Ornithinibacter aureus (DSM 23364, CGMCC 1.10341, HB09001)

Name: Ornithinibacter aureus (DSM 23364, CGMCC 1.10341, HB09001)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6312

Type strain

Strain Designation HB09001

Culture col. no. DSM 23364 CGMCC 1.10341 HB09001 JCM 17738

NCBI tax ID(s) 622664

Special Collections DSMZ JCM Wink compendium Literature strains

History DSMZ <- C. Xiao, Chinese Academy Tropical Agricultural Sci., Haikou, China; CGMCC 1.10341 <- J. Ye JCM <-- CGMCC 1.10341 <-- C. Xiao HB09001.

Links

Ornithinibacter aureus HB09001 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from seawater.

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

Name and taxonomic classification

SI-ID 398106

JCM 17738,DSM 23364

@ref 20215

Last LPSN update 2026-05-29 08:26:22

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Intrasporangiaceae

Genus Ornithinibacter

Species Ornithinibacter aureus

Full scientific name Ornithinibacter aureus Xiao et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29855	positive	0.94 µm	0.69 µm	rod-shaped
125438	positive				90.136
125439					94.298
125439	positive				99.559

Colony morphology

@ref	Colony color	Incubation period	Medium used
21371	Golden yellow (1004)	10-14 days	ISP 2
21371	Traffic yellow (1023)	10-14 days	ISP 3
21371		10-14 days	ISP 4
21371		10-14 days	ISP 5
21371	Ocher brown (8001)	10-14 days	ISP 7
21371	Brown beige (1011)	10-14 days	suter with tyrosine
21371		10-14 days	suter without tyrosine

Multicellular morphology

@ref	Forms multicellular complex	Medium name
21371		ISP 2
21371		ISP 3
21371		ISP 4
21371		ISP 5
21371		ISP 7
21371		Suter with tyrosine
21371		Suter without tyrosine

Pigmentation

29855

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16807	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
21371	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
21371	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:
21371	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
21371	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
21371	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
21371	suter with tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21371	suter without tyrosine		Name: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

Culture temp

@ref	Growth	Type	Temperature (°C)
16807	positive	growth	28
29855	positive	growth	04-45
29855	positive	optimum	34
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
29855	positive	optimum	7.2
29855	positive	growth	5-10.2	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29855	aerobe
125439	facultative anaerobe	95.367

Spore formation

29855

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
21371	NaCl	positive	maximum	2.5 %
29855	NaCl	positive	growth	0-5 %
29855	NaCl	positive	optimum	1 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
21371	22599 ChEBI	arabinose	+
21371	62968 ChEBI	cellulose	+
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
21371	28757 ChEBI	fructose	+
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
21371	17234 ChEBI	glucose	+
29855	15428 ChEBI	glycine	+	carbon source
68379	28087 ChEBI	glycogen	+	fermentation	from API Coryne
68379	17716 ChEBI	lactose	+	fermentation	from API Coryne
68379	17306 ChEBI	maltose	+	fermentation	from API Coryne
21371	37684 ChEBI	mannose	+
21371	17268 ChEBI	myo-inositol	+
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
29855	26271 ChEBI	proline	+	carbon source
21371	16634 ChEBI	raffinose	+
21371	26546 ChEBI	rhamnose	+
29855	26546 ChEBI	rhamnose	+	carbon source
21371	17992 ChEBI	sucrose	+
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
21371	18222 ChEBI	xylose	+

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29855	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
29855	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
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
29855	catalase	+	1.11.1.6
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

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
21371	+	-	-	+	-	+	+	-	+	-	-	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
21371	not determinedn.d.	+	+	+	-	+	+/-	+/-	-	+	+	+	+	+	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16807	seawater	Hainan, South China Sea	China	CHN	Asia
67770	Seawater in the South China Sea	Hainan	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ796074 (>99% sequence identity) for Ornithinibacter aureus subclade from Microbeatlas

Aquatic Samples	176
Soil Samples	33
Animal Samples	40
Plant Samples	3
Total Samples	252

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16807	1	Risk group (German 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	ASM985824v1 assembly for Ornithinibacter aureus DSM 23364	contig	GCA_009858245	622664.3	2756170161	622664	76.33
124043	ASM3954127v1 assembly for Ornithinibacter aureus JCM 17738	scaffold	GCA_039541275			622664	59.91

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16807	Ornithinibacter aureus strain HB09001 16S ribosomal RNA gene, partial sequence	FJ796074	1441		622664

GC content

@ref	GC-content (mol%)	Method
16807	69.6	high performance liquid chromatography (HPLC)
29855	69.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM985824v1 assembly for Ornithinibacter aureus DSM 23364
NCBI: GCA_009858245

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.37	no
125439	gram_stain	BacteriaNetⓘ	positive	99.56	no
125439	motility	BacteriaNetⓘ	no	94.30	no
125439	spore_formation	BacteriaNetⓘ	yes	58.23	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ornithinibacter aureus strain DSM 23364
PATRIC: 622664.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.14	yes
125438	anaerobic	anaerobicⓘ	no	96.53	yes
125438	spore-forming	spore-formingⓘ	no	71.04	yes
125438	aerobic	aerobicⓘ	yes	87.47	no
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oryzobacter terrae gen. nov., sp. nov., isolated from paddy soil.	Kim SJ, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijsem.0.000398	2015
Phylogeny	Ornithinibacter aureus gen. nov., sp. nov., a novel member of the family Intrasporangiaceae.	Xiao C, Huang H, Ye J, Wu X, Zhu J, Zhan B, Bao S	Int J Syst Evol Microbiol	10.1099/ijs.0.022806-0	2010

References

#16807	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23364
#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 )
#21371	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#26229	IJSEM 659 2011 ( DOI 10.1099/ijs.0.022806-0 , PubMed 20400663 )
#29855	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26229
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Ornithinibacter aureus (DSM 23364, CGMCC 1.10341, HB09001)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_009858245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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