Beutenbergia cavernae (DSM 12333, ATCC BAA-8, IFO 16432)

Name: Beutenbergia cavernae (DSM 12333, ATCC BAA-8, IFO 16432)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1678

Type strain

Strain Designation 2163-026

Culture col. no. DSM 12333 ATCC BAA-8 IFO 16432 NBRC 16432 CCUG 43141 5 more

NCBI tax ID(s) 471853 84757

Special Collections DSMZ CCUG JCM CIP Wink compendium

Links

Beutenbergia cavernae 2163-026 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from cave, soil between rocks.

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

Name and taxonomic classification

SI-ID 44250

ATCC BAA-8,DSM 12333,IFO 16432,CIP 106362,NCIMB 13614,JCM 11478,CCUG 43141,NBRC 16432

@ref 20215

Last LPSN update 2025-12-16 09:47:09

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Beutenbergiaceae

Genus Beutenbergia

Species Beutenbergia cavernae

Full scientific name Beutenbergia cavernae Groth et al. 1999

BacDive ID	Other strains from **Beutenbergia cavernae** (3)	Type strain
1679	B. cavernae 2163-008, DSM 12334, HKI 0132
103262	B. cavernae ST033334(HKI),
103263	B. cavernae SF008615(FSU),

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
117221	positive	rod-shaped
125439	positive		99.8
125438			92

Colony morphology

@ref	Colony color	Incubation period	Medium used
19736	Zinc yellow (1018)	10-14 days	5006
19736		10-14 days	ISP 2
19736		10-14 days	ISP 3
19736		10-14 days	ISP 4
117221

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19736		5006
19736		ISP 2
19736		ISP 3
19736		ISP 4

Multimedia

@ref:	66793
multimedia content:	EM_DSM_12333_1.jpg
multimedia.multimedia content:	EM_DSM_12333_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4698	RICH MEDIUM (DSMZ Medium 736)	Medium recipe at MediaDive	Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
19736	5006		Medium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
19736	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
19736	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:
19736	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
32959	MEDIUM 29- Brain heart agar		Distilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
117221	CIP Medium 29	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4698	positive	growth	28	mesophilic
19736	positive	optimum	28	mesophilic
32959	positive	growth	30	mesophilic
55688	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
117221	positive	growth	15-37
117221	negative	growth	10
117221	negative	growth	41
117221	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
55688	aerobe
117221	obligate aerobe
125439	obligate aerobe	99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
19736	NaCl	positive	maximum	5 %
117221	NaCl	positive	growth	2-4 %
117221	NaCl		growth	6 %
117221	NaCl		growth	8 %
117221	NaCl		growth	10 %

Murein

@ref	Murein short key	Type
4698	A11.54	A4alpha L-Lys-L-Glu

Observation

67770

Observationquinones: MK-8(H₄), MK-8(₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
19736	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
19736	62968 ChEBI	cellulose	+
117221	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
117221	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
19736	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
19736	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
117221	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
19736	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
19736	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
117221	17632 ChEBI	nitrate	+	reduction
117221	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
19736	16634 ChEBI	raffinose	+
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
19736	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
19736	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
19736	18222 ChEBI	xylose	+

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
117221	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
117221	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
117221	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	+			from API 20E
117221	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
117221	alcohol dehydrogenase	-	1.1.1.1
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	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
117221	amylase	-
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	+	3.2.1.23	from API zym
117221	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
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
117221	caseinase	+	3.4.21.50
117221	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
117221	DNase	-
117221	gamma-glutamyltransferase	-	2.3.2.2
117221	gelatinase	+/-
68379	gelatinase	-		from API Coryne
68368	gelatinase	-		from API 20E
117221	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
117221	lipase	-
68382	lipase (C 14)	-		from API zym
117221	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
117221	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
117221	oxidase	-
117221	phenylalanine ammonia-lyase	-	4.3.1.24
117221	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
117221	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
117221	tween esterase	-
117221	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	cellulose degradation	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	pentose phosphate pathway	100	11 of 11
66794	cardiolipin biosynthesis	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	starch degradation	100	10 of 10
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	lactate fermentation	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	lipoate biosynthesis	100	5 of 5
66794	heme metabolism	92.86	13 of 14
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
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	valine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	degradation of sugar acids	88	22 of 25
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	pyrimidine metabolism	84.44	38 of 45
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	82.98	78 of 94
66794	metabolism of disaccharids	81.82	9 of 11
66794	myo-inositol biosynthesis	80	8 of 10
66794	gallate degradation	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	leucine metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	butanoate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	degradation of pentoses	75	21 of 28
66794	proline metabolism	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	degradation of hexoses	72.22	13 of 18
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	phosphatidylethanolamine bioynthesis	69.23	9 of 13
66794	tryptophan metabolism	68.42	26 of 38
66794	non-pathway related	68.42	26 of 38
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	methionine metabolism	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	oxidative phosphorylation	63.74	58 of 91
66794	degradation of sugar alcohols	62.5	10 of 16
66794	arginine metabolism	62.5	15 of 24
66794	vitamin B1 metabolism	61.54	8 of 13
66794	factor 420 biosynthesis	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	lipid A biosynthesis	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	urea cycle	53.85	7 of 13
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	lysine metabolism	50	21 of 42
66794	cyclohexanol degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	catecholamine biosynthesis	50	2 of 4
66794	tyrosine metabolism	50	7 of 14
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	propanol degradation	42.86	3 of 7
66794	O-antigen biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	carotenoid biosynthesis	36.36	8 of 22
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	sulfate reduction	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18

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
19736	-	-	-	-	-	-	+	-	-	+	-	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
19736	-	-	-	+	-	+	+	-	+/-	+	-	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
19736	not determinedn.d.	+	-	-	-	+	-	-	-	-	+	+	+	+	-	+	-	+	+	-
117221	-	+	+	+	-	+	-	-	-	-	+	+	+	+	-	+	-	+	+	+

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
117221	not determinedn.d.	+	-	+	+	+	+	-	+	-	+	+	+	+	-	+	-	-	-	-	+	-	-	-	-	+	+	+	+	+	+	+	+	-	-	+	-	-	+	+	+	+	-	+	+	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
4698	cave, soil between rocks	China, Guilin, "cave of the reed flutes"	China	CHN	Asia
55688	Cave,soil between rocks		China	CHN	Asia
67770	Soil between rocks, Reed Flute Cave	near Guilin Guangxi	China	CHN	Asia
117221	Environment, Soil, cellar	Guilin	China	CHN	Asia	1997

Taxonmaps

69479

Global distribution of 16S sequence Y18378 (>99% sequence identity) for Beutenbergia cavernae subclade from Microbeatlas

Aquatic Samples	228
Soil Samples	443
Animal Samples	157
Plant Samples	38
Total Samples	866

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4698	1	Risk group (German classification) According to TRBA 466
19736	1	Risk group (German classification) According to TRBA 466
117221	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
66792	ASM2310v1 assembly for Beutenbergia cavernae DSM 12333	complete	GCA_000023105	471853.5	643692008	471853	98.64

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4698	Beutenbergia cavernosa 16S rRNA gene	Y18378	1485		471853

GC content

@ref	GC-content (mol%)	Method
4698	71.4	high performance liquid chromatography (HPLC)
67770	71	high performance liquid chromatography (HPLC)
67770	73.12	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Beutenbergia cavernae DSM 12333
NCBI: GCA_000023105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	67.50	no
125439	motility	BacteriaNetⓘ	no	76.10	no
125439	gram_stain	BacteriaNetⓘ	positive	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Beutenbergia cavernae DSM 12333 DSM 12333
NCBI: GCA_000023105.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.48	no
125438	anaerobic	anaerobicⓘ	no	96.23	yes
125438	aerobic	aerobicⓘ	yes	85.30	yes
125438	spore-forming	spore-formingⓘ	no	72.60	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	92.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Pancreatic Cancer Resistance to Treatment: The Role of Microbiota.	Nista EC, Del Gaudio A, Del Vecchio LE, Mezza T, Pignataro G, Piccioni A, Gasbarrini A, Franceschi F, Candelli M.	Biomedicines	10.3390/biomedicines11010157	2023
	The Pancreatic Microbiome is Associated with Carcinogenesis and Worse Prognosis in Males and Smokers.	Chakladar J, Kuo SZ, Castaneda G, Li WT, Gnanasekar A, Yu MA, Chang EY, Wang XQ, Ongkeko WM.	Cancers (Basel)	10.3390/cancers12092672	2020
	Proteomic Analysis of the Xanthan-Degrading Pathway of Microbacterium sp. XT11.	Sun Z, Liu H, Wang X, Yang F, Li X.	ACS Omega	10.1021/acsomega.9b02313	2019
	Analysis of EAWAG-BBD pathway prediction system for the identification of malathion degrading microbes.	Sivakumar S, Anitha P, Ramesh B, Suresh G.	Bioinformation	10.6026/97320630013073	2017
	In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID.	Michalska K, Tan K, Chang C, Li H, Hatzos-Skintges C, Molitsky M, Alkire R, Joachimiak A.	J Synchrotron Radiat	10.1107/s1600577515016598	2015
Genetics	Characterizing the native codon usages of a genome: an axis projection approach.	Davis JJ, Olsen GJ.	Mol Biol Evol	10.1093/molbev/msq185	2011
Metabolism	Cellodextrin utilization by bifidobacterium breve UCC2003.	Pokusaeva K, O'Connell-Motherway M, Zomer A, Macsharry J, Fitzgerald GF, van Sinderen D.	Appl Environ Microbiol	10.1128/aem.01786-10	2011
Phylogeny	Phenotypic and genotypic properties of Microbacterium yannicii, a recently described multidrug resistant bacterium isolated from a lung transplanted patient with cystic fibrosis in France.	Sharma P, Diene SM, Thibeaut S, Bittar F, Roux V, Gomez C, Reynaud-Gaubert M, Rolain JM.	BMC Microbiol	10.1186/1471-2180-13-97	2013
Metabolism	Evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in Bacillus subtilis biofilm formation.	Burrell M, Hanfrey CC, Murray EJ, Stanley-Wall NR, Michael AJ.	J Biol Chem	10.1074/jbc.m110.163154	2010
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
	Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion.	Puri V, Goyal A, Sankaranarayanan R, Enright AJ, Vaidya T.	BMC Evol Biol	10.1186/1471-2148-11-334	2011
Genetics	Genomic basis for natural product biosynthetic diversity in the actinomycetes.	Nett M, Ikeda H, Moore BS.	Nat Prod Rep	10.1039/b817069j	2009
Genetics	Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences.	Chandra G, Chater KF.	FEMS Microbiol Rev	10.1111/1574-6976.12047	2014
	Xenobiotic efflux in bacteria and fungi: a genomics update.	Barabote RD, Thekkiniath J, Strauss RE, Vediyappan G, Fralick JA, San Francisco MJ.	Adv Enzymol Relat Areas Mol Biol	10.1002/9780470920541.ch6	2011
Phylogeny	Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.	Gao B, Gupta RS.	Microbiol Mol Biol Rev	10.1128/mmbr.05011-11	2012
Enzymology	Crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum.	Tian D, Fu X, Cao W, Yuan H.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x20005336	2020
Genetics	Genome sequencing and annotation of Cellulomonas sp. HZM.	Chua P, Har ZM, Austin CM, Yule CM, Dykes GA, Lee SM.	Genom Data	10.1016/j.gdata.2015.05.009	2015
Metabolism	Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria.	Li Y, Huang Y.	Microbiol Spectr	10.1128/spectrum.02380-21	2022
	Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis.	Wan T, Horova M, Khetrapal V, Li S, Jones C, Schacht A, Sun X, Zhang L.	J Biol Chem	10.1016/j.jbc.2023.104777	2023
Genetics	Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition.	Wang C, Dong D, Wang H, Muller K, Qin Y, Wang H, Wu W.	Biotechnol Biofuels	10.1186/s13068-016-0440-2	2016
Metabolism	Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds.	Axenov-Gribanov DV, Voytsekhovskaya IV, Tokovenko BT, Protasov ES, Gamaiunov SV, Rebets YV, Luzhetskyy AN, Timofeyev MA.	PLoS One	10.1371/journal.pone.0149216	2016
Metabolism	Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals.	Severi E, Rudden M, Bell A, Palmer T, Juge N, Thomas GH.	Microb Genom	10.1099/mgen.0.000614	2021
	Complete genome sequence of Cellulomonas flavigena type strain (134).	Abt B, Foster B, Lapidus A, Clum A, Sun H, Pukall R, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.	Stand Genomic Sci	10.4056/sigs.1012662	2010
Enzymology	A putative serine protease, SpSsp1, from Saprolegnia parasitica is recognised by sera of rainbow trout, Oncorhynchus mykiss.	Minor KL, Anderson VL, Davis KS, Van Den Berg AH, Christie JS, Lobach L, Faruk AR, Wawra S, Secombes CJ, Van West P.	Fungal Biol	10.1016/j.funbio.2014.04.008	2014
Enzymology	Functional characterization of Corynebacterium glutamicum mycothiol S-conjugate amidase.	Si M, Long M, Chaudhry MT, Xu Y, Zhang P, Zhang L, Shen X.	PLoS One	10.1371/journal.pone.0115075	2014
Metabolism	Characterization of three mycobacterial DinB (DNA polymerase IV) paralogs highlights DinB2 as naturally adept at ribonucleotide incorporation.	Ordonez H, Uson ML, Shuman S.	Nucleic Acids Res	10.1093/nar/gku752	2014
Genetics	Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand.	Somboonna N, Assawamakin A, Wilantho A, Tangphatsornruang S, Tongsima S.	BMC Genomics	10.1186/1471-2164-13-s7-s29	2012
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
Genetics	Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122).	Land M, Pukall R, Abt B, Goker M, Rohde M, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jefferies CC, Saunders E, Brettin T, Detter JC, Han C, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A	Stand Genomic Sci	10.4056/sigs.1162	2009
Metabolism	The genome sequences of Cellulomonas fimi and "Cellvibrio gilvus" reveal the cellulolytic strategies of two facultative anaerobes, transfer of "Cellvibrio gilvus" to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov.	Christopherson MR, Suen G, Bramhacharya S, Jewell KA, Aylward FO, Mead D, Brumm PJ.	PLoS One	10.1371/journal.pone.0053954	2013
Phylogeny	Miniimonas arenae gen. nov., sp. nov., an actinobacterium isolated from sea sand.	Ue H, Matsuo Y, Kasai H, Yokota A.	Int J Syst Evol Microbiol	10.1099/ijs.0.019596-0	2011
Phylogeny	Salana multivorans gen. nov., sp. nov., a novel actinobacterium isolated from an anaerobic bioreactor and capable of selenate reduction.	von Wintzingerode F, Gobel UB, Siddiqui RA, Rosick U, Schumann P, Fruhling A, Rohde M, Pukall R, Stackebrandt E.	Int J Syst Evol Microbiol	10.1099/00207713-51-5-1653	2001
Phylogeny	Beutenbergia cavernae gen. nov., sp. nov., an L-lysine-containing actinomycete isolated from a cave.	Groth I, Schumann P, Schuetze B, Augsten K, Kramer I, Stackebrandt E	Int J Syst Bacteriol	10.1099/00207713-49-4-1733	1999

References

#4698	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12333
#19736	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 )
#32959	; Curators of the CIP;
#55688	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 43141
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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 .
#117221	Collection of Institut Pasteur ; Curators of the CIP; CIP 106362
#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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Beutenbergia cavernae (DSM 12333, ATCC BAA-8, IFO 16432)

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

Murein

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20E

API coryne

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_000023105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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