Gordonia rhizosphera (DSM 44383, IFO 16068, NBRC 16068)

Name: Gordonia rhizosphera (DSM 44383, IFO 16068, NBRC 16068)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10596

Type strain

Strain Designation 141

Culture col. no. DSM 44383 IFO 16068 NBRC 16068 141 VKM Ac-2072 6 more

NCBI tax ID(s) 1108045 83341

Special Collections DSMZ JCM KCTC CIP Wink compendium

History DSMZ <- IFO; 141 JCM <-- IFO 16068 <-- M. Takeuchi 141. CIP <- 1998, IFO <- K. Hatano: strain 141

Links

Gordonia rhizosphera 141 is an obligate aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil of the Mangrove rhizosphere.

Gram-positive rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 50603

CIP 105727,IFO 16068,DSM 44383,JCM 10426,VKM Ac-2072,KCTC 9824,NBRC 16068,BCRC 16393,CCRC 16393,NCIMB 13848

@ref 20215

Last LPSN update 2026-05-29 08:27:22

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Gordoniaceae

Genus Gordonia

Species Gordonia rhizosphera

Full scientific name Gordonia rhizosphera Takeuchi and Hatano 1998

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122213	positive	rod-shaped
125438			92.5
125438	positive		93.247
125439	positive		92.789

Colony morphology

@ref	Colony color	Incubation period	Medium used	Hemolysis ability
20052	Salmon orange (2012)	10-14 days	ISP 2
20052	Salmon orange (2012)	10-14 days	ISP 3
20052	Salmon orange (2012)	10-14 days	ISP 4
20052	Salmon orange (2012)	10-14 days	ISP 5
20052	Salmon orange (2012)	10-14 days	ISP 6
20052	Salmon orange (2012)	10-14 days	ISP 7
122213				0

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20052		ISP 2
20052		ISP 3
20052		ISP 4
20052		ISP 5
20052		ISP 6
20052		ISP 7

Multimedia

@ref:	11504
multimedia content:	DSM_44383.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44383.jpg
caption:	Medium 535 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11504	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20052	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20052	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20052	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20052	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20052	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20052	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
39324	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
122213	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11504	positive	growth	28
20052	positive	optimum	28
39324	positive	growth	30
67770	positive	growth	28
122213	positive	growth	25-37
122213	negative	growth	10
122213	negative	growth	41
122213	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
122213	obligate aerobe
125439	obligate aerobe	99.105

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122213	NaCl	positive	growth	0-6 %
122213	NaCl		growth	8 %
122213	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
20052	22599 ChEBI	arabinose	-
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
20052	62968 ChEBI	cellulose	-
122213	16947 ChEBI	citrate	+	carbon source
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68371	17108 ChEBI	D-arabinose	+	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
122213	4853 ChEBI	esculin	+	hydrolysis
20052	28757 ChEBI	fructose	+
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
20052	17234 ChEBI	glucose	+
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
122213	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	+	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	+	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
20052	29864 ChEBI	mannitol	+
68371	6731 ChEBI	melezitose	+	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
20052	17268 ChEBI	myo-inositol	+
68371	17268 ChEBI	myo-inositol	+	builds acid from	from API 50CH acid
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
122213	17632 ChEBI	nitrate	-	reduction
122213	17632 ChEBI	nitrate	-	respiration
122213	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
20052	16634 ChEBI	raffinose	-
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
20052	26546 ChEBI	rhamnose	+
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
20052	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
20052	18222 ChEBI	xylose	-

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
122213	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
122213	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
122213	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-			from API 20E
122213	17234 ChEBI	glucose		-
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
122213	alcohol dehydrogenase	-	1.1.1.1
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
122213	amylase	-
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
122213	beta-galactosidase	-	3.2.1.23
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
122213	caseinase	-	3.4.21.50
122213	catalase	+	1.11.1.6
122213	DNase	-
122213	gamma-glutamyltransferase	-	2.3.2.2
122213	gelatinase	-
68379	gelatinase	-		from API Coryne
68368	gelatinase	-		from API 20E
122213	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
122213	lipase	-
68382	lipase (C 14)	-		from API zym
122213	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
122213	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
122213	oxidase	-
122213	phenylalanine ammonia-lyase	-	4.3.1.24
122213	protease	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
122213	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
122213	tween esterase	-
122213	urease	+	3.5.1.5
68379	urease	+	3.5.1.5	from API Coryne
68368	urease	+	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	propanol degradation	100	7 of 7
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	3-chlorocatechol degradation	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	cardiolipin biosynthesis	100	7 of 7
66794	butanoate fermentation	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	hydrogen production	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	starch degradation	100	10 of 10
66794	enterobactin biosynthesis	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	resorcinol degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	vitamin K metabolism	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	cyanate degradation	100	3 of 3
66794	myo-inositol biosynthesis	100	10 of 10
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	kanosamine biosynthesis II	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	flavin biosynthesis	93.33	14 of 15
66794	citric acid cycle	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	purine metabolism	89.36	84 of 94
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	ketogluconate metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	phenol degradation	85	17 of 20
66794	urea cycle	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glycolysis	82.35	14 of 17
66794	proline metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	factor 420 biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	gallate degradation	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	arginine metabolism	79.17	19 of 24
66794	tryptophan metabolism	78.95	30 of 38
66794	d-mannose degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	carotenoid biosynthesis	77.27	17 of 22
66794	methionine metabolism	76.92	20 of 26
66794	vitamin B1 metabolism	76.92	10 of 13
66794	vitamin E metabolism	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	lipid metabolism	74.19	23 of 31
66794	glutathione metabolism	71.43	10 of 14
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	sulfate reduction	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	lysine metabolism	66.67	28 of 42
66794	tyrosine metabolism	64.29	9 of 14
66794	oxidative phosphorylation	63.74	58 of 91
66794	metabolism of disaccharids	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of hexoses	61.11	11 of 18
66794	creatinine degradation	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	benzoyl-CoA degradation	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	degradation of pentoses	53.57	15 of 28
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	CMP-KDO biosynthesis	50	2 of 4
66794	polyamine pathway	47.83	11 of 23
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	d-xylose degradation	45.45	5 of 11
66794	cholesterol biosynthesis	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	coenzyme M biosynthesis	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	arachidonic acid metabolism	33.33	6 of 18
66794	methanogenesis from CO2	33.33	4 of 12
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
20052	-	+	+	+	+	-	+	-	-	-	-	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

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
20052	-	-	-	-	-	-	-	-	-	+	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
20052	not determinedn.d.	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-
122213	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122213	not determinedn.d.	-	-	+	-	-	-	-	-	-	-	+	+	+/-	-	+	-	+	+	-	-	-	+/-	-	-	+/-	-	+	+	-	-	+	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122213	not determinedn.d.	+	+	-	+	-	-	-	+	-	+	+	-	-	-	-	+	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	+	-	-	-	-	-	+	+	-	+	+	+	-	+	+	+	-	-	+	-	-	+	+	-	-	-	+	+	-	-	-	+	-	+	-	+	-	-	-	-	+	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Mangrove
#Environmental	#Terrestrial	#Soil
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
11504	soil of the Mangrove rhizosphere			Japan	JPN	Asia
67770	Soil and the surface of fine roots in rhizosphere of Bruguiera gymnorrhiza (mangrove)	Bruguiera gymnorrhiza	Shiira River estuary, Iriomote Island	Japan	JPN	Asia
122213	Environment, Mangrove rhizosphere, root		Iriomote Island	Japan	JPN	Asia	1995

Taxonmaps

69479

Global distribution of 16S sequence AB004729 (>99% sequence identity) for Gordonia from Microbeatlas

Aquatic Samples	31
Soil Samples	6
Animal Samples	164
Plant Samples	10
Total Samples	211

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11504	1	Risk group (German classification) According to TRBA 466
20052	1	German classification According to TRBA 466
122213	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM5130314v1 assembly for Gordonia rhizosphera NBRC 16068	scaffold	GCA_051303145			1108045	67.33
67770	ASM29819v1 assembly for Gordonia rhizosphera NBRC 16068	contig	GCA_000298195	1108045.3	2523231044	1108045	23.84

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
11504	Gordonia rhizosphera gene for 16S rRNA, partial sequence	AB004729	1475		1108045

GC content

@ref	GC-content (mol%)	Method
11504	66.8
67770	66.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM5130314v1 assembly for Gordonia rhizosphera NBRC 16068
NCBI: GCA_051303145

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.11	no
125439	gram_stain	BacteriaNetⓘ	positive	92.79	no
125439	motility	BacteriaNetⓘ	no	77.76	no
125439	spore_formation	BacteriaNetⓘ	no	88.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gordonia rhizosphera NBRC 16068
PATRIC: 1108045.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.25	no
125438	anaerobic	anaerobicⓘ	no	98.22	yes
125438	spore-forming	spore-formingⓘ	no	52.24	no
125438	aerobic	aerobicⓘ	yes	88.15	no
125438	thermophilic	thermophileⓘ	no	96.96	no
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Molecular Detection and Phylogenetic Analysis of the alkB Gene in Klebsiella oxytoca Strains Isolated from the Gut of Tenebrio molitor.	Mupamhadzi TL, Machona O, Chidzwondo F, Mangoyi R.	ScientificWorldJournal	10.1155/2024/3350591	2024
Metabolism	Identification of a cyclosporine-specific P450 hydroxylase gene through targeted cytochrome P450 complement (CYPome) disruption in Sebekia benihana.	Lee MJ, Kim HB, Yoon YJ, Han K, Kim ES.	Appl Environ Microbiol	10.1128/aem.03722-12	2013
	Insights into the phylogenetic diversity, biological activities, and biosynthetic potential of mangrove rhizosphere Actinobacteria from Hainan Island.	Ye JJ, Zou RJ, Zhou DD, Deng XL, Wu NL, Chen DD, Xu J.	Front Microbiol	10.3389/fmicb.2023.1157601	2023
Phylogeny	Molecular detection and phylogenetic analysis of the catechol 1,2-dioxygenase gene from Gordonia spp.	Shen FT, Lin JL, Huang CC, Ho YN, Arun AB, Young LS, Young CC.	Syst Appl Microbiol	10.1016/j.syapm.2009.04.002	2009
	Search for genes gained by horizontal gene transfer in an entomopoxvirus, with special reference to the analysis of the transfer of an ABC transporter gene.	Sugimoto TN, Jouraku A, Mitsuhashi W.	Virus Res	10.1016/j.virusres.2024.199418	2024
Phylogeny	Gordonia soli sp. nov., a novel actinomycete isolated from soil.	Shen FT, Goodfellow M, Jones AL, Chen YP, Arun AB, Lai WA, Rekha PD, Young CC.	Int J Syst Evol Microbiol	10.1099/ijs.0.64492-0	2006
Genetics	Genomic insights into Gordonia diversity: proposal of three novel species (Gordonia. altitudinis sp. nov., Gordonia. ligustrum sp. nov., and Gordonia. pistacia sp. nov.) with distinct environmental and biomedical traits.	Li CJ, Zhang J, Su J, Yu LY, Chen HH, Zhang YQ.	BMC Microbiol	10.1186/s12866-025-04362-0	2025
Phylogeny	Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan.	Xie Y, Zhou S, Xu Y, Wu W, Xia W, Zhang R, Huang D, Huang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.004310	2020
Phylogeny	Gordonia sediminis sp. nov., an actinomycete isolated from mangrove sediment.	Sangkanu S, Suriyachadkun C, Phongpaichit S	Int J Syst Evol Microbiol	10.1099/ijsem.0.003399	2019
Phylogeny	Gordonia oryzae sp. nov., isolated from rice plant stems (Oryza sativa L.).	Muangham S, Lipun K, Thamchaipenet A, Matsumoto A, Duangmal K	Int J Syst Evol Microbiol	10.1099/ijsem.0.003368	2019
Phylogeny	Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere.	Takeuchi M, Hatano K	Int J Syst Bacteriol	10.1099/00207713-48-3-907	1998

References

#11504	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44383
#20052	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 )
#39324	; Curators of the CIP;
#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 .
#68371	Automatically annotated from API 50CH acid .
#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 .
#122213	Collection of Institut Pasteur ; Curators of the CIP; CIP 105727
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 .
#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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Gordonia rhizosphera (DSM 44383, IFO 16068, NBRC 16068)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20E

API coryne

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_051303145

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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