Name: Ornithinibacter aureus HB09001
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6312

Type strain:

Species: Ornithinibacter aureus

Strain Designation: HB09001

Culture col. no.: DSM 23364, CGMCC 1.10341, JCM 17738

Strain history: CGMCC 1.10341 <-- C. Xiao HB09001.

NCBI tax ID(s): 622664 (species)

SI-ID 398106

DSM 23364

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Intrasporangiaceae*
	Genus	*Ornithinibacter*
	Species	**Ornithinibacter aureus**
	Full Scientific Name (LPSN)	Ornithinibacter aureus Xiao et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29855]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29855]	Cell length	0.94 µm

[Ref.: #29855]	Cell width	0.69 µm

[Ref.: #29855]	Cell shape	rod-shaped

[Ref.: #29855]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %93.989

[Ref.: #21371]	Colony color	Golden yellow (1004)
[Ref.: #21371]	Incubation period	10-14 days
[Ref.: #21371]	Cultivation medium used	ISP 2

[Ref.: #21371]	Colony color	Traffic yellow (1023)
[Ref.: #21371]	Incubation period	10-14 days
[Ref.: #21371]	Cultivation medium used	ISP 3

[Ref.: #21371]	Colony color	Ocher brown (8001)
[Ref.: #21371]	Incubation period	10-14 days
[Ref.: #21371]	Cultivation medium used	ISP 7

[Ref.: #21371]	Colony color	Brown beige (1011)
[Ref.: #21371]	Incubation period	10-14 days
[Ref.: #21371]	Cultivation medium used	suter with tyrosine

[Ref.: #21371]	Incubation period	10-14 days
[Ref.: #21371]	Cultivation medium used	ISP 4

[Ref.: #21371]	Incubation period	10-14 days
[Ref.: #21371]	Cultivation medium used	ISP 5

[Ref.: #21371]	Incubation period	10-14 days
[Ref.: #21371]	Cultivation medium used	suter without tyrosine

[Ref.: #29855]

Pigment production

yes

[Ref.: #21371]	Multicellular complex forming ability	no
[Ref.: #21371]	Medium Name (multicellularity)	ISP 2

[Ref.: #21371]	Multicellular complex forming ability	no
[Ref.: #21371]	Medium Name (multicellularity)	ISP 3

[Ref.: #21371]	Multicellular complex forming ability	no
[Ref.: #21371]	Medium Name (multicellularity)	ISP 4

[Ref.: #21371]	Multicellular complex forming ability	no
[Ref.: #21371]	Medium Name (multicellularity)	ISP 5

[Ref.: #21371]	Multicellular complex forming ability	no
[Ref.: #21371]	Medium Name (multicellularity)	ISP 7

[Ref.: #21371]	Multicellular complex forming ability	no
[Ref.: #21371]	Medium Name (multicellularity)	Suter with tyrosine

[Ref.: #21371]	Multicellular complex forming ability	no
[Ref.: #21371]	Medium Name (multicellularity)	Suter without tyrosine

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16807]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #16807]

Culture medium growth

[Ref.: #16807]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #21371]

Culture medium

ISP 2

[Ref.: #21371]

Culture medium growth

[Ref.: #21371]

Culture medium composition

expand / minimize

[Ref.: #21371]

Culture medium

ISP 3

[Ref.: #21371]

Culture medium growth

[Ref.: #21371]

Culture medium composition

expand / minimize

[Ref.: #21371]

Culture medium

ISP 4

[Ref.: #21371]

Culture medium growth

[Ref.: #21371]

Culture medium composition

expand / minimize

[Ref.: #21371]

Culture medium

ISP 5

[Ref.: #21371]

Culture medium growth

[Ref.: #21371]

Culture medium composition

expand / minimize

[Ref.: #21371]

Culture medium

ISP 7

[Ref.: #21371]

Culture medium growth

[Ref.: #21371]

Culture medium composition

expand / minimize

[Ref.: #21371]

Culture medium

suter with tyrosine

[Ref.: #21371]

Culture medium growth

[Ref.: #21371]

Culture medium composition

expand / minimize

[Ref.: #21371]

Culture medium

suter without tyrosine

[Ref.: #21371]

Culture medium growth

[Ref.: #21371]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16807]	growth	28 °C
[Ref.: #29855]	growth	04-45 °C
[Ref.: #29855]	optimum	34 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #16807]	Temperature range	mesophilic
[Ref.: #29855]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29855]			optimum	7.2
[Ref.: #29855]			growth	5-10.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29855]

Oxygen tolerance

aerobe

[Ref.: #29855]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.963

	Salt		Salt conc.
[Ref.: #21371]	NaCl	maximum	2.5	%
[Ref.: #29855]	NaCl	growth	0-5	%
[Ref.: #29855]	NaCl	optimum	1	%

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #21371]	arabinose ChEBI	+
[Ref.: #21371]	cellulose ChEBI	+
[Ref.: #68379]	D-glucose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #21371]	fructose ChEBI	+
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21371]	glucose ChEBI	+
[Ref.: #29855]	glycine ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	+	fermentation	* from API Coryne
[Ref.: #21371]	mannose ChEBI	+
[Ref.: #21371]	myo-inositol ChEBI	+
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #29855]	proline ChEBI	+	carbon source
[Ref.: #21371]	raffinose ChEBI	+
[Ref.: #21371]	rhamnose ChEBI	+
[Ref.: #29855]	rhamnose ChEBI	+	carbon source
[Ref.: #21371]	sucrose ChEBI	+
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21371]	xylose ChEBI	+
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #29855]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #29855]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym, API Coryne
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym, API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #29855]	catalase	+	1.11.1.6
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #21371]	500	+	-	-	+	-	+	+	-	+	-	-	not determinedn.d.	+	-	-	-	+	+	-	+	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #21371]	1012	not determinedn.d.	+	+	+	-	+	+/-	+/-	-	+	+	+	+	+	-	+	+	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16807]	Sample type/isolated from	seawater
[Ref.: #16807]	Geographic location (country and/or sea, region)	Hainan, South China Sea
[Ref.: #16807]	Country	China
[Ref.: #16807]	Country ISO 3 Code	CHN
[Ref.: #16807]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Seawater in the South China Sea
[Ref.: #67770]	Geographic location (country and/or sea, region)	Hainan
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16807]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16807]	Ornithinibacter aureus strain HB09001 16S ribosomal RNA gene, partial sequence	FJ796074	1441	ENA	622664 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Ornithinibacter aureus DSM 23364	GCA_009858245	contig	GenBank	622664 tax ID
[Ref.: #66792]	Ornithinibacter aureus strain DSM 23364	622664.3	wgs	PATRIC	622664 tax ID	*
[Ref.: #66792]	Ornithinibacter aureus DSM 23364	2756170161	draft	JGI IMG/M	622664 tax ID	*

[Ref.: #16807]	GC-content	69.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29855]	GC-content	69.6 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Ornithinibacter aureus strain DSM 23364 PATRIC: 622664.3
[Ref.: #69481]	spore-forming	no	73	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ornithinibacter aureus strain DSM 23364 PATRIC: 622664.3
[Ref.: #69480]	gram-positive	yes	88.362	yes
[Ref.: #69480]	anaerobic	no	96.96	no
[Ref.: #69480]	halophile	no	92.592	no
[Ref.: #69480]	spore-forming	no	89.164	yes
[Ref.: #69480]	glucose-util	yes	88.19	no
[Ref.: #69480]	thermophile	no	96.968	yes
[Ref.: #69480]	flagellated	no	98.556	yes
[Ref.: #69480]	aerobic	yes	87.17	yes
[Ref.: #69480]	motile	no	94.434	yes
[Ref.: #69480]	glucose-ferment	no	83.33	yes

Availability in culture collections External links

[Ref.: #16807]

Culture collection no.

DSM 23364, CGMCC 1.10341, JCM 17738

[Ref.: #75786]

SI-ID 398106

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 .

#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 (see below)

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75786

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID398106.1 )

#26229

IJSEM 659 2011 ( DOI 10.1099/ijs.0.022806-0 , PubMed 20400663 )

* These data were automatically processed and therefore are not curated

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Ornithinibacter aureus strain DSM 23364

Ornithinibacter aureus strain DSM 23364

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