Duganella violaceinigra (DSM 15887, CCUG 50881, CIP 108077)

Name: Duganella violaceinigra (DSM 15887, CCUG 50881, CIP 108077)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11377

Type strain

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

NCBI tax ID(s) 1121480 246602

Special Collections DSMZ CCUG KCTC CIP

History <- W.-J. Li <- W.-J. Li and C.-L. Jiang 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 31327 <- WJ Li, China CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 31327

Links

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

Gram-negative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 265457

CIP 108077,KCTC 12193,DSM 15887,CCUG 50881

@ref 20215

Last LPSN update 2026-02-09 11:20:32

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Duganella

Species Duganella violaceinigra

Full scientific name Duganella violaceinigra Li et al. 2004

Synonyms (2)

Pseudoduganella violaceinigra
"Massilia violaceinigrum"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
67771	negative
123851	negative	rod-shaped
125439	negative		99.6
125438	negative		97.4

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6139	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37406	MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
123851	CIP Medium 116	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6139	positive	growth	28
37406	positive	growth	30
59038	positive	growth	30
67771	positive	growth	30
123851	positive	growth	10-30
123851	negative	growth	37
123851	negative	growth	41
123851	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
59038	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
123851	NaCl	positive	growth	0 %
123851	NaCl		growth	2 %
123851	NaCl		growth	4 %
123851	NaCl		growth	6 %
123851	NaCl		growth	8 %
123851	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
123851	16947 ChEBI	citrate	-	carbon source
123851	4853 ChEBI	esculin	+	hydrolysis
123851	606565 ChEBI	hippurate	+	hydrolysis
123851	17632 ChEBI	nitrate	-	reduction
123851	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123851	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
123851	15688 ChEBI	acetoin	-
123851	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
123851	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
123851	beta-galactosidase	-	3.2.1.23
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123851	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
123851	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
123851	gamma-glutamyltransferase	+	2.3.2.2
123851	gelatinase	+
123851	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
123851	lipase	+
68382	lipase (C 14)	+		from API zym
123851	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123851	ornithine decarboxylase	-	4.1.1.17
123851	oxidase	-
123851	phenylalanine ammonia-lyase	+	4.3.1.24
123851	protease	+
68382	trypsin	+	3.4.21.4	from API zym
123851	tryptophan deaminase	-
123851	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123851	-	+	+	+	+	+	+	+	+	-	+	+	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6139	forest soil		Yunnan province	China	CHN	Asia
59038	Soil,forest	2000	Yunnan Province	China	CHN	Asia
67771	From a forest soil		Yunnan Province	China	CHN	Asia
123851	Environment, Soil, forest		Yunnan	China	CHN	Asia	2000

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6139	1	Risk group (German classification) According to TRBA 466
123851	1	Risk group (French 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	ASM42538v1 assembly for Pseudoduganella violaceinigra DSM 15887	scaffold	GCA_000425385	1121480.5	2523533621	1121480	69.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6139	Duganella violaceinigra strain YIM 31327 16S ribosomal RNA gene, partial sequence	AY376163	1439		1121480

GC content

@ref	GC-content (mol%)	Method
6139	62.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoduganella violaceinigra DSM 15887
NCBI: GCA_000425385

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	89.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	80.70	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.40	yes
125438	anaerobic	anaerobicⓘ	no	96.32	yes
125438	aerobic	aerobicⓘ	yes	88.92	no
125438	spore-forming	spore-formingⓘ	no	82.77	no
125438	thermophilic	thermophileⓘ	no	97.49	no
125438	flagellated	motile2+ⓘ	yes	83.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Biotechnology	Recent Advances in Synthetic, Industrial and Biological Applications of Violacein and Its Heterologous Production.	Ahmed A, Ahmad A, Li R, Al-Ansi W, Fatima M, Mushtaq BS, Basharat S, Li Y, Bai Z.	J Microbiol Biotechnol	10.4014/jmb.2107.07045	2021
Enzymology	Purification of Natural Pigments Violacein and Deoxyviolacein Produced by Fermentation Using Yarrowia lipolytica.	Nemer G, Louka N, Rabiller Blandin P, Maroun RG, Vorobiev E, Rossignol T, Nicaud JM, Guenin E, Koubaa M.	Molecules	10.3390/molecules28114292	2023
Metabolism	Use of plate-wash samples to monitor the fates of culturable bacteria in mercury- and trichloroethylene-contaminated soils.	Mera N, Iwasaki K.	Appl Microbiol Biotechnol	10.1007/s00253-007-1152-0	2007
Metabolism	Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field.	Cretoiu MS, Korthals GW, Visser JH, van Elsas JD.	Appl Environ Microbiol	10.1128/aem.01361-13	2013
	Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils.	Gomez Exposito R, de Bruijn I, Postma J, Raaijmakers JM.	Front Microbiol	10.3389/fmicb.2017.02529	2017
Metabolism	Formation of Se (0) nanoparticles by Duganella sp. and Agrobacterium sp. isolated from Se-laden soil of North-East Punjab, India.	Bajaj M, Schmidt S, Winter J.	Microb Cell Fact	10.1186/1475-2859-11-64	2012
	Growth-promoting characteristics of potential nitrogen-fixing bacteria in the root of an invasive plant Ageratina adenophora.	Fang K, Bao ZS, Chen L, Zhou J, Yang ZP, Dong XF, Zhang HB.	PeerJ	10.7717/peerj.7099	2019
Genetics	The Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and L. pneumophila LqsA autoinducer synthases.	Hornung C, Poehlein A, Haack FS, Schmidt M, Dierking K, Pohlen A, Schulenburg H, Blokesch M, Plener L, Jung K, Bonge A, Krohn-Molt I, Utpatel C, Timmermann G, Spieck E, Pommerening-Roser A, Bode E, Bode HB, Daniel R, Schmeisser C, Streit WR.	PLoS One	10.1371/journal.pone.0055045	2013
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 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
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 .
#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 .
#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 )

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Duganella violaceinigra (DSM 15887, CCUG 50881, CIP 108077)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000425385

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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