Name: Agrobacterium tumefaciens A 1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13581

Type strain:

Species: Agrobacterium tumefaciens

Strain Designation: A 1

Culture col. no.: CCUG 3355, DSM 30150, ATCC 4720, CCM 1000, IAM 14141, IAM 1524, NCIB 8150, JCM 21034, CIP 104335, LMG 182, NCIMB 8150

Strain history: CIP <- 1995, ATCC, Agrobacterium tumefaciens <- I.L. Baldwin: strain A 1

NCBI tax ID(s): 358 (species)

SI-ID 550

LMG 182, ATCC 4720, CCM 1000, CCUG 3355, DSM 30150, IAM 1524, ICMP 5793, NCIB 8150, NCPPB 2992, PDDCC 5793, CIP 104335, IAM 14141, NCIMB 8150, CCUG3555, VKM B-1573, CECT 4304, CFBP 2412, CBMAI 198, CCT 4774, CCT 5075, NCAIM B.01409, CFBP 5493, JCM 21034

Section

Agrobacterium tumefaciens A 1 is a mesophilic, motile human pathogen that was isolated from Presumably subclone of T5 from black raspberry.

motile
human pathogen
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	*Rhizobiaceae*
	Genus	*Agrobacterium*
	Species	**Agrobacterium tumefaciens**
	Full Scientific Name (LPSN)	Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 (Approved Lists 1980)

Synonym

"Bacterium tumefaciens"

Information on morphological and physiological properties Morphology

[Ref.: #122120]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.992

[Ref.: #122120]	Cell shape	rod-shaped

[Ref.: #122120]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %90.129

Information on culture and growth conditions Culture and growth conditions

[Ref.: #41367]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #41367]

Culture medium growth

[Ref.: #41367]

Culture medium composition

expand / minimize

[Ref.: #9170]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #9170]

Culture medium growth

[Ref.: #9170]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9170]

Culture medium composition

expand / minimize

[Ref.: #122120]

Culture medium

CIP Medium 3

[Ref.: #122120]

Culture medium growth

[Ref.: #122120]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #68368]

Culture medium

MacConkey medium * from API 20E

[Ref.: #68368]

Culture medium growth

* from API 20E

	Kind of temperature		Temperature
[Ref.: #9170]		growth	26 °C
[Ref.: #41367]		growth	30 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #122120]		growth	10-30 °C
[Ref.: #122120]	no	growth	5 °C
[Ref.: #122120]	no	growth	41 °C

[Ref.: #9170]	Temperature range	mesophilic
[Ref.: #41367]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #122120]	Temperature range	psychrophilic
[Ref.: #122120]	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 %99.998

[Ref.: #9170]

Name of produced compound

3 ketolactose

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	-	fermentation	* from API 20E
[Ref.: #122120]	esculin ChEBI	+	hydrolysis
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #122120]	glucose ChEBI	-	fermentation
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #122120]	lactose ChEBI	-	fermentation
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	+	fermentation	* from API 20E
[Ref.: #122120]	nitrate ChEBI	+	reduction
[Ref.: #68368]	nitrate ChEBI	-	reduction	* from API 20E
[Ref.: #122120]	nitrite ChEBI	+	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #122120]	sodium thiosulfate ChEBI	+	builds gas from
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #122120]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite	Production
[Ref.: #122120]	indole ChEBI	no
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E
[Ref.: #68368]	nitrite ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #122120]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #122120]	amylase	-
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #122120]	beta-galactosidase	+	3.2.1.23
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #122120]	caseinase	-	3.4.21.50
[Ref.: #122120]	catalase	+	1.11.1.6
[Ref.: #68368]	cytochrome oxidase	+	1.9.3.1	* from API 20E
[Ref.: #122120]	DNase	-
[Ref.: #122120]	gelatinase	-
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #122120]	lecithinase	+
[Ref.: #122120]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #122120]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #122120]	oxidase	+
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #122120]	tween esterase	+
[Ref.: #122120]	urease	+	3.5.1.5
[Ref.: #68368]	urease	+	3.5.1.5	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #9170]	16857	+	-	-	-	+	-	+	-	-	+	-	-	-	+	-	+	+	-	+	+	+	-	not determinedn.d.	not determinedn.d.	+	not determinedn.d.	not determinedn.d.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #122120]	639	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	-	-	+	-	-	-	+	+	+	+	-	-	+	+	+	+	-	+	+	-	+	+	+	-	-	-	-	-	+	+	-	+	-	+	-	-	-	+	+	-	-	-	-	-	+	-	+	+	+	+	-	+	+	-	+	-	-

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

[Ref.: #44649]	Sample type/isolated from	Presumably subclone of T5 from black raspberry
[Ref.: #44649]	Geographic location (country and/or sea, region)	Iowa
[Ref.: #44649]	Country	USA
[Ref.: #44649]	Country ISO 3 Code	USA
[Ref.: #44649]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Shrub (Scrub)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence M11223 (>99% sequence identity) for Agrobacterium from Microbeatlas

Aquatic Samples	6
Soil Samples	7
Animal Samples	33
Plant Samples	42
Total Samples	88

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

[Ref.: #9170]	Pathogenicity (human)	yes, in single cases
[Ref.: #9170]	Pathogenicity (plant)	yes
[Ref.: #9170]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122120]	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 tumefaciens 16S rRNA gene	M11223	1489	ENA	358 tax ID	*
[Ref.: #20218]	Agrobacterium tumefaciens gene for 16S rRNA, strain: IAM 14141	D13294	1439	ENA	358 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agrobacterium tumefaciens ATCC 4720	GCA_011684035	contig	GenBank	358 tax ID
[Ref.: #66792]	Agrobacterium tumefaciens strain ATCC 4720	358.278	wgs	PATRIC	358 tax ID	*

[Ref.: #9170]	GC-content	62.1 mol%
[Ref.: #9170]	GC-content	61.0 mol%

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 tumefaciens strain ATCC 4720 PATRIC: 358.278
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agrobacterium tumefaciens strain ATCC 4720 PATRIC: 358.278
[Ref.: #69480]	gram-positive	no	98.412	no
[Ref.: #69480]	anaerobic	no	98.473	no
[Ref.: #69480]	halophile	no	93.363	no
[Ref.: #69480]	spore-forming	no	96.099	no
[Ref.: #69480]	glucose-util	yes	92.352	no
[Ref.: #69480]	motile	yes	85.342	no
[Ref.: #69480]	flagellated	no	73.868	no
[Ref.: #69480]	thermophile	no	99.578	yes
[Ref.: #69480]	aerobic	yes	94.243	no
[Ref.: #69480]	glucose-ferment	no	90.103	yes

Availability in culture collections External links

[Ref.: #9170]

Culture collection no.

CCUG 3355, DSM 30150, ATCC 4720, CCM 1000, IAM 14141, IAM 1524, NCIB 8150, JCM 21034, CIP 104335, LMG 182, NCIMB 8150

[Ref.: #82768]

SI-ID 550

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Strain ATCC 4720(T) is the authentic type strain of Agrobacterium tumefaciens, which is not a later heterotypic synonym of Agrobacterium radiobacter.	Velazquez E, Flores-Felix JD, Sanchez-Juanes F, Igual JM, Peix A	Int J Syst Evol Microbiol	10.1099/ijsem.0.004443	2020	*

References

#9170

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30150

#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 )

#41367 ; Curators of the CIP;
#44649 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 3355

#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;

#68368

Automatically annotated from API 20E .

#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 )

#82768

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-ID550.1 )

#122120 Collection of Institut Pasteur ; Curators of the CIP; CIP 104335
* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Agrobacterium radiobacter in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Agrobacterium tumefaciens strain ATCC 4720

Agrobacterium tumefaciens strain ATCC 4720

Change proposal

Change proposal