Name: Agrobacterium rubi TR3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13573

Type strain:

Species: Agrobacterium rubi

Strain Designation: TR3, TR 3

Culture col. no.: DSM 6772, ATCC 13335, NCPPB 1854, JCM 20918, CFBP 1317, CIP 104332, HAMBI 1812, IAM 13569, ICMP 6428, ICPB TR3, IFO 13261, LMG 13935, LMG 156, NBRC 13261

Strain history: CIP <- 1995, ATCC <- M.P. Starr: strain TR 3 <- E.M. Hildebrand

NCBI tax ID(s): 1368415 (strain), 28099 (species)

SI-ID 447

LMG 156, ATCC 13335, CIP 104332, IAM 13569, ICMP 6428, LMG 17935, NCPPB 1854, PDDCC 6428, DSM 6772, IFO 13261, CECT 4118, CCRC 12820, KCTC 2434, ICMP 11833, NBRC 13261, CFBP 1317, HAMBI 1812, BCRC 12820, KCTC 12454, KACC 10739, JCM 20918, CGMCC 1.2558, CFBP 5509, CFBP 6448

Other strains from Agrobacterium rubi

A. rubi DSM 30149, ATCC 13334, ICPB TR2, ...

Section

Agrobacterium rubi TR3 is a mesophilic, Gram-negative plant pathogen that was isolated from probably boysenberry .

Gram-negative
mesophilic
plant pathogen
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	*Rhizobiaceae*
	Genus	*Agrobacterium*
	Species	**Agrobacterium rubi**
	Full Scientific Name (LPSN)	Agrobacterium rubi (Hildebrand 1940) Starr and Weiss 1943 (Approved Lists 1980)

	Synonym	"Phytomonas* rubi"*
	Synonym	Rhizobium rubi

Information on morphological and physiological properties Morphology

[Ref.: #122281]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.975

[Ref.: #122281]	Cell shape	rod-shaped

[Ref.: #122281]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #34681]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #34681]

Culture medium growth

[Ref.: #34681]

Culture medium composition

expand / minimize

[Ref.: #2810]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #2810]

Culture medium growth

[Ref.: #2810]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2810]

Culture medium composition

expand / minimize

[Ref.: #122281]

Culture medium

CIP Medium 3

[Ref.: #122281]

Culture medium growth

[Ref.: #122281]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #2810]		growth	26 °C
[Ref.: #34681]		growth	30 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #122281]		growth	30 °C
[Ref.: #122281]	no	growth	5 °C
[Ref.: #122281]	no	growth	10 °C
[Ref.: #122281]	no	growth	41 °C

[Ref.: #2810]	Temperature range	mesophilic
[Ref.: #34681]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #122281]	Temperature range	mesophilic
[Ref.: #122281]	Temperature range	psychrophilic
[Ref.: #122281]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #122281]	esculin ChEBI	-	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #122281]	glucose ChEBI	+	degradation
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #122281]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #122281]	nitrite ChEBI	-	reduction
[Ref.: #122281]	sodium thiosulfate ChEBI	-	builds gas from
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #122281]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #122281]		indole ChEBI	no
[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.: #122281]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #122281]	amylase	-
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #122281]	beta-galactosidase	+	3.2.1.23
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #122281]	caseinase	-	3.4.21.50
[Ref.: #122281]	catalase	-	1.11.1.6
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #122281]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #122281]	lecithinase	-
[Ref.: #122281]	lysine decarboxylase	-	4.1.1.18
[Ref.: #122281]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #122281]	oxidase	-
[Ref.: #122281]	tween esterase	-
[Ref.: #122281]	urease	+	3.5.1.5
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

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.: #2810]	24895	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	-	+	-	-	+

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

[Ref.: #2810]	Sample type/isolated from	probably boysenberry (Rubus ursinus var. loganobaccus)
[Ref.: #2810]	Host species	Rubus ursinus var. Loganobaccus

[Ref.: #67770]	Sample type/isolated from	Cane gall of Rubus ursinus
[Ref.: #67770]	Host species	Rubus ursinus
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America

[Ref.: #122281]	Sample type/isolated from	Black raspberry
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Fruit (Seed)

What are isolation sources categories?

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

[Ref.: #2810]	Pathogenicity (plant)	yes
[Ref.: #2810]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122281]	Biosafety level	1	Risk group (French classification)

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Rhizobium rubi strain DSM 6772 clone 1 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence	AF345276	1259	ENA	28099 tax ID	*
[Ref.: #20218]	Rhizobium rubi strain DSM 6772 clone 2 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence	AF345277	1248	ENA	28099 tax ID	*
[Ref.: #20218]	Agrobacterium rubi gene for 16S rRNA, strain: IAM 13569	D12787	1438	ENA	28099 tax ID	*
[Ref.: #20218]	Agrobacterium rubi strain ICMP 11833 16S ribosomal RNA gene, partial sequence	AY626395	1336	ENA	28099 tax ID	*
[Ref.: #20218]	Agrobacterium rubi gene for 16S ribosomal RNA, complete sequence	D14503	1472	ENA	28099 tax ID	*
[Ref.: #20218]	Agrobacterium rubi partial 16S rRNA gene, strain LMG 156	X67228	1436	ENA	28099 tax ID	*
[Ref.: #20218]	Agrobacterium rubi partial 16S rRNA gene, strain LMG 17935	AM181759	1426	ENA	28099 tax ID	*
[Ref.: #20218]	Agrobacterium rubi gene for 16S rRNA, partial sequence, strain: NBRC 13261	AB680385	1410	ENA	28099 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agrobacterium rubi TR3 = NBRC 13261	GCA_000739935	contig	GenBank	1368415 tax ID
[Ref.: #66792]	Agrobacterium rubi DSM 6772	GCA_017873055	contig	GenBank	28099 tax ID	*
[Ref.: #66792]	Agrobacterium rubi strain DSM 6772	28099.16	wgs	PATRIC	28099 tax ID	*
[Ref.: #66792]	Rhizobium rubi NBRC 13261	1220582.3	wgs	PATRIC	1368415 tax ID	*
[Ref.: #66792]	Agrobacterium rubi NBRC 13261	2600255076	draft	JGI IMG/M	1368415 tax ID	*
[Ref.: #66792]	Rhizobium rubi DSM 6772	2913290767	draft	JGI IMG/M	28099 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: Agrobacterium rubi strain DSM 6772 PATRIC: 28099.16
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium rubi NBRC 13261 PATRIC: 1220582.3
[Ref.: #69480]	motile	yes	81.456	no
[Ref.: #69480]	gram-positive	no	98.293	no
[Ref.: #69480]	anaerobic	no	97.863	no
[Ref.: #69480]	aerobic	yes	89.437	no
[Ref.: #69480]	halophile	no	89.656	no
[Ref.: #69480]	spore-forming	no	96.151	no
[Ref.: #69480]	thermophile	no	99.666	yes
[Ref.: #69480]	glucose-util	yes	90.674	yes
[Ref.: #69480]	flagellated	no	81.778	no
[Ref.: #69480]	glucose-ferment	no	89.695	yes

Availability in culture collections External links

[Ref.: #2810]

Culture collection no.

DSM 6772, ATCC 13335, NCPPB 1854, JCM 20918, CFBP 1317, CIP 104332, HAMBI 1812, IAM 13569, ICMP 6428, ICPB TR3, IFO 13261, LMG 13935, LMG 156, NBRC 13261

[Ref.: #82760]

SI-ID 447

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia.	Zahradnik J, Nunvar J, Parizkova H, Kolarova L, Palyzova A, Maresova H, Grulich M, Kyslikova E, Kyslik P	Syst Appl Microbiol	10.1016/j.syapm.2018.01.003	2018	*
Phylogeny	Rhizobium skierniewicense sp. nov., isolated from tumours on chrysanthemum and cherry plum.	Pulawska J, Willems A, Sobiczewski P	Int J Syst Evol Microbiol	10.1099/ijs.0.032532-0	2011	*
Phylogeny	Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.).	Panday D, Schumann P, Das SK	Int J Syst Evol Microbiol	10.1099/ijs.0.028407-0	2010	*
Genetics	Agrobacterium rubi(T) DSM 6772 produces a lipophilic polysaccharide capsule whose degree of acetylation is growth modulated.	De Castro C, Gargiulo V, Lanzetta R, Parrilli M	Biomacromolecules	10.1021/bm061081f	2007	*

References

#2810

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6772

#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 )

#34681 ; Curators of the CIP;

#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;

#68369

Automatically annotated from API 20NE .

#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 )

#82760

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-ID447.1 )

#122281 Collection of Institut Pasteur ; Curators of the CIP; CIP 104332
* These data were automatically processed and therefore are not curated

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Agrobacterium rubi strain DSM 6772

Rhizobium rubi NBRC 13261

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