Microbacterium oxydans (DSM 20578, CIP 6612, NCIB 9944)

Name: Microbacterium oxydans (DSM 20578, CIP 6612, NCIB 9944)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7369

Type strain

Strain Designation X98

Culture col. no. DSM 20578 CIP 6612 NCIB 9944 NRRL B-24236 CCUG 58056 13 more

NCBI tax ID(s) 82380

Special Collections DSMZ CCUG JCM KCTC CIP Wink compendium

Links

Microbacterium oxydans X98 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from air.

Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49650

NCTC 13564,DSM 20578,NCIB 9944,CIP 6612,NCIMB 9944,IFO15586,VKM Ac-2116,CIP 66.12,KCTC 3256,NBRC 15586,JCM 12414,BCRC 12117,CCRC 12117,LMG 23389,NRRL B-24236,IAM 15197,CCUG 58056

@ref 20215

Last LPSN update 2025-12-16 09:48:34

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Microbacterium

Species Microbacterium oxydans

Full scientific name Microbacterium oxydans (Chatelain and Second 1966) Schumann et al. 1999

Synonyms (1)

Brevibacterium oxydans

BacDive ID	Other strains from **Microbacterium oxydans** (19)	Type strain
134483	M. oxydans X 95, CIP 66.13
134755	M. oxydans CIP 60.8, ATCC 7762, NCTC 6701
134756	M. oxydans 4B, CIP 60.9
135591	M. oxydans 30003, CIP 56.40
136022	M. oxydans CIP 101877
137639	M. oxydans 67-82, CIP 102950
137715	M. oxydans CIP 102791
137792	M. oxydans 983-85, CIP 101976
137802	M. oxydans 229.87, CIP 102957
138693	M. oxydans 40-86, CIP 102128
145393	M. oxydans CCUG 28354
145395	M. oxydans CCUG 28358
146734	M. oxydans CCUG 32039
147061	M. oxydans CCUG 32767
147984	M. oxydans CCUG 34623
150377	M. oxydans CCUG 39774
152265	M. oxydans CCUG 46251
152683	M. oxydans CCUG 47351
156196	M. oxydans CCUG 60687

Morphology

Cell morphology

@ref	Gram stain
67771	positive
121487	positive
125439	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
18450	Beige (1001)	10-14 days	ISP 2
18450	Zinc yellow (1018)	10-14 days	ISP 3
18450	Beige (1001)	10-14 days	ISP 4
18450	Beige (1001)	10-14 days	ISP 5
18450	Beige (1001)	10-14 days	ISP 6
18450	Beige (1001)	10-14 days	ISP 7
121487

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18450		ISP 2
18450		ISP 3
18450		ISP 4
18450		ISP 5
18450		ISP 6
18450		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Composition
18450	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
18450	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
18450	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:
18450	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
18450	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
18450	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
8928	CORYNEBACTERIUM AGAR (DSMZ Medium 53)	Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
37612	MEDIUM 3 - Columbia agar	Columbia agar (39.000 g);distilled water (1000.000 ml)
121487	CIP Medium 3

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8928	positive	growth	30	mesophilic
18450	positive	optimum	28	mesophilic
37612	positive	growth	30	mesophilic
61577	positive	growth	37	mesophilic
67770	positive	growth	28	mesophilic
67771	positive	growth	30	mesophilic
121487	positive	growth	10-37
121487	negative	growth	41
121487	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
61577	aerobe
67771	aerobe
121487	obligate aerobe
125439	obligate aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121487	NaCl	positive	growth	0-6 %
121487	NaCl		growth	8 %
121487	NaCl		growth	10 %

Murein

@ref	Murein short key	Type
8928	B06	B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

Observation

67770

Observationquinones: MK-11, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121487	16947 ChEBI	citrate	+	carbon source
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	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
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
121487	4853 ChEBI	esculin	+	hydrolysis
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
68371	24265 ChEBI	gluconate	-	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
121487	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	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
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68371	28053 ChEBI	melibiose	-	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
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
121487	17632 ChEBI	nitrate	-	reduction
121487	17632 ChEBI	nitrate	-	respiration
121487	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
121487	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121487	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
121487	15688 ChEBI	acetoin	-
121487	17234 ChEBI	glucose

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121487	alcohol dehydrogenase	-	1.1.1.1
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
121487	amylase	+
121487	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121487	caseinase	+	3.4.21.50
121487	catalase	+	1.11.1.6
68379	catalase	+	1.11.1.6	from API Coryne
121487	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121487	gamma-glutamyltransferase	-	2.3.2.2
121487	gelatinase	+
68379	gelatinase	+		from API Coryne
121487	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121487	lipase	-
121487	lysine decarboxylase	-	4.1.1.18
121487	ornithine decarboxylase	-	4.1.1.17
121487	oxidase	-
121487	phenylalanine ammonia-lyase	-	4.3.1.24
121487	protease	+
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
121487	tryptophan deaminase	-
121487	tween esterase	-
121487	urease	-	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	starch degradation	100	10 of 10
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	pentose phosphate pathway	100	11 of 11
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	gallate degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	lipoate biosynthesis	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	photosynthesis	92.86	13 of 14
66794	Entner Doudoroff pathway	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	glycolysis	88.24	15 of 17
66794	gluconeogenesis	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	phenylalanine metabolism	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	metabolism of disaccharids	81.82	9 of 11
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	vitamin B1 metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	degradation of hexoses	72.22	13 of 18
66794	degradation of sugar acids	72	18 of 25
66794	degradation of pentoses	71.43	20 of 28
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	degradation of sugar alcohols	68.75	11 of 16
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	heme metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	oxidative phosphorylation	62.64	57 of 91
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	3-chlorocatechol degradation	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	phenol degradation	55	11 of 20
66794	lysine metabolism	54.76	23 of 42
66794	CMP-KDO biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	tyrosine metabolism	50	7 of 14
66794	cyclohexanol degradation	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	vitamin B6 metabolism	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	lipid A biosynthesis	44.44	4 of 9
66794	glutathione metabolism	42.86	6 of 14
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	carotenoid biosynthesis	36.36	8 of 22
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	coenzyme M biosynthesis	30	3 of 10
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	sulfate reduction	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9

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
18450	-	-	-	-	-	-	+	-	+	+	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.
61577	-	-	-	+	-	+	+	+	+	-	+	-	-	-	-	-	-	-	-	-	+

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
18450	not determinedn.d.	-	+	+	-	+	+	+	+	+	+	-	-	+	-	+	+	-	+	+
61577	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	+	+	+	-
121487	-	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	+	+	+	+

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
8928	-	+	-	-	-	+/-	-	-	-	-	+	+	+	+	-	+	-	-	+	-	-	+	-	+	+	+	+	+	+	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-
121487	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
121487	not determinedn.d.	+	+	+	+	+	-	-	+	-	+	+	-	-	-	-	+	+	-	+	+	-	-	+	+	+	+	-	-	+	-	-	+	-	+	+	+	-	-	+	-	-	+	-	-	-	-	-	-	-	+	-	-	-	+	+	-	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+	+	+	-	-	-	-	-	+	-	-	-	+	+	-	+	-	-	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Air

Isolation

@ref	Sample type
8928	air
61577	Air contaminant,hospital
67770	Air
121487	Environment, Contaminating air

Taxonmaps

69479

Global distribution of 16S sequence Y17227 (>99% sequence identity) for Microbacterium from Microbeatlas

Aquatic Samples	9581
Soil Samples	10113
Animal Samples	16954
Plant Samples	5605
Total Samples	42253

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8928	1	Risk group (German classification) According to TRBA 466
18450	1	German classification According to TRBA 466
121487	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	ASM886802v1 assembly for Microbacterium oxydans DSM 20578	contig	GCA_008868025	82380.43	8117014482	82380	77.38
67770	ASM654008v1 assembly for Microbacterium oxydans NBRC 15586	contig	GCA_006540085	82380.42		82380	75.08
124043	ASM3952779v1 assembly for Microbacterium oxydans JCM 12414	scaffold	GCA_039527795			82380	59.36

Genome browser: GCA_008868025

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Microbacterium oxydans strain DSM 20578 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	HQ853347	500	82380
20218	Microbacterium oxydans 16S rRNA gene	Y17227	1466	82380
8928	Microbacterium oxydans strain DSM 20578 16S ribosomal RNA, partial sequence	NR_044931	1466	82380
124043	Microbacterium oxydans strain DSM 20578 16S ribosomal RNA gene, partial sequence.	OR801634	1466	82380
124043	Microbacterium oxydans strain DSM 20578(T) 16S ribosomal RNA gene, partial sequence.	MH321609	1393	82380

GC content

@ref	GC-content (mol%)
8928	67.0
67770	70

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Microbacterium oxydans NBRC 15586
NCBI: GCA_006540085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	75.50	no
125439	motility	BacteriaNetⓘ	no	68.30	no
125439	gram_stain	BacteriaNetⓘ	positive	97.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microbacterium oxydans strain DSM 20578
PATRIC: 82380.43

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.33	yes
125438	anaerobic	anaerobicⓘ	no	97.71	yes
125438	aerobic	aerobicⓘ	yes	87.19	no
125438	spore-forming	spore-formingⓘ	no	71.76	no
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	76.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Microbacterium strain A8/3-1 isolated from the root nodule of Oxytropis tragacanthoides, growing in the Altai region.	Guro P, Sazanova A, Belimov A, Karlov D, Kuznetsova I, Safronova V.	Microbiol Resour Announc	10.1128/mra.00817-24	2024
	Bacteraemia due to Microbacterium paraoxydans in a patient with chronic kidney disease, refractory hypertension and sarcoidosis.	Chorost MS, Smith NC, Hutter JN, Ong AC, Stam JA, McGann PT, Hinkle MK, Schaecher KE, Kamau E.	JMM Case Rep	10.1099/jmmcr.0.005169	2018
	Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables.	Acuna JJ, Hu J, Inostroza NG, Valenzuela T, Perez P, Epstein S, Sessitsch A, Zhang Q, Jorquera MA.	Sci Rep	10.1038/s41598-023-47099-4	2023
	Effect of volatile compounds produced by the cotton endophytic bacterial strain Bacillus sp. T6 against Verticillium wilt.	Zhang L, Wang Y, Lei S, Zhang H, Liu Z, Yang J, Niu Q.	BMC Microbiol	10.1186/s12866-022-02749-x	2023
Phylogeny	Characterization of bacterial communities associated with the exotic and heavy metal tolerant wetland plant Spartina alterniflora.	Yang Y, Ding J, Chi Y, Yuan J.	Sci Rep	10.1038/s41598-020-75041-5	2020
Phylogeny	Identification of a bacterial strain isolated from the liver of a laboratory mouse as Microbacterium paraoxydans and emended description of the species Microbacterium paraoxydans Laffineur et al 2003.	Buczolits S, Schumann P, Valens M, Rossello-Mora R, Busse HJ.	Indian J Microbiol	10.1007/s12088-008-0035-0	2008
Enzymology	Cultivable microbiota associated with Aurelia aurita and Mnemiopsis leidyi.	Weiland-Brauer N, Prasse D, Brauer A, Jaspers C, Reusch TBH, Schmitz RA.	Microbiologyopen	10.1002/mbo3.1094	2020
Enzymology	Evaluation of Bioaerosol Bacterial Components of a Wastewater Treatment Plant Through an Integrate Approach and In Vivo Assessment.	Bruni E, Simonetti G, Bovone B, Casagrande C, Castellani F, Riccardi C, Pomata D, Di Filippo P, Federici E, Buiarelli F, Uccelletti D.	Int J Environ Res Public Health	10.3390/ijerph17010273	2019
Pathogenicity	Antibiotic-resistant bacteria in the guts of insects feeding on plants: prospects for discovering plant-derived antibiotics.	Ignasiak K, Maxwell A.	BMC Microbiol	10.1186/s12866-017-1133-0	2017
	Parallel evolution of alternate morphotypes of Chryseobacterium gleum during experimental evolution with Caenorhabditis elegans.	Duckett M, Taylor MN, Bowman C, Vega NM.	FEMS Microbiol Ecol	10.1093/femsec/fiae039	2024
Pathogenicity	Genome Sequencing of the Antibiotic-Resistant Leucobacter sp. HNU-1 and Its Developmental Toxicity in Caenorhabditis elegans.	Ju J, Lu X, Gao Z, Yin H, Xu S, Li H.	Int J Mol Sci	10.3390/ijms26083673	2025
Genetics	Genome-Based Analysis of the Potential Bioactivity of the Terrestrial Streptomyces vinaceusdrappus Strain AC-40.	Sedeek AM, Salah I, Kamel HL, Soltan MA, Nour E, Alshammari A, Riaz Rajoka MS, Elsayed TR.	Biology (Basel)	10.3390/biology12030345	2023
Phylogeny	Microbacterium algeriense sp. nov., a novel actinobacterium isolated from Algerian oil production waters.	Lenchi N, Anzil A, Servais P, Kebbouche-Gana S, Gana ML, Lliros M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004434	2020

References

#8928	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20578
#18450	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 )
#37612	; Curators of the CIP;
#61577	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58056
#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;
#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 .
#121487	Collection of Institut Pasteur ; Curators of the CIP; CIP 66.12
#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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Microbacterium oxydans (DSM 20578, CIP 6612, NCIB 9944)

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

Murein

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

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_008868025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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