Thermomonospora umbrina (DSM 43927, ATCC 49502, IFO 14346)

Name: Thermomonospora umbrina (DSM 43927, ATCC 49502, IFO 14346)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16974

Type strain

Culture col. no. DSM 43927 ATCC 49502 IFO 14346 IMET 9746 INA 2309 7 more

NCBI tax ID(s) 111806

Special Collections DSMZ JCM KCTC CIP Wink compendium

Links

Thermomonospora umbrina DSM 43927 is a facultative anaerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.

Gram-positive rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 125862

VKM Ac-1086,ATCC 49502,IFO 14346,CIP 105485,DSM 43927,IMET 9746,JCM 6837,NRRL B-16244,KCTC 9343,NBRC 14346

@ref 20215

Last LPSN update 2025-12-16 09:50:58

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Thermomonosporaceae

Genus Thermomonospora

Species Thermomonospora umbrina

Full scientific name Thermomonospora umbrina (Galatenko et al. 1987) Nouioui et al. 2018

Synonyms (1)

Actinomadura umbrina

BacDive ID	Other strains from **Thermomonospora umbrina** (14)	Type strain
128627	T. umbrina STH00427(ZIMET), HKI 0427
128628	T. umbrina STH00383(ZIMET), MRC 303, HKI 0383
128629	T. umbrina SF005255(FSU),
128630	T. umbrina SF005258(FSU),
128631	T. umbrina SF005260(FSU),
128632	T. umbrina SF005261(FSU),
128633	T. umbrina SF005256(FSU),
128634	T. umbrina SF005257(FSU),
128635	T. umbrina SF005262(FSU),
128636	T. umbrina SF005263(FSU),
128637	T. umbrina SF000752(FSU),
128638	T. umbrina SF000753(FSU),
128639	T. umbrina SF005253(FSU),
128640	T. umbrina SF005259(FSU),

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.9
125439		95.2
123721	positive

Colony morphology

@ref	Colony color	Incubation period	Medium used
19619	Pastel orange	10-14 days	ISP 2
19619	Pastel orange	10-14 days	ISP 3
19619	Pastel orange	10-14 days	ISP 4
19619	Pastel orange	10-14 days	ISP 5
19619	Pastel orange	10-14 days	ISP 6
19619	Pastel orange	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19619		ISP 2
19619		ISP 3
19619		ISP 4
19619		ISP 5
19619		ISP 6
19619		ISP 7

Multimedia

@ref:	11276
multimedia content:	DSM_43927.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_43927.jpg
caption:	Medium 554 37°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11276	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	Medium recipe at MediaDive	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
11276	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19619	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
19619	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:
19619	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
19619	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
19619	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
19619	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
40507	MEDIUM 129 - for Pseudonocardia, Nocardia, Skermania and Streptomyces seoulensis, Streptomyces stramineus		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (10.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
11276	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
123721	CIP Medium 129	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11276	positive	growth	37	mesophilic
19619	positive	optimum	28	mesophilic
40507	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
123721	positive	growth	25-30	mesophilic
123721	negative	growth	5
123721	negative	growth	15
123721	negative	growth	37
123721	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
123721	facultative anaerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		95.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19619	NaCl	positive	maximum	2.5 %
123721	NaCl	positive	growth	2-4 %
123721	NaCl		growth	0 %
123721	NaCl		growth	6 %
123721	NaCl		growth	8 %
123721	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-9(H₆), MK-9(H₈), MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
19619	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
19619	62968 ChEBI	cellulose	+/-
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	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
123721	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
19619	28757 ChEBI	fructose	+/-
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
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
19619	17234 ChEBI	glucose	+
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
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
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
19619	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
19619	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
123721	17632 ChEBI	nitrate	-	reduction
123721	17632 ChEBI	nitrate	+	respiration
123721	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
19619	16634 ChEBI	raffinose	+/-
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
19619	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
19619	17992 ChEBI	sucrose	+/-
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
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
19619	18222 ChEBI	xylose	+/-

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
123721	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
123721	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-	from API 20E
123721	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
123721	alcohol dehydrogenase	+	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
123721	amylase	-
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
123721	beta-galactosidase	+	3.2.1.23
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123721	caseinase	+	3.4.21.50
123721	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
123721	DNase	-
68382	esterase lipase (C 8)	+		from API zym
123721	gamma-glutamyltransferase	-	2.3.2.2
123721	gelatinase	+/-
68368	gelatinase	+		from API 20E
123721	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
123721	lipase	-
68382	lipase (C 14)	+		from API zym
123721	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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123721	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
123721	oxidase	-
123721	phenylalanine ammonia-lyase	-	4.3.1.24
123721	protease	+
68382	trypsin	+	3.4.21.4	from API zym
123721	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
123721	tween esterase	-
123721	urease	-	3.5.1.5
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	cellulose degradation	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	enterobactin biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	photosynthesis	100	14 of 14
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	urea cycle	100	13 of 13
66794	valine metabolism	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	cardiolipin biosynthesis	100	7 of 7
66794	Entner Doudoroff pathway	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	phenylalanine metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
66794	myo-inositol biosynthesis	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glycolysis	82.35	14 of 17
66794	pentose phosphate pathway	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	peptidoglycan biosynthesis	80	12 of 15
66794	factor 420 biosynthesis	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	tryptophan metabolism	76.32	29 of 38
66794	pyrimidine metabolism	75.56	34 of 45
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	non-pathway related	73.68	28 of 38
66794	vitamin B12 metabolism	73.53	25 of 34
66794	metabolism of disaccharids	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	aclacinomycin biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	methionine metabolism	69.23	18 of 26
66794	oxidative phosphorylation	67.03	61 of 91
66794	lysine metabolism	66.67	28 of 42
66794	acetoin degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	arginine metabolism	66.67	16 of 24
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	sphingosine metabolism	66.67	4 of 6
66794	d-mannose degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glutathione metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	histidine metabolism	62.07	18 of 29
66794	sulfate reduction	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	arachidonate biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	carotenoid biosynthesis	59.09	13 of 22
66794	tyrosine metabolism	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	cholesterol biosynthesis	54.55	6 of 11
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	glycine metabolism	50	5 of 10
66794	carnitine metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	d-xylose degradation	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of pentoses	42.86	12 of 28
66794	gallate degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
19619	+	+	+	+	+	-	+	-	-	-	+	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 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
19619	not determinedn.d.	+	-	+	+	+	+	+	+	+	+	+	-	-	-	+	+	+	-	-
123721	-	+	+	+	+	+	+	+	+	+	+	+	-	-	-	+	+	+	-	-

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
123721	not determinedn.d.	+	-	-	-	+/-	-	-	-	-	+	+	+/-	+	-	-	-	-	-	+/-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
11276	soil
67770	Soil
123721	Environment, Soil

Taxonmaps

69479

Global distribution of 16S sequence AJ293713 (>99% sequence identity) for Thermomonospora umbrina subclade from Microbeatlas

Aquatic Samples	3
Soil Samples	45
Animal Samples	3
Plant Samples	1
Total Samples	52

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11276	1	Risk group (German classification) According to TRBA 466
19619	1	Risk group (German classification) According to TRBA 466
123721	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	ASM338655v1 assembly for Thermomonospora umbrina DSM 43927	contig	GCA_003386555	111806.3	2778260945	111806	76.1

Genome browser: GCA_003386555

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Actinomadura umbrina partial 16S rRNA gene, strain IMSNU 22165T	AJ293713	1439	111806
20218	Actinomadura umbrina 16S ribosomal RNA gene, partial sequence	AF163121	1446	111806
20218	Actinomadura umbrina 16S-23S ribosomal RNA intergenic spacer sequence	AF163132	614	111806

GC content

@ref	GC-content (mol%)	Method
67770	71.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thermomonospora umbrina DSM 43927
NCBI: GCA_003386555

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	95.40	no
125439	motility	BacteriaNetⓘ	no	95.20	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Actinomadura umbrina strain DSM 43927
PATRIC: 111806.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.55	no
125438	anaerobic	anaerobicⓘ	no	95.40	yes
125438	spore-forming	spore-formingⓘ	yes	78.68	no
125438	aerobic	aerobicⓘ	yes	79.47	yes
125438	thermophilic	thermophileⓘ	no	93.75	no
125438	flagellated	motile2+ⓘ	no	86.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
	[Expression, thermal stability modification and application in PHB degradation of polyhydroxyalkanoate depolymerase from Thermomonospora umbrina].	Li Z, Chen S, Kong D, Chen S, Wang L, Wu J.	Sheng Wu Gong Cheng Xue Bao	10.13345/j.cjb.220996	2023
Phylogeny	[New species of Actinomadura isolated from soils in Turkmenia and their antagonistic properties].	Galatenko OA, Terekhova LP, Preobrazhenskaia TP	Antibiotiki		1981
	Actinomadura welshii sp. nov., a New Mycetoma Agent in Mexico.	Vera-Cabrera L, Molina-Torres CA, Crane AE, Cantu-Alvarez MG, Aguilera-Valenciano MA, Gallardo-Rocha A, Escalante-Fuentes WG, Ocampo-Candiani J, Avanzi C.	PLoS Negl Trop Dis	10.1371/journal.pntd.0013016	2025
Phylogeny	Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil.	Jiao JY, Liu L, Zhou EM, Wei DQ, Ming H, Xian WD, Yuan CG, Zhong JM, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-015-0465-8	2015

References

#11276	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43927
#19619	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 )
#40507	; 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 .
#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 .
#123721	Collection of Institut Pasteur ; Curators of the CIP; CIP 105485
#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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Thermomonospora umbrina (DSM 43927, ATCC 49502, IFO 14346)

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

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20E

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003386555

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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