-05-29 08:27:28

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Rhodococcus

Species Rhodococcus erythropolis

Full scientific name Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980)

Synonyms (9)

Rhodococcus jialingiae
Rhodococcus degradans
Rhodococcus qingshengii
"Nocardia erythropolis"
Rhodococcus enclensis
"Mycobacterium erythropolis"
Rhodococcus baikonurensis
Nocardia calcarea
Arthrobacter picolinophilus

BacDive ID	Other strains from **Rhodococcus erythropolis** (68)	Type strain
10866	R. erythropolis A-0201, N11, DSM 43066, ATCC 25544, ATCC ... (type strain)
10851	R. erythropolis huber, 2411, DSM 312, ATCC 15591, CCUG 27198
10852	R. erythropolis B-297, DSM 313, ATCC 19140
10853	R. erythropolis DSM 743, ATCC 25544, CCM 277, NCIB 9158
10854	R. erythropolis B-286, DSM 772, DSM 43296
10855	R. erythropolis HA1, DSM 6344
10856	R. erythropolis CAA2, DSM 7337
10857	R. erythropolis MPropP3, DSM 8424
10858	R. erythropolis MP50, DSM 9675
10859	R. erythropolis C3II, DSM 9685
10860	R. erythropolis K2a, DSM 11397
10861	R. erythropolis EK2, DSM 12788
10862	R. erythropolis EK5, DSM 12789
10863	R. erythropolis DSM 20665, ATCC 27854, JCM 11573, CCM 2769, ...
10864	R. erythropolis T-16, DSM 43135, LBG A 3116, NCIB 9409, ETH ...
10865	R. erythropolis No 52, DSM 43060, ATCC 11048, CCM 2595, NCIB ...
10867	R. erythropolis DSM 43188, ATCC 19369, CBS 613.67, CCM 2597, ...
10868	R. erythropolis DSM 43200, DSM 314, NCIB 9905
10869	R. erythropolis A 20-17, Schering 254, DSM 43288, ATCC 14559
10870	R. erythropolis B-286, Schering 270, DSM 43296, ATCC 17895
10871	R. erythropolis B-285, Schering 271, DSM 43297, ATCC 17896
10872	R. erythropolis DSM 43574, CBS 611.67, SN 6400
10873	R. erythropolis TTD-1, DSM 43933
10874	R. erythropolis N63, DSM 43958
10876	R. erythropolis N60, DSM 43957
10877	R. erythropolis DSM 44235
10878	R. erythropolis 404-97, H1aT1, PWD28, DSM 44308
10879	R. erythropolis MAWF, DSM 44522
10880	R. erythropolis DTB, DSM 44534
10914	R. erythropolis 81 N Fr, DSM 43590
10996	R. erythropolis DSM 1069
130481	R. erythropolis DSM 26610, NCIMB 8147
131916	R. erythropolis Stev11, DSM 103048
134648	R. erythropolis TA 57, CIP 107391
137083	R. erythropolis CIP 104497, ATCC 15963, IAM 1399, IFO 12538, ...
137086	R. erythropolis P-8-1, CIP 104499, ATCC 15961, IAM 1484, ...
137088	R. erythropolis CIP 104500, ATCC 15962, IAM 1494, JCM 2895
137854	R. erythropolis IFP 192 P, CIP 101879
138041	R. erythropolis CIP 102573
138089	R. erythropolis CIP 104646, ATCC 21035, IFO 12320
138358	R. erythropolis CIP 106505, NRRL B-16531, ATCC 15960, JCM ...
139251	R. erythropolis CIP 104647, IAM 1414, IFO 12539, JCM 20158, ...
139773	R. erythropolis ACN1, DSM 105063
145711	R. erythropolis CCUG 29360
146519	R. erythropolis CCUG 31366
146583	R. erythropolis CCUG 31495
150997	R. erythropolis CCUG 42976
151111	R. erythropolis CCUG 43294
151622	R. erythropolis CCUG 44470
152104	R. erythropolis CCUG 45793
152657	R. erythropolis CCUG 47303
152710	R. erythropolis CCUG 47441
152741	R. erythropolis CCUG 47521
154681	R. erythropolis CCUG 54830
156842	R. erythropolis CCUG 66020
157817	R. erythropolis BG43, DSM 46869
157818	R. erythropolis Stevenage 150518_C15, DSM 107796
160170	R. erythropolis CCMMB1294, GK12, DSM 102980
162788	R. erythropolis JCM 20154, IAM 1400
162791	R. erythropolis JCM 20161, CIP 104648, IAM 1428, IFO 12540, ...
162792	R. erythropolis JCM 20165, IAM 1440
162796	R. erythropolis JCM 20170, IAM 1452
162803	R. erythropolis JCM 20186, IAM 1503
163709	R. erythropolis JCM 3011, CGMCC 4.1481, IFM 0020
166074	R. erythropolis JCM 9803
166075	R. erythropolis JCM 9804
166076	R. erythropolis JCM 9805
178953	R. erythropolis IMET 07252, STI07252

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32188	positive	ovoid-shaped
125438			90.5
125439			90.614

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15685	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
15685	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

Culture temp

@ref	Growth	Type	Temperature (°C)
15685	positive	growth	28
32188	positive	optimum	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH
32188	positive	optimum	7.75

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32188	aerobe
125439	obligate aerobe	96.887

Observation

67770

Observationquinones: MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32188	28644 ChEBI	2-oxopentanoate	+	carbon source
32188	30089 ChEBI	acetate	+	carbon source
32188	16449 ChEBI	alanine	+	carbon source
32188	23652 ChEBI	dextrin	+	carbon source
32188	28757 ChEBI	fructose	+	carbon source
32188	24265 ChEBI	gluconate	+	carbon source
32188	17234 ChEBI	glucose	+	carbon source
32188	17754 ChEBI	glycerol	+	carbon source
32188	21217 ChEBI	L-alaninamide	+	carbon source
32188	25115 ChEBI	malate	+	carbon source
32188	37684 ChEBI	mannose	+	carbon source
32188	33942 ChEBI	ribose	+	carbon source
32188	17992 ChEBI	sucrose	+	carbon source
32188	53423 ChEBI	tween 40	+	carbon source
32188	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32188	catalase	+	1.11.1.6
32188	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15685	carbendazim-contaminated soil sample from a vegetable field	Jiangsu province	China	CHN	Asia
67770	Carbendazim-contaminated soil from a vegetable field	Jiangsu Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ090961 (>99% sequence identity) for Nocardiaceae from Microbeatlas

Aquatic Samples	6494
Soil Samples	7777
Animal Samples	11681
Plant Samples	2835
Total Samples	28787

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15685	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	ASM2322159v1 assembly for Rhodococcus qingshengii JCM 15477 djl-6	complete	GCA_023221595	1303681.9	8113001176	1303681	97.73
67770	ASM164674v1 assembly for Rhodococcus qingshengii JCM 15477	contig	GCA_001646745	334542.13	2744054616	334542	52.95
66792	ASM131344v1 assembly for Rhodococcus qingshengii JCM 15477	contig	GCA_001313445	1303681.3	2734481946	1303681	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
15685	Rhodococcus qingshengii strain djl-6 16S ribosomal RNA gene, partial sequence	DQ090961	1484	1303681
124043	Rhodococcus qingshengii JCM 15477 strain H44 16S ribosomal RNA gene, partial sequence.	OR122181	1226	1303681
124043	Rhodococcus qingshengii strain JCM 15477 (T) 16S ribosomal RNA gene, partial sequence.	MK424306	1440	334542
124043	Rhodococcus qingshengii strain JCM 15477 16S ribosomal RNA gene, partial sequence.	MW111164	599	334542

GC content

@ref	GC-content (mol%)	Method
15685	59.1
67770	62.4	genome sequence analysis
67770	59.1	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2322159v1 assembly for Rhodococcus qingshengii JCM 15477 djl-6
NCBI: GCA_023221595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.89	no
125439	gram_stain	BacteriaNetⓘ	positive	84.86	no
125439	motility	BacteriaNetⓘ	no	90.61	no
125439	spore_formation	BacteriaNetⓘ	no	71.88	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodococcus qingshengii JCM 15477 djl-6
NCBI: GCA_023221595.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.34	yes
125438	anaerobic	anaerobicⓘ	no	97.47	yes
125438	aerobic	aerobicⓘ	yes	85.77	no
125438	spore-forming	spore-formingⓘ	yes	56.36	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	90.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome-Based Characterization of Plant-Associated Rhodococcus qingshengii RL1 Reveals Stress Tolerance and Plant-Microbe Interaction Traits.	Kuhl T, Chowdhury SP, Uhl J, Rothballer M.	Front Microbiol	10.3389/fmicb.2021.708605	2021
	Complete Genome Sequence of Rhodococcus qingshengii Strain CL-05, Isolated from Concrete.	Kiledal EA, McDermott SG, Shevchenko O, Ross J, Bediako S, Maresca JA.	Microbiol Resour Announc	10.1128/mra.00376-21	2021
	Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species.	Nahar A, Baker AL, Nichols DS, Bowman JP, Britz ML.	Microorganisms	10.3390/microorganisms9061253	2021
	iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments.	Dos Santos JDN, Joao SA, Martin J, Vicente F, Reyes F, Lage OM.	Microorganisms	10.3390/microorganisms10071471	2022
Genetics	Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8.	Thompson D, Cognat V, Goodfellow M, Koechler S, Heintz D, Carapito C, Van Dorsselaer A, Mahmoud H, Sangal V, Ismail W.	Front Microbiol	10.3389/fmicb.2020.01417	2020
	Biological conversion of aromatic monolignol compounds by a Pseudomonas isolate from sediments of the Baltic Sea.	Ravi K, Garcia-Hidalgo J, Nobel M, Gorwa-Grauslund MF, Liden G.	AMB Express	10.1186/s13568-018-0563-x	2018
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
	Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome.	Chuang S, Yang H, Wang X, Xue C, Jiang J, Hong Q	J Hazard Mater	10.1016/j.jhazmat.2021.125496	2021
Metabolism	Biodegradation of carbendazim by a novel actinobacterium Rhodococcus jialingiae djl-6-2.	Wang Z, Wang Y, Gong F, Zhang J, Hong Q, Li S	Chemosphere	10.1016/j.chemosphere.2010.08.040	2010
Metabolism	Functional analysis, diversity, and distribution of carbendazim hydrolases MheI and CbmA, responsible for the initial step in carbendazim degradation.	Zhang M, Bai X, Li Q, Zhang L, Zhu Q, Gao S, Ke Z, Jiang M, Hu J, Qiu J, Hong Q	Environ Microbiol	10.1111/1462-2920.16139	2022
Metabolism	Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium.	Xu JL, He J, Wang ZC, Wang K, Li WJ, Tang SK, Li SP.	Int J Syst Evol Microbiol	10.1099/ijs.0.65095-0	2007

References

#15685	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45222
#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 )
#28430	IJSEM 2754 2007 ( DOI 10.1099/ijs.0.65095-0 , PubMed 18048720 )
#32188	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 #28430
#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;
#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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Rhodococcus erythropolis (DSM 45222, CGMCC 1.6580, KCTC 19205)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_023221595

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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