Name: Labedaea rhizosphaerae RS-49
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13517

Type strain:

Species: Labedaea rhizosphaerae

Strain Designation: RS-49

Culture col. no.: DSM 45361, KCTC 19662, JCM 31489

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 598644 (species)

SI-ID 397978

DSM 45361

Section

Labedaea rhizosphaerae RS-49 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from rhizosphere soil of the cliff-associated plant Peucedanum japonicum Thunb..

Gram-positive
spore-forming
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Labedaea*
	Species	**Labedaea rhizosphaerae**
	Full Scientific Name (LPSN)	Labedaea rhizosphaerae Lee 2012

Information on morphological and physiological properties Morphology

[Ref.: #30357]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30357]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.788

[Ref.: #69388]	Colony color	Fawn brown (8007), Pale brown (8025)
[Ref.: #69388]	Cultivation medium used	suter with tyrosine

[Ref.: #69388]	Colony color	Ivory (1014)
[Ref.: #69388]	Cultivation medium used	ISP 2

[Ref.: #69388]	Colony color	Ivory (1014)
[Ref.: #69388]	Cultivation medium used	ISP 3

[Ref.: #69388]	Colony color	Ivory (1014)
[Ref.: #69388]	Cultivation medium used	ISP 6

[Ref.: #69388]	Colony color	Light ivory (1015)
[Ref.: #69388]	Cultivation medium used	ISP 4

[Ref.: #69388]	Colony color	Light ivory (1015)
[Ref.: #69388]	Cultivation medium used	ISP 5

[Ref.: #69388]	Colony color	Light ivory (1015)
[Ref.: #69388]	Cultivation medium used	ISP 7

[Ref.: #69388]	Colony color	Sepia brown (8014), Brown beige (1011)
[Ref.: #69388]	Cultivation medium used	suter without tyrosine

[Ref.: #30357]	Pigment production	no
[Ref.: #69388]	Pigment production	no
[Ref.: #69388]	Pigment name	Melanin
[Ref.: #69388]	Pigment production	yes
[Ref.: #69388]	Pigmentation color	Ochre brown (8001)
[Ref.: #69388]	Pigment name	soluble pigment

[Ref.: #69388]	Multicellular complex forming ability	no
[Ref.: #69388]	Multicellular complex name	Aerial mycelium
[Ref.: #69388]	Medium Name (multicellularity)	ISP 2

[Ref.: #69388]	Multicellular complex forming ability	no
[Ref.: #69388]	Multicellular complex name	Aerial mycelium
[Ref.: #69388]	Medium Name (multicellularity)	ISP 3

[Ref.: #69388]	Multicellular complex forming ability	yes
[Ref.: #69388]	Multicellular complex name	Aerial mycelium
[Ref.: #69388]	Multicellular complex color	Pure white (9010)
[Ref.: #69388]	Medium Name (multicellularity)	ISP 4

[Ref.: #69388]	Multicellular complex forming ability	no
[Ref.: #69388]	Multicellular complex name	Aerial mycelium
[Ref.: #69388]	Medium Name (multicellularity)	ISP 5

[Ref.: #69388]	Multicellular complex forming ability	no
[Ref.: #69388]	Multicellular complex name	Aerial mycelium
[Ref.: #69388]	Medium Name (multicellularity)	ISP 6

[Ref.: #69388]	Multicellular complex forming ability	yes
[Ref.: #69388]	Multicellular complex name	Aerial mycelium
[Ref.: #69388]	Multicellular complex color	Traffic white (9016)
[Ref.: #69388]	Medium Name (multicellularity)	ISP 7

[Ref.: #69388]	Multicellular complex forming ability	no
[Ref.: #69388]	Multicellular complex name	Aerial mycelium
[Ref.: #69388]	Medium Name (multicellularity)	suter with tyrosine

[Ref.: #69388]	Multicellular complex forming ability	no
[Ref.: #69388]	Multicellular complex name	Aerial mycelium
[Ref.: #69388]	Medium Name (multicellularity)	suter without tyrosine

Multimedia content

[Ref.: #69388]

Caption:

Plates (553, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69388]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

[Ref.: #69388]

Caption:

Plates (553, ISP2, ISP3, ISP4, ISP5, ISP7)

[Ref.: #69388]

Intellectual property rights:

Helmholtz-Zentrum für Infektionsforschung GmbH

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16409]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #16409]

Culture medium growth

[Ref.: #16409]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16409]

Culture medium composition

expand / minimize

[Ref.: #16409]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #16409]

Culture medium growth

[Ref.: #16409]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16409]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16409]	growth	28 °C
[Ref.: #30357]	growth	25-42 °C
[Ref.: #30357]	optimum	33.5 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #16409]	Temperature range	mesophilic
[Ref.: #30357]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30357]			optimum	7.75
[Ref.: #30357]			growth	5.1-10.1

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30357]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #30357]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30357]		NaCl		growth	<3	%
[Ref.: #69388]		NaCl		growth	0-10	%

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-8, MK-9(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69388]	arabinose ChEBI	-	growth
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30357]	cellobiose ChEBI	+	carbon source
[Ref.: #69388]	cellulose ChEBI	-	growth
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE, API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30357]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE, API Coryne
[Ref.: #30357]	fructose ChEBI	+	carbon source
[Ref.: #69388]	fructose ChEBI	-	growth
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE, API Coryne
[Ref.: #30357]	glucose ChEBI	+	carbon source
[Ref.: #69388]	glucose ChEBI	-	growth
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #69388]	inositol ChEBI	-	growth
[Ref.: #30357]	lactose ChEBI	+	carbon source
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #30357]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #30357]	mannitol ChEBI	+	carbon source
[Ref.: #69388]	mannose ChEBI	-	growth
[Ref.: #30357]	melibiose ChEBI	+	carbon source
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE, API Coryne
[Ref.: #30357]	raffinose ChEBI	+	carbon source
[Ref.: #69388]	raffinose ChEBI	-	growth
[Ref.: #30357]	rhamnose ChEBI	+	carbon source
[Ref.: #69388]	rhamnose ChEBI	-	growth
[Ref.: #30357]	sucrose ChEBI	+	carbon source
[Ref.: #69388]	sucrose ChEBI	-	growth
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #30357]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE, API Coryne
[Ref.: #30357]	xylose ChEBI	+	carbon source
[Ref.: #69388]	xylose ChEBI	-	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	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.: #68379]	alpha-glucosidase	+	3.2.1.20	* from API Coryne
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68379]	beta-galactosidase	-	3.2.1.23	* from API Coryne, API zym
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne, API 20NE
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #30357]	gelatinase	+
[Ref.: #68379]	gelatinase	+		* from API Coryne, API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API Coryne, API zym
[Ref.: #68379]	pyrazinamidase	+	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne, API 20NE
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #16409]	25365	-	-	-	-	-	+	+	-	+/-	+/-	-	+/-	+/-	-	+/-	-	+/-	+/-	-	-	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.: #69388]	3881	-	+	+	-	-	-	+	+	+	-	+	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.: #16409]	14341	-	+/-	-	-	-	+	-	-	-	-	+	+/-	-	-	-	+/-	-	+	-	-
[Ref.: #69388]	6065	not determinedn.d.	+/-	+	+	+/-	+	+	+/-	+/-	+/-	+	-	+	-	-	+	+	+	+	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	daunorubicin biosynthesis	100	9 of 9
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	3-chlorocatechol degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	85.71	6 of 7
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	cysteine metabolism	77.78	14 of 18
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	non-pathway related	73.68	28 of 38
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	benzoyl-CoA degradation	57.14	4 of 7
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	cholesterol biosynthesis	54.55	6 of 11
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[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]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
		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.: #16409]	Sample type/isolated from	rhizosphere soil of the cliff-associated plant Peucedanum japonicum Thunb.
[Ref.: #16409]	Host species	Peucedanum japonicum
[Ref.: #16409]	Geographic location (country and/or sea, region)	Jeju, Mara Island
[Ref.: #16409]	Country	Republic of Korea
[Ref.: #16409]	Country ISO 3 Code	KOR
[Ref.: #16409]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Rhizosphere soil of a cliff-associated plant (Peucedanum japonicum Thunb.) on Mara Island
[Ref.: #67770]	Host species	Peucedanum japonicum
[Ref.: #67770]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From rhizosphere)
[Ref.: #67771]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	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 FM998036 (>99% sequence identity) for Kibdelosporangium from Microbeatlas

Aquatic Samples	43
Soil Samples	946
Animal Samples	76
Plant Samples	668
Total Samples	1733

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

[Ref.: #16409]

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.: #16409]	Labedaea rhizosphaerae partial 16S rRNA gene, type strain RS-49T	FM998036	1424	ENA	598644 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Labedaea rhizosphaerae DSM 45361	GCA_004362825	scaffold	GenBank	598644 tax ID
[Ref.: #66792]	Labedaea rhizosphaerae strain DSM 45361	598644.3	wgs	PATRIC	598644 tax ID	*
[Ref.: #66792]	Labedaea rhizosphaerae DSM 45361	2795385470	draft	JGI IMG/M	598644 tax ID	*

[Ref.: #16409]	GC-content	64.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30357]	GC-content	64.2 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Labedaea rhizosphaerae DSM 45361 NCBI: GCA_004362825.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Labedaea rhizosphaerae strain DSM 45361 PATRIC: 598644.3
[Ref.: #69480]	gram-positive	yes	86.756	yes
[Ref.: #69480]	anaerobic	no	98.929	yes
[Ref.: #69480]	halophile	no	94.022	no
[Ref.: #69480]	spore-forming	yes	90.211	yes
[Ref.: #69480]	glucose-util	yes	89.561	no
[Ref.: #69480]	flagellated	no	97.406	yes
[Ref.: #69480]	aerobic	yes	92.407	no
[Ref.: #69480]	thermophile	no	97.004	yes
[Ref.: #69480]	motile	no	93.932	yes
[Ref.: #69480]	glucose-ferment	no	92.047	yes

Availability in culture collections External links

[Ref.: #16409]

Culture collection no.

DSM 45361, KCTC 19662, JCM 31489

[Ref.: #82708]

SI-ID 397978

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Labedaea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere soil.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.034355-0	2011	*

References

#16409

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45361

#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 )

#30357

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 #26697 (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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69388

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

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82708

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-ID397978.1 )

#26697

IJSEM 1772 2012 ( DOI 10.1099/ijs.0.034355-0 , PubMed 21948095 )

* These data were automatically processed and therefore are not curated

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Labedaea rhizosphaerae DSM 45361

Labedaea rhizosphaerae strain DSM 45361

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