Agrobacterium skierniewicense (DSM 26438, CFBP 7420, HAMBI 3460)

Name: Agrobacterium skierniewicense (DSM 26438, CFBP 7420, HAMBI 3460)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13647

Type strain

Strain Designation Ch11

Culture col. no. DSM 26438 CFBP 7420 HAMBI 3460 LMG 26191 Ch11

NCBI tax ID(s) 984260

Special Collections DSMZ Literature strains

History DSMZ <- LMG <- J. Pulawska; Ch11

Links

Agrobacterium skierniewicense Ch11 is an aerobe, Gram-negative, rod-shaped plant pathogen that was isolated from gall on chrysanthemum.

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

Name and taxonomic classification

SI-ID 376037

DSM 26438,LMG 26191,CFBP 7420

@ref 20215

Last LPSN update 2026-05-29 08:28:05

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Agrobacterium

Species Agrobacterium skierniewicense

Full scientific name Agrobacterium skierniewicense (Pulawska et al. 2012) Mousavi et al. 2016

Synonyms (1)

Rhizobium skierniewicense

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30286	negative	2.5-3.0 µm	0.5 µm	rod-shaped
125439	negative				97.644
125438	negative				99.333

Colony morphology

18222

Incubation period3-7 days

Pigmentation

30286

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18222	RHIZOBIUM MEDIUM (DSMZ Medium 98)		Medium recipe at MediaDive	Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
18222	positive	growth	30
30286	positive	growth	26

Physiology and metabolism

Oxygen tolerance

30286

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
30286
125439		99.682
125438		90.12

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30286	NaCl	positive	growth	2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30286	37054 ChEBI	3-hydroxybutyrate	+	carbon source
30286	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
30286	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
30286	22653 ChEBI	asparagine	+	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
30286	28757 ChEBI	fructose	+	carbon source
30286	33984 ChEBI	fucose	+	carbon source
30286	24148 ChEBI	galactonate	+	carbon source
30286	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
30286	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
30286	17234 ChEBI	glucose	+	carbon source
30286	29987 ChEBI	glutamate	+	carbon source
30286	17754 ChEBI	glycerol	+	carbon source
30286	17596 ChEBI	inosine	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
30286	18403 ChEBI	L-arabitol	+	carbon source
30286	17716 ChEBI	lactose	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
30286	15792 ChEBI	malonate	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
30286	29864 ChEBI	mannitol	+	carbon source
30286	37684 ChEBI	mannose	+	carbon source
30286	28053 ChEBI	melibiose	+	carbon source
30286	37657 ChEBI	methyl D-glucoside	+	carbon source
30286	17268 ChEBI	myo-inositol	+	carbon source
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
30286	18257 ChEBI	ornithine	+	carbon source
30286	26271 ChEBI	proline	+	carbon source
30286	26490 ChEBI	quinate	+	carbon source
30286	26546 ChEBI	rhamnose	+	carbon source
30286	15963 ChEBI	ribitol	+	carbon source
30286	30031 ChEBI	succinate	+	carbon source
30286	17992 ChEBI	sucrose	+	carbon source
30286	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
30286	16704 ChEBI	uridine	+	carbon source
30286	18222 ChEBI	xylose	+	carbon source

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
30286	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
18222	catalase	-	1.11.1.6
30286	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
18222	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
18222	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+	-	-	+	-	-	+
18222	-	-	-	-	+	+	-	+	+	+	+	+	+/-	+	+	-	-	+	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Infection	#Plant infections	#Gall

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
18222	gall on chrysanthemum	Skierniewice	Poland	POL	Europe

Taxonmaps

69479

Global distribution of 16S sequence HQ823551 (>99% sequence identity) for Agrobacterium from Microbeatlas

Aquatic Samples	101
Soil Samples	173
Animal Samples	477
Plant Samples	797
Total Samples	1548

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
18222		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	Rhizobium skierniewicense DSM 26438	complete			2738541311	984260	87.91
66792	ASM1419651v1 assembly for Rhizobium skierniewicense DSM 26438	contig	GCA_014196515	984260.5	2829908084	984260	72.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18222	Rhizobium skierniewicense strain Ch11 16S ribosomal RNA gene, partial sequence	HQ823551	1400		1368417

GC content

18222

GC-content (mol%)57.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1419651v1 assembly for Rhizobium skierniewicense DSM 26438
NCBI: GCA_014196515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	86.23	no
125439	motility	BacteriaNetⓘ	yes	53.79	no
125439	gram_stain	BacteriaNetⓘ	negative	97.64	no
125439	spore_formation	BacteriaNetⓘ	no	99.68	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium skierniewicense strain DSM 26438
PATRIC: 984260.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.33	yes
125438	anaerobic	anaerobicⓘ	no	96.51	yes
125438	aerobic	aerobicⓘ	yes	85.03	no
125438	spore-forming	spore-formingⓘ	no	90.12	yes
125438	thermophilic	thermophileⓘ	no	98.60	yes
125438	flagellated	motile2+ⓘ	yes	68.45	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium skierniewicense sp. nov., isolated from tumours on chrysanthemum and cherry plum.	Pulawska J, Willems A, Sobiczewski P	Int J Syst Evol Microbiol	10.1099/ijs.0.032532-0	2011

References

#18222	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26438
#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 )
#26627	IJSEM 895 2012 ( DOI 10.1099/ijs.0.032532-0 , PubMed 21642489 )
#30286	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 #26627
#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 )

Content

About us

Agrobacterium skierniewicense (DSM 26438, CFBP 7420, HAMBI 3460)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

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

Genome browser: GCA_014196515

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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