Name: Brucella oryzae CCUG 54940
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1887

Type strain:

Species: Brucella oryzae

Culture col. no.: CCUG 54940, DSM 17471, MTCC 4195, NBRC 102588

Strain history: <- M. Schloter <- A. K. Tripathi et al.

NCBI tax ID(s): 335286 (species)

SI-ID 292771

DSM 17471, NBRC 102588

Section

Brucella oryzae CCUG 54940 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from deep water rice roots .

colony-forming
Gram-negative
motile
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Brucellaceae*
	Genus	*Brucella*
	Species	**Brucella oryzae**
	Full Scientific Name (LPSN)	Brucella oryzae (Tripathi et al. 2006) Hördt et al. 2020

Synonym

Ochrobactrum oryzae

Information on morphological and physiological properties Morphology

[Ref.: #23337]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #23337]	Cell length	1.4 µm

[Ref.: #23337]	Cell width	0.8 µm

[Ref.: #23337]	Cell shape	rod-shaped

[Ref.: #23337]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %90.497

[Ref.: #23337]	Flagellum arrangement	monotrichous, polar

[Ref.: #23337]	Colony color	milky white, translucent
[Ref.: #23337]	Colony shape	circular
[Ref.: #23337]	Cultivation medium used	Nutrient agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7006]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #7006]

Culture medium growth

[Ref.: #7006]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7006]

Culture medium composition

expand / minimize

[Ref.: #23337]

Culture medium

Nutrient agar (NA)

[Ref.: #23337]

Culture medium growth

		Temperature
[Ref.: #7006]	growth	28 °C
[Ref.: #23337]	growth	10-37 °C
[Ref.: #23337]	optimum	30 °C
[Ref.: #60400]	growth	30-37 °C

[Ref.: #7006]	Temperature range	mesophilic
[Ref.: #23337]	Temperature range	mesophilic
[Ref.: #60400]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23337]			optimum	6.0-7.0
[Ref.: #23337]			growth	4.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23337]	Oxygen tolerance	aerobe
[Ref.: #60400]	Oxygen tolerance	aerobe

[Ref.: #23337]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23337]	4-hydroxy-L-proline ChEBI	+
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #23337]	bromosuccinate ChEBI	+
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	cis-aconitate ChEBI	+
[Ref.: #23337]	citrate ChEBI	-
[Ref.: #68371]	D-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	D-galactonic acid lactone ChEBI	+
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #23337]	D-glucosaminic acid ChEBI	+
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	D-serine ChEBI	+
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #23337]	erythritol ChEBI	+
[Ref.: #68371]	erythritol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #23337]	ethanolamine ChEBI	-
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	gamma-aminobutyric acid ChEBI	+
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	glycyl L-aspartic acid ChEBI	+
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	itaconate ChEBI	-
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	L-aspartate ChEBI	+
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	L-histidine ChEBI	+
[Ref.: #23337]	L-leucine ChEBI	+
[Ref.: #23337]	L-ornithine ChEBI	+
[Ref.: #23337]	L-phenylalanine ChEBI	-
[Ref.: #68371]	L-rhamnose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	L-threonine ChEBI	+
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	lactate ChEBI	+
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	N-acetylgalactosamine ChEBI	+	respiration
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #23337]	phenylethylamine ChEBI	-
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	ribitol ChEBI	+
[Ref.: #68371]	ribitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #23337]	sucrose ChEBI	-
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68371]	turanose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #23337]	catalase	+	1.11.1.6
[Ref.: #23337]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #7006]	23786	+	-	-	-	+	-	-	-	+	+	+	-	+	+	+/-	-	-	+	-	-	not determinedn.d.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #7006]	14183	-	-	+	+	+	-	-	-	+	-	+	+	+	+	-	+	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	+	-	+	-	-	+	-	-	+	-

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

[Ref.: #7006]	Sample type/isolated from	deep water rice roots (endophyte)
[Ref.: #7006]	Geographic location (country and/or sea, region)	Suraha Tal Lake
[Ref.: #7006]	Country	India
[Ref.: #7006]	Country ISO 3 Code	IND
[Ref.: #7006]	Continent	Asia

[Ref.: #23337]	Sample type/isolated from	surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa)
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Host Body-Site	#Plant	#Root (Rhizome)
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Fruit (Seed)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681868 (>99% sequence identity) for Ochrobactrum oryzae subclade from Microbeatlas

Aquatic Samples	55
Soil Samples	28
Animal Samples	94
Plant Samples	30
Total Samples	207

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

[Ref.: #7006]

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.: #7006]	Ochrobactrum oryzae partial 16S rRNA gene, strain MTCC 4195T	AM041247	1477	ENA	335286 tax ID
[Ref.: #20218]	Ochrobactrum oryzae gene for 16S rRNA, partial sequence, strain: NBRC 102588	AB681868	1412	ENA	335286 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Brucella oryzae NBRC 102588	GCA_012103035	contig	GenBank	335286 tax ID	*
[Ref.: #66792]	Ochrobactrum oryzae strain NBRC 102588	335286.8	wgs	PATRIC	335286 tax ID	*

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: Ochrobactrum oryzae strain NBRC 102588 PATRIC: 335286.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ochrobactrum oryzae strain NBRC 102588 PATRIC: 335286.8
[Ref.: #69480]	gram-positive	no	98.492	no
[Ref.: #69480]	anaerobic	no	97.445	yes
[Ref.: #69480]	halophile	no	94.929	no
[Ref.: #69480]	spore-forming	no	96.758	yes
[Ref.: #69480]	glucose-util	yes	91.479	yes
[Ref.: #69480]	motile	yes	62.091	yes
[Ref.: #69480]	flagellated	no	94.646	no
[Ref.: #69480]	thermophile	no	98.819	no
[Ref.: #69480]	aerobic	yes	87.144	yes
[Ref.: #69480]	glucose-ferment	no	91.277	yes

Availability in culture collections External links

[Ref.: #7006]

Culture collection no.

CCUG 54940, DSM 17471, MTCC 4195, NBRC 102588

[Ref.: #71531]

SI-ID 292771

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India.	Tripathi AK, Verma SC, Chowdhury SP, Lebuhn M, Gattinger A, Schloter M	Int J Syst Evol Microbiol	10.1099/ijs.0.63934-0	2006	*

References

#7006

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17471

#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 )

#23337

Anil K. Tripathi, Subhash C. Verma, Soumitra Paul Chowdhury, Michael Lebuhn, Andreas Gattinger, Michael Schloter: Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. IJSEM 56: 1677 - 1680 2006 ( DOI 10.1099/ijs.0.63934-0 , PubMed 16825649 )

#60400 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54940

#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) .

#68369

Automatically annotated from API 20NE .

#68371

Automatically annotated from API 50CH acid .

#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 )

#71531

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-ID292771.1 )

* These data were automatically processed and therefore are not curated

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Ochrobactrum oryzae strain NBRC 102588

Ochrobactrum oryzae strain NBRC 102588

Change proposal

Change proposal