Agrobacterium radiobacter (DSM 30147, ATCC 19358, IFO 13532)

Name: Agrobacterium radiobacter (DSM 30147, ATCC 19358, IFO 13532)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13580

Type strain

Culture col. no. DSM 30147 ATCC 19358 IFO 13532 NBRC 13532 NCIB 9042 16 more

NCBI tax ID(s) 1336745 362

Special Collections DSMZ CCUG JCM KCTC CIP

History <- ATCC <- NCIB <- Lab. Microbiol. Delft, EX 3.24.2 (L 624) IAM 12048 <-- ATCC 19358 <-- NCIB 9042 <-- Lab. Micorbiol., Delft; EX3.24.2. CIP <- 1995, ATCC <- NCIB <- Lab. Microbiol., Delft: strain EX 3.24.2

Links

Agrobacterium radiobacter DSM 30147 is an aerobe, mesophilic, Gram-negative plant pathogen that was isolated from Ditch water.

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

Name and taxonomic classification

SI-ID 311029

LMG 140,ATCC 19358,CCUG 3354,DSM 30147,IAM 12048,ICMP 5785,IFO 13532,NCIB 9042,NCPPB 3001,PDDCC 5785,CIP 104325,NCIMB 9042,LMD 27.5,CECT 4112,CCRC 10372,CFBP 2414,NCCB 27005,NBRC 13532,HAMBI 1814,BCRC 10372,KACC 10798,CGMCC 1.2557,CFBP 5522,JCM 20371,KCTC 22091

@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 radiobacter

Full scientific name Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980)

Synonyms (3)

"Bacillus radiobacter"
Rhizobium radiobacter
Beijerinckia fluminensis

BacDive ID	Other strains from **Agrobacterium radiobacter** (59)	Type strain
13581	A. radiobacter A 1, CCUG 3355, DSM 30150, ATCC 4720, CCM ... (type strain)
13576	A. radiobacter AK205, DSM 7215
13577	A. radiobacter d3I, DSM 9674
13579	A. radiobacter DSM 13874, NCPPB 4043
13582	A. radiobacter M 2/1, DSM 30199, DSM 60577, JCM 20987, IAM ...
13584	A. radiobacter B 6, B6, DSM 30205, ATCC 23308, CCM 1040, ...
13585	A. radiobacter F/1, DSM 30206, DSM 60575
13586	A. radiobacter 3/1, DSM 30207, DSM 60576
13587	A. radiobacter H-100, DSM 30208, DSM 60579, NCPPB 3837, ...
13589	A. radiobacter DSM 2108, CRIPP D57
100184	A. radiobacter ST032833(HKI), E008,
100185	A. radiobacter ST033150(HKI),
100186	A. radiobacter ST032607(HKI), F114a,
24476	A. radiobacter DSM 2327, UQM 1685, CCUG 53676, CIP 106281, ...
24823	A. radiobacter GV3101(pMP90), DSM 12364
134748	A. radiobacter B6 Tr, CIP 74.29
134990	A. radiobacter CIP 102835
136296	A. radiobacter CIP 104327, ATCC 6466, IFO 13127, JCM 20200, ...
136689	A. radiobacter 90A, CIP 107749, CCUG 51326
137356	A. radiobacter B62, CIP 104334, ATCC 11157
137357	A. radiobacter TT134, 6-1-2, CIP 104336, ATCC 15955
137527	A. radiobacter 500, CIP 70.51, ATCC 17983
137660	A. radiobacter 81.83, CIP 100088
137664	A. radiobacter C58, CIP 104333, ATCC 33970
137832	A. radiobacter CIP 101091
137982	A. radiobacter 358-86, CIP 102371
139082	A. radiobacter CIP 104326, ATCC 4718, JCM 20199, IAM 1526, ...
139214	A. radiobacter 572-85, CIP 101768
141516	A. radiobacter CCUG 2516, NRRL B-181
141594	A. radiobacter CCUG 3370
142441	A. radiobacter CCUG 12508
142442	A. radiobacter CCUG 12509, LMG 385
143154	A. radiobacter CCUG 17511
145747	A. radiobacter CCUG 29471
146695	A. radiobacter CCUG 31962
146956	A. radiobacter CCUG 32540
146960	A. radiobacter CCUG 32544
147074	A. radiobacter CCUG 32799
147077	A. radiobacter CCUG 32804
147384	A. radiobacter CCUG 33502
147440	A. radiobacter CCUG 33585
150676	A. radiobacter CCUG 41940
150928	A. radiobacter CCUG 42766
152911	A. radiobacter CCUG 47961
153141	A. radiobacter CCUG 48560
153176	A. radiobacter CCUG 48648
153197	A. radiobacter CCUG 48700 B
153447	A. radiobacter CCUG 49619
153627	A. radiobacter CCUG 50385 B
157291	A. radiobacter IMI 347314
157292	A. radiobacter IMI 350781
157293	A. radiobacter IMI 347313
157294	A. radiobacter IMI 347316
157295	A. radiobacter IMI 347322
157296	A. radiobacter IMI 347323
157297	A. radiobacter IMI 347324
157298	A. radiobacter IMI 347312
157514	A. radiobacter IMI 389299
157515	A. radiobacter IMI 505624a

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122119	negative	rod-shaped
125438	negative		93.562
125439	negative		99.6

Colony morphology

9167

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
37042	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
9167	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
122119	CIP Medium 3	Medium recipe at CIP
122119	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
9167	positive	growth	30	mesophilic
37042	positive	growth	30	mesophilic
44648	positive	growth	37	mesophilic
67770	positive	growth	25	mesophilic
122119	positive	growth	30	mesophilic
122119	negative	growth	5
122119	negative	growth	10
122119	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44648	aerobe
122119	obligate aerobe
125439	obligate aerobe	97.3

Spore formation

@ref	Spore formation	Confidence
125439		98.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	+	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	+	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
122119	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
122119	17234 ChEBI	glucose	+/-	degradation
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	+	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
122119	17632 ChEBI	nitrate	+	reduction
122119	16301 ChEBI	nitrite	+	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
122119	132112 ChEBI	sodium thiosulfate	+	builds gas from
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
122119	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
122119	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
122119	alcohol dehydrogenase	-	1.1.1.1
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
122119	beta-galactosidase	+	3.2.1.23
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122119	caseinase	-	3.4.21.50
9167	catalase	+	1.11.1.6
122119	catalase	+	1.11.1.6
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
9167	cytochrome-c oxidase	+	1.9.3.1
122119	DNase	-
122119	gelatinase	-
68369	gelatinase	-		from API 20NE
122119	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
122119	lysine decarboxylase	-	4.1.1.18
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
122119	ornithine decarboxylase	-	4.1.1.17
122119	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
122119	tween esterase	+
122119	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
9167	-	+/-	-	-	-	+	+/-	-	+	-	-	-	-	-	-	+	+/-	+	-	-
122119	-	+	+	+	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-

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
9167	+/-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	+/-	+	-	-	not determinedn.d.
9167	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	-	+	-	-	+
9167	+	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	-	+	-	-	+
9167	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	+/-	+	-	-	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122119	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
122119	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	-	-	-	-	-	-	+	+	-	+	-	-	+	+	+	-	-	+	+	-	+	+	+	-	-	-	-	-	-	+	-	+	-	+	-	-	-	+	+	-	-	-	-	-	+	-	+	+	+	+	-	+	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Engineered	#Built environment	-

Isolation

44648

Sample typeDitch water

Taxonmaps

69479

Global distribution of 16S sequence AM181758 (>99% sequence identity) for Agrobacterium from Microbeatlas

Aquatic Samples	822
Soil Samples	595
Animal Samples	3746
Plant Samples	731
Total Samples	5894

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity plant	Biosafety level	Biosafety level comment
9167	yes, in single cases		1	Risk group (German classification) According to TRBA 466
122119			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	ASM154130v1 assembly for Agrobacterium radiobacter NCPPB 3001	contig	GCA_001541305	358.72		358	74.94
67770	ASM200821v1 assembly for Agrobacterium radiobacter LMG 140	contig	GCA_002008215	358.128	2868989325	358	74.88
67770	ASM880138v1 assembly for Agrobacterium radiobacter CCUG 3354	contig	GCA_008801385	358.266		358	73.94
124043	AR_v2 assembly for Agrobacterium radiobacter DSM 30147	contig	GCA_963360635	1336745.18		1336745	50.85
67770	ASM1168400v1 assembly for Agrobacterium radiobacter NCIB 9042	contig	GCA_011684005	358.277	2916111912	2756240	42.24
67770	genome assembly for Agrobacterium radiobacter DSM 30147	contig	GCA_000421945	1336745.4	2571042120	1336745

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Agrobacterium radiobacter 16S rRNA gene, strain ATCC19358	AJ389904	1437	358
20218	Agrobacterium tumefaciens strain LMG 140 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence and 23S ribosomal RNA gene, partial sequence	AF541973	1086	358
20218	Agrobacterium radiobacter partial 16S rRNA gene, strain LMG 140	AM181758	1426	358
20218	Agrobacterium tumefaciens gene for 16S rRNA, partial sequence, strain: NBRC 13532	AB680423	1410	358
9167	Agrobacterium tumefaciens genes for 16S rRNA, tRNA-Ile, tRNA-Ala, 23S rRNA 150-b fragment, IVS, 23S rRNA 1.3-kb fragment A, partial and complete sequence, strain: IAM 12048	AB247615	2738	358
124043	Agrobacterium radiobacter DSM 30147 partial 16S rRNA gene, isolate N-67	LS999519	1350	1336745

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Agrobacterium radiobacter DSM 30147
NCBI: GCA_000421945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	yes	58.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agrobacterium radiobacter DSM 30147
PATRIC: 1336745.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.56	no
125438	anaerobic	anaerobicⓘ	no	94.84	yes
125438	spore-forming	spore-formingⓘ	no	89.66	no
125438	aerobic	aerobicⓘ	yes	82.59	yes
125438	thermophilic	thermophileⓘ	no	97.20	yes
125438	flagellated	motile2+ⓘ	yes	63.41	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Exploring gingerol glucosides with enhanced anti-inflammatory activity through a newly identified alpha-glucosidase (ArG) from Agrobacterium radiobacter DSM 30147.	Chang TS, Wu JY, Ding HY, Lin HY, Wang TY.	J Biosci Bioeng	10.1016/j.jbiosc.2024.06.004	2024
	Enzymatic Glycosylation of Ganoderma Terpenoid via Bacterial Glycosyltransferases and Glycoside Hydrolases.	Chang TS, Wu JY, Ding HY, Wang TY.	Biomolecules	10.3390/biom15050655	2025
	Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach.	Hiergeist A, Ruelle J, Emler S, Gessner A.	PLoS One	10.1371/journal.pone.0280870	2023
Metabolism	In silico analysis of the chemotactic system of Agrobacterium tumefaciens.	Xu N, Wang M, Yang X, Xu Y, Guo M.	Microb Genom	10.1099/mgen.0.000460	2020
Enzymology	Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans.	Han ND, Cheng J, Delannoy-Bruno O, Webber D, Terrapon N, Henrissat B, Rodionov DA, Arzamasov AA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Desai C, Marion S, Barratt MJ, Heath AC, Gordon JI.	Cell	10.1016/j.cell.2022.06.004	2022
Metabolism	The biofilm of Burkholderia cenocepacia H111 contains an exopolysaccharide composed of l-rhamnose and l-mannose: Structural characterization and molecular modelling.	Bellich B, Jou IA, Buriola C, Ravenscroft N, Brady JW, Fazli M, Tolker-Nielsen T, Rizzo R, Cescutti P.	Carbohydr Res	10.1016/j.carres.2020.108231	2021
	In vivo manipulation of human gut Bacteroides fitness by abiotic oligosaccharides.	Wesener DA, Beller ZW, Hill MF, Yuan H, Belanger DB, Frankfater C, Terrapon N, Henrissat B, Rodionov DA, Leyn SA, Osterman A, van Hylckama Vlieg JET, Gordon JI.	Nat Chem Biol	10.1038/s41589-024-01763-6	2025
	Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition.	Barratt MJ, Nuzhat S, Ahsan K, Frese SA, Arzamasov AA, Sarker SA, Islam MM, Palit P, Islam MR, Hibberd MC, Hibberd MC, Nakshatri S, Cowardin CA, Guruge JL, Byrne AE, Venkatesh S, Sundaresan V, Henrick B, Duar RM, Mitchell RD, Casaburi G, Prambs J, Flannery R, Mahfuz M, Rodionov DA, Osterman AL, Kyle D, Ahmed T, Gordon JI.	Sci Transl Med	10.1126/scitranslmed.abk1107	2022
	Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition.	Chang HW, Lee EM, Wang Y, Zhou C, Pruss KM, Henrissat S, Chen RY, Kao C, Hibberd MC, Lynn HM, Webber DM, Crane M, Cheng J, Rodionov DA, Arzamasov AA, Castillo JJ, Couture G, Chen Y, Balcazo NP, Lebrilla CB, Terrapon N, Henrissat B, Ilkayeva O, Muehlbauer MJ, Newgard CB, Mostafa I, Das S, Mahfuz M, Osterman AL, Barratt MJ, Ahmed T, Gordon JI.	Nat Microbiol	10.1038/s41564-024-01628-7	2024
	Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo.	Wesener DA, Beller ZW, Peters SL, Rajabi A, Dimartino G, Giannone RJ, Hettich RL, Gordon JI.	Elife	10.7554/elife.64478	2021
Metabolism	Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium.	Wolf AR, Wesener DA, Cheng J, Houston-Ludlam AN, Beller ZW, Hibberd MC, Giannone RJ, Peters SL, Hettich RL, Leyn SA, Rodionov DA, Osterman AL, Gordon JI.	Cell Host Microbe	10.1016/j.chom.2019.09.001	2019
Metabolism	Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition.	Weagley JS, Zaydman M, Venkatesh S, Sasaki Y, Damaraju N, Yenkin A, Buchser W, Rodionov DA, Osterman A, Ahmed T, Barratt MJ, DiAntonio A, Milbrandt J, Gordon JI.	Cell Rep	10.1016/j.celrep.2022.110738	2022
Metabolism	Genes and enzymes of azetidine-2-carboxylate metabolism: detoxification and assimilation of an antibiotic.	Gross C, Felsheim R, Wackett LP.	J Bacteriol	10.1128/jb.02022-07	2008
	Differentiation of gram-negative, nonfermentative bacteria isolated from biofilters on the basis of Fatty Acid composition, quinone system, and physiological reaction profiles.	Lipski A, Klatte S, Bendinger B, Altendorf K.	Appl Environ Microbiol	10.1128/aem.58.6.2053-2065.1992	1992
	Case of bacterial endophthalmitis caused by an Agrobacterium radiobacter-like organism.	Miller JM, Novy C, Hiott M.	J Clin Microbiol	10.1128/jcm.34.12.3212-3213.1996	1996
	Differentiating Indigenous Soybean Bradyrhizobium and Rhizobium spp. of Indian Soils.	Ansari PG, Rao DL.	Indian J Microbiol	10.1007/s12088-013-0430-z	2014
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
Enzymology	Superiority of molecular techniques for identification of gram-negative, oxidase-positive rods, including morphologically nontypical Pseudomonas aeruginosa, from patients with cystic fibrosis.	Wellinghausen N, Kothe J, Wirths B, Sigge A, Poppert S.	J Clin Microbiol	10.1128/jcm.43.8.4070-4075.2005	2005
Phylogeny	Comparison of thirty-seven strains of Vd-3 bacteria with Agrobacterium radiobacter: morphological and physiological observations.	Riley PS, Weaver RE.	J Clin Microbiol	10.1128/jcm.5.2.172-177.1977	1977
	Growth of Escherichia coli in model distribution system biofilms exposed to hypochlorous acid or monochloramine.	Williams MM, Braun-Howland EB.	Appl Environ Microbiol	10.1128/aem.69.9.5463-5471.2003	2003
	PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid.	Greisen K, Loeffelholz M, Purohit A, Leong D.	J Clin Microbiol	10.1128/jcm.32.2.335-351.1994	1994
	NMR analysis of succinoglycans from different microbial sources: partial assignment of their 1H and 13C NMR spectra and location of the succinate and the acetate groups.	Matulova M, Toffanin R, Navarini L, Gilli R, Paoletti S, Cesaro A.	Carbohydr Res	10.1016/0008-6215(94)00227-4	1994
Genetics	Draft genome sequence of Agrobacterium pusense strain CMT1: A promising growth-promoting bacterium isolated from nodules of soybean (Glycine max L. Merrill) crops for the One Health approach in Paraguay.	Samudio Oggero A, Valdez Borda M, Felix Pablos CM, Leguizamon G, Morinigo FM, Gonzalez Caballero V, Farias A, Nakayama H, de Los Santos Villalobos S.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100259	2024
	Draft Genome Sequence of Agrobacterium radiobacter Strain MD22b, Isolated from a Grape Plant in Tajikistan.	Dzhuraeva M, Bobodzhanova K, Javier-Lopez R, Tediashvili M, Jaiani E, Birkeland NK.	Microbiol Resour Announc	10.1128/mra.01131-22	2023
	Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia.	Cummings SP, Gyaneshwar P, Vinuesa P, Farruggia FT, Andrews M, Humphry D, Elliott GN, Nelson A, Orr C, Pettitt D, Shah GR, Santos SR, Krishnan HB, Odee D, Moreira FM, Sprent JI, Young JP, James EK.	Environ Microbiol	10.1111/j.1462-2920.2009.01975.x	2009
Stress	Characterization and rheological properties analysis of the succinoglycan produced by a high-yield mutant of Rhizobium radiobacter ATCC 19358.	Gao H, Yang L, Tian J, Huang L, Huang D, Zhang W, Xie F, Niu Y, Jin M, Jia C, Zou C, Huang J, Chang Z, Yang X, Jiang D	Int J Biol Macromol	10.1016/j.ijbiomac.2020.10.087	2020
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
	Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4.	Gan HM, Lee MVL, Savka MA	PeerJ	10.7717/peerj.6366	2019
	Genomic analysis of Agrobacterium radiobacter DSM 30147(T) and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993.	Zhang L, Li X, Zhang F, Wang G	Stand Genomic Sci	10.4056/sigs.4688352	2014
Phylogeny	Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia.	Humphry DR, Andrews M, Santos SR, James EK, Vinogradova LV, Perin L, Reis VM, Cummings SP	Antonie Van Leeuwenhoek	10.1007/s10482-006-9100-z	2007
Enzymology	Purification and characterization of 2,6-dihydroxybenzoate decarboxylase reversibly catalyzing nonoxidative decarboxylation.	Yoshida T, Hayakawa Y, Matsui T, Nagasawa T	Arch Microbiol	10.1007/s00203-004-0668-2	2004
Biotechnology	Modeling growth and succinoglucan production by Agrobacterium radiobacter NCIB 9042 in batch cultures.	Dussap CG, De Vita D, Pons A	Biotechnol Bioeng	10.1002/bit.260380109	1991
Phylogeny	Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture.	Zhao J, Zhao X, Wang J, Gong Q, Zhang X, Zhang G	Microorganisms	10.3390/microorganisms8040608	2020
Phylogeny	Agrobacterium salinitolerans sp. nov., a saline-alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina.	Yan J, Li Y, Yan H, Chen WF, Zhang X, Wang ET, Han XZ, Xie ZH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001885	2017
Phylogeny	Agrobacterium deltaense sp. nov., an endophytic bacteria isolated from nodule of Sesbania cannabina.	Yan J, Li Y, Han XZ, Chen WF, Zou WX, Xie Z, Li M	Arch Microbiol	10.1007/s00203-017-1367-0	2017
Phylogeny	Rhizobium nepotum sp. nov. isolated from tumors on different plant species.	Pulawska J, Willems A, De Meyer SE, Sule S	Syst Appl Microbiol	10.1016/j.syapm.2012.03.001	2012
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
Phylogeny	Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Muller 1986 as Rhizobium aggregatum comb. nov.	Kaur J, Verma M, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.017491-0	2010
Phylogeny	Rhizobium borbori sp. nov., aniline-degrading bacteria isolated from activated sludge.	Zhang GX, Ren SZ, Xu MY, Zeng GQ, Luo HD, Chen JL, Tan ZY, Sun GP	Int J Syst Evol Microbiol	10.1099/ijs.0.022228-0	2010

References

#9167	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30147
#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 )
#37042	; Curators of the CIP;
#44648	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 3354
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#122119	Collection of Institut Pasteur ; Curators of the CIP; CIP 104325
#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 radiobacter (DSM 30147, ATCC 19358, IFO 13532)

Name and taxonomic classification

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Physiology and metabolism

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