Brucella oryzae (CCUG 54940, DSM 17471, MTCC 4195)

Name: Brucella oryzae (CCUG 54940, DSM 17471, MTCC 4195)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1887

Type strain

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

NCBI tax ID(s) 335286

Special Collections DSMZ CCUG Literature strains

History <- M. Schloter <- A. K. Tripathi et al.

Links

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

Gram-negative motile rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 292771

MTCC 4195,DSM 17471,NBRC 102588,CCUG 54940T

@ref 20215

Last LPSN update 2026-02-09 11:18:12

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Brucellaceae

Genus Brucella

Species Brucella oryzae

Full scientific name Brucella oryzae (Tripathi et al. 2006) Hördt et al. 2020

Synonyms (1)

Ochrobactrum oryzae

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
23337	negative	1.4 µm	0.8 µm	rod-shaped	monotrichous, polar
125438	negative					99.5
125439	negative					98.5

Colony morphology

@ref	Colony color	Colony shape	Medium used
23337	milky white, translucent	circular	Nutrient agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7006	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
23337	Nutrient agar (NA)

Culture temp

@ref	Growth	Type	Temperature (°C)
7006	positive	growth	28
23337	positive	growth	10-37
23337	positive	optimum	30
60400	positive	growth	30-37

Culture pH

@ref	Ability	Type	PH	PH range
23337	positive	optimum	6.0-7.0
23337	positive	growth	4.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23337	aerobe
60400	aerobe
125439	aerobe	93.4

Spore formation

@ref	Spore formation	Confidence
23337
125439		98.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23337	18240 ChEBI	4-hydroxy-L-proline	+
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
23337	73706 ChEBI	bromosuccinate	+
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
23337	16383 ChEBI	cis-aconitate	+
23337	16947 ChEBI	citrate	-
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
23337	15895 ChEBI	D-galactonic acid lactone	+
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
23337	17784 ChEBI	D-glucosaminic acid	+
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
23337	16523 ChEBI	D-serine	+
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	+	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
23337	17113 ChEBI	erythritol	+
68371	17113 ChEBI	erythritol	+	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
23337	16000 ChEBI	ethanolamine	-
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
23337	16865 ChEBI	gamma-aminobutyric acid	+
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
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
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
23337	73804 ChEBI	glycyl L-aspartic acid	+
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
23337	17240 ChEBI	itaconate	-
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
23337	29991 ChEBI	L-aspartate	+
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
23337	15971 ChEBI	L-histidine	+
23337	15603 ChEBI	L-leucine	+
23337	15729 ChEBI	L-ornithine	+
23337	17295 ChEBI	L-phenylalanine	-
68371	62345 ChEBI	L-rhamnose	+	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
23337	16857 ChEBI	L-threonine	+
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
23337	24996 ChEBI	lactate	+
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
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
23337	28037 ChEBI	N-acetylgalactosamine	+	respiration
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
23337	50048 ChEBI	phenylethylamine	-
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
23337	15963 ChEBI	ribitol	+
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
23337	17992 ChEBI	sucrose	-
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
23337	catalase	+	1.11.1.6
23337	cytochrome oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	+	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
7006	+	-	-	-	+	-	-	-	+	+	+	-	+	+	+/-	-	-	+	-	-	not determinedn.d.

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
7006	-	-	+	+	+	-	-	-	+	-	+	+	+	+	-	+	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	+	-	+	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7006	deep water rice roots (endophyte)	Suraha Tal Lake	India	IND	Asia
23337	surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa)

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7006	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
124043	ASM4192996v1 assembly for Brucella oryzae DSM 17471	scaffold	GCA_041929965		335286	29.86
66792	O.oryzae_NBRC_102588.fasta assembly for Brucella oryzae NBRC 102588	contig	GCA_012103035	335286.8	335286	5.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Ochrobactrum oryzae gene for 16S rRNA, partial sequence, strain: NBRC 102588	AB681868	1412		335286
7006	Ochrobactrum oryzae partial 16S rRNA gene, strain MTCC 4195T	AM041247	1477		335286

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Brucella oryzae NBRC 102588
NCBI: GCA_012103035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.30	no
125439	motility	BacteriaNetⓘ	yes	65.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	93.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ochrobactrum oryzae strain NBRC 102588
PATRIC: 335286.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	yes
125438	anaerobic	anaerobicⓘ	no	93.66	yes
125438	spore-forming	spore-formingⓘ	no	89.65	yes
125438	aerobic	aerobicⓘ	yes	82.79	yes
125438	thermophilic	thermophileⓘ	no	98.99	yes
125438	flagellated	motile2+ⓘ	yes	61.21	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
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 .
#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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Brucella oryzae (CCUG 54940, DSM 17471, MTCC 4195)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_041929965

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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