Name: Dermacoccus nishinomiyaensis 59
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3922

Type strain:

Species: Dermacoccus nishinomiyaensis

Strain Designation: 59, 8094

Culture col. no.: DSM 20448, ATCC 29093, CCM 2140, CCUG 33028, JCM 11613, CECT 544, CIP 81.71, IAM 13592, IFO 15356, IMSNU 21319, LMG 14222, NBRC 15356, NCDO 2358, NCIMB 702358, NCTC 11039, VKM Ac-2160, VKM B-1818

Strain history: CIP <- 1981, CCM <- Osaka University, Japan: strain 8094 <- M. Oda: strain 59

NCBI tax ID(s): 1274 (species)

SI-ID 9313

LMG 14222, ATCC 29093, CCM 2140, IAM 13592, IFO 15356, NCFB 2358, NCTC 11039, CCUG 33028, NCDO 2358, NCIMB 702358, VKM B-1818, CECT 544, IMET 11365, JCM 11613, NBRC 15356, VKM Ac-2160, DSM 20448, CIP 81.71

Special Collections

Other strains from Dermacoccus nishinomiyaensis

Section

When using BacDive for research please cite our paper

Dermacoccus nishinomiyaensis 59 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from water.

coccus-shaped
Gram-positive
facultative anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Dermacoccaceae*
	Genus	*Dermacoccus*
	Species	**Dermacoccus nishinomiyaensis**
	Full Scientific Name (LPSN)	Dermacoccus nishinomiyaensis (Oda 1935) Stackebrandt et al. 1995

Synonym

Micrococcus nishinomiyaensis

Information on morphological and physiological properties Morphology

[Ref.: #121306]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %94.675
[Ref.: #125439]	Gram stain	positive Confidence in %99.7

[Ref.: #121306]	Cell shape	coccus-shaped

[Ref.: #121306]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %90.5

[Ref.: #18747]	Colony color	Chrome yellow
[Ref.: #18747]	Incubation period	10-14 days
[Ref.: #18747]	Cultivation medium used	5006

[Ref.: #18747]	Colony color	Chrome yellow
[Ref.: #18747]	Incubation period	10-14 days
[Ref.: #18747]	Cultivation medium used	5425

[Ref.: #18747]	Colony color	Chrome yellow
[Ref.: #18747]	Incubation period	10-14 days
[Ref.: #18747]	Cultivation medium used	5428

[Ref.: #18747]	Colony color	Chrome yellow
[Ref.: #18747]	Incubation period	10-14 days
[Ref.: #18747]	Cultivation medium used	ISP 2

[Ref.: #18747]	Colony color	Chrome yellow
[Ref.: #18747]	Incubation period	10-14 days
[Ref.: #18747]	Cultivation medium used	ISP 6

[Ref.: #18747]	Multicellular complex forming ability	no
[Ref.: #18747]	Medium Name (multicellularity)	ISP 2

[Ref.: #18747]	Multicellular complex forming ability	no
[Ref.: #18747]	Medium Name (multicellularity)	5006

[Ref.: #18747]	Multicellular complex forming ability	no
[Ref.: #18747]	Medium Name (multicellularity)	5425

[Ref.: #18747]	Multicellular complex forming ability	no
[Ref.: #18747]	Medium Name (multicellularity)	5428

[Ref.: #18747]	Multicellular complex forming ability	no
[Ref.: #18747]	Medium Name (multicellularity)	ISP 6

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8820]

Culture medium

CORYNEBACTERIUM AGAR (DSMZ Medium 53)

[Ref.: #8820]

Culture medium growth

[Ref.: #8820]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8820]

Culture medium composition

expand / minimize

[Ref.: #18747]

Culture medium

ISP 2

[Ref.: #18747]

Culture medium growth

[Ref.: #18747]

Culture medium composition

expand / minimize

[Ref.: #18747]

Culture medium

5006

[Ref.: #18747]

Culture medium growth

[Ref.: #18747]

Culture medium composition

expand / minimize

[Ref.: #18747]

Culture medium

5425

[Ref.: #18747]

Culture medium growth

[Ref.: #18747]

Culture medium composition

expand / minimize

[Ref.: #18747]

Culture medium

5428

[Ref.: #18747]

Culture medium growth

[Ref.: #18747]

Culture medium

ISP 6

[Ref.: #18747]

Culture medium growth

[Ref.: #18747]

Culture medium composition

expand / minimize

[Ref.: #38082]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #38082]

Culture medium growth

[Ref.: #38082]

Culture medium composition

expand / minimize

[Ref.: #121306]

Culture medium

CIP Medium 72

[Ref.: #121306]

Culture medium growth

[Ref.: #121306]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121306]

Culture medium

CIP Medium 3

[Ref.: #121306]

Culture medium growth

[Ref.: #121306]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8820]	growth	30 °C
[Ref.: #18747]	optimum	28 °C
[Ref.: #38082]	growth	30 °C
[Ref.: #67770]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #121306]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.7

[Ref.: #8820]	Murein short key	A11.39
[Ref.: #8820]	Murein types	A4alpha L-Lys-L-Ser₂-D-Glu

[Ref.: #67770]

Observation

quinones: MK-8(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne, API 20E
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #121306]	nitrate ChEBI	-	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #121306]	nitrite ChEBI	-	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne, API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #121306]	indole ChEBI	no
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	-	3.1.3.1	* from API Coryne
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #121306]	catalase	+	1.11.1.6
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne, API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	+	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #121306]	oxidase	+
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #121306]	urease	-	3.5.1.5
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne, API 20E
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #51331]

Fatty acid	Percentage	ECL
C17:1 ω8c	22.2	16.792
C17:0 iso	16.4	16.629
C16:0 10-methyl	15	16.433
C16:1 ω7c	13.6	15.819
C15:0 ISO	10.6	14.621
C16:0 iso	9.3	15.626
C18:1 ω9c	5.9	17.769
C17:0 anteiso	4	16.722
C17:0 10-methyl	3	17.41

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #18747]	231	+	+	+	-	+	-	+	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #18747]	190	-	-	-	-	-	-	+	-	-	+	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #18747]	319	not determinedn.d.	-	-	+	-	+	-	-	-	-	+	-	-	-	-	+	-	-	-	-
[Ref.: #121306]	13498	-	+	+	+	-	+	+	+	+	-	+	-	-	-	-	+	-	-	-	-

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8820]	Sample type/isolated from	water

[Ref.: #67770]	Sample type/isolated from	Water ("miyamizu")
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #121306]	Sample type/isolated from	Environment, Water
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X87757 (>99% sequence identity) for Dermacoccus from Microbeatlas

Aquatic Samples	2728
Soil Samples	2219
Animal Samples	18144
Plant Samples	1181
Total Samples	24272

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #18747]	Biosafety level	1	Risk group (German classification)
[Ref.: #8820]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121306]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8820]	M.nishinomyaensis 16S rRNA gene	X87757	1464	GenBank ENA	1274 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Dermacoccus nishinomiyaensis NCTC11039	GCA_900447535	contig	GenBank ENA	1274 tax ID
[Ref.: #66792]	Dermacoccus nishinomiyaensis strain FDAARGOS_1119	1274.37	complete	PATRIC	1274 tax ID	*
[Ref.: #66792]	Dermacoccus nishinomiyaensis strain NCTC11039	1274.14	wgs	PATRIC	1274 tax ID	*
[Ref.: #66792]	Dermacoccus nishinomiyaensis NCTC 11039	2832479645	draft	JGI IMG/M	1274 tax ID	*

[Ref.: #8820]	GC-content	67.8 mol%
[Ref.: #67770]	GC-content	67.8 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dermacoccus nishinomiyaensis strain FDAARGOS_1119 strain Not applicable PATRIC: 1274.37
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	94.675	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.895	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	74.949	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	74.385	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.583	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	90.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dermacoccus nishinomiyaensis NCTC11039 NCBI: GCA_900447535
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	99.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	83
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	68.4

Availability in culture collections External links

[Ref.: #8820]

Culture collection no.

DSM 20448, ATCC 29093, CCM 2140, CCUG 33028, JCM 11613, CECT 544, CIP 81.71, IAM 13592, IFO 15356, IMSNU 21319, LMG 14222, NBRC 15356, NCDO 2358, NCIMB 702358, NCTC 11039, VKM Ac-2160, VKM B-1818

[Ref.: #73431]

SI-ID 9313

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dermacoccus abyssi sp. nov., a piezotolerant actinomycete isolated from the Mariana Trench.	Pathom-Aree W, Nogi Y, Sutcliffe IC, Ward AC, Horikoshi K, Bull AT, Goodfellow M	Int J Syst Evol Microbiol	10.1099/ijs.0.64133-0	2006	*

References

#8820

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20448

#18747

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 )

#38082 ; Curators of the CIP;
#51331 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 33028

#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) .

#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;

#68368

Automatically annotated from API 20E .

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#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 .

#73431

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID9313.1 )

#121306 Collection of Institut Pasteur ; Curators of the CIP; CIP 81.71

#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 .

* These data were automatically processed and therefore are not curated

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Dermacoccus nishinomiyaensis strain FDAARGOS_1119 strain Not applicable

Dermacoccus nishinomiyaensis NCTC11039

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