Nocardioides simplex (CCUG 23611, JCM 1363, DSM 20130)

Name: Nocardioides simplex (CCUG 23611, JCM 1363, DSM 20130)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11100

Type strain

Culture col. no. CCUG 23611 JCM 1363 DSM 20130 ATCC 6946 CCM 1652 28 more

NCBI tax ID(s) 2045

Special Collections DSMZ CCUG JCM KCTC CIP Wink compendium

History <- NCIB <- NCTC <- H.L. Jensen (Corynebacterium simplex) K. Suzuki CNF 035 <-- AJ 1420 <-- ATCC 6946 <-- NCTC 4215 <-- H. L. Jensen. CIP <- 1982, ATCC <- NCTC, Corynebacterium simplex <- H.L. Jensen

Links

Nocardioides simplex CCUG 23611 is a mesophilic prokaryote that was isolated from soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 88162

LMG 16261,ATCC 6946,CCM 1652,DSM 20130,IMET 10368,NCIMB 8929,NCTC 4215,ATCC 15799,IAM 1660,NCIB 8929,CCUG 23611,JCM 1363,DSM 776,CCRC 10381,IFO 12069,IFO 3530,CECT466,VKM Ac-925,KCTC 9106,NCAIM B.01106,VKM B-667,KCTC 1003,IAM 3530,KCTC 3187,KCTC 9606,NBRC 12069,NBRC 3530,NRRL B-14051,NRRL B-3157,NCCB 39010,CCM 1908,LMD 39.10,NCIB 8913,HAMBI 1861,HAMBI 90,BCRC 10381,CCT 3022,KCTC 1002,NCIM 2449,CDBB 18,VKM Ac-1118,CIP 82.106

@ref 20215

Last LPSN update 2025-12-16 09:49:30

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides simplex

Full scientific name Nocardioides simplex (Jensen 1934) O'Donnell et al. 1983

Synonyms (3)

"Corynebacterium simplex"
Pimelobacter simplex
Arthrobacter simplex

BacDive ID	Other strains from **Nocardioides simplex** (8)	Type strain
11101	N. simplex DSM 20299, IAM 1398, JCM 1366, IFO 12679, ...
104699	N. simplex STH00414(ZIMET), F-1360, HKI 0414, FERM P-5362
104700	N. simplex SF002835(FSU),
104701	N. simplex SF000322(FSU),
104702	N. simplex SF001744(FSU),
104703	N. simplex SF005254(FSU),
144251	N. simplex CCUG 23927, LMG 3810
161393	N. simplex JCM 1367, IAM 1413, KCTC 9622

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.9

Colony morphology

@ref	Colony color	Incubation period	Medium used
18625	Colorless	10-14 days	ISP 2
18625	Colorless	10-14 days	ISP 3
18625	Colorless	10-14 days	ISP 4
18625	Colorless	10-14 days	ISP 5
18625	Colorless	10-14 days	ISP 6
18625	Colorless	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18625		ISP 2
18625		ISP 3
18625		ISP 4
18625		ISP 5
18625		ISP 6
18625		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8555	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18625	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
18625	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:
18625	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
18625	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
18625	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
18625	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
37734	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
8555	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
122620	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8555	positive	growth	28	mesophilic
37734	positive	growth	25	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98

Compound production

@ref	Compound
8555	steroids, 7-cyano
8555	pregnadienes
8555	5' nucleotides
8555	dienes
8555	steroids, 3-ketoDelta¹^,⁴

Murein

@ref	Murein short key	Type
8555	A41.01	A3gamma LL-Dpm-Gly

Observation

67770

Observationquinones: MK-8(H₄)

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	biotin biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	ethanol fermentation	100	2 of 2
66794	propanol degradation	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	resorcinol degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	taurine degradation	100	1 of 1
66794	IAA biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	citric acid cycle	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	urea cycle	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	arginine metabolism	83.33	20 of 24
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	vitamin B12 metabolism	82.35	28 of 34
66794	pyrimidine metabolism	82.22	37 of 45
66794	pentose phosphate pathway	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	starch degradation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	histidine metabolism	79.31	23 of 29
66794	glutathione metabolism	78.57	11 of 14
66794	lysine metabolism	78.57	33 of 42
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	tryptophan metabolism	76.32	29 of 38
66794	lactate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	methionine metabolism	73.08	19 of 26
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenol degradation	70	14 of 20
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	oxidative phosphorylation	69.23	63 of 91
66794	non-pathway related	68.42	26 of 38
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	3-phenylpropionate degradation	60	9 of 15
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	creatinine degradation	60	3 of 5
66794	elloramycin biosynthesis	60	3 of 5
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	tyrosine metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	degradation of hexoses	55.56	10 of 18
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	d-xylose degradation	54.55	6 of 11
66794	ascorbate metabolism	54.55	12 of 22
66794	cholesterol biosynthesis	54.55	6 of 11
66794	degradation of sugar acids	52	13 of 25
66794	quinate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of pentoses	46.43	13 of 28
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	glycine metabolism	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	chlorophyll metabolism	27.78	5 of 18
66794	polyamine pathway	26.09	6 of 23
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
8555	soil
47831	Rice soil
67770	Soil
122620	Environment, Rice soil

Taxonmaps

69479

Global distribution of 16S sequence Z78212 (>99% sequence identity) for Pimelobacter simplex from Microbeatlas

Aquatic Samples	68
Soil Samples	197
Animal Samples	61
Plant Samples	48
Total Samples	374

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8555	1	Risk group (German classification) According to TRBA 466
18625	1	Hazard group According to TRBA 466
122620	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
67770	IMG-taxon 2687453782 annotated assembly for Pimelobacter simplex ATCC 6946	scaffold	GCA_900114845	2045.9	2687453782	2045	74.7
67770	ASM653896v1 assembly for Pimelobacter simplex NBRC 12069	contig	GCA_006538965	2045.10		2045	69.61

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Nocardioides simplex 16S ribosomal RNA gene, partial sequence	AF005013	1474	2045
20218	Nocardioides simplex strain ATCC 15799 16S-23S internal transcribed spacer, complete sequence	AF017499	386	2045
20218	N.simplex 16S rRNA gene	Z78212	1468	2045
20218	Pimelobacter simplex strain KCTC 9106 16S ribosomal RNA gene, partial sequence	AF005009	1474	2045
20218	Nocardioides simplex strain KCTC 9106 16S-23S internal transcribed spacer, complete sequence	AF017494	386	2045
20218	Nocardioides simplex partial 16S rRNA	X53213	1392	2045
67770	Arthobacter simplex small subunit ribosomal RNA	M37693	1517	2045

GC content

@ref	GC-content (mol%)	Method
8555	71.7
67770	71.7	thermal denaturation, midpoint method (Tm)
67770	73	thermal denaturation, midpoint method (Tm)
67770	74
67770	74.4	thermal denaturation, midpoint method (Tm)
67770	72.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pimelobacter simplex ATCC 6946
NCBI: GCA_900114845

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	72.90	no
125439	motility	BacteriaNetⓘ	no	83.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pimelobacter simplex strain ATCC 6946
PATRIC: 2045.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.72	no
125438	anaerobic	anaerobicⓘ	no	95.82	no
125438	spore-forming	spore-formingⓘ	no	51.44	no
125438	aerobic	aerobicⓘ	yes	85.86	no
125438	thermophilic	thermophileⓘ	no	95.89	yes
125438	flagellated	motile2+ⓘ	no	63.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Building trans-bicyclo[4.4.0]decanes/decenes in complex multifunctional frameworks: the case for antibiotic development.	Zhang W, Kaplan AR, Davison EK, Freeman JL, Brimble MA, Wuest WM.	Nat Prod Rep	10.1039/d0np00052c	2021
Metabolism	Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil.	Rabus R, Fukui M, Wilkes H, Widdle F.	Appl Environ Microbiol	10.1128/aem.62.10.3605-3613.1996	1996
Enzymology	Expression, purification, crystallization and preliminary X-ray studies of histamine dehydrogenase from Nocardioides simplex.	Reed TM, Hirakawa H, Mure M, Scott EE, Limburg J.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309108023336	2008
Metabolism	Large-scale production of coenzyme F420-5,6 by using Mycobacterium smegmatis.	Isabelle D, Simpson DR, Daniels L.	Appl Environ Microbiol	10.1128/aem.68.11.5750-5755.2002	2002
	FR171456 is a specific inhibitor of mammalian NSDHL and yeast Erg26p.	Helliwell SB, Karkare S, Bergdoll M, Rahier A, Leighton-Davis JR, Fioretto C, Aust T, Filipuzzi I, Frederiksen M, Gounarides J, Hoepfner D, Hofmann A, Imbert PE, Jeker R, Knochenmuss R, Krastel P, Margerit A, Memmert K, Miault CV, Rao Movva N, Muller A, Naegeli HU, Oberer L, Prindle V, Riedl R, Schuierer S, Sexton JA, Tao J, Wagner T, Yin H, Zhang J, Roggo S, Reinker S, Parker CN.	Nat Commun	10.1038/ncomms9613	2015
	Compilation of small ribosomal subunit RNA structures.	Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.	Nucleic Acids Res	10.1093/nar/21.13.3025	1993
Metabolism	Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate.	Shtratnikova VY, Sshelkunov MI, Fokina VV, Bragin EY, Shutov AA, Donova MV.	BMC Biotechnol	10.1186/s12896-021-00668-9	2021
	Degradation of C₁₉-Steroids and Effect of Androstenedione on Gene Expression in Nocardioides simplex.	Fokina V, Lobastova T, Tarlachkov S, Shutov A, Kazantsev A, Donova M.	Curr Microbiol	10.1007/s00284-025-04105-4	2025
Enzymology	Reconstruction of the Steroid 1(2)-Dehydrogenation System from Nocardioides simplex VKM Ac-2033D in Mycolicibacterium Hosts.	Fufaeva SR, Dovbnya DV, Ivashina TV, Shutov AA, Donova MV.	Microorganisms	10.3390/microorganisms11112720	2023
	Radical Ring-Opening Reaction of Non-Activated Oximes Catalyzed by Aldoxime Dehydratases.	Kato S, Nishiwaki H, Endo K, Hayashi T.	Angew Chem Int Ed Engl	10.1002/anie.202511590	2025
	Cholesterol Assay Based on Recombinant Cholesterol Oxidase, ABTS, and Horseradish Peroxidase.	Sviridov AV, Karpov MV, Fokina VV, Donova MV.	Methods Mol Biol	10.1007/978-1-0716-3385-4_9	2023
	Recombinant Extracellular Cholesterol Oxidase from Nocardioides simplex.	Fokina VV, Karpov MV, Kollerov VV, Bragin EY, Epiktetov DO, Sviridov AV, Kazantsev AV, Shutov AA, Donova MV.	Biochemistry (Mosc)	10.1134/s0006297922090048	2022
	Boldenone and Testosterone Production from Phytosterol via One-Pot Cascade Biotransformations.	Kollerov VV, Timakova TA, Shutov AA, Donova MV.	J Fungi (Basel)	10.3390/jof10120830	2024
	Tuber indicum colonization enhances plant drought tolerance by modifying physiological, rhizosphere metabolic and bacterial community responses in Pinus armandii.	Huang L, Wan S, Liu Y, Zhan J, Zhang F, Yang H, Zhang F, Xie X, Shi X, Wang Y, Yu F.	Front Plant Sci	10.3389/fpls.2025.1642071	2025
Metabolism	Bioconversion of 6-(N-methyl-N-phenyl)aminomethyl androstane steroids by Nocardioides simplex.	Sukhodolskaya G, Fokina V, Shutov A, Nikolayeva V, Savinova T, Grishin Y, Kazantsev A, Lukashev N, Donova M.	Steroids	10.1016/j.steroids.2016.11.001	2017
Enzymology	Modulating Substrate Specificity of Rhizobium sp. Histamine Dehydrogenase through Protein Engineering for Food Quality Applications.	Rodriguez-Nunez K, Cortes-Monroy A, Serey M, Ensari Y, Davari MD, Bernal C, Martinez R, Martinez R.	Molecules	10.3390/molecules28093748	2023
Metabolism	Genome-Wide Transcriptome Profiling Provides Insight on Cholesterol and Lithocholate Degradation Mechanisms in Nocardioides simplex VKM Ac-2033D.	Shtratnikova VY, Schelkunov MI, Fokina VV, Bragin EY, Lobastova TG, Shutov AA, Kazantsev AV, Donova MV.	Genes (Basel)	10.3390/genes11101229	2020
	Screening for Microbial Metal-Chelating Siderophores for the Removal of Metal Ions from Solutions.	Hofmann M, Heine T, Malik L, Hofmann S, Joffroy K, Senges CHR, Bandow JE, Tischler D.	Microorganisms	10.3390/microorganisms9010111	2021
Enzymology	Bioproduction of testosterone from phytosterol by Mycolicibacterium neoaurum strains: "one-pot", two modes.	Tekucheva DN, Nikolayeva VM, Karpov MV, Timakova TA, Shutov AV, Donova MV.	Bioresour Bioprocess	10.1186/s40643-022-00602-7	2022
Metabolism	Structural Insights into 6-Hydroxypseudooxynicotine Amine Oxidase from Pseudomonas geniculata N1, the Key Enzyme Involved in Nicotine Degradation.	Liu G, Wang W, He F, Zhang P, Xu P, Tang H.	Appl Environ Microbiol	10.1128/aem.01559-20	2020
Metabolism	Stopped flow kinetic studies on reductive half-reaction of histamine dehydrogenase from Nocardioides simplex with histamine.	Tsutsumi M, Tsujimura S, Shirai O, Kano K.	J Biochem	10.1093/jb/mvq032	2010
Enzymology	Site-directed mutation at residues near the catalytic site of histamine dehydrogenase from Nocardioides simplex and its effects on substrate inhibition.	Tsutsumi M, Tsuse N, Fujieda N, Kano K.	J Biochem	10.1093/jb/mvp162	2010
Genetics	A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry.	Sekiguchi Y, Teramoto K, Tourlousse DM, Ohashi A, Hamajima M, Miura D, Yamada Y, Iwamoto S, Tanaka K.	Genome Biol	10.1186/s13059-023-03096-4	2023
Enzymology	Thermodynamic redox properties governing the half-reduction characteristics of histamine dehydrogenase from Nocardioides simplex.	Tsutsumi M, Fujieda N, Tsujimura S, Shirai O, Kano K.	Biosci Biotechnol Biochem	10.1271/bbb.70665	2008
	Bioactive Compounds from an Endophytic Pezicula sp. Showing Antagonistic Effects against the Ash Dieback Pathogen	Demir O, Zeng H, Schulz B, Schrey H, Steinert M, Stadler M, Surup F.	Biomolecules		2023
Metabolism	Production of completely flavinylated histamine dehydrogenase, unique covalently bound flavin, and iron-sulfur cluster-containing enzyme of nocardioides simplex in Escherichia coli, and its properties.	Fujieda N, Tsuse N, Satoh A, Ikeda T, Kano K.	Biosci Biotechnol Biochem	10.1271/bbb.69.2459	2005
Enzymology	Crystallization and preliminary crystallographic analysis of histamine dehydrogenase from Natrinema gari BCC 24369.	Zhou D, Visessanguan W, Chaikaew S, Benjakul S, Oda K, Wlodawer A.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x14011327	2014
Enzymology	Cloning and characterization of histamine dehydrogenase from Nocardioides simplex.	Limburg J, Mure M, Klinman JP.	Arch Biochem Biophys	10.1016/j.abb.2004.11.024	2005
Enzymology	6-S-cysteinyl flavin mononucleotide-containing histamine dehydrogenase from Nocardioides simplex: molecular cloning, sequencing, overexpression, and characterization of redox centers of enzyme.	Fujieda N, Satoh A, Tsuse N, Kano K, Ikeda T.	Biochemistry	10.1021/bi049061q	2004
	The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome.	Chamankar B, Maleki-Ravasan N, Karami M, Forouzan E, Karimian F, Naeimi S, Choobdar N.	Microbiome	10.1186/s40168-022-01456-z	2023
Metabolism	[The 1(2)-dehydrogenation of steroid substrates by Nocardioides simplex VKM Ac-2033D].	Fokina VV, Sukhodol'skaia GV, Gulevskaia SA, Gavrish EIu, Evtushenko LI, Donova MV.	Mikrobiologiia		2003
	Four Aromatic Intradiol Ring Cleavage Dioxygenases from Aspergillus niger.	Semana P, Powlowski J.	Appl Environ Microbiol	10.1128/aem.01786-19	2019
Pathogenicity	A fermentation product of phytosterol including campestenone reduces body fat storage and body weight gain in mice.	Suzuki K, Konno R, Shimzu T, Nagashima T, Kimura A.	J Nutr Sci Vitaminol (Tokyo)	10.3177/jnsv.53.63	2007
	Steroid Metabolism in Thermophilic Actinobacterium Saccharopolyspora hirsuta VKM Ac-666^T.	Lobastova T, Fokina V, Tarlachkov S, Shutov A, Bragin E, Kazantsev A, Donova M.	Microorganisms	10.3390/microorganisms9122554	2021
Enzymology	Histamine dehydrogenase from Rhizobium sp.: gene cloning, expression in Escherichia coli, characterization and application to histamine determination.	Bakke M, Sato T, Ichikawa K, Nishimura I.	J Biotechnol	10.1016/j.jbiotec.2005.04.005	2005
	SmI2-mediated dimerization of indolylbutenones and synthesis of the myxobacterial natural product indiacen B.	Marsch N, Jones PG, Lindel T.	Beilstein J Org Chem	10.3762/bjoc.11.184	2015
Metabolism	Role of N,N-Dimethylglycine and Its Catabolism to Sarcosine in Chromohalobacter salexigens DSM 3043.	Yang T, Shao YH, Guo LZ, Meng XL, Yu H, Lu WD.	Appl Environ Microbiol	10.1128/aem.01186-20	2020
Metabolism	Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil.	Piutti S, Semon E, Landry D, Hartmann A, Dousset S, Lichtfouse E, Topp E, Soulas G, Martin-Laurent F.	FEMS Microbiol Lett	10.1016/s0378-1097(03)00168-x	2003
Phylogeny	Reclassification of Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis.	Yoon JH, Lee JS, Shin YK, Park YH, Lee ST.	Int J Syst Bacteriol	10.1099/00207713-47-3-904	1997
Enzymology	Crystal structure of histamine dehydrogenase from Nocardioides simplex.	Reed T, Lushington GH, Xia Y, Hirakawa H, Travis DM, Mure M, Scott EE, Limburg J.	J Biol Chem	10.1074/jbc.m109.084301	2010
Phylogeny	Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences.	Yoon JH, Lee ST, Park YH.	Int J Syst Bacteriol	10.1099/00207713-48-1-187	1998
	Genetic analyses of the genus Nocardioides and related taxa based on 16S-23S rDNA internally transcribed spacer sequences.	Yoon HJ, Lee ST, Park YH.	Int J Syst Bacteriol	10.1099/00207713-48-3-641	1998
	Reduction of histamine and biogenic amines during salted fish fermentation by Bacillus polymyxa as a starter culture.	Lee YC, Kung HF, Huang CY, Huang TC, Tsai YH.	J Food Drug Anal	10.1016/j.jfda.2015.02.002	2016
	Gram-positive cell wall structure of the A3 gamma type in heliobacteria.	Pickett MW, Weiss N, Kelly DJ.	FEMS Microbiol Lett	10.1111/j.1574-6968.1994.tb07135.x	1994
Metabolism	Degradation of 2,4,5-trichlorophenoxyacetic acid by a Nocardioides simplex culture.	Golovleva LA, Pertsova RN, Evtushenko LI, Baskunov BP.	Biodegradation	10.1007/bf00119763	1990
Enzymology	Degradation of histamine by Bacillus polymyxa isolated from salted fish products.	Lee YC, Lin CS, Liu FL, Huang TC, Tsai YH.	J Food Drug Anal	10.1016/j.jfda.2015.02.003	2015
Metabolism	Genomic and transcriptomic analyses of Agrobacterium tumefaciens S33 reveal the molecular mechanism of a novel hybrid nicotine-degrading pathway.	Huang H, Yu W, Wang R, Li H, Xie H, Wang S.	Sci Rep	10.1038/s41598-017-05320-1	2017
Metabolism	Isolation and characterization of a thermostable F₄₂₀:NADPH oxidoreductase from Thermobifida fusca.	Kumar H, Kumar H, Nguyen QT, Binda C, Mattevi A, Fraaije MW.	J Biol Chem	10.1074/jbc.m117.787754	2017
Metabolism	A progesterone biosensor derived from microbial screening.	Grazon C, Baer RC, Kuzmanovic U, Nguyen T, Chen M, Zamani M, Chern M, Aquino P, Zhang X, Lecommandoux S, Fan A, Cabodi M, Klapperich C, Grinstaff MW, Dennis AM, Galagan JE.	Nat Commun	10.1038/s41467-020-14942-5	2020
Metabolism	Nitrite elimination and hydrolytic ring cleavage in 2,4,6-trinitrophenol (picric acid) degradation.	Hofmann KW, Knackmuss HJ, Heiss G.	Appl Environ Microbiol	10.1128/aem.70.5.2854-2860.2004	2004
Enzymology	Discovery and characterization of an F₄₂₀-dependent glucose-6-phosphate dehydrogenase (Rh-FGD1) from Rhodococcus jostii RHA1.	Nguyen QT, Trinco G, Binda C, Mattevi A, Fraaije MW.	Appl Microbiol Biotechnol	10.1007/s00253-016-8038-y	2017
Phylogeny	Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) lochhead in the genus Nocardioides (Prauser) emend. O'Donnell et al. as Nocardioides simplex comb. nov.	O'Donnell AG, Goodfellow M, Minnikin DE.	Arch Microbiol	10.1007/bf00521299	1982
Enzymology	Periplasmic Nicotine Dehydrogenase NdhAB Utilizes Pseudoazurin as Its Physiological Electron Acceptor in Agrobacterium tumefaciens S33.	Yu W, Wang R, Huang H, Xie H, Wang S.	Appl Environ Microbiol	10.1128/aem.01050-17	2017
Metabolism	Nicotine Dehydrogenase Complexed with 6-Hydroxypseudooxynicotine Oxidase Involved in the Hybrid Nicotine-Degrading Pathway in Agrobacterium tumefaciens S33.	Li H, Xie K, Yu W, Hu L, Huang H, Xie H, Wang S.	Appl Environ Microbiol	10.1128/aem.03909-15	2016
Phylogeny	Use of randomly amplified polymorphic DNA as a means of developing genus- and strain-specific Streptomyces DNA probes.	Roberts MA, Crawford DL.	Appl Environ Microbiol	10.1128/aem.66.6.2555-2564.2000	2000
Metabolism	Characterization of S-triazine herbicide metabolism by a Nocardioides sp. isolated from agricultural soils.	Topp E, Mulbry WM, Zhu H, Nour SM, Cuppels D.	Appl Environ Microbiol	10.1128/aem.66.8.3134-3141.2000	2000
Metabolism	3-nitroadipate, a metabolic intermediate for mineralization of 2, 4-dinitrophenol by a new strain of a Rhodococcus species.	Blasco R, Moore E, Wray V, Pieper D, Timmis K, Castillo F.	J Bacteriol	10.1128/jb.181.1.149-152.1999	1999
Metabolism	Formation of hydride-Meisenheimer complexes of picric acid (2,4, 6-trinitrophenol) and 2,4-dinitrophenol during mineralization of picric acid by Nocardioides sp. strain CB 22-2.	Behrend C, Heesche-Wagner K.	Appl Environ Microbiol	10.1128/aem.65.4.1372-1377.1999	1999
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
Enzymology	Enzyme immobilization on alpha-1,3-glucan: development of flow reactor with fusion protein of alpha-1,3-glucan binding domains and histamine dehydrogenase.	Nagahashi Y, Hasegawa K, Takagi K, Yano S.	J Gen Appl Microbiol	10.2323/jgam.2023.04.002	2024
	Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism.	Lee DH, Zo YG, Kim SJ.	Appl Environ Microbiol	10.1128/aem.62.9.3112-3120.1996	1996
Metabolism	Increased yield of biotransformation of exemestane with beta-cyclodextrin complexation technique.	Li G, Li F, Deng L, Fang X, Zou H, Xu K, Li T, Tan G	Steroids	10.1016/j.steroids.2013.07.009	2013
Metabolism	Enhancement of androstadienedione production from progesterone by biotransformation using the hydroxypropyl-beta-cyclodextrin complexation technique.	Manosroi A, Saowakhon S, Manosroi J	J Steroid Biochem Mol Biol	10.1016/j.jsbmb.2007.05.032	2007
Metabolism	Conversion of liposomal 4-androsten-3,17-dione by A. simplex immobilized cells in calcium pectate.	Llanes N, Pendas J, Falero A, Perez C, Hung BR, Moreira T	J Steroid Biochem Mol Biol	10.1016/s0960-0760(01)00176-5	2002
Enzymology	Purification and characterization of histamine dehydrogenase from Nocardioides simplex IFO 12069.	Siddiqui JA, Shoeb SM, Takayama S, Shimizu E, Yorifuji T	FEMS Microbiol Lett	10.1111/j.1574-6968.2000.tb09227.x	2000
Phylogeny	Mineralization of 2,4,6-trinitrophenol (picric acid): characterization and phylogenetic identification of microbial strains.	Rajan J, Valli K, Perkins RE, Sariaslani FS, Barns SM, Reysenbach AL, Rehm S, Ehringer M, Pace NR	J Ind Microbiol	10.1007/BF01570041	1996
Enzymology	Purification and characterization of the 3-ketosteroid-delta 1-dehydrogenase of Arthrobacter simplex produced in Streptomyces lividans.	Choi KP, Molnar I, Yamashita M, Murooka Y	J Biochem	10.1093/oxfordjournals.jbchem.a124804	1995
Metabolism	Delta'-dehydrogenation of steroids by Arthrobacter simplex immobilized in calcium polygalacturonate beads.	Montes MC, Magana I	J Ind Microbiol	10.1007/BF01576064	1991
	Ultrasound-enhanced bioprocess. II: Dehydrogenation of hydrocortisone by Arthrobacter simplex.	Zabaneh M, Bar R	Biotechnol Bioeng	10.1002/bit.260371103	1991
Metabolism	The use of free and immobilised Arthrobacter simplex in organic solvent/aqueous two-liquid-phase reactors.	Hocknull MD, Lilly MD	Appl Microbiol Biotechnol	10.1007/BF00176516	1990
Phylogeny	Nocardioides flava sp. nov., isolated from rhizosphere of poppy plant, Republic of Korea.	Singh H, Yin CS.	Arch Microbiol	10.1007/s00203-015-1178-0	2016
Phylogeny	Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil.	Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi TH.	Int J Syst Evol Microbiol	10.1099/ijsem.0.000730	2016
Phylogeny	Nocardioides ginsengisoli sp. nov., isolated from soil of a ginseng field.	Cui YS, Lee ST, Im WT.	Int J Syst Evol Microbiol	10.1099/ijs.0.010025-0	2009
Phylogeny	Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field.	Cho CH, Lee JS, An DS, Whon TW, Kim SG.	Int J Syst Evol Microbiol	10.1099/ijs.0.012690-0	2010
Phylogeny	Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium.	Yoon JH, Lee JK, Jung SY, Kim JA, Kim HK, Oh TK.	Int J Syst Evol Microbiol	10.1099/ijs.0.64120-0	2006
Metabolism	Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments.	Kubota M, Kawahara K, Sekiya K, Uchida T, Hattori Y, Futamata H, Hiraishi A.	Syst Appl Microbiol	10.1016/j.syapm.2004.10.002	2005
Phylogeny	Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium.	Yoon JH, Cho YG, Lee ST, Suzuki K, Nakase T, Park YH.	Int J Syst Bacteriol	10.1099/00207713-49-2-675	1999
Phylogeny	Nocardioides soli sp. nov., a bacterium isolated from a mountain soil.	Srinivasan S, Lee SS, Lee JJ, Kim MK	Antonie Van Leeuwenhoek	10.1007/s10482-014-0191-7	2014
Phylogeny	Nocardioides caeni sp. nov., isolated from wastewater.	Yoon JH, Kang SJ, Park S, Kim W, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.010124-0	2009
Phylogeny	Nocardioides humi sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.	Kim MK, Srinivasan S, Park MJ, Sathiyaraj G, Kim YJ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.008821-0	2009

References

#8555	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20130
#18625	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 )
#37734	; Curators of the CIP;
#47831	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 23611
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#122620	Collection of Institut Pasteur ; Curators of the CIP; CIP 82.106
#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 )

Rate our new design

Content

About us

Nocardioides simplex (CCUG 23611, JCM 1363, DSM 20130)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Murein

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900114845

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media