Strain identifier
BacDive ID: 1939
Type strain:
Species: Burkholderia vietnamiensis
Strain Designation: TVV75
Strain history: CIP <- 1999, CFBP <- LMG <- T. Heulin, CNRS, unidentified <- V. Tran Van, Binh Thanh, Vietnam
NCBI tax ID(s): 1449978 (strain), 60552 (species)
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 id | Matching level |
---|---|
1449978 | strain |
60552 | species |
strain history
@ref | history |
---|---|
4295 | <- BCCM; LMG 10929 <- T. Heulin; <- T. V. Van; TVV75 |
67770 | LMG 10929 <-- T. Heulin CNRS <-- T. V. Van TVV75. |
123840 | CIP <- 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 91.342 | ||
69480 | 99.922 | negative | ||
123840 | yes | negative | rod-shaped |
pigmentation
- @ref: 123840
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4295 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf | |
4295 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf | |
40243 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
123840 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4295 | positive | growth | 28 | mesophilic |
40243 | positive | growth | 30 | mesophilic |
51960 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
123840 | positive | growth | 30-41 | |
123840 | no | growth | 5 | psychrophilic |
123840 | no | growth | 10 | psychrophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
51960 | aerobe |
123840 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.933 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123840 | NaCl | positive | growth | 0-2 % |
123840 | NaCl | no | growth | 4 % |
123840 | NaCl | no | growth | 6 % |
123840 | NaCl | no | growth | 8 % |
123840 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
123840 | 16947 | citrate | + | carbon source |
123840 | 4853 | esculin | - | hydrolysis |
123840 | 17632 | nitrate | + | reduction |
123840 | 16301 | nitrite | - | reduction |
123840 | 17632 | nitrate | - | 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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
123840 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
123840 | oxidase | + | |
123840 | beta-galactosidase | + | 3.2.1.23 |
123840 | alcohol dehydrogenase | - | 1.1.1.1 |
123840 | gelatinase | - | |
123840 | amylase | - | |
123840 | DNase | - | |
123840 | caseinase | - | 3.4.21.50 |
123840 | catalase | + | 1.11.1.6 |
123840 | tween esterase | + | |
123840 | lecithinase | + | |
123840 | lipase | + | |
123840 | lysine decarboxylase | - | 4.1.1.18 |
123840 | ornithine decarboxylase | - | 4.1.1.17 |
123840 | protease | + | |
123840 | tryptophan deaminase | - | |
123840 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123840 | - | + | + | + | + | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4295 | + | - | - | - | - | - | - | + | + | + | + | + | + | - | + | + | - | + | + | + | + |
4295 | + | - | - | - | - | - | - | + | + | + | + | + | + | - | + | + | - | + | + | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123840 | + | + | + | + | + | - | - | + | - | - | - | - | - | + | - | - | - | - | - | + | + | + | - | - | + | - | + | - | - | + | + | + | + | + | - | - | + | - | - | + | - | - | - | + | + | - | - | - | + | + | + | + | + | + | + | + | + | - | + | + | + | + | + | + | + | - | - | + | - | + | - | + | + | + | + | + | + | + | + | + | + | + | + | + | + | - | + | + | + | + | + | + | + | + | + | + | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
4295 | rice rhizosphere soil | Binh Thanh | Vietnam | VNM | Asia | 10.8106 | 106.709 |
51960 | Soil,rice rhizosphere | Binh Thanh | Vietnam | VNM | Asia | ||
67770 | Rice rhizosphere soil | Bình Thanh | Vietnam | VNM | Asia | ||
123840 | Environment, Rhizosphere soil |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
4295 | 2 | Risk group (German classification) |
123840 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Burkholderia vietnamiensis strain LMG 10929 16S ribosomal RNA gene, partial sequence | AF416383 | 174 | ena | 60552 |
20218 | Burkholderia vietnamiensis strain LMG 10929 16S ribosomal RNA gene, partial sequence | HQ849107 | 1124 | ena | 60552 |
20218 | Burkholderia vietnamiensis 16S ribosomal RNA gene, partial sequence | U96928 | 1526 | ena | 60552 |
4295 | Burkholderia vietnamiensis strain LMG 10929 16S ribosomal RNA gene, partial sequence | AF097534 | 1494 | ena | 60552 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Burkholderia vietnamiensis LMG 10929 | GCA_000959445 | complete | ncbi | 1449978 |
66792 | Burkholderia vietnamiensis LMG 10929 | GCA_902830295 | scaffold | ncbi | 60552 |
66792 | Burkholderia vietnamiensis LMG 10929 | 1449978.3 | complete | patric | 1449978 |
66792 | Burkholderia vietnamiensis LMG 10929 | 1449978.4 | plasmid | patric | 1449978 |
66792 | Burkholderia vietnamiensis strain FDAARGOS_1488 | 60552.132 | complete | patric | 60552 |
66792 | Burkholderia vietnamiensis strain LMG 10929 | 60552.72 | wgs | patric | 60552 |
66792 | Burkholderia vietnamiensis LMG 10929 | 2636415515 | complete | img | 1449978 |
66792 | Burkholderia vietnamiensis TVV75 | 2582581767 | draft | img | 60552 |
67770 | Burkholderia vietnamiensis BAA-248 | GCA_001527445 | contig | ncbi | 60552 |
66792 | Burkholderia vietnamiensis strain FDAARGOS_1488 | 60552.174 | complete | patric | 60552 |
66792 | Burkholderia vietnamiensis strain FDAARGOS_1488 | 60552.136 | complete | patric | 60552 |
66792 | Burkholderia vietnamiensis strain FDAARGOS_1488 | 60552.154 | complete | patric | 60552 |
GC content
- @ref: 67770
- GC-content: 67.9
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 88.422 | no |
flagellated | no | 86.179 | no |
gram-positive | no | 98.277 | no |
anaerobic | no | 98.338 | no |
aerobic | yes | 88.035 | no |
halophile | no | 95.767 | no |
spore-forming | no | 94.823 | no |
glucose-util | yes | 90.209 | no |
thermophile | no | 99.436 | yes |
glucose-ferment | no | 88.652 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11375196 | Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution. | Estrada-De Los Santos P, Bustillos-Cristales R, Caballero-Mellado J | Appl Environ Microbiol | 10.1128/AEM.67.6.2790-2798.2001 | 2001 | Bacterial 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/*microbiology | Phenotype |
Pathogenicity | 11425720 | Effects of rice seed surface sterilization with hypochlorite on inoculated Burkholderia vietnamiensis. | Miche L, Balandreau J | Appl Environ Microbiol | 10.1128/AEM.67.7.3046-3052.2001 | 2001 | Anti-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/*methods | Genetics |
Phylogeny | 11846770 | Detection and activity of insertion sequences in environmental strains of Burkholderia. | Miche L, Faure D, Blot M, Cabanne-Giuli E, Balandreau J | Environ Microbiol | 10.1046/j.1462-2920.2001.00251.x | 2001 | Blotting, Southern, Burkholderia/classification/*genetics, DNA Transposable Elements/*genetics, *Genes, Bacterial, Molecular Sequence Data, Phylogeny, Polymorphism, Restriction Fragment Length, Statistics as Topic | Genetics |
Phylogeny | 17406771 | Effects 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 C | Microb Ecol | 10.1007/s00248-007-9247-9 | 2007 | Burkholderia/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, DNA | Enzymology |
Phylogeny | 21349327 | Five 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 R | Res Microbiol | 10.1016/j.resmic.2011.02.007 | 2011 | Acids/*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/*metabolism | Metabolism |
Pathogenicity | 23544536 | Structure of a novel exopolysaccharide produced by Burkholderia vietnamiensis, a cystic fibrosis opportunistic pathogen. | Cescutti P, Cuzzi B, Herasimenka Y, Rizzo R | Carbohydr Polym | 10.1016/j.carbpol.2013.01.047 | 2013 | Burkholderia 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 Ionization | Genetics |
Pathogenicity | 35862731 | Differential 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 L | Appl Environ Microbiol | 10.1128/aem.00642-22 | 2022 | Animals, *Burkholderia/metabolism, *Burkholderia cepacia complex/genetics, *Burkholderiaceae/genetics, Humans, Mutagenesis, Insertional, *Oryza/microbiology, Plants/genetics | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4295 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11319) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11319 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
40243 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17942 | ||||
51960 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 34169) | https://www.ccug.se/strain?id=34169 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
71584 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10342.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123840 | Curators of the CIP | Collection of Institut Pasteur (CIP 105875) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105875 |