Allorhizobium borbori (DSM 26385, CICC 10378, HAMBI 3454)

Name: Allorhizobium borbori (DSM 26385, CICC 10378, HAMBI 3454)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13641

Type strain

Strain Designation DN316

Culture col. no. DSM 26385 CICC 10378 HAMBI 3454 LMG 23925 DN316

NCBI tax ID(s) 485907

Special Collections DSMZ Literature strains

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Allorhizobium borbori DN316 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from activated sludge of a textile-printing wastewater-treatment plant.

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

Name and taxonomic classification

SI-ID 377102

DSM 26385,LMG 23925,DSM 22790,LMG 25371

@ref 20215

Last LPSN update 2025-12-16 09:50:08

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Allorhizobium

Species Allorhizobium borbori

Full scientific name Allorhizobium borbori (Zhang et al. 2011) Mousavi et al. 2016

Synonyms (2)

"Ectorhizobium borbori"
Rhizobium borbori

Morphology

Cell morphology

@ref	Gram stain	Cell shape
29839	negative	rod-shaped
125439	negative
125438	negative

Colony morphology

@ref	Type of hemolysis	Incubation period
18209	gamma	1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18209	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
18209	positive	growth	30	mesophilic
29839	positive	growth	4.0-37
29839	positive	optimum	28	mesophilic

Culture pH

@ref	Ability	Type	PH
29839	positive	optimum	6.9
29839	positive	growth	5.0-9.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29839	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
29839
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29839	NaCl	positive	growth	0.0-0.5 %
29839	NaCl	positive	optimum	0.25 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29839	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
29839	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
29839	17057 ChEBI	cellobiose	+	carbon source
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
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
29839	28757 ChEBI	fructose	+	carbon source
29839	33984 ChEBI	fucose	+	carbon source
29839	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
29839	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
29839	18403 ChEBI	L-arabitol	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
29839	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
29839	29864 ChEBI	mannitol	+	carbon source
29839	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
29839	17272 ChEBI	propionate	+	carbon source
29839	30911 ChEBI	sorbitol	+	carbon source
29839	17992 ChEBI	sucrose	+	carbon source
29839	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
18209	catalase	+	1.11.1.6
18209	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
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
18209	+	-	-	-	+	+	-	+	+	+	+	+	-	+	-	-	-	+	+	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Industrial
#Engineered	#Waste
#Engineered	#Waste
#Engineered	#Waste

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
18209	activated sludge of a textile-printing wastewater-treatment plant	Guangzhou	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF125187 (>99% sequence identity) for Rhizobiaceae from Microbeatlas

Aquatic Samples	179
Soil Samples	162
Animal Samples	35
Plant Samples	105
Total Samples	481

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18209	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	IMG accession	NCBI tax ID	Score
66792	Rhizobium borbori LMG 23925	complete	2739367697	485907	85.57
66792	ASM1419653v1 assembly for Allorhizobium borbori DSM 26385	scaffold	2829903426	485907	65.21

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18209	Rhizobium borbori strain DN316 16S ribosomal RNA gene, partial sequence	EF125187	1353		485907

GC content

18209

GC-content (mol%)60.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Allorhizobium borbori DSM 26385
NCBI: GCA_014196535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	yes	70.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium borbori DSM 26385
NCBI: GCA_014196535.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	94.54	yes
125438	aerobic	aerobicⓘ	yes	79.30	no
125438	spore-forming	spore-formingⓘ	no	89.28	yes
125438	thermophilic	thermophileⓘ	no	96.63	no
125438	flagellated	motile2+ⓘ	yes	69.16	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica.	Rozahon M, Ismayil N, Hamood B, Erkin R, Abdurahman M, Mamtimin H, Abdukerim M, Lal R, Rahman E	Int J Syst Evol Microbiol	10.1099/ijs.0.061416-0	2014
Phylogeny	Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis).	Kittiwongwattana C, Thawai C	Int J Syst Evol Microbiol	10.1099/ijs.0.051888-0	2013
Phylogeny	Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand.	Ramana CV, Parag B, Girija KR, Ram BR, Ramana VV, Sasikala C	Int J Syst Evol Microbiol	10.1099/ijs.0.041442-0	2012
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

#18209	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26385
#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 )
#29839	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26215 (see below)
#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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Allorhizobium borbori (DSM 26385, CICC 10378, HAMBI 3454)

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

Halophily

Metabolite utilization

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

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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