Cite this strain

"Agrobacterium fabrum" (CIP 104333, ATCC 33970, C58)

BacDive ID 137664

Type strain

Strain Designation C58

Culture col. no. CIP 104333 ATCC 33970 C58

NCBI tax ID(s) 1176649 362

Special Collections CIP

Links

"Agrobacterium fabrum" C58 is an obligate aerobe, mesophilic, Gram-negative prokaryote of the family Rhizobiaceae.

Gram-negative motile rod-shaped obligate aerobe mesophilic genome sequence

Name and taxonomic classification

SI-ID 624

LMG 287,ATCC 33970,CIP 104333,LMD 85.29,NCCB 85029,CGMCC 1.1488,CFBP 1903,CFBP 6552

@ref 20215

Last LPSN update 2025-12-16 10:02:52

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Agrobacterium

Species "Agrobacterium fabrum"

Full scientific name Agrobacterium fabrum Lassalle et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
38495	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
38495	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
38495	CIP Medium 3			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
38495	positive	growth	30	mesophilic
38495	positive	growth	10-30
38495	negative	growth	5
38495	negative	growth	41

Physiology and metabolism

Oxygen tolerance

38495

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125438		97.432

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
38495	4853 ChEBI	esculin	+	hydrolysis
38495	17234 ChEBI	glucose	-	fermentation
38495	17716 ChEBI	lactose	-	fermentation
38495	17632 ChEBI	nitrate	+	reduction
38495	16301 ChEBI	nitrite	+	reduction
38495	132112 ChEBI	sodium thiosulfate	+	builds gas from

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
38495	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
38495	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
38495	alcohol dehydrogenase	-	1.1.1.1
38495	amylase	-
38495	beta-galactosidase	+	3.2.1.23
38495	caseinase	-	3.4.21.50
38495	catalase	+	1.11.1.6
38495	DNase	-
38495	gelatinase	-
38495	lecithinase	+
38495	lysine decarboxylase	-	4.1.1.18
38495	ornithine decarboxylase	-	4.1.1.17
38495	oxidase	+
38495	tween esterase	+
38495	urease	+	3.5.1.5

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
38495	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	-	-	-	-	-	-	+	+	+	+	-	-	+	+	+	+	-	+	+	-	+	+	+	-	-	-	-	-	+	+	-	+	-	+	-	-	-	+	+	-	-	-	-	-	+	-	+	+	+	+	-	+	+	-	+	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
38495		New-York	USA	USA	North America
38495	Cherry, gall	New York	United States of America	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
38495	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM9202v1 assembly for Agrobacterium fabrum str. C58	complete	GCA_000092025	176299.10	639279302	176299	98.94

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agrobacterium fabrum str. C58
PATRIC: 176299.53

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	65.10	no
125438	anaerobic	anaerobicⓘ	no	86.24	yes
125438	spore-forming	spore-formingⓘ	no	97.43	no
125438	aerobic	aerobicⓘ	yes	50.56	yes
125438	thermophilic	thermophileⓘ	no	93.50	no
125438	flagellated	motile2+ⓘ	no	75.36	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Transcriptome	Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium.	Slater S, Setubal JC, Goodner B, Houmiel K, Sun J, Kaul R, Goldman BS, Farrand SK, Almeida N, Burr T, Nester E, Rhoads DM, Kadoi R, Ostheimer T, Pride N, Sabo A, Henry E, Telepak E, Cromes L, Harkleroad A, Oliphant L, Pratt-Szegila P, Welch R, Wood D.	Appl Environ Microbiol	10.1128/aem.03192-12	2013

References

#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 )
#38495	Collection of Institut Pasteur ; Curators of the CIP; CIP 104333
#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) .
#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 )
#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 fabrum" (CIP 104333, ATCC 33970, C58)

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

Enzymes

API biotype100

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000092025

Genome-based predictions

Predictions

Literature

Literature

References

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