Name: Duganella danionis E3/2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133214

Type strain:

Species: Duganella danionis

Strain Designation: E3/2

Culture col. no.: LMG 29678, CCM 8698, DSM 103461, CIP 111103

Strain history: CIP <- 2016, P. Kämpfer, Giessen Univ., Giessen, Germany: strain E3/2

NCBI tax ID(s): 1890295 (species)

SI-ID 404155

DSM 103461

Special Collections

Section

When using BacDive for research please cite our paper

Duganella danionis E3/2 is an aerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from zebrafish, Daniorerio.

colony-forming
Gram-negative
motile
rod-shaped
aerobe
chemoorganotroph
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Duganella*
	Species	**Duganella danionis**
	Full Scientific Name (LPSN)	Duganella danionis (Kämpfer et al. 2016) Lu et al. 2020

Synonym

Pseudoduganella danionis

Information on morphological and physiological properties Morphology

[Ref.: #25016]	Gram stain	negative
[Ref.: #118855]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.3
[Ref.: #125438]	Gram stain	negative Confidence in %98.5

[Ref.: #25016]	Cell length	1.6-2.2 µm

[Ref.: #25016]	Cell width	0.9-1.1 µm

[Ref.: #25016]	Cell shape	rod-shaped
[Ref.: #118855]	Cell shape	rod-shaped

[Ref.: #25016]	Motility	yes
[Ref.: #118855]	Motility	no

[Ref.: #25016]	Colony color	beige pigmented
[Ref.: #25016]	Colony shape	circular
[Ref.: #25016]	Incubation period	3 days
[Ref.: #25016]	Cultivation medium used	R2A

[Ref.: #25016]	Pigment production	yes
[Ref.: #25016]	Pigmentation color	beige

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25016]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #25016]

Culture medium growth

[Ref.: #64832]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #64832]

Culture medium growth

[Ref.: #64832]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64832]

Culture medium composition

expand / minimize

[Ref.: #118855]

Culture medium

CIP Medium 566

[Ref.: #118855]

Culture medium growth

[Ref.: #118855]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #25016]		optimum	20-30 °C
[Ref.: #25016]	negative	growth	40 °C
[Ref.: #64832]		growth	25 °C

	Kind of pH		pH
[Ref.: #25016]		optimum	6
[Ref.: #25016]	no	growth	5
[Ref.: #25016]	no	growth	9
[Ref.: #25016]		growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25016]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %98.2

[Ref.: #25016]

Nutrition type

chemoorganotroph

[Ref.: #125439]

Ability of spore formation

no Confidence in %97.3

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25016]	adipate ChEBI	-	assimilation
[Ref.: #25016]	D-glucose ChEBI	-	builds acid from
[Ref.: #25016]	D-mannitol ChEBI	-	assimilation
[Ref.: #25016]	D-mannose ChEBI	-	builds acid from
[Ref.: #25016]	decanoate ChEBI	-	assimilation
[Ref.: #25016]	esculin ChEBI	+	hydrolysis
[Ref.: #25016]	L-arabinose ChEBI	-	builds acid from
[Ref.: #25016]	L-arabinose ChEBI	-	assimilation
[Ref.: #25016]	lactose ChEBI	-	builds acid from
[Ref.: #25016]	malate ChEBI	-	builds acid from
[Ref.: #25016]	maltose ChEBI	-	builds acid from
[Ref.: #25016]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25016]	nitrate ChEBI	+	reduction
[Ref.: #25016]	phenylacetate ChEBI	-	assimilation
[Ref.: #25016]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #25016]	sodium citrate ChEBI	-	assimilation
[Ref.: #25016]	sucrose ChEBI	-	assimilation
[Ref.: #25016]	tryptophan ChEBI	-	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25016]		indole ChEBI	no

	Physiological tests	Metabolite	Indole test
[Ref.: #25016]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25016]	acid phosphatase	+	3.1.3.2
[Ref.: #25016]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25016]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25016]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25016]	beta-galactosidase	-	3.2.1.23
[Ref.: #25016]	beta-glucosidase	+	3.2.1.21
[Ref.: #25016]	catalase	-	1.11.1.6
[Ref.: #25016]	cystine arylamidase	+	3.4.11.3
[Ref.: #25016]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25016]	esterase (C 4)	+
[Ref.: #25016]	esterase lipase (C 8)	+
[Ref.: #25016]	leucine arylamidase	+	3.4.11.1
[Ref.: #25016]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25016]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25016]	urease	-	3.5.1.5
[Ref.: #25016]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #25016]	Sample type/isolated from	zebrafish, Daniorerio

[Ref.: #64832]	Sample type/isolated from	zebrafish (Danio rerio) maintained in E3 medium
[Ref.: #64832]	Country	Chile
[Ref.: #64832]	Country ISO 3 Code	CHL
[Ref.: #64832]	Continent	Middle and South America

[Ref.: #118855]	Sample type/isolated from	Zebrafish, Danio rerio
[Ref.: #118855]	Country	Chile
[Ref.: #118855]	Country ISO 3 Code	CHL
[Ref.: #118855]	Continent	Middle and South America
[Ref.: #118855]	Isolation date	2014-01-02
* marker position based on {}

Isolation sources categories

#Host

#Fishes

#Zebrafish

What are isolation sources categories?

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

[Ref.: #64832]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118855]	Biosafety level	1	Risk group (French classification)

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.: #64832]	Pseudoduganella danionis strain E3/2 16S ribosomal RNA gene, partial sequence	KX427103	1448	GenBank ENA	1890295 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoduganella danionis DSM 103461	GCA_009720775	scaffold	GenBank ENA	1890295 tax ID	*
[Ref.: #66792]	Pseudoduganella danionis strain DSM 103461	1890295.3	wgs	PATRIC	1890295 tax ID	*
[Ref.: #66792]	Pseudoduganella danionis DSM 103461	2914572788	draft	JGI IMG/M	1890295 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudoduganella danionis DSM 103461 NCBI: GCA_009720775.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.5	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.778	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	78.709	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	89.603	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.839	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	84.92	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoduganella danionis DSM 103461 NCBI: GCA_009720775
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	89.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.2

Availability in culture collections External links

[Ref.: #64832]

Culture collection no.

LMG 29678, CCM 8698, DSM 103461, CIP 111103

[Ref.: #91394]

SI-ID 404155

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella.	Lu HB, Cai ZP, Yang YG, Xu MY	Antonie Van Leeuwenhoek	10.1007/s10482-020-01422-5	2020	*
Phylogeny	Pseudoduganella danionis sp. nov., isolated from zebrafish (Danio rerio).	Kampfer P, Irgang R, Busse HJ, Poblete-Morales M, Kleinhagauer T, Glaeser SP, Avendano-Herrera R	Int J Syst Evol Microbiol	10.1099/ijsem.0.001408	2016	*

References

#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 )

#25016

P. I. Kämpfer, R.,Busse, H. J.,Poblete-Morales, M.,Kleinhagauer, T.,Glaeser, S. P.,Avendaño-Herrera, R.: Pseudoduganella danionis sp. nov., isolated from zebrafish (Danio rerio). IJSEM 66: 4671 - 4675 2016 ( DOI 10.1099/ijsem.0.001408 , PubMed 27506663 )

#64832

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103461

#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) .

#91394

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-ID404155.1 )

#118855 Collection of Institut Pasteur ; Curators of the CIP; CIP 111103

#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 .

* These data were automatically processed and therefore are not curated

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Pseudoduganella danionis DSM 103461

Pseudoduganella danionis DSM 103461

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