Nocardioides simplex (DSM 20299, IAM 1398, NBRC 12679)

Name: Nocardioides simplex (DSM 20299, IAM 1398, NBRC 12679)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11101

Type strain

Culture col. no. DSM 20299 IAM 1398 NBRC 12679 KCTC 9621 IFO 12679 1 more

NCBI tax ID(s) 2045

Special Collections DSMZ JCM KCTC

History DSMZ <- H.G. Schlegel <- K. Komagata <- IAM (Brevibacterium lipolyticum) JCM <-- IAM 1398 <-- H. Iizuka and K. Komagata P-18.

Links

Nocardioides simplex DSM 20299 is a bacterium that was isolated from Soil of petroleum zone.

16S sequence Bacteria

Name and taxonomic classification

SI-ID 49603

DSM 20299,IAM 1398,JCM 1366,IFO 12679,KCTC 9621,NBRC 12679,CECT 848

@ref 20215

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

Domain Bacteria

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)

Pimelobacter simplex
Arthrobacter simplex
"Corynebacterium simplex"

BacDive ID	Other strains from **Nocardioides simplex** (11)	Type strain
11100	N. simplex CCUG 23611, JCM 1363, DSM 20130, ATCC 6946, ... (type strain)
104700	N. simplex SF002835,
104701	N. simplex SF000322,
104702	N. simplex SF001744,
104703	N. simplex SF005254,
144251	N. simplex CCUG 23927, LMG 3810
161393	N. simplex JCM 1367, IAM 1413, KCTC 9622
179095	N. simplex IMET 10624, STI10624
179097	N. simplex IMET 10626, STI10626
179082	N. simplex IMET 10283, STI10283
179096	N. simplex IMET 10625, STI10625

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8702	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

Culture temp

@ref	Growth	Type	Temperature (°C)
8702	positive	growth	28
67770	positive	growth	30

Physiology and metabolism

Murein

@ref	Murein short key	Type
8702	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

@ref	Sample type	Country	Country ISO 3 Code	Continent
67770	Soil of petroleum zone	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AF005010 (>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
8702	1	Risk group (German classification) According to TRBA 466

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Nocardioides simplex 16S ribosomal RNA gene, partial sequence	AF005010	1474		2045
124043	Nocardioides simplex strain JCM 1366 16S-23S internal transcribed spacer, complete sequence	AF017495	386		2045

GC content

@ref	GC-content (mol%)	Method
8702	70.7
67770	73.5	thermal denaturation, midpoint method (Tm)
67770	70.7	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Literature

References

#8702	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20299
#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 )
#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 .
#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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