Name: Duganella violaceinigra DSM 15887
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11377

Type strain:

Species: Duganella violaceinigra

Culture col. no.: DSM 15887, CCUG 50881, CIP 108077, KCTC 12193, YIM 31327

Strain history: CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 31327

NCBI tax ID(s): 1121480 (strain), 246602 (species)

SI-ID 265457

CIP 108077, KCTC 12193, DSM 15887, CCUG 50881

Special Collections

Section

When using BacDive for research please cite our paper

Duganella violaceinigra DSM 15887 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from forest soil.

Gram-negative
aerobe
mesophilic
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 violaceinigra**
	Full Scientific Name (LPSN)	Duganella violaceinigra Li et al. 2004

	Synonym	"Massilia* violaceinigrum"*
	Synonym	Pseudoduganella violaceinigra

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #123851]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.6
[Ref.: #125438]	Gram stain	negative Confidence in %97.4

[Ref.: #123851]	Cell shape	rod-shaped

[Ref.: #123851]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6139]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #6139]

Culture medium growth

[Ref.: #6139]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6139]

Culture medium composition

expand / minimize

[Ref.: #37406]

Culture medium

MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum

[Ref.: #37406]

Culture medium growth

[Ref.: #37406]

Culture medium composition

expand / minimize

[Ref.: #123851]

Culture medium

CIP Medium 116

[Ref.: #123851]

Culture medium growth

[Ref.: #123851]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6139]		growth	28 °C
[Ref.: #37406]		growth	30 °C
[Ref.: #59038]		growth	30 °C
[Ref.: #67771]		growth	30 °C
[Ref.: #123851]		growth	10-30 °C
[Ref.: #123851]	no	growth	37 °C
[Ref.: #123851]	no	growth	41 °C
[Ref.: #123851]	no	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #59038]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #125439]

Ability of spore formation

no Confidence in %99.5

	Salt	Tested relation		Salt conc.
[Ref.: #123851]	NaCl		growth	0	%
[Ref.: #123851]	NaCl	no	growth	2	%
[Ref.: #123851]	NaCl	no	growth	4	%
[Ref.: #123851]	NaCl	no	growth	6	%
[Ref.: #123851]	NaCl	no	growth	8	%
[Ref.: #123851]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #123851]	citrate ChEBI	-	carbon source
[Ref.: #123851]	esculin ChEBI	+	hydrolysis
[Ref.: #123851]	hippurate ChEBI	+	hydrolysis
[Ref.: #123851]	nitrate ChEBI	-	reduction
[Ref.: #123851]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #123851]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #123851]		acetoin ChEBI	-
[Ref.: #123851]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #123851]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #123851]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #123851]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #123851]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #123851]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #123851]	gelatinase	+
[Ref.: #123851]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #123851]	lipase	+
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #123851]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #123851]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #123851]	oxidase	-
[Ref.: #123851]	phenylalanine ammonia-lyase	+	4.3.1.24
[Ref.: #123851]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #123851]	tryptophan deaminase	-
[Ref.: #123851]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #123851]	10865	-	+	+	+	+	+	+	+	+	-	+	+	-	-	-	+	+	-	-	-

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

[Ref.: #6139]	Sample type/isolated from	forest soil
[Ref.: #6139]	Geographic location (country and/or sea, region)	Yunnan province
[Ref.: #6139]	Country	China
[Ref.: #6139]	Country ISO 3 Code	CHN
[Ref.: #6139]	Continent	Asia

[Ref.: #59038]	Sample type/isolated from	Soil,forest
[Ref.: #59038]	Sampling date	2000
[Ref.: #59038]	Geographic location (country and/or sea, region)	Yunnan Province
[Ref.: #59038]	Country	China
[Ref.: #59038]	Country ISO 3 Code	CHN
[Ref.: #59038]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From a forest soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Yunnan Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #123851]	Sample type/isolated from	Environment, Soil, forest
[Ref.: #123851]	Geographic location (country and/or sea, region)	Yunnan
[Ref.: #123851]	Country	China
[Ref.: #123851]	Country ISO 3 Code	CHN
[Ref.: #123851]	Continent	Asia
[Ref.: #123851]	Isolation date	2000
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #6139]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123851]	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.: #6139]	Duganella violaceinigra strain YIM 31327 16S ribosomal RNA gene, partial sequence	AY376163	1439	GenBank ENA	1121480 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoduganella violaceinigra DSM 15887	GCA_000425385	scaffold	GenBank ENA	1121480 tax ID	*
[Ref.: #66792]	Duganella violaceinigra DSM 15887	1121480.5	wgs	PATRIC	1121480 tax ID	*
[Ref.: #66792]	Pseudoduganella violaceinigra DSM 15887	2523533621	draft	JGI IMG/M	1121480 tax ID	*

[Ref.: #6139]

GC-content

62.8 mol%

thermal denaturation, midpoint method (Tm)

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 violaceinigra DSM 15887 DSM 15887 NCBI: GCA_000425385.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.4	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.32	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	88.92	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	82.77	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.491	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	83.272	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoduganella violaceinigra DSM 15887 NCBI: GCA_000425385
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	89.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	80.7

Availability in culture collections External links

[Ref.: #6139]

Culture collection no.

DSM 15887, CCUG 50881, CIP 108077, KCTC 12193, YIM 31327

[Ref.: #80607]

SI-ID 265457

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	Psedoduganella eburnea sp. nov., isolated from lagoon sediments.	Jin DH, Subhash Y, Lee SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.002460	2017	*
Pathogenicity	High-level production of violacein by the newly isolated Duganella violaceinigra str. NI28 and its impact on Staphylococcus aureus.	Choi SY, Kim S, Lyuck S, Kim SB, Mitchell RJ	Sci Rep	10.1038/srep15598	2015	*
Phylogeny	Duganella phyllosphaerae sp. nov., isolated from the leaf surface of Trifolium repens and proposal to reclassify Duganella violaceinigra into a novel genus as Pseudoduganella violceinigra gen. nov., comb. nov.	Kampfer P, Wellner S, Lohse K, Martin K, Lodders N	Syst Appl Microbiol	10.1016/j.syapm.2011.10.003	2011	*
Phylogeny	Duganella violaceinigra sp. nov., a novel mesophilic bacterium isolated from forest soil.	Li WJ, Zhang YQ, Park DJ, Li CT, Xu LH, Kim CJ, Jiang CL	Int J Syst Evol Microbiol	10.1099/ijs.0.63141-0	2004	*

References

#6139

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15887

#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 )

#37406 ; Curators of the CIP;
#59038 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50881

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68382

Automatically annotated from API zym .

#80607

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-ID265457.1 )

#123851 Collection of Institut Pasteur ; Curators of the CIP; CIP 108077

#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 violaceinigra DSM 15887 DSM 15887

Pseudoduganella violaceinigra DSM 15887

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