Agrobacterium rubi (DSM 6772, ATCC 13335, NCPPB 1854)

Name: Agrobacterium rubi (DSM 6772, ATCC 13335, NCPPB 1854)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13573

Type strain

Strain Designation TR3, TR 3

Culture col. no. DSM 6772 ATCC 13335 NCPPB 1854 TR3 NBRC 13261 11 more

NCBI tax ID(s) 1368415 28099

Special Collections DSMZ JCM CIP

Links

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

Gram-negative rod-shaped mesophilic plant pathogen genome sequence 16S sequence

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2025-12-16 09:50:07

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Agrobacterium

Species Agrobacterium rubi

Full scientific name Agrobacterium rubi (Hildebrand 1940) Starr and Weiss 1943 (Approved Lists 1980)

Synonyms (2)

"Phytomonas rubi"
Rhizobium rubi

BacDive ID	Other strains from **Agrobacterium rubi** (1)	Type strain
13574	A. rubi DSM 30149, ATCC 13334, ICPB TR2, IFO 13260, ...

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122281	negative	rod-shaped
125438	negative		98.333
125439	negative		96

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
34681	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
2810	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
122281	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2810	positive	growth	26	mesophilic
34681	positive	growth	30	mesophilic
67770	positive	growth	25	mesophilic
122281	positive	growth	30	mesophilic
122281	negative	growth	5
122281	negative	growth	10
122281	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	91.8

Spore formation

@ref	Spore formation	Confidence
125439		97.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
122281	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
122281	17234 ChEBI	glucose	+	degradation
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
122281	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
122281	16301 ChEBI	nitrite	-	reduction
122281	132112 ChEBI	sodium thiosulfate	-	builds gas from
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
122281	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
122281	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
122281	alcohol dehydrogenase	-	1.1.1.1
122281	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
122281	beta-galactosidase	+	3.2.1.23
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
122281	caseinase	-	3.4.21.50
122281	catalase	-	1.11.1.6
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
122281	gelatinase	-
68369	gelatinase	-		from API 20NE
122281	lecithinase	-
122281	lysine decarboxylase	-	4.1.1.18
122281	ornithine decarboxylase	-	4.1.1.17
122281	oxidase	-
122281	tween esterase	-
122281	urease	+	3.5.1.5
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
2810	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Fruit (Seed)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
2810	probably boysenberry (Rubus ursinus var. loganobaccus)	Rubus ursinus var. Loganobaccus
67770	Cane gall of Rubus ursinus	Rubus ursinus	USA	USA	North America
122281	Black raspberry

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
2810		1	Risk group (German classification) According to TRBA 466
122281		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1787305v1 assembly for Agrobacterium rubi DSM 6772	contig	GCA_017873055	28099.16	2913290767	28099	71.95
67770	ASM73993v1 assembly for Agrobacterium rubi TR3 = NBRC 13261	contig	GCA_000739935	1220582.3	2600255076	1368415	67.56

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Agrobacterium rubi gene for 16S rRNA, strain: IAM 13569	D12787	1438	28099
20218	Agrobacterium rubi strain ICMP 11833 16S ribosomal RNA gene, partial sequence	AY626395	1336	28099
20218	Agrobacterium rubi gene for 16S ribosomal RNA, complete sequence	D14503	1472	28099
20218	Agrobacterium rubi partial 16S rRNA gene, strain LMG 156	X67228	1436	28099
20218	Agrobacterium rubi partial 16S rRNA gene, strain LMG 17935	AM181759	1426	28099
20218	Agrobacterium rubi gene for 16S rRNA, partial sequence, strain: NBRC 13261	AB680385	1410	28099

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Agrobacterium rubi DSM 6772
NCBI: GCA_017873055

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.80	no
125439	motility	BacteriaNetⓘ	yes	57.10	no
125439	gram_stain	BacteriaNetⓘ	negative	96.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium rubi NBRC 13261
PATRIC: 1220582.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.33	no
125438	anaerobic	anaerobicⓘ	no	97.48	no
125438	spore-forming	spore-formingⓘ	no	89.44	no
125438	aerobic	aerobicⓘ	yes	84.15	no
125438	thermophilic	thermophileⓘ	no	97.75	yes
125438	flagellated	motile2+ⓘ	yes	63.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Analysis of stable low-molecular-weight RNA profiles of members of the family Rhizobiaceae.	Velazquez E, Cruz-Sanchez JM, Mateos PF, Martinez-Molina E.	Appl Environ Microbiol	10.1128/aem.64.4.1555-1559.1998	1998
	Minimum requirements of flagellation and motility for infection of Agrobacterium sp. strain H13-3 by flagellotropic bacteriophage 7-7-1.	Yen JY, Broadway KM, Scharf BE.	Appl Environ Microbiol	10.1128/aem.01082-12	2012
	An efficient direct screening system for microorganisms that activate plant immune responses based on plant-microbe interactions using cultured plant cells.	Kurokawa M, Nakano M, Kitahata N, Kuchitsu K, Furuya T.	Sci Rep	10.1038/s41598-021-86560-0	2021
Genetics	Comparative Genomics Reveals Potential Mechanisms of Plant Beneficial Effects of a Novel Bamboo-Endophytic Bacterial Isolate Paraburkholderia sacchari Suichang626.	Wang K, Wu Y, Ye M, Yang Y, Asiegbu FO, Overmyer K, Liu S, Cui F.	Front Microbiol	10.3389/fmicb.2021.686998	2021
Phylogeny	Estimating Divergence Times and Substitution Rates in Rhizobia.	Chriki-Adeeb R, Chriki A.	Evol Bioinform Online	10.4137/ebo.s39070	2016
Enzymology	Specific detection of Bradyrhizobium and Rhizobium strains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer-targeted PCR.	Tan Z, Hurek T, Vinuesa P, Muller P, Ladha JK, Reinhold-Hurek B.	Appl Environ Microbiol	10.1128/aem.67.8.3655-3664.2001	2001
Phylogeny	Discordant phylogenies within the rrn loci of Rhizobia.	van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindstrom K, Eardly BD.	J Bacteriol	10.1128/jb.185.10.2988-2998.2003	2003
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
Genetics	Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.	Singh NK, Lavire C, Nesme J, Vial L, Nesme X, Mason CE, Lassalle F, Venkateswaran K.	Front Microbiol	10.3389/fmicb.2021.765943	2021
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

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 .
#122281	Collection of Institut Pasteur ; Curators of the CIP; CIP 104332
#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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Agrobacterium rubi (DSM 6772, ATCC 13335, NCPPB 1854)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017873055

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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