Nocardia crassostreae (DSM 44597, ATCC 700418, NB4H)

Name: Nocardia crassostreae (DSM 44597, ATCC 700418, NB4H)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10765

Type strain

Strain Designation NB4H

Culture col. no. DSM 44597 ATCC 700418 NB4H NBRC 100342 IFM 10173 3 more

NCBI tax ID(s) 53428

Special Collections DSMZ CCUG JCM CIP Wink compendium

Links

Nocardia crassostreae NB4H is a mesophilic, Gram-positive, rod-shaped animal pathogen that was isolated from diseased Pacific oyster.

Gram-positive rod-shaped mesophilic animal pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 43927

ATCC 700418,CIP 105895,JCM 10500,DSM 44597,CCUG46826,NBRC 100342

@ref 20215

Last LPSN update 2025-12-16 09:49:25

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Nocardia

Species Nocardia crassostreae

Full scientific name Nocardia crassostreae Friedman et al. 1998

Morphology

Cell morphology

@ref	Gram stain	Cell shape
118778	positive	rod-shaped
125438	positive
125439	positive
125439

Colony morphology

@ref	Colony color	Incubation period	Medium used
20078	Beige (1001)	10-14 days	ISP 2
20078	Beige (1001)	10-14 days	ISP 3
20078	Beige (1001)	10-14 days	ISP 4
20078	Beige (1001)	10-14 days	ISP 5
20078	Beige (1001)	10-14 days	ISP 6
20078	Beige (1001)	10-14 days	ISP 7
118778

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20078		ISP 2
20078		ISP 3
20078		ISP 4
20078		ISP 5
20078		ISP 6
20078		ISP 7

Multimedia

@ref:	11912
multimedia content:	DSM_44597.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44597.jpg
caption:	Medium 553 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11912	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
11912	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
20078	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
20078	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:
20078	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
20078	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
20078	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
20078	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
40271	MEDIUM 9 - Brain heart infusion BHI		Distilled water make up to (1000.000 ml);Brain heart infusion (37.000 g)
118778	CIP Medium 9	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11912	positive	growth	28	mesophilic
20078	positive	optimum	28	mesophilic
40271	positive	growth	22	psychrophilic
67770	positive	growth	25	mesophilic
118778	positive	growth	10-30
118778	negative	growth	37
118778	negative	growth	41
118778	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.2

Spore formation

@ref	Spore formation	Confidence
125439		97.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118778	NaCl	positive	growth	0-4 %
118778	NaCl		growth	6 %
118778	NaCl		growth	8 %
118778	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-8(H₄, ω-cycl)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
118778	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
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
118778	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
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
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
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
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	17814 ChEBI	salicin	+	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	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118778	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
118778	15688 ChEBI	acetoin	-
118778	17234 ChEBI	glucose

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118778	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
118778	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
118778	beta-galactosidase	-	3.2.1.23
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
118778	caseinase	-	3.4.21.50
118778	catalase	+	1.11.1.6
118778	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118778	gamma-glutamyltransferase	-	2.3.2.2
118778	gelatinase	-
68379	gelatinase	+		from API Coryne
118778	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118778	lipase	-
68382	lipase (C 14)	-		from API zym
118778	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
118778	ornithine decarboxylase	-	4.1.1.17
118778	oxidase	-
118778	phenylalanine ammonia-lyase	-	4.3.1.24
118778	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
118778	tryptophan deaminase	-
118778	tween esterase	+
118778	urease	-	3.5.1.5
68379	urease	+	3.5.1.5	from API Coryne

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
20078	-	-	-	+	-	-	-	-	-	+	+	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
20078	not determinedn.d.	+	+	+	-	+	+	+	+	-	+	-	-	-	-	+	-	-	-	-
118778	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	+	-	-	-	-

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
118778	not determinedn.d.	-	-	-	-	+	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	+/-	+	+	+	+/-	+	-	-	-	+	-	-	-	+	+	-	-	+	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Mollusca

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11912	diseased Pacific oyster	British Columbia, Nanoose Bay	Canada	CAN	North America
67770	Pacific oyster (Crassostrea gigas)	Nanoose Bay, Vancouver Island, British Columbia	Canada	CAN	North America
118778	Pacific oysters	Nanoose bay, British Columbia	Canada	CAN	North America

Taxonmaps

69479

Global distribution of 16S sequence Z37989 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples	25
Soil Samples	21
Animal Samples	10
Plant Samples
Total Samples	56

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11912	1	Risk group (German classification) According to TRBA 466
20078	1	German classification According to TRBA 466
118778	2	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	ASM161340v1 assembly for Nocardia crassostreae NBRC 100342	contig	GCA_001613405	53428.4	2713896925	53428	63.9

Genome browser: GCA_001613405

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Nocardia crassostreae strain ATCC 700418 16S ribosomal RNA gene, partial sequence	AY756548	606	53428
20218	N.crassostrae gene for 16S ribosomal RNA (partial)	Z37989	1473	53428
20218	Nocardia crassostreae strain JCM 10500 16S ribosomal RNA gene, complete sequence	AF430049	1493	53428
20218	Nocardia crassostreae strain JCM 10500 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequence	AF536418	297	53428
20218	Nocardia crassostreae strain JCM 10500 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequence	AF536419	297	53428

GC content

@ref	GC-content (mol%)
11912	68.6
67770	67.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia crassostreae NBRC 100342
NCBI: GCA_001613405

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	97.90	no
125439	motility	BacteriaNetⓘ	no	95.60	no
125439	gram_stain	BacteriaNetⓘ	positive	99.80	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 crassostreae strain NBRC 100342
PATRIC: 53428.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.09	no
125438	anaerobic	anaerobicⓘ	no	98.03	no
125438	spore-forming	spore-formingⓘ	yes	65.23	no
125438	aerobic	aerobicⓘ	yes	88.04	no
125438	thermophilic	thermophileⓘ	no	94.90	yes
125438	flagellated	motile2+ⓘ	no	85.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardia crassostreae sp. nov., the causal agent of nocardiosis in Pacific oysters.	Friedman CS, Beaman BL, Chun J, Goodfellow M, Gee A, Hedrick RP	Int J Syst Bacteriol	10.1099/00207713-48-1-237	1998

References

#11912	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44597
#20078	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 )
#40271	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#118778	Collection of Institut Pasteur ; Curators of the CIP; CIP 105895
#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 crassostreae (DSM 44597, ATCC 700418, NB4H)

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

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_001613405

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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