Agrobacterium tumefaciens (CCUG 3355, DSM 30150, ATCC 4720)

Name: Agrobacterium tumefaciens (CCUG 3355, DSM 30150, ATCC 4720)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13581

Type strain

Strain Designation A 1

Culture col. no. CCUG 3355 DSM 30150 ATCC 4720 CCM 1000 IAM 14141 7 more

NCBI tax ID(s) 362 358

Special Collections DSMZ CCUG JCM CIP

Links

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

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

Name and taxonomic classification

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

@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 tumefaciens

Full scientific name Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 (Approved Lists 1980)

Synonyms (1)

"Bacterium tumefaciens"

Morphology

Cell morphology

@ref	Gram stain	Cell shape
122120	negative	rod-shaped
125439	negative
125438	negative

Culture and growth conditions

Culture medium

@ref	Name	Composition
41367	MEDIUM 3 - Columbia agar	Columbia agar (39.000 g);distilled water (1000.000 ml)
9170	NUTRIENT AGAR (DSMZ Medium 1)	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
68368	MacConkey medium		from API 20E
122120	CIP Medium 3

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
9170	positive	growth	26	mesophilic
41367	positive	growth	30	mesophilic
67770	positive	growth	25	mesophilic
122120	positive	growth	10-30
122120	negative	growth	5
122120	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95

Spore formation

@ref	Spore formation	Confidence
125439		98.6
125438		92.321

Compound production

9170

Compound3 ketolactose

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	-	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
122120	4853 ChEBI	esculin	+	hydrolysis
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
122120	17234 ChEBI	glucose	-	fermentation
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
122120	17716 ChEBI	lactose	-	fermentation
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	+	fermentation	from API 20E
122120	17632 ChEBI	nitrate	+	reduction
68368	17632 ChEBI	nitrate	-	reduction	from API 20E
122120	16301 ChEBI	nitrite	+	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
122120	132112 ChEBI	sodium thiosulfate	+	builds gas from
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	+	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
122120	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
122120	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E
68368	16301 ChEBI	nitrite	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
68368	15688 ChEBI	acetoin	+	from API 20E
68368	35581 ChEBI	indole		from API 20E

Enzymes

@ref	Value	Activity	Ec
122120	alcohol dehydrogenase	-	1.1.1.1
122120	amylase	-
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
122120	beta-galactosidase	+	3.2.1.23
68368	beta-galactosidase	+	3.2.1.23	from API 20E
122120	caseinase	-	3.4.21.50
122120	catalase	+	1.11.1.6
68368	cytochrome oxidase	+	1.9.3.1	from API 20E
122120	DNase	-
122120	gelatinase	-
68368	gelatinase	-		from API 20E
122120	lecithinase	+
122120	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
122120	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
122120	oxidase	+
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
122120	tween esterase	+
122120	urease	+	3.5.1.5
68368	urease	+	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
9170	+	-	-	-	+	-	+	-	-	+	-	-	-	+	-	+	+	-	+	+	+	-	not determinedn.d.	not determinedn.d.	+	not determinedn.d.	not determinedn.d.

API biotype100

@ref	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
122120	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	-	-	+	-	-	-	+	+	+	+	-	-	+	+	+	+	-	+	+	-	+	+	+	-	-	-	-	-	+	+	-	+	-	+	-	-	-	+	+	-	-	-	-	-	+	-	+	+	+	+	-	+	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Shrub (Scrub)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
44649	Presumably subclone of T5 from black raspberry	Iowa	USA	USA	North America

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity plant	Biosafety level	Biosafety level comment
9170	yes, in single cases		1	Risk group (German classification) According to TRBA 466
122120			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
67770	ASM1168403v1 assembly for Agrobacterium tumefaciens ATCC 4720	contig	GCA_011684035	358.278	8116548949	358	64.38

Genome browser: GCA_011684035

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Agrobacterium tumefaciens gene for 16S rRNA, strain: IAM 14141	D13294	1439	358
20218	Agrobacterium tumefaciens 16S rRNA gene	M11223	1489	358
124043	Agrobacterium tumefaciens strain ATCC 4720, type 16S ribosomal RNA gene, partial sequence.	MT534522	1437	358

GC content

@ref	GC-content (mol%)
9170	62.1
9170	61.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Agrobacterium tumefaciens ATCC 4720
NCBI: GCA_011684035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.60	no
125439	motility	BacteriaNetⓘ	yes	63.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agrobacterium tumefaciens strain ATCC 4720
PATRIC: 358.278

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.33	no
125438	anaerobic	anaerobicⓘ	no	94.21	no
125438	spore-forming	spore-formingⓘ	no	92.32	no
125438	aerobic	aerobicⓘ	yes	86.28	no
125438	thermophilic	thermophileⓘ	no	99.75	yes
125438	flagellated	motile2+ⓘ	yes	67.85	no

Literature

Title	Authors	Journal	DOI	Year
Lupins in the genome editing era: advances in plant cell culture, double haploid technology and genetic transformation for crop improvement.	Pathi KM, Sprink T.	Front Plant Sci	10.3389/fpls.2025.1601216	2025
Golden Standard: a complete standard, portable, and interoperative MoClo tool for model and non-model proteobacteria.	Blazquez B, Leon DS, Torres-Bacete J, Gomez-Luengo A, Kniewel R, Martinez I, Sordon S, Wilczak A, Salgado S, Huszcza E, Poplonski J, Prieto A, Nogales J.	Nucleic Acids Res	10.1093/nar/gkad758	2023
Solution structure of RNase P RNA.	Kazantsev AV, Rambo RP, Karimpour S, Santalucia J, Tainer JA, Pace NR.	RNA	10.1261/rna.2563511	2011
A new Agrobacterium strain isolated from aerial tumors on Ficus benjamina L.	Bouzar H, Chilton WS, Nesme X, Dessaux Y, Vaudequin V, Petit A, Jones JB, Hodge NC.	Appl Environ Microbiol	10.1128/aem.61.1.65-73.1995	1995
Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling.	Schmalenberger A, Schwieger F, Tebbe CC.	Appl Environ Microbiol	10.1128/aem.67.8.3557-3563.2001	2001
Myxothiazol, a new antibiotic interfering with respiration.	Thierbach G, Reichenbach H.	Antimicrob Agents Chemother	10.1128/aac.19.4.504	1981
Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil.	Janssen PH, Schuhmann A, Morschel E, Rainey FA.	Appl Environ Microbiol	10.1128/aem.63.4.1382-1388.1997	1997
Judicial Opinions 123-127.	Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, Ventosa A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005708	2022
Antimicrobial and Antiviral Compounds of Phlomis viscosa Poiret.	Yarmolinsky L, Nakonechny F, Budovsky A, Zeigerman H, Khalfin B, Sharon E, Yarmolinsky L, Ben-Shabat S, Nisnevitch M.	Biomedicines	10.3390/biomedicines11020441	2023
Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers.	Portier P, Fischer-Le Saux M, Mougel C, Lerondelle C, Chapulliot D, Thioulouse J, Nesme X.	Appl Environ Microbiol	10.1128/aem.00018-06	2006
Novel tellurite-amended media and specific chromosomal and Ti plasmid probes for direct analysis of soil populations of Agrobacterium biovars 1 and 2.	Mougel C, Cournoyer B, Nesme X.	Appl Environ Microbiol	10.1128/aem.67.1.65-74.2001	2001
Psychrotolerant bacteria isolated from arctic soil that degrade polychlorinated biphenyls at low temperatures	Master ER, Mohn WW.	Appl Environ Microbiol	10.1128/aem.64.12.4823-4829.1998	1998
The sequence of the single 16S rRNA gene of the thermophilic eubacterium Rhodothermus marinus reveals a distant relationship to the group containing Flexibacter, Bacteroides, and Cytophaga species.	Andresson OS, Fridjonsson OH.	J Bacteriol	10.1128/jb.176.20.6165-6169.1994	1994
Aromatic-degrading Sphingomonas isolates from the deep subsurface.	Fredrickson JK, Balkwill DL, Drake GR, Romine MF, Ringelberg DB, White DC.	Appl Environ Microbiol	10.1128/aem.61.5.1917-1922.1995	1995
Phylogenetic analysis of the bacterial communities in marine sediments.	Gray JP, Herwig RP.	Appl Environ Microbiol	10.1128/aem.62.11.4049-4059.1996	1996
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
#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 .
#122120	Collection of Institut Pasteur ; Curators of the CIP; CIP 104335
#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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Agrobacterium tumefaciens (CCUG 3355, DSM 30150, ATCC 4720)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API 20E

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_011684035

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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