Gordonia alkanivorans (DSM 44369, IFO 16433, JCM 10677)

Name: Gordonia alkanivorans (DSM 44369, IFO 16433, JCM 10677)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10585

Type strain

Strain Designation 2102-488

Culture col. no. DSM 44369 IFO 16433 JCM 10677 NBRC 16433 HKI 0136 5 more

NCBI tax ID(s) 1027371 84096

Special Collections DSMZ JCM KCTC CIP Wink compendium

Links

Gordonia alkanivorans 2102-488 is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from tar and phenol contaminated soil.

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

Name and taxonomic classification

SI-ID 50595

CIP 106363,DSM 44369,IFO 16433,JCM 10677,KCTC 9951,NBRC 16433,NCIMB 13615

@ref 20215

Last LPSN update 2025-12-16 09:49:22

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Gordoniaceae

Genus Gordonia

Species Gordonia alkanivorans

Full scientific name Gordonia alkanivorans Kummer et al. 1999

Synonyms (1)

Gordonia nitida

BacDive ID	Other strains from **Gordonia alkanivorans** (6)	Type strain
10581	G. alkanivorans S564, DSM 777, IAM 1038
10582	G. alkanivorans Vera, DSM 2354
10583	G. alkanivorans 335, Schering 258, DSM 43290, ATCC 14346, ...
10584	G. alkanivorans MoAcy 2, DSM 44187
10586	G. alkanivorans DSM 44499, KCCM 80004, KCTC 0605BP, LE 31, ...
104719	G. alkanivorans ST033346(HKI),

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
116254	positive	rod-shaped
125438			92
125438	positive		91.35
125439	positive		97.9

Colony morphology

@ref	Colony color	Incubation period	Medium used
19655	Pure orange	10-14 days	ISP 2
19655	Pure orange	10-14 days	ISP 3
19655	Pure orange	10-14 days	ISP 4
19655	Pure orange	10-14 days	ISP 5
19655	Pure orange	10-14 days	ISP 6
19655	Pure orange	10-14 days	ISP 7
116254

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19655		ISP 2
19655		ISP 3
19655		ISP 4
19655		ISP 5
19655		ISP 6
19655		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11710	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
19655	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
19655	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:
19655	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
19655	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
19655	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
19655	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
40303	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116254	CIP Medium 29	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11710	positive	growth	28	mesophilic
19655	positive	optimum	28	mesophilic
40303	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
116254	positive	growth	25-41
116254	negative	growth	10
116254	negative	growth	45

Physiology and metabolism

Oxygen tolerance

116254

Oxygen toleranceobligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19655	NaCl	positive	maximum	5 %
116254	NaCl	positive	growth	0-6 %
116254	NaCl		growth	8 %
116254	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-9(H₂), MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
19655	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
19655	62968 ChEBI	cellulose	+
116254	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
68371	16024 ChEBI	D-mannose	-	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
116254	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
19655	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
19655	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
116254	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
19655	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
19655	17268 ChEBI	myo-inositol	-
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
116254	17632 ChEBI	nitrate	+	reduction
116254	17632 ChEBI	nitrate	-	respiration
116254	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
19655	16634 ChEBI	raffinose	-
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
19655	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
19655	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
19655	18222 ChEBI	xylose	-

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
116254	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
116254	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
116254	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-			from API 20E
116254	17234 ChEBI	glucose		-
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116254	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
116254	amylase	-
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
116254	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
116254	caseinase	-	3.4.21.50
116254	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
116254	DNase	+
68382	esterase lipase (C 8)	+		from API zym
116254	gamma-glutamyltransferase	-	2.3.2.2
116254	gelatinase	-
68379	gelatinase	-		from API Coryne
68368	gelatinase	-		from API 20E
116254	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116254	lipase	-
68382	lipase (C 14)	-		from API zym
116254	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
116254	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
116254	oxidase	-
116254	phenylalanine ammonia-lyase	-	4.3.1.24
116254	protease	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
116254	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
116254	tween esterase	+
116254	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

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
19655	-	+	+	+	+	-	+	-	-	-	-	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
19655	-	-	-	+	-	-	+	-	-	+	-	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
19655	not determinedn.d.	+	-	+	-	+	+	+	+	-	+	+	-	-	-	+	+	-	-	-
116254	-	+	+	+	-	+	+	+	-	-	+	+	-	+	-	+	+	-	-	-

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
116254	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
116254	not determinedn.d.	+	+	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	+	+	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	+	-	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Engineered	#Industrial	#Engineered product
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
11710	tar and phenol contaminated soil	Thuringia, Rosnitz, area of the former tar factory	Germany	DEU	Europe
67770	Tar- and phenol-contaminated soil of the former tar factory	Rositz	Germany	DEU	Europe
116254	Environment, Tar and phenol contaminated soil	Thuringia	Germany	DEU	Europe	1996

Taxonmaps

69479

Global distribution of 16S sequence Y18054 (>99% sequence identity) for Gordonia from Microbeatlas

Aquatic Samples	238
Soil Samples	155
Animal Samples	301
Plant Samples	12
Total Samples	706

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11710	1	Risk group (German classification) According to TRBA 466
19655	1	Risk group (German classification) According to TRBA 466
116254	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
67770	ASM22550v1 assembly for Gordonia alkanivorans NBRC 16433	contig	GCA_000225505	1027371.3	2512047058	1027371	51.32

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Gordonia alkanivorans strain CIP 106363 16S ribosomal RNA gene, partial sequence	DQ020577	464		1027371
20218	Gordonia alkalivorans 16S rRNA gene	Y18054	1490		84096

GC content

@ref	GC-content (mol%)	Method
11710	68
67770	68	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: Gordonia alkanivorans NBRC 16433
NCBI: GCA_000225505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	75.50	no
125439	motility	BacteriaNetⓘ	no	74.70	no
125439	gram_stain	BacteriaNetⓘ	positive	97.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gordonia alkanivorans NBRC 16433
PATRIC: 1027371.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.35	no
125438	anaerobic	anaerobicⓘ	no	98.80	no
125438	spore-forming	spore-formingⓘ	no	61.92	no
125438	aerobic	aerobicⓘ	yes	89.36	yes
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	no	92.00	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
Genetics	Genomic analysis provides insights into the Gordonia sp. W3S5 taxonomy and sulfur metabolism-related genes.	Parveen S, Akhtar N, Akram J.	3 Biotech	10.1007/s13205-021-02850-4	2021
	Isolation and identification of Alcaligenes faecalis W2-3 with high-yield production of dimethyl disulfide.	Wu P, Deng S, Li J, Wei X, Zheng R, Men X, Zhang H.	Sci Rep	10.1038/s41598-025-04904-6	2025
Genetics	Comparative Genomic Analysis of the Hydrocarbon-Oxidizing Dibenzothiophene-Desulfurizing Gordonia Strains.	Frantsuzova E, Delegan Y, Bogun A, Sokolova D, Nazina T.	Microorganisms	10.3390/microorganisms11010004	2022
	In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2.	Nahurira R, Wang J, Yan Y, Jia Y, Fan S, Khokhar I, Eltoukhy A.	AMB Express	10.1186/s13568-019-0733-5	2019
Phylogeny	Phylogenetic analysis reveals the taxonomically diverse distribution of the Pseudomonas putida group.	Yonezuka K, Shimodaira J, Tabata M, Ohji S, Hosoyama A, Kasai D, Yamazoe A, Fujita N, Ezaki T, Fukuda M.	J Gen Appl Microbiol	10.2323/jgam.2016.06.003	2017
	Antibiotic resistance patterns of environmental bacteria from sewage water in Vellore, India: isolation, virulence analysis, and characterization	Barnwal S, Saleh A.	Front Microbiol		2025
	Cloning and characterization of Kluyveromyces marxianus Hog1 gene	Qian J, Qin X, Yin Q, Chu J, Wang Y.	Biotechnol Lett		2011
	Larvicidal, growth inhibitory and biochemical effects of soil bacterium, Pseudomonas sp. EN4 against Spodoptera litura (Fab.) (Lepidoptera: Noctuidae).	Sarkhandia S, Devi M, Sharma G, Mahajan R, Chadha P, Saini HS, Kaur S.	BMC Microbiol	10.1186/s12866-023-02841-w	2023
Metabolism	Cloning and characterization of Kluyveromyces marxianus Hog1 gene.	Qian J, Qin X, Yin Q, Chu J, Wang Y.	Biotechnol Lett	10.1007/s10529-010-0458-7	2011
	Investigating the antibacterial effects of some Lactobacillus, Bifidobacterium and acetobacter strains killed by different methods on Streptococcus mutans and Escherichia coli.	Safari MS, Keyhanfar M, Shafiei R.	Mol Biol Res Commun	10.22099/mbrc.2019.33582.1399	2019
	Biodecolorization and Biodegradation of Azo Dye Reactive Orange-16 by Marine Nocardiopsis sp.	Chittal V, Gracias M, Anu A, Saha P, Bhaskara Rao KV.	Iran J Biotechnol	10.29252/ijb.1551	2019
	Marinoterpins A-C: Rare Linear Merosesterterpenoids from Marine-Derived Actinomycete Bacteria of the Family Streptomycetaceae.	Kim MC, Winter JM, Asolkar RN, Boonlarppradab C, Cullum R, Fenical W.	J Org Chem	10.1021/acs.joc.1c00262	2021
	Strategy of Salt Tolerance and Interactive Impact of Azotobacter chroococcum and/or Alcaligenes faecalis Inoculation on Canola (Brassica napus L.) Plants Grown in Saline Soil.	Abdel Latef AAH, Omer AM, Badawy AA, Osman MS, Ragaey MM.	Plants (Basel)	10.3390/plants10010110	2021
	Extracellular Xylanopectinolytic Enzymes by Bacillus subtilis ADI1 from EFB's Compost.	Nawawi MH, Mohamad R, Tahir PM, Saad WZ.	Int Sch Res Notices	10.1155/2017/7831954	2017
Metabolism	Role of the pectinolytic enzyme in the lactic acid fermentation of potato pulp by Rhizopus oryzae.	Saito K, Kawamura Y, Oda Y.	J Ind Microbiol Biotechnol	10.1007/s10295-003-0071-z	2003
	Mechanisms of halotolerant plant growth promoting Alcaligenes sp. involved in salt tolerance and enhancement of the growth of rice under salinity stress.	Fatima T, Mishra I, Verma R, Arora NK.	3 Biotech	10.1007/s13205-020-02348-5	2020
Genetics	Exploring K2G30 Genome: A High Bacterial Cellulose Producing Strain in Glucose and Mannitol Based Media.	Gullo M, La China S, Petroni G, Di Gregorio S, Giudici P.	Front Microbiol	10.3389/fmicb.2019.00058	2019
Metabolism	The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2).	Pisciotta A, Manteca A, Alduina R.	Sci Rep	10.1038/s41598-018-32027-8	2018
	The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages.	Nielsen TK, Carstens AB, Browne P, Lametsch R, Neve H, Kot W, Hansen LH.	Sci Rep	10.1038/s41598-017-13911-1	2017
Metabolism	Agarolytic bacterium Persicobacter sp. CCB-QB2 exhibited a diauxic growth involving galactose utilization pathway.	Furusawa G, Lau NS, Suganthi A, Amirul AA.	Microbiologyopen	10.1002/mbo3.405	2017
Enzymology	Comprehensive Analysis of a Vibrio parahaemolyticus Strain Extracellular Serine Protease VpSP37.	Salamone M, Nicosia A, Bennici C, Quatrini P, Catania V, Mazzola S, Ghersi G, Cuttitta A.	PLoS One	10.1371/journal.pone.0126349	2015
	Diverse alkane hydroxylase genes in microorganisms and environments.	Nie Y, Chi CQ, Fang H, Liang JL, Lu SL, Lai GL, Tang YQ, Wu XL.	Sci Rep	10.1038/srep04968	2014
Genetics	Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens.	Ye L, Hildebrand F, Dingemans J, Ballet S, Laus G, Matthijs S, Berendsen R, Cornelis P.	PLoS One	10.1371/journal.pone.0110038	2014
	Deciphering the biodesulfurization potential of two novel Rhodococcus isolates from a unique Greek environment.	Glekas PD, Martzoukou O, Mastrodima ME, Zarkadoulas E, Kanakoglou DS, Kekos D, Pachnos M, Mavridis G, Mamma D, Hatzinikolaou DG.	AIMS Microbiol	10.3934/microbiol.2022032	2022
	Microbial consortia degrade several widely used organic UV filters, but a number of hydrophobic filters remain recalcitrant to biodegradation.	Fagervold SK, Rohee C, Lebaron P.	Environ Sci Pollut Res Int	10.1007/s11356-023-31063-w	2023
	Detection of horizontal gene transfers from phylogenetic comparisons.	Pylro VS, Vespoli Lde S, Duarte GF, Yotoko KS.	Int J Evol Biol	10.1155/2012/813015	2012
Phylogeny	Gordonia nitida Yoon et al. 2000 is a later synonym of Gordonia alkanivorans Kummer et al. 1999.	Arenskotter M, Linos A, Schumann P, Kroppenstedt RM, Steinbuchel A	Int J Syst Evol Microbiol	10.1099/ijs.0.63400-0	2005
Phylogeny	Pseudomonas boreofloridensis sp. nov., and Pseudomonas citrulli sp. nov., isolated from watermelon in Florida.	Fullem KR, MacLellan MP, Poudel M, Goss EM, Potnis N, Minsavage GV, Jones JB, Paret ML.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006596	2024
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 westfalica sp. nov., a novel rubber-degrading actinomycete.	Linos A, Berekaa MM, Steinbuchel A, Kim KK, Sproer C, Kroppenstedt RM	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1133	2002
Phylogeny	Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete.	Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow M	Int J Syst Evol Microbiol	10.1099/00207713-50-6-2031	2000
Phylogeny	Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil.	Kummer C, Schumann P, Stackebrandt E	Int J Syst Bacteriol	10.1099/00207713-49-4-1513	1999

References

#11710	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44369
#19655	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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#40303	; Curators of the CIP;
#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 .
#116254	Collection of Institut Pasteur ; Curators of the CIP; CIP 106363
#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 alkanivorans (DSM 44369, IFO 16433, JCM 10677)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

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_000225505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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