Dermacoccus nishinomiyaensis (DSM 105519, C3b-C13)

Name: Dermacoccus nishinomiyaensis (DSM 105519, C3b-C13)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 157782

Type strain

Strain Designation C3b-C13

Culture col. no. DSM 105519 C3b-C13

NCBI tax ID(s) 1274

Special Collections DSMZ ESA

History <- European Space Agency, Noordwijk, Netherlands <- C. Moissl-Eichinger, Medical Univ. Graz, Austria; C3b-C13

Links

Dermacoccus nishinomiyaensis C3b-C13 is a bacterium that was isolated from cleanroom facility, TAS-I.

Bacteria

Name and taxonomic classification

SI-ID 401694

DSM 105519

@ref 20215

Last LPSN update 2026-02-09 11:38:09

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Dermacoccaceae

Genus Dermacoccus

Species Dermacoccus nishinomiyaensis

Full scientific name Dermacoccus nishinomiyaensis (Oda 1935) Stackebrandt et al. 1995

Synonyms (1)

Micrococcus nishinomiyaensis

BacDive ID	Other strains from **Dermacoccus nishinomiyaensis** (10)	Type strain
3922	D. nishinomiyaensis 59, 8094, DSM 20448, ATCC 29093, CCM 2140, ... (type strain)
103245	D. nishinomiyaensis STI09589(IMET), IMET 09688, INA 4035
136592	D. nishinomiyaensis CIP 82.60, CCM 2669, RM 3
147191	D. nishinomiyaensis CCUG 33029, CCM 2673
153991	D. nishinomiyaensis CCUG 51868
157779	D. nishinomiyaensis C3a-C1, DSM 105516
157780	D. nishinomiyaensis C3b-C3, DSM 105517
157781	D. nishinomiyaensis C3b-C12, DSM 105518
157783	D. nishinomiyaensis K25-1, DSM 109490
159005	D. nishinomiyaensis Fh040319_C13, DSM 109537

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64354	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)
64354	positive	growth	28

Physiology and metabolism

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	proline metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	vitamin K metabolism	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	chorismate metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	alanine metabolism	75.86	22 of 29
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	pyrimidine metabolism	73.33	33 of 45
66794	histidine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	cyanate degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	oxidative phosphorylation	64.84	59 of 91
66794	metabolism of disaccharids	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	NAD metabolism	61.11	11 of 18
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	Entner Doudoroff pathway	60	6 of 10
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	d-mannose degradation	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	ethanol fermentation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glutathione metabolism	50	7 of 14
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	phenylmercury acetate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	d-xylose degradation	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	tyrosine metabolism	42.86	6 of 14
66794	carotenoid biosynthesis	40.91	9 of 22
66794	ascorbate metabolism	40.91	9 of 22
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	degradation of pentoses	35.71	10 of 28
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	#Clean room

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
64354	cleanroom facility, TAS-I	Turin	Italy	ITA	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64354	1	Risk group (German classification)

Sequence information

Genome-based predictions

Literature

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 )
#64354	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105519
#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 )
#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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