Name: Pantoea vagans BD 765
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5011

Type strain:

Species: Pantoea vagans

Strain Designation: BD 765, R-21566

Culture col. no.: DSM 23078, BCC 105, LMG 24199

Strain history: <- T. A. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; R-21566

NCBI tax ID(s): 470934 (species)

SI-ID 127387

BCC105, LMG 24199, BCC 005

Section

Pantoea vagans BD 765 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from Eucalyptus sp..

Gram-negative
motile
facultative anaerobe
mesophilic
plant pathogen
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Erwiniaceae*
	Genus	*Pantoea*
	Species	**Pantoea vagans**
	Full Scientific Name (LPSN)	Pantoea vagans Brady et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29239]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.986

[Ref.: #29239]	Cell length	1.5-3.0 µm

[Ref.: #29239]	Cell width	0.9 µm

[Ref.: #29239]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.606

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16695]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #16695]

Culture medium growth

[Ref.: #16695]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16695]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #16695]			growth	28 °C

[Ref.: #16695]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29239]

Oxygen tolerance

facultative anaerobe

[Ref.: #29239]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.963

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29239]	alanine ChEBI	+	carbon source
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #29239]	arabinose ChEBI	+	carbon source
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #29239]	aspartate ChEBI	+	carbon source
[Ref.: #29239]	cellobiose ChEBI	+	carbon source
[Ref.: #29239]	citrate ChEBI	+	carbon source
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #29239]	fructose ChEBI	+	carbon source
[Ref.: #29239]	galactose ChEBI	+	carbon source
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #29239]	glucose ChEBI	+	carbon source
[Ref.: #29239]	glutamate ChEBI	+	carbon source
[Ref.: #29239]	glycerol ChEBI	+	carbon source
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #29239]	malonate ChEBI	+	carbon source
[Ref.: #29239]	maltose ChEBI	+	carbon source
[Ref.: #29239]	mannitol ChEBI	+	carbon source
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	+	fermentation	* from API 20E
[Ref.: #29239]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #29239]	ornithine ChEBI	+	carbon source
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #29239]	proline ChEBI	+	carbon source
[Ref.: #29239]	rhamnose ChEBI	+	carbon source
[Ref.: #29239]	ribose ChEBI	+	carbon source
[Ref.: #29239]	serine ChEBI	+	carbon source
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #29239]	succinate ChEBI	+	carbon source
[Ref.: #29239]	sucrose ChEBI	+	carbon source
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #29239]	trehalose ChEBI	+	carbon source
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #29239]	tween 40 ChEBI	+	carbon source
[Ref.: #29239]	tween 80 ChEBI	+	carbon source
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
[Ref.: #29239]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	+		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #16695]	18043	+	-	-	-	+	-	-	-	-	+	+	+	+	+	-	+	+	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16695]	Sample type/isolated from	Eucalyptus sp.
[Ref.: #16695]	Host species	Eucalyptus
[Ref.: #16695]	Country	Uganda
[Ref.: #16695]	Country ISO 3 Code	UGA
[Ref.: #16695]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host	#Plants	#Tree

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY173021 (>99% sequence identity) for Pantoea ananatis from Microbeatlas

Aquatic Samples	764
Soil Samples	845
Animal Samples	5045
Plant Samples	2149
Total Samples	8803

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16695]	Pathogenicity (plant)	yes
[Ref.: #16695]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16695]	Pantoea vagans strain LMG 24199 16S ribosomal RNA gene, partial sequence	EF688012	1429	ENA	470934 tax ID
[Ref.: #20218]	Pantoea ananatis strain BCC0105 16S ribosomal RNA gene, partial sequence	AY173021	1325	ENA	553 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pantoea vagans LMG 24199	GCA_004792415	complete	GenBank	470934 tax ID	*
[Ref.: #66792]	Pantoea vagans strain LMG 24199	470934.52	complete	PATRIC	470934 tax ID	*
[Ref.: #66792]	Pantoea vagans LMG 24199	2844050306	complete	JGI IMG/M	470934 tax ID	*

[Ref.: #16695]	GC-content	55.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29239]	GC-content	55.4 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pantoea vagans LMG 24199 NCBI: GCA_004792415.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pantoea vagans LMG 24199 NCBI: GCA_004792415.1
[Ref.: #69480]	motile	yes	92.552	yes
[Ref.: #69480]	flagellated	no	65.168	no
[Ref.: #69480]	gram-positive	no	97.915	no
[Ref.: #69480]	anaerobic	no	98.821	yes
[Ref.: #69480]	aerobic	no	73.348	yes
[Ref.: #69480]	halophile	no	85.557	no
[Ref.: #69480]	spore-forming	no	94.136	yes
[Ref.: #69480]	glucose-util	yes	95.356	yes
[Ref.: #69480]	thermophile	no	99.251	no
[Ref.: #69480]	glucose-ferment	yes	89.791	yes

Availability in culture collections External links

[Ref.: #16695]

Culture collection no.

DSM 23078, BCC 105, LMG 24199

[Ref.: #74506]

SI-ID 127387

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov.	Brady CL, Venter SN, Cleenwerck I, Engelbeen K, Vancanneyt M, Swings J, Coutinho TA	Int J Syst Evol Microbiol	10.1099/ijs.0.009241-0	2009	*

References

#16695

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23078

#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 )

#29239

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 #25659 (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) .

#68368

Automatically annotated from API 20E .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#74506

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID127387.1 )

#25659

IJSEM 2339 2009 ( DOI 10.1099/ijs.0.009241-0 , PubMed 19620357 )

* These data were automatically processed and therefore are not curated

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Pantoea vagans LMG 24199

Pantoea vagans LMG 24199

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