Strain identifier

BacDive ID: 11377

Type strain: Yes

Species: Duganella violaceinigra

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

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

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General

@ref: 6139

BacDive-ID: 11377

DSM-Number: 15887

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

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

NCBI tax id

NCBI tax idMatching level
246602species
1121480strain

strain history

@refhistory
6139<- W.-J. Li <- W.-J. Li and C.-L. Jiang
374062003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 31327
67771<- WJ Li, China
123851CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 31327

doi: 10.13145/bacdive11377.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • 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

    @refsynonym
    20215Massilia violaceinigrum
    20215Pseudoduganella violaceinigra

@ref: 6139

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Pseudoduganella

species: Pseudoduganella violaceinigra

full scientific name: Pseudoduganella violaceinigra (Li et al. 2004) Kämpfer et al. 2012

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
67771negative
69480yes96.554
69480negative99.992
123851negativeyesrod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6139NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37406MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
123851CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
6139positivegrowth28mesophilic
37406positivegrowth30mesophilic
59038positivegrowth30mesophilic
67771positivegrowth30mesophilic
123851positivegrowth10-30
123851nogrowth37mesophilic
123851nogrowth41thermophilic
123851nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59038aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.979

halophily

@refsaltgrowthtested relationconcentration
123851NaClpositivegrowth0 %
123851NaClnogrowth2 %
123851NaClnogrowth4 %
123851NaClnogrowth6 %
123851NaClnogrowth8 %
123851NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12385116947citrate-carbon source
1238514853esculin+hydrolysis
123851606565hippurate+hydrolysis
12385117632nitrate-reduction
12385116301nitrite-reduction

metabolite production

  • @ref: 123851
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12385115688acetoin-
12385117234glucose-

enzymes

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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123851-++++++++-++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6139forest soilYunnan provinceChinaCHNAsia
59038Soil,forestYunnan ProvinceChinaCHNAsia2000
67771From a forest soilYunnan ProvinceChinaCHNAsia
123851Environment, Soil, forestYunnanChinaCHNAsia2000

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61391Risk group (German classification)
1238511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6139
  • description: Duganella violaceinigra strain YIM 31327 16S ribosomal RNA gene, partial sequence
  • accession: AY376163
  • length: 1439
  • database: ena
  • NCBI tax ID: 1121480

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella violaceinigra DSM 15887GCA_000425385scaffoldncbi1121480
66792Duganella violaceinigra DSM 158871121480.5wgspatric1121480
66792Pseudoduganella violaceinigra DSM 158872523533621draftimg1121480

GC content

  • @ref: 6139
  • GC-content: 62.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.491no
flagellatedyes76.556no
gram-positiveno98.309yes
anaerobicno98.677yes
aerobicyes90.023no
halophileno96.37no
spore-formingno88.638no
thermophileno99.316yes
glucose-utilyes80.62no
glucose-fermentno88.156no

External links

@ref: 6139

culture collection no.: DSM 15887, CCUG 50881, CIP 108077, KCTC 12193, YIM 31327

straininfo link

  • @ref: 80607
  • straininfo: 265457

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388748Duganella violaceinigra sp. nov., a novel mesophilic bacterium isolated from forest soil.Li WJ, Zhang YQ, Park DJ, Li CT, Xu LH, Kim CJ, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63141-02004Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA/genetics, Hydrogen-Ion Concentration, Microscopy, Microscopy, Electron, Molecular Sequence Data, Movement, Oxalobacteraceae/*classification/cytology/*isolation & purification/physiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial, Temperature, Ubiquinone/analysisEnzymology
Phylogeny22169565Duganella 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 NSyst Appl Microbiol10.1016/j.syapm.2011.10.0032011Bacterial Typing Techniques, Carbon/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/chemistry/*classification/genetics/*isolation & purification, Phospholipids/analysis, Phylogeny, Plant Leaves/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Trifolium/*microbiologyGenetics
Pathogenicity26489441High-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 RJSci Rep10.1038/srep155982015Anti-Bacterial Agents/*administration & dosage/chemistry/metabolism, Bacterial Typing Techniques, Humans, Indoles/*administration & dosage/chemistry/metabolism, Methicillin-Resistant Staphylococcus aureus/*drug effects/pathogenicity, Oxalobacteraceae/chemistry/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Staphylococcal Infections/*drug therapy/microbiologyPhylogeny
Phylogeny29087279Psedoduganella eburnea sp. nov., isolated from lagoon sediments.Jin DH, Subhash Y, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0024602017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, North Carolina, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyTranscriptome
Phylogeny32361957Duganella 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 MYAntonie Van Leeuwenhoek10.1007/s10482-020-01422-52020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genome, Bacterial, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phosphatidylethanolamines, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitle
6139Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15887)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15887
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
37406Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5659
59038Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50881)https://www.ccug.se/strain?id=50881
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80607Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265457.1StrainInfo: A central database for resolving microbial strain identifiers
123851Curators of the CIPCollection of Institut Pasteur (CIP 108077)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108077