Strain identifier
BacDive ID: 2066
Type strain:
Species: Pandoraea vervacti
Strain Designation: 561, NS15
Strain history: <- N. Sahin, Mugla University, Kötekli, Turkey; NS15
NCBI tax ID(s): 656178 (species)
General
@ref: 17291
BacDive-ID: 2066
DSM-Number: 23571
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Pandoraea vervacti 561 is a mesophilic, Gram-negative, motile bacterium that was isolated from uncultivated field soil.
NCBI tax id
- NCBI tax id: 656178
- Matching level: species
strain history
- @ref: 17291
- history: <- N. Sahin, Mugla University, Kötekli, Turkey; NS15
doi: 10.13145/bacdive2066.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiaceae
- genus: Pandoraea
- species: Pandoraea vervacti
- full scientific name: Pandoraea vervacti Sahin et al. 2011
@ref: 17291
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Pandoraea
species: Pandoraea vervacti
full scientific name: Pandoraea vervacti Sahin et al. 2011
strain designation: 561, NS15
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
23368 | negative | 2.8 µm | 0.9 µm | rod-shaped | yes | |
69480 | yes | 95.793 | ||||
69480 | negative | 99.982 |
colony morphology
@ref | incubation period | colony size | colony color | medium used |
---|---|---|---|---|
17291 | 1-2 days | |||
23368 | 2 days | 1-2 mm | cream | TSA |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
17291 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
23368 | Trypticase Soy Agar (TSA) | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17291 | positive | growth | 28 | mesophilic |
23368 | positive | growth | 30-42 |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.963 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
23368 | NaCl | positive | growth | 3 %(w/v) |
23368 | NaCl | no | growth | 4.5 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23368 | 17128 | adipate | - | carbon source |
23368 | 17057 | cellobiose | - | respiration |
23368 | 14314 | D-glucose 6-phosphate | - | respiration |
23368 | 17992 | sucrose | - | respiration |
23368 | 16523 | D-serine | - | respiration |
23368 | 32323 | glucuronamide | - | respiration |
23368 | 28087 | glycogen | - | respiration |
23368 | 73804 | glycyl L-aspartic acid | - | respiration |
23368 | 30849 | L-arabinose | - | respiration |
23368 | 15792 | malonate | - | respiration |
23368 | 73784 | glycyl-l-glutamate | - | respiration |
23368 | 41865 | sebacic acid | - | respiration |
23368 | 27689 | decanoate | + | carbon source |
23368 | 16947 | citrate | + | carbon source |
23368 | 24265 | gluconate | + | carbon source |
23368 | 17234 | glucose | + | carbon source |
23368 | 25115 | malate | + | carbon source |
23368 | 18401 | phenylacetate | + | carbon source |
23368 | 64552 | 2-hydroxybutyrate | + | respiration |
23368 | 16763 | 2-oxobutanoate | + | respiration |
23368 | 28644 | 2-oxopentanoate | + | respiration |
23368 | 37054 | 3-hydroxybutyrate | + | respiration |
23368 | 16724 | 4-hydroxybutyrate | + | respiration |
23368 | 30089 | acetate | + | respiration |
23368 | 17925 | alpha-D-glucose | + | respiration |
23368 | 73706 | bromosuccinate | + | respiration |
23368 | 16383 | cis-aconitate | + | respiration |
23368 | 16947 | citrate | + | respiration |
23368 | 8391 | D-gluconate | + | respiration |
23368 | 17784 | D-glucosaminic acid | + | respiration |
23368 | 15740 | formate | + | respiration |
23368 | 17754 | glycerol | + | respiration |
23368 | 21217 | L-alaninamide | + | respiration |
23368 | 73786 | L-alanylglycine | + | respiration |
23368 | 17196 | L-asparagine | + | respiration |
23368 | 29985 | L-glutamate | + | respiration |
23368 | 15971 | L-histidine | + | respiration |
23368 | 15603 | L-leucine | + | respiration |
23368 | 17295 | L-phenylalanine | + | respiration |
23368 | 17203 | L-proline | + | respiration |
23368 | 18183 | L-pyroglutamic acid | + | respiration |
23368 | 17115 | L-serine | + | respiration |
23368 | 16857 | L-threonine | + | respiration |
23368 | 24996 | lactate | + | respiration |
23368 | 51850 | methyl pyruvate | + | respiration |
23368 | 53426 | tween 80 | + | respiration |
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 |
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | - | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | - | fermentation |
68368 | 17634 | D-glucose | - | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | + | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
antibiotic resistance
- @ref: 23368
- ChEBI: 27902
- metabolite: tetracycline
- is antibiotic: yes
- is resistant: no
- resistance conc.: 30 µg
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
68369 | 35581 | indole | - | |
68368 | 15688 | acetoin | - | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23368 | acid phosphatase | + | 3.1.3.2 |
23368 | alkaline phosphatase | + | 3.1.3.1 |
23368 | catalase | + | 1.11.1.6 |
23368 | cystine arylamidase | - | 3.4.11.3 |
23368 | cytochrome oxidase | + | 1.9.3.1 |
23368 | esterase (C 4) | + | |
23368 | esterase lipase (C 8) | - | |
23368 | esterase lipase (C 8) | + | |
23368 | leucine arylamidase | + | 3.4.11.1 |
23368 | naphthol-AS-BI-phosphohydrolase | + | |
23368 | nitrate reductase | - | 1.7.99.4 |
23368 | urease | + | 3.5.1.5 |
23368 | valine arylamidase | - | |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | + | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | + | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
17291 | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
17291 | - | - | - | - | + | - | - | - | + | - | - | - | - | - | + | + | - | + | + | + | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
17291 | uncultivated field soil | Mugla | Turkey | TUR | Asia |
23368 | field soil after enrichment with oxalate in mineral medium |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Laboratory | #Lab enrichment |
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_814.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_494;97_563;98_648;99_814&stattab=map
- Last taxonomy: Pandoraea
- 16S sequence: AB510956
- Sequence Identity:
- Total samples: 20583
- soil counts: 6943
- aquatic counts: 4192
- animal counts: 3605
- plant counts: 5843
Safety information
risk assessment
- @ref: 17291
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17291
- description: Pandoraea vervacti gene for 16S rRNA, partial sequence, strain: NS15
- accession: AB510956
- length: 1378
- database: ena
- NCBI tax ID: 656178
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pandoraea vervacti NS15 | GCA_000934605 | complete | ncbi | 656178 |
66792 | Pandoraea vervacti strain NS15 | 656178.9 | plasmid | patric | 656178 |
66792 | Pandoraea vervacti strain NS15 | 656178.5 | complete | patric | 656178 |
66792 | Pandoraea vervacti NS15 | 2927181219 | complete | img | 656178 |
GC content
@ref | GC-content | method |
---|---|---|
17291 | 65.8 | thermal denaturation, midpoint method (Tm) |
23368 | 65.8 | Thermal denaturation, fluorometry |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 88.68 | no |
motile | yes | 88.68 | no |
flagellated | no | 58.531 | no |
flagellated | no | 58.531 | no |
gram-positive | no | 98.717 | no |
gram-positive | no | 98.717 | no |
anaerobic | no | 98.81 | no |
anaerobic | no | 98.81 | no |
aerobic | yes | 90.975 | no |
aerobic | yes | 90.975 | no |
halophile | no | 94.024 | no |
halophile | no | 94.024 | no |
spore-forming | no | 94.044 | no |
spore-forming | no | 94.044 | no |
glucose-util | yes | 64.918 | yes |
glucose-util | yes | 64.918 | yes |
thermophile | no | 98.902 | yes |
thermophile | no | 98.902 | yes |
glucose-ferment | no | 89.565 | yes |
glucose-ferment | no | 89.565 | yes |
External links
@ref: 17291
culture collection no.: DSM 23571, CCM 7667, NBRC 106088
straininfo link
- @ref: 71713
- straininfo: 378120
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20952546 | Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. | Sahin N, Tani A, Kotan R, Sedlacek I, Kimbara K, Tamer AU | Int J Syst Evol Microbiol | 10.1099/ijs.0.026138-0 | 2010 | Aerobiosis, Bacterial Typing Techniques, Burkholderiaceae/*classification/genetics/*isolation & purification/metabolism, Cluster Analysis, Culture Media/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalates/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
Genetics | 25848988 | Complete genome sequence of oxalate-degrading bacterium Pandoraea vervacti DSM 23571(T). | Ee R, Yong D, Lim YL, Yin WF, Chan KG | J Biotechnol | 10.1016/j.jbiotec.2015.03.020 | 2015 | Base Composition, Base Sequence, Burkholderiaceae/*genetics/metabolism, Gene Components, Genome, Bacterial/*genetics, Industrial Microbiology, Metabolic Networks and Pathways/genetics, Molecular Sequence Data, Oxalates/metabolism, Sequence Analysis, DNA, *Soil Microbiology, Turkey | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
17291 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23571) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23571 | |||
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 | |||
23368 | Nurettin Sahin, Akio Tani, Recep Kotan, Ivo Sedlácek, Kazuhide Kimbara, Abdurrahman U. Tamer | 10.1099/ijs.0.026138-0 | Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture | IJSEM 61: 2247-2253 2011 | 20952546 | |
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) | |||
68368 | Automatically annotated from API 20E | |||||
68369 | Automatically annotated from API 20NE | |||||
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 | |||
71713 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID378120.1 | StrainInfo: A central database for resolving microbial strain identifiers |