Name: Geodermatophilus ruber DSM 45317
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5823

Type strain:

Species: Geodermatophilus ruber

Culture col. no.: DSM 45317, CCM 7619, CPCC 201356, JCM 17967

Strain history: CCM 7619 <-- Y.-Q. Zhang CPCC 201356.

NCBI tax ID(s): 504800 (species)

SI-ID 404418

DSM 45317

Special Collections

Section

When using BacDive for research please cite our paper

Geodermatophilus ruber DSM 45317 is a mesophilic, Gram-positive, motile bacterium that was isolated from rhizosphere soil of Astragalus membranaceus.

coccus-shaped
Gram-positive
motile
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	*Geodermatophilales*
	Family	*Geodermatophilaceae*
	Genus	*Geodermatophilus*
	Species	**Geodermatophilus ruber**
	Full Scientific Name (LPSN)	Geodermatophilus ruber Zhang et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29776]	Gram stain	positive
[Ref.: #125439]	Gram stain	positive Confidence in %99.3

[Ref.: #29776]	Cell shape	coccus-shaped

[Ref.: #29776]	Motility	yes

[Ref.: #21393]	Colony color	Sand yellow (1002)
[Ref.: #21393]	Incubation period	10-14 days
[Ref.: #21393]	Cultivation medium used	ISP 2

[Ref.: #21393]	Colony color	Orange brown (8023)
[Ref.: #21393]	Incubation period	10-14 days
[Ref.: #21393]	Cultivation medium used	ISP 7

[Ref.: #21393]	Colony color	Ochre brown (8001)
[Ref.: #21393]	Incubation period	10-14 days
[Ref.: #21393]	Cultivation medium used	Suter with tyrosine

[Ref.: #21393]	Colony color	Beige (1001)
[Ref.: #21393]	Incubation period	10-14 days
[Ref.: #21393]	Cultivation medium used	Suter without tyrosine

[Ref.: #21393]	Incubation period	10-14 days
[Ref.: #21393]	Cultivation medium used	ISP 3

[Ref.: #21393]	Incubation period	10-14 days
[Ref.: #21393]	Cultivation medium used	ISP 4

[Ref.: #21393]	Incubation period	10-14 days
[Ref.: #21393]	Cultivation medium used	ISP 5

[Ref.: #29776]

Pigment production

yes

[Ref.: #21393]	Multicellular complex forming ability	no
[Ref.: #21393]	Medium Name (multicellularity)	ISP 2

[Ref.: #21393]	Multicellular complex forming ability	no
[Ref.: #21393]	Medium Name (multicellularity)	ISP 3

[Ref.: #21393]	Multicellular complex forming ability	no
[Ref.: #21393]	Medium Name (multicellularity)	ISP 4

[Ref.: #21393]	Multicellular complex forming ability	no
[Ref.: #21393]	Medium Name (multicellularity)	ISP 5

[Ref.: #21393]	Multicellular complex forming ability	no
[Ref.: #21393]	Medium Name (multicellularity)	ISP 7

[Ref.: #21393]	Multicellular complex forming ability	no
[Ref.: #21393]	Medium Name (multicellularity)	Suter with tyrosine

[Ref.: #21393]	Multicellular complex forming ability	no
[Ref.: #21393]	Medium Name (multicellularity)	Suter without tyrosine

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16221]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #16221]

Culture medium growth

[Ref.: #16221]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16221]

Culture medium composition

expand / minimize

[Ref.: #16221]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #16221]

Culture medium growth

[Ref.: #16221]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16221]

Culture medium composition

expand / minimize

[Ref.: #21393]

Culture medium

ISP 2

[Ref.: #21393]

Culture medium growth

[Ref.: #21393]

Culture medium composition

expand / minimize

[Ref.: #21393]

Culture medium

ISP 3

[Ref.: #21393]

Culture medium growth

[Ref.: #21393]

Culture medium composition

expand / minimize

[Ref.: #21393]

Culture medium

ISP 4

[Ref.: #21393]

Culture medium growth

[Ref.: #21393]

Culture medium composition

expand / minimize

[Ref.: #21393]

Culture medium

ISP 5

[Ref.: #21393]

Culture medium growth

[Ref.: #21393]

Culture medium composition

expand / minimize

[Ref.: #21393]

Culture medium

ISP 7

[Ref.: #21393]

Culture medium growth

[Ref.: #21393]

Culture medium composition

expand / minimize

[Ref.: #21393]

Culture medium

Suter with tyrosine

[Ref.: #21393]

Culture medium growth

[Ref.: #21393]

Culture medium composition

expand / minimize

[Ref.: #21393]

Culture medium

Suter without tyrosine

[Ref.: #21393]

Culture medium growth

[Ref.: #21393]

Culture medium composition

expand / minimize

[Ref.: #16221]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #16221]

Culture medium growth

[Ref.: #16221]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16221]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16221]	growth	28 °C
[Ref.: #29776]	growth	10-40 °C
[Ref.: #29776]	optimum	26 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #29776]			optimum	7.25
[Ref.: #29776]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %99.8

	Salt		Salt conc.
[Ref.: #21393]	NaCl	growth	0	%
[Ref.: #29776]	NaCl	growth	<1	%
[Ref.: #29776]	NaCl	optimum	0.5	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29776]	acetate ChEBI	+	carbon source
[Ref.: #21393]	arabinose ChEBI	-
[Ref.: #21393]	cellulose ChEBI	-
[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.: #21393]	fructose ChEBI	+
[Ref.: #29776]	fructose ChEBI	+	carbon source
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21393]	glucose ChEBI	-
[Ref.: #29776]	glucose ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #29776]	inosine ChEBI	+	carbon source
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29776]	malate ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #21393]	mannose ChEBI	+
[Ref.: #29776]	mannose ChEBI	+	carbon source
[Ref.: #21393]	myo-inositol ChEBI	-
[Ref.: #29776]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #29776]	proline ChEBI	+	carbon source
[Ref.: #29776]	quinate ChEBI	+	carbon source
[Ref.: #21393]	raffinose ChEBI	-
[Ref.: #21393]	rhamnose ChEBI	-
[Ref.: #29776]	succinate ChEBI	+	carbon source
[Ref.: #21393]	sucrose ChEBI	-
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21393]	xylose ChEBI	-
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29776]	acid phosphatase	+	3.1.3.2
[Ref.: #29776]	alkaline phosphatase	+	3.1.3.1
[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.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[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.: #29776]	catalase	+	1.11.1.6
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[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.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #21393]	519	-	-	-	-	-	-	-	-	-	-	-	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.: #21393]	1034	not determinedn.d.	+/-	+	+	-	+	-	+/-	-	-	+/-	+	-	-	-	+/-	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	myo-inositol biosynthesis	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	glycolysis	88.24	15 of 17
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	3-phenylpropionate degradation	86.67	13 of 15
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	phenol degradation	80	16 of 20
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	65.93	60 of 91
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	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]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		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.: #16221]	Sample type/isolated from	rhizosphere soil of Astragalus membranaceus
[Ref.: #16221]	Host species	Astragalus membranaceus
[Ref.: #16221]	Geographic location (country and/or sea, region)	Qinghai Province, Xining (37° 35' N 101° 49' E; elevation 2800 m)
[Ref.: #16221]	Country	China
[Ref.: #16221]	Country ISO 3 Code	CHN
[Ref.: #16221]	Continent	Asia
[Ref.: #16221]	Geographic location	37.5833°/101.8170°

[Ref.: #67770]	Sample type/isolated from	rhRizosphere soil of the plant Astragalus membranaceus from Xining
[Ref.: #67770]	Host species	Astragalus membranaceus
[Ref.: #67770]	Geographic location (country and/or sea, region)	Qinghai Province, north-west China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU438905 (>99% sequence identity) for Geodermatophilus ruber from Microbeatlas

Aquatic Samples	99
Soil Samples	856
Animal Samples	27
Plant Samples	132
Total Samples	1114

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

[Ref.: #16221]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #16221]	Geodermatophilus ruber strain CPCC 201356 16S ribosomal RNA gene, partial sequence	EU438905	1449	GenBank ENA	504800 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Geodermatophilus ruber DSM 45317	GCA_900114385	scaffold	GenBank ENA	504800 tax ID
[Ref.: #66792]	Geodermatophilus ruber strain DSM 45317	504800.3	wgs	PATRIC	504800 tax ID	*
[Ref.: #66792]	Geodermatophilus ruber DSM 45317	2622736605	draft	JGI IMG/M	504800 tax ID	*

[Ref.: #16221]	GC-content	72.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29776]	GC-content	72.8 mol%

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: Geodermatophilus ruber strain DSM 45317 PATRIC: 504800.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	87.596	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.511	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	59.376	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	89.647	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	92.714	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	57.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Geodermatophilus ruber DSM 45317 NCBI: GCA_900114385
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	52.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	73.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	99.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.8

Availability in culture collections External links

[Ref.: #16221]

Culture collection no.

DSM 45317, CCM 7619, CPCC 201356, JCM 17967

[Ref.: #75305]

SI-ID 404418

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Geodermatophilus telluris sp. nov., an actinomycete isolated from Saharan desert sand.	Montero-Calasanz MDC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Klenk HP, Gorbushina AA	Int J Syst Evol Microbiol	10.1099/ijs.0.046888-0	2012	*
Phylogeny	Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant.	Zhang YQ, Chen J, Liu HY, Zhang YQ, Li WJ, Yu LY	Int J Syst Evol Microbiol	10.1099/ijs.0.020610-0	2010	*

References

#16221

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45317

#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 )

#21393

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#29776

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 #26156 (see below)

#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;

#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 .

#75305

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-ID404418.1 )

#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 .

#26156

IJSEM 190 2011 ( DOI 10.1099/ijs.0.020610-0 , PubMed 20190022 )

* These data were automatically processed and therefore are not curated

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Geodermatophilus ruber strain DSM 45317

Geodermatophilus ruber DSM 45317

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