Strain identifier

BacDive ID: 1939

Type strain: Yes

Species: Burkholderia vietnamiensis

Strain Designation: TVV75

Strain history: CIP <- 1999, CFBP <- LMG <- T. Heulin, CNRS, unidentified <- V. Tran Van, Binh Thanh, Vietnam

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4295

BacDive-ID: 1939

DSM-Number: 11319

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Burkholderia vietnamiensis TVV75 is an aerobe, mesophilic, motile bacterium that was isolated from rice rhizosphere soil.

NCBI tax id

NCBI tax idMatching level
1449978strain
60552species

strain history

@refhistory
4295<- BCCM; LMG 10929 <- T. Heulin; <- T. V. Van; TVV75
67770LMG 10929 <-- T. Heulin CNRS <-- T. V. Van TVV75.
123840CIP <- 1999, CFBP <- LMG <- T. Heulin, CNRS, unidentified <- V. Tran Van, Binh Thanh, Vietnam

doi: 10.13145/bacdive1939.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Burkholderia
  • species: Burkholderia vietnamiensis
  • full scientific name: Burkholderia vietnamiensis Gillis et al. 1995

@ref: 4295

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia vietnamiensis

full scientific name: Burkholderia vietnamiensis Gillis et al. 1995

strain designation: TVV75

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes91.342
6948099.922negative
123840yesnegativerod-shaped

pigmentation

  • @ref: 123840
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4295COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
4295TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
40243MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123840CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4295positivegrowth28mesophilic
40243positivegrowth30mesophilic
51960positivegrowth37mesophilic
67770positivegrowth28mesophilic
123840positivegrowth30-41
123840nogrowth5psychrophilic
123840nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51960aerobe
123840obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.933

halophily

@refsaltgrowthtested relationconcentration
123840NaClpositivegrowth0-2 %
123840NaClnogrowth4 %
123840NaClnogrowth6 %
123840NaClnogrowth8 %
123840NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12384016947citrate+carbon source
1238404853esculin-hydrolysis
12384017632nitrate+reduction
12384016301nitrite-reduction
12384017632nitrate-respiration

antibiotic resistance

  • @ref: 123840
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12384035581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123840oxidase+
123840beta-galactosidase+3.2.1.23
123840alcohol dehydrogenase-1.1.1.1
123840gelatinase-
123840amylase-
123840DNase-
123840caseinase-3.4.21.50
123840catalase+1.11.1.6
123840tween esterase+
123840lecithinase+
123840lipase+
123840lysine decarboxylase-4.1.1.18
123840ornithine decarboxylase-4.1.1.17
123840protease+
123840tryptophan deaminase-
123840urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123840-+++++----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4295+------++++++-++-++++
4295+------++++++-++-+++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123840+++++--+-----+-----+++--+-+--+++++--+--+---++---+++++++++-+++++++--+-+-++++++++++++++-++++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
4295rice rhizosphere soilBinh ThanhVietnamVNMAsia10.8106106.709
51960Soil,rice rhizosphereBinh ThanhVietnamVNMAsia
67770Rice rhizosphere soilBình ThanhVietnamVNMAsia
123840Environment, Rhizosphere soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_198.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_18;97_18;98_21;99_198&stattab=map
  • Last taxonomy: Burkholderia
  • 16S sequence: U96928
  • Sequence Identity:
  • Total samples: 5054
  • soil counts: 1055
  • aquatic counts: 564
  • animal counts: 1930
  • plant counts: 1505

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42952Risk group (German classification)
1238401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia vietnamiensis strain LMG 10929 16S ribosomal RNA gene, partial sequenceAF416383174ena60552
20218Burkholderia vietnamiensis strain LMG 10929 16S ribosomal RNA gene, partial sequenceHQ8491071124ena60552
20218Burkholderia vietnamiensis 16S ribosomal RNA gene, partial sequenceU969281526ena60552
4295Burkholderia vietnamiensis strain LMG 10929 16S ribosomal RNA gene, partial sequenceAF0975341494ena60552

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Burkholderia vietnamiensis LMG 10929GCA_000959445completencbi1449978
66792Burkholderia vietnamiensis LMG 10929GCA_902830295scaffoldncbi60552
66792Burkholderia vietnamiensis LMG 109291449978.3completepatric1449978
66792Burkholderia vietnamiensis LMG 109291449978.4plasmidpatric1449978
66792Burkholderia vietnamiensis strain FDAARGOS_148860552.132completepatric60552
66792Burkholderia vietnamiensis strain LMG 1092960552.72wgspatric60552
66792Burkholderia vietnamiensis LMG 109292636415515completeimg1449978
66792Burkholderia vietnamiensis TVV752582581767draftimg60552
67770Burkholderia vietnamiensis BAA-248GCA_001527445contigncbi60552
66792Burkholderia vietnamiensis strain FDAARGOS_148860552.174completepatric60552
66792Burkholderia vietnamiensis strain FDAARGOS_148860552.136completepatric60552
66792Burkholderia vietnamiensis strain FDAARGOS_148860552.154completepatric60552

GC content

  • @ref: 67770
  • GC-content: 67.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.422no
flagellatedno86.179no
gram-positiveno98.277no
anaerobicno98.338no
aerobicyes88.035no
halophileno95.767no
spore-formingno94.823no
glucose-utilyes90.209no
thermophileno99.436yes
glucose-fermentno88.652no

External links

@ref: 4295

culture collection no.: CCUG 34169, DSM 11319, LMG 10929, JCM 10562, ATCC BAA 248, CCM 4901, CIP 105875, KCTC 2974, NCIMB 13446, CFBP 4796

straininfo link

  • @ref: 71584
  • straininfo: 10342

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11375196Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution.Estrada-De Los Santos P, Bustillos-Cristales R, Caballero-Mellado JAppl Environ Microbiol10.1128/AEM.67.6.2790-2798.20012001Bacterial Proteins/isolation & purification, Bacterial Typing Techniques, Burkholderia/classification/genetics/*metabolism, Coffee/*microbiology, DNA, Bacterial/genetics, Genes, Bacterial, Geography, Magnoliopsida/microbiology, Mexico, Nitrogen Fixation/*genetics, Phenotype, Plant Roots/*microbiology, *Soil Microbiology, Zea mays/*microbiologyPhenotype
Pathogenicity11425720Effects of rice seed surface sterilization with hypochlorite on inoculated Burkholderia vietnamiensis.Miche L, Balandreau JAppl Environ Microbiol10.1128/AEM.67.7.3046-3052.20012001Anti-Bacterial Agents/pharmacology, Burkholderia/drug effects/genetics/*growth & development, Colony Count, Microbial, DNA Gyrase, DNA Topoisomerases, Type II/genetics, DNA-Directed RNA Polymerases/genetics, Drug Resistance, Microbial/genetics, Hydrogen Peroxide/pharmacology, Hypochlorous Acid/*pharmacology, Molecular Sequence Data, Mutation, Nalidixic Acid/pharmacology, Oryza/drug effects/growth & development/*microbiology, Polymerase Chain Reaction, Rifampin/pharmacology, Seeds/drug effects/*microbiology, Sterilization/*methodsGenetics
Phylogeny11846770Detection and activity of insertion sequences in environmental strains of Burkholderia.Miche L, Faure D, Blot M, Cabanne-Giuli E, Balandreau JEnviron Microbiol10.1046/j.1462-2920.2001.00251.x2001Blotting, Southern, Burkholderia/classification/*genetics, DNA Transposable Elements/*genetics, *Genes, Bacterial, Molecular Sequence Data, Phylogeny, Polymorphism, Restriction Fragment Length, Statistics as TopicGenetics
Phylogeny17406771Effects of the inoculation of Burkholderia vietnamensis and related endophytic diazotrophic bacteria on grain yield of rice.Govindarajan M, Balandreau J, Kwon SW, Weon HY, Lakshminarasimhan CMicrob Ecol10.1007/s00248-007-9247-92007Burkholderia/classification/genetics/*growth & development/isolation & purification, Colony Count, Microbial, Crops, Agricultural, Culture Media, Genes, rRNA, Gram-Negative Bacteria/classification/genetics/*growth & development/isolation & purification, India, Molecular Sequence Data, *Nitrogen Fixation, Oryza/*growth & development/*microbiology, Phylogeny, Plant Roots/microbiology, Plant Shoots/microbiology, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNAEnzymology
Phylogeny21349327Five novel acid-tolerant oligotrophic thiosulfate-metabolizing chemolithotrophic acid mine drainage strains affiliated with the genus Burkholderia of Betaproteobacteria and identification of two novel soxB gene homologues.Bhowal S, Chakraborty RRes Microbiol10.1016/j.resmic.2011.02.0072011Acids/*metabolism, Bacterial Proteins/*genetics/metabolism, Betaproteobacteria/classification/genetics/isolation & purification/metabolism, Burkholderia/classification/genetics/*isolation & purification/metabolism, Chemoautotrophic Growth, Mining, Molecular Sequence Data, Phylogeny, Thiosulfates/*metabolismMetabolism
Pathogenicity23544536Structure of a novel exopolysaccharide produced by Burkholderia vietnamiensis, a cystic fibrosis opportunistic pathogen.Cescutti P, Cuzzi B, Herasimenka Y, Rizzo RCarbohydr Polym10.1016/j.carbpol.2013.01.0472013Burkholderia cepacia complex/*metabolism, Carbohydrate Conformation, Carbohydrate Sequence, Cystic Fibrosis/microbiology, Humans, Hydrolysis, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Opportunistic Infections/microbiology, Polysaccharides, Bacterial/biosynthesis/*chemistry, Spectrometry, Mass, Electrospray IonizationGenetics
Pathogenicity35862731Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp. japonica and O. sativa subsp. indica, as Revealed by Transposon Mutagenesis Sequencing.Wallner A, Busset N, Lachat J, Guigard L, King E, Rimbault I, Mergaert P, Bena G, Moulin LAppl Environ Microbiol10.1128/aem.00642-222022Animals, *Burkholderia/metabolism, *Burkholderia cepacia complex/genetics, *Burkholderiaceae/genetics, Humans, Mutagenesis, Insertional, *Oryza/microbiology, Plants/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4295Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11319)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11319
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40243Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17942
51960Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34169)https://www.ccug.se/strain?id=34169
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
71584Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10342.1StrainInfo: A central database for resolving microbial strain identifiers
123840Curators of the CIPCollection of Institut Pasteur (CIP 105875)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105875