Name: Agrobacterium rubi DSM 30149
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13574

Type strain:

Species: Agrobacterium rubi

Culture col. no.: DSM 30149, ATCC 13334, ICPB TR2, IFO 13260, NBRC 13260, NCPPB 1856, JCM 20917, CIP 104331, IAM 13568, LMG 159

Strain history: CIP <- 1995, ATCC <- M.P. Starr: strain TR 2 <- E.M. Hildebrand

NCBI tax ID(s): 28099 (species)

SI-ID 449

LMG 159, ATCC 13334, DSM 30149, IFO 13260, NCPPB 1856, CIP 104331, IAM 13568, ICMP 8643, CECT 4303, CFBP 999, NBRC 13260, KACC 11194, JCM 20917

Special Collections

Other strains from Agrobacterium rubi

Section

Agrobacterium rubi DSM 30149 is an obligate aerobe, Gram-negative, rod-shaped plant pathogen that was isolated from Probably black raspberry gall.

Gram-negative
rod-shaped
obligate aerobe
plant pathogen
16S sequence
Bacteria

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.: #122280]	Gram stain	negative

[Ref.: #122280]	Cell shape	rod-shaped

Information on culture and growth conditions Culture and growth conditions

[Ref.: #41366]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #41366]

Culture medium growth

[Ref.: #41366]

Culture medium composition

expand / minimize

[Ref.: #9169]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #9169]

Culture medium growth

[Ref.: #9169]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9169]

Culture medium composition

expand / minimize

[Ref.: #122280]

Culture medium

CIP Medium 3

[Ref.: #122280]

Culture medium growth

[Ref.: #122280]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #9169]		growth	26 °C
[Ref.: #41366]		growth	30 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #122280]		growth	30 °C
[Ref.: #122280]	no	growth	5 °C
[Ref.: #122280]	no	growth	10 °C
[Ref.: #122280]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #122280]

Oxygen tolerance

obligate aerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #122280]	esculin ChEBI	-	hydrolysis
[Ref.: #122280]	glucose ChEBI	+/-	degradation
[Ref.: #122280]	nitrate ChEBI	-	reduction
[Ref.: #122280]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #122280]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #122280]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #122280]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #122280]	amylase	-
[Ref.: #122280]	beta-galactosidase	+	3.2.1.23
[Ref.: #122280]	caseinase	-	3.4.21.50
[Ref.: #122280]	catalase	-	1.11.1.6
[Ref.: #122280]	gelatinase	-
[Ref.: #122280]	lecithinase	-
[Ref.: #122280]	lysine decarboxylase	-	4.1.1.18
[Ref.: #122280]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #122280]	oxidase	-
[Ref.: #122280]	tween esterase	+
[Ref.: #122280]	urease	+	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #67770]	Sample type/isolated from	Probably black raspberry gall
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America

[Ref.: #122280]	Sample type/isolated from	Probably black raspberry
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence AB680384 (>99% sequence identity) for Agrobacterium from Microbeatlas

Aquatic Samples	101
Soil Samples	173
Animal Samples	477
Plant Samples	797
Total Samples	1548

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

[Ref.: #9169]	Pathogenicity (plant)	yes
[Ref.: #9169]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122280]	Biosafety level	1	Risk group (French classification)

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.: #20218]	Agrobacterium rubi gene for 16S rRNA, partial sequence, strain: NBRC 13260	AB680384	1410	GenBank ENA	28099 tax ID	*
[Ref.: #124043]	Agrobacterium rubi partial 16S rRNA gene, strain LMG 159	FR828341	1380	GenBank ENA	28099 tax ID	*

[Ref.: #9169]	GC-content	58.8 mol%
[Ref.: #67770]	GC-content	58.8 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #9169]

Culture collection no.

DSM 30149, ATCC 13334, ICPB TR2, IFO 13260, NBRC 13260, NCPPB 1856, JCM 20917, CIP 104331, IAM 13568, LMG 159

[Ref.: #82761]

SI-ID 449

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A novel capsular polysaccharide from Rhizobium rubi strain DSM 30149.	De Castro C, Fregolino E, Gargiulo V, Lanzetta R, Parrilli M	Carbohydr Res	10.1016/j.carres.2008.04.024	2008	*

References

#9169

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30149

#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 )

#41366 ; Curators of the CIP;
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#82761

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-ID449.1 )

#122280 Collection of Institut Pasteur ; Curators of the CIP; CIP 104331

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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