Bradyrhizobium betae (DSM 17288, CECT 5829, LMG 21987)

Name: Bradyrhizobium betae (DSM 17288, CECT 5829, LMG 21987)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1813

Type strain

Strain Designation P17Hg1, PL7HG1

Culture col. no. DSM 17288 CECT 5829 LMG 21987 NBRC 103048 CCUG 55850 2 more

NCBI tax ID(s) 244734

Special Collections DSMZ CCUG Literature strains

History DSMZ <- E. Velázquez, Univ. Salamanca, Spain; P17Hg1

Links

Bradyrhizobium betae P17Hg1 is an aerobe, Gram-negative bacterium that was isolated from roots of sugar beet Beta vulgaris affected by tumour-like deformations.

Gram-negative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 128240

LMG 21987,CECT 5829,DSM 17288,NBRC 103048,CCUG 55850T

@ref 20215

Last LPSN update 2026-05-29 08:25:21

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Nitrobacteraceae

Genus Bradyrhizobium

Species Bradyrhizobium betae

Full scientific name Bradyrhizobium betae Rivas et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Confidence
23328	negative
125439	negative	91.337
125438	negative	97.8

Colony morphology

@ref	Colony color	Medium used
23328	pearl white	YMA

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6873	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
23328	YMA

Culture temp

@ref	Growth	Type	Temperature (°C)
6873	positive	growth	28
23328	positive	optimum	28
60755	positive	growth	30

Culture pH

@ref	Ability	Type	PH
23328	positive	optimum	7.0-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
60755	aerobe
125439	obligate aerobe	98.74

Spore formation

@ref	Spore formation	Confidence
125439		98.459

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
23328	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
23328	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
23328	17234 ChEBI	glucose	+	carbon source
23328	30849 ChEBI	L-arabinose	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
23328	62345 ChEBI	L-rhamnose	-	growth
23328	17266 ChEBI	L-sorbose	+	carbon source
23328	17716 ChEBI	lactose	-	growth
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
23328	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
23328	29864 ChEBI	mannitol	+	carbon source
23328	37684 ChEBI	mannose	+	carbon source
23328	506227 ChEBI	N-acetylglucosamine	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
23328	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
23328	16634 ChEBI	raffinose	-	growth
23328	15963 ChEBI	ribitol	-	growth
23328	17992 ChEBI	sucrose	-	growth
23328	27082 ChEBI	trehalose	-	growth
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.	Intermediate conc.
23328	2676	amoxicillin
23328	3515	cefuroxime	30 µg
23328	100241	ciprofloxacin	5 µg
23328	49566	cloxacillin		1 µg
23328	48923	erythromycin			2 µg
23328	17833	gentamicin		10 µg
23328	7507	neomycin	5 µg
23328	27701	oxytetracycline		30 µg
23328	17334	penicillin		10 Unit
23328	8309	polymyxin b		300 Unit

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
23328	6-phospho-beta-galactosidase	+	3.2.1.85
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
23328	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

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
60755	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	-	-
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
6873	roots of sugar beet Beta vulgaris affected by tumour-like deformations	Beta vulgaris		northern Spain	Spain	ESP	Europe
60755	Beta vulgaris tumor-like deformations	Beta vulgaris	2002	Salamanca	Spain	ESP	Europe

Taxonmaps

69479

Global distribution of 16S sequence AY372184 (>99% sequence identity) for Bradyrhizobium from Microbeatlas

Aquatic Samples	2827
Soil Samples	5001
Animal Samples	4320
Plant Samples	739
Total Samples	12887

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6873	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM893211v1 assembly for Bradyrhizobium betae PL7HG1	complete	GCA_008932115	244734.9	8109381866	244734	95.02
66792	ASM2480687v1 assembly for Bradyrhizobium betae CECT 5829	contig	GCA_024806875	244734.18	2824350403	244734	71.19

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bradyrhizobium betae gene for 16S rRNA, partial sequence, strain: NBRC 103048	AB681928	1414	244734
20218	Bradyrhizobium betae internal transcribed spacer between 16S and 23S rRNA genes	AJ631967	789	244734
6873	Bradyrhizobium betae 16S ribosomal RNA gene, partial sequence	AY372184	1483	244734

GC content

@ref	GC-content (mol%)	Method
6873	63.7
23328	63.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM893211v1 assembly for Bradyrhizobium betae PL7HG1
BV-BRC: 244734.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.74	no
125439	gram_stain	BacteriaNetⓘ	negative	91.34	no
125439	motility	BacteriaNetⓘ	yes	56.01	no
125439	spore_formation	BacteriaNetⓘ	no	98.46	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bradyrhizobium betae PL7HG1
NCBI: GCA_008932115.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.80	yes
125438	anaerobic	anaerobicⓘ	no	90.93	no
125438	aerobic	aerobicⓘ	yes	85.13	yes
125438	spore-forming	spore-formingⓘ	no	84.84	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	yes	76.21	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis.	Azevedo H, Lopes F, Silla P, Hungria M.	BMC Genomics	10.1186/1471-2164-16-s5-s10	2015
	Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae.	Stepkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP.	Genes (Basel)	10.3390/genes9030163	2018
Genetics	Analysis of the Complete Genome Sequence of the Widely Studied Strain Bradyrhizobium betae PL7HG1(T) Reveals the Presence of Photosynthesis Genes and a Putative Plasmid.	Cloutier S, Bromfield ESP	Microbiol Resour Announc	10.1128/MRA.01282-19	2019
Phylogeny	Bradyrhizobium daqingense sp. nov., isolated from soybean nodules.	Wang JY, Wang R, Zhang YM, Liu HC, Chen WF, Wang ET, Sui XH, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.034280-0	2012
Phylogeny	Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations.	Rivas R, Willems A, Palomo JL, Garcia-Benavides P, Mateos PF, Martinez-Molina E, Gillis M, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.02971-0	2004

References

#6873	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17288
#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 )
#23328	Raúl Rivas, Anne Willems, José Luis Palomo, Pablo García-Benavides, Pedro F. Mateos, Eustoquio Martínez-Molina, Monique Gillis, Encarna Velázquez: Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations. IJSEM 54: 1271 - 1275 2004 ( DOI 10.1099/ijs.0.02971-0 , PubMed 15280302 )
#60755	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55850
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#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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About us

Bradyrhizobium betae (DSM 17288, CECT 5829, LMG 21987)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_008932115

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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