Name: Pantoea brenneri BD 873
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5015

Type strain:

Species: Pantoea brenneri

Strain Designation: BD 873

Culture col. no.: DSM 24232, LMG 5343

Strain history: <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; BD 873

NCBI tax ID(s): 472694 (species)

SI-ID 3812

LMG 5343, ATCC 29921

Section

Pantoea brenneri BD 873 is a mesophilic bacterium that was isolated from human urethra.

mesophilic
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 brenneri**
	Full Scientific Name (LPSN)	Pantoea brenneri Brady et al. 2010

Information on culture and growth conditions Culture and growth conditions

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Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #17572]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #17572]			growth	30 °C
[Ref.: #17572]			growth	28 °C

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Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[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.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[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.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* 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.: #17572]	17896	+	-	-	-	+	-	-	-	-	-	+	+	+	+	-	+	+	+	+	+	+	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.: #17572]	Sample type/isolated from	human urethra
[Ref.: #17572]	Geographic location (country and/or sea, region)	Montana
[Ref.: #17572]	Country	USA
[Ref.: #17572]	Country ISO 3 Code	USA
[Ref.: #17572]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Urogenital tract	#Urethra
#Infection	#Patient	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ611808 (>99% sequence identity) for Pantoea from Microbeatlas

Aquatic Samples	948
Soil Samples	442
Animal Samples	4423
Plant Samples	1924
Total Samples	7737

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

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Biosafety level

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.: #17572]	Pantoea brenneri strain LMG 5343 16S ribosomal RNA gene, partial sequence	EU216735	1344	ENA	472694 tax ID
[Ref.: #20218]	Pantoea brenneri strain LMG 5343 16S ribosomal RNA gene, partial sequence	FJ611808	1376	ENA	472694 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pantoea brenneri LMG 5343	GCA_002095305	contig	GenBank	472694 tax ID	*
[Ref.: #66792]	Pantoea brenneri strain LMG 5343	472694.3	wgs	PATRIC	472694 tax ID	*
[Ref.: #66792]	Pantoea brenneri LMG 5343	2791355168	draft	JGI IMG/M	472694 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pantoea brenneri strain LMG 5343 PATRIC: 472694.3
[Ref.: #69480]	gram-positive	no	97.994	no
[Ref.: #69480]	anaerobic	no	98.602	no
[Ref.: #69480]	halophile	no	86.944	no
[Ref.: #69480]	spore-forming	no	94.445	no
[Ref.: #69480]	glucose-util	yes	94.851	no
[Ref.: #69480]	aerobic	no	57.458	no
[Ref.: #69480]	flagellated	no	67.091	no
[Ref.: #69480]	thermophile	no	99.062	no
[Ref.: #69480]	motile	yes	90.213	no
[Ref.: #69480]	glucose-ferment	yes	89.51	yes

Availability in culture collections External links

[Ref.: #17572]

Culture collection no.

DSM 24232, LMG 5343

[Ref.: #74510]

SI-ID 3812

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.	Brady CL, Cleenwerck I, Venter SN, Engelbeen K, De Vos P, Coutinho TA	Int J Syst Evol Microbiol	10.1099/ijs.0.017301-0	2009	*

References

#17572

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24232

#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 )

#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) .

#74510

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-ID3812.1 )

* These data were automatically processed and therefore are not curated

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Pantoea brenneri strain LMG 5343

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