Nocardia otitidiscaviarum (CCUG 21087, IMRU 738, ATCC 14630)

Name: Nocardia otitidiscaviarum (CCUG 21087, IMRU 738, ATCC 14630)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 143705

Type strain

Culture col. no. CCUG 21087 IMRU 738 ATCC 14630

NCBI tax ID(s) 1823

Special Collections CCUG

Links

Nocardia otitidiscaviarum CCUG 21087 is a mesophilic prokaryote that was isolated from Bone marrow.

mesophilic genome sequence

Name and taxonomic classification

SI-ID 45562

ATCC 14630,CCUG 21087

@ref 20215

Last LPSN update 2025-12-16 10:04:26

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Nocardia

Species Nocardia otitidiscaviarum

Full scientific name Nocardia otitidiscaviarum corrig. Snijders 1924 (Approved Lists 1980)

Synonyms (1)

"Nocardia caviae"

BacDive ID	Other strains from **Nocardia otitidiscaviarum** (21)	Type strain
10679	N. otitidiscaviarum DSM 43242, ATCC 14629, NCTC 1934, CCUG 10075, ... (type strain)
10676	N. otitidiscaviarum N65, R 1315, Ts 23115, DSM 43010
10677	N. otitidiscaviarum A0930-H-5187, DSM 43398, IMRU 1088
10678	N. otitidiscaviarum DSM 43400, IMRU 1316
10680	N. otitidiscaviarum S639, DSM 44565
10681	N. otitidiscaviarum TSH 1, DSM 45036
10682	N. otitidiscaviarum Gdf N313, DSM 46009, CIP 751, IMET 7154, ...
10683	N. otitidiscaviarum N206, Schaal 206, DSM 46056, IMET 7457
10684	N. otitidiscaviarum N 210, N210, Schaal N210, DSM 46057, IMET ...
137218	N. otitidiscaviarum CIP 102918
138108	N. otitidiscaviarum CIP 104836, IFM 0273, JCM 7792
161658	N. otitidiscaviarum JCM 15858, IFM 0167
161667	N. otitidiscaviarum JCM 15867, IFM 0181
161668	N. otitidiscaviarum JCM 15868, IFM 0192
161682	N. otitidiscaviarum JCM 15883, IFM 0313
161683	N. otitidiscaviarum JCM 15884, IFM 0314
161684	N. otitidiscaviarum JCM 15885, IFM 0315
161685	N. otitidiscaviarum JCM 15886, IFM 0316
161686	N. otitidiscaviarum JCM 15887, IFM 0317
161687	N. otitidiscaviarum JCM 15888, IFM 0318
161689	N. otitidiscaviarum JCM 15892, IFM 0362

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	90.918
125439	positive	99.5
125439		92.3

Colony morphology

47273

Incubation period2 days

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
47273	positive	growth	25-30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	91.479
125439	obligate aerobe	99.2

Spore formation

@ref	Spore formation	Confidence
125439		91.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68379	catalase	-	1.11.1.6	from API Coryne
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
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
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
68379	urease	+	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	acetate fermentation	100	4 of 4
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	glycogen metabolism	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	phenylalanine metabolism	100	13 of 13
66794	palmitate biosynthesis	100	22 of 22
66794	photosynthesis	100	14 of 14
66794	cardiolipin biosynthesis	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	threonine metabolism	100	10 of 10
66794	octane oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	cyanate degradation	100	3 of 3
66794	ceramide biosynthesis	100	1 of 1
66794	isoleucine metabolism	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	aerobactin biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	heme metabolism	92.86	13 of 14
66794	citric acid cycle	92.86	13 of 14
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	propanol degradation	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	urea cycle	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	vitamin B12 metabolism	82.35	28 of 34
66794	pyrimidine metabolism	82.22	37 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	purine metabolism	81.91	77 of 94
66794	proline metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	methionine metabolism	80.77	21 of 26
66794	propionate fermentation	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	factor 420 biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	histidine metabolism	79.31	23 of 29
66794	allantoin degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	tryptophan metabolism	76.32	29 of 38
66794	lactate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	sulfopterin metabolism	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	lipid metabolism	74.19	23 of 31
66794	lysine metabolism	73.81	31 of 42
66794	metabolism of disaccharids	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	arginine metabolism	70.83	17 of 24
66794	myo-inositol biosynthesis	70	7 of 10
66794	phenol degradation	70	14 of 20
66794	sulfate reduction	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	oxidative phosphorylation	68.13	62 of 91
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	tyrosine metabolism	64.29	9 of 14
66794	carotenoid biosynthesis	63.64	14 of 22
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	3-chlorocatechol degradation	60	3 of 5
66794	D-cycloserine biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of hexoses	55.56	10 of 18
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	cholesterol biosynthesis	54.55	6 of 11
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	sphingosine metabolism	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	polyamine pathway	47.83	11 of 23
66794	degradation of pentoses	46.43	13 of 28
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	arachidonic acid metabolism	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of sugar acids	40	10 of 25
66794	coenzyme M biosynthesis	40	4 of 10
66794	carnitine metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	sulfoquinovose degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4

Fatty acid profile

Metadata FA analysis

@ref

47273

Fatty acid	Percentage	ECL
C16:0	23.3	16
C18:1 ω9c	22.2	17.769
C16:1 ω7c/C15:0 ISO 2OH	12.2	15.85
TBSA 10Me18:0	11.8	18.392
C17:1 ω8c	7.3	16.792
C17:0	4.8	17
C18:0	4.6	18
C15:0	4.5	15
C17:0 10-methyl	3.5	17.41
C19:1 ω11c/19:1 ω9c	2.9	18.762
C14:0	0.9	14
C20:1 ω9c	0.8	19.77
C19:0	0.7	19
C15:1 ω5c	0.6	14.904

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
47273	+	-	-	+	-	-	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-

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
47273	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body-Site	#Other	#Bone

Isolation

47273

Sample typeBone marrow

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM736229v1 assembly for Nocardia otitidiscaviarum NEB252	complete	GCA_007362295	1823.6	8121179994	1823	97.13

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia otitidiscaviarum strain NEB252
PATRIC: 1823.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	91.30	no
125439	motility	BacteriaNetⓘ	no	92.30	no
125439	gram_stain	BacteriaNetⓘ	positive	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia otitidiscaviarum strain NEB252
PATRIC: 1823.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.92	no
125438	anaerobic	anaerobicⓘ	no	98.32	no
125438	spore-forming	spore-formingⓘ	yes	59.46	no
125438	aerobic	aerobicⓘ	yes	91.48	no
125438	thermophilic	thermophileⓘ	no	96.90	no
125438	flagellated	motile2+ⓘ	no	86.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Fatty acid characterization of rapidly growing pathogenic aerobic actinomycetes as a means of identification.	McNabb A, Shuttleworth R, Behme R, Colby WD.	J Clin Microbiol	10.1128/jcm.35.6.1361-1368.1997	1997
Phylogeny	Clinical and laboratory features of the Nocardia spp. based on current molecular taxonomy.	Brown-Elliott BA, Brown JM, Conville PS, Wallace RJ.	Clin Microbiol Rev	10.1128/cmr.19.2.259-282.2006	2006

References

#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 )
#47273	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 21087
#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 )
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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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Nocardia otitidiscaviarum (CCUG 21087, IMRU 738, ATCC 14630)

Name and taxonomic classification