Strain identifier
BacDive ID: 1974
Type strain:
Species: Burkholderia oklahomensis
Strain Designation: C6786
Strain history: CIP <- 2011, DSMZ <- LMG <- M.B. Glass, CDC, Atlanta, USA: strain C6786
NCBI tax ID(s): 342113 (species)
General
@ref: 15939
BacDive-ID: 1974
DSM-Number: 21774
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Burkholderia oklahomensis C6786 is an aerobe, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from 27-year-old male in farming accident, left thigh wound.
NCBI tax id
- NCBI tax id: 342113
- Matching level: species
strain history
@ref | history |
---|---|
15939 | <- LMG; LMG 23618 <- M. B. Glass, CDC, Atlanta; C6786 <- CDC, Atlanta; |
121408 | CIP <- 2011, DSMZ <- LMG <- M.B. Glass, CDC, Atlanta, USA: strain C6786 |
doi: 10.13145/bacdive1974.20230509.8.1
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 oklahomensis
- full scientific name: Burkholderia oklahomensis Glass et al. 2006
@ref: 15939
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Burkholderia
species: Burkholderia oklahomensis
full scientific name: Burkholderia oklahomensis Glass et al. 2006
strain designation: C6786
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
23158 | negative | rod-shaped | yes | |
69480 | yes | 92.823 | ||
69480 | negative | 99.987 | ||
121408 | negative | rod-shaped | yes |
colony morphology
- @ref: 23158
- colony color: white
- colony shape: irregular
- incubation period: 3 days
- medium used: 5 % sheep blood agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15939 | 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 |
23158 | 5 % sheep blood agar | yes | ||
37596 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
15939 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
121408 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15939 | positive | growth | 37 | mesophilic |
23158 | positive | growth | 25-37 | mesophilic |
23158 | positive | maximum | 42 | thermophilic |
37596 | positive | growth | 37 | mesophilic |
59160 | positive | growth | 25-37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
23158 | aerobe |
59160 | aerobe |
121408 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 96 |
69480 | no | 99.993 |
halophily
- @ref: 23158
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23158 | 27897 | tryptophan | - | energy source |
23158 | 16136 | hydrogen sulfide | - | growth |
23158 | 65327 | D-xylose | + | assimilation |
23158 | 17234 | glucose | + | assimilation |
23158 | 17716 | lactose | + | assimilation |
23158 | 17306 | maltose | + | assimilation |
23158 | 29864 | mannitol | + | assimilation |
23158 | 17992 | sucrose | + | assimilation |
23158 | 17632 | nitrate | + | reduction |
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 | 17632 | nitrate | + | reduction |
121408 | 17632 | nitrate | + | reduction |
121408 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
23158 | 35581 | indole | no |
121408 | 35581 | indole | no |
metabolite tests
- @ref: 23158
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
15939 | catalase | + | 1.11.1.6 |
15939 | cytochrome-c oxidase | - | 1.9.3.1 |
23158 | arginine decarboxylase | + | 4.1.1.19 |
23158 | arginine dihydrolase | + | 3.5.3.6 |
23158 | catalase | + | 1.11.1.6 |
23158 | cytochrome oxidase | + | 1.9.3.1 |
23158 | lysine decarboxylase | - | 4.1.1.18 |
23158 | ornithine decarboxylase | - | 4.1.1.17 |
23158 | tryptophan deaminase | - | 4.1.99.1 |
23158 | urease | - | 3.5.1.5 |
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 |
121408 | oxidase | + | |
121408 | catalase | + | 1.11.1.6 |
121408 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121408 | - | + | + | + | + | + | - | - | - | - | + | + | - | - | - | - | - | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15939 | + | - | - | + | - | + | + | - | + | - | + | + | + | - | + | + | + | + | + | + | + |
15939 | + | + | - | + | - | + | + | - | + | - | + | + | + | - | + | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
15939 | 27-year-old male in farming accident, left thigh wound | Oklahoma | USA | USA | North America | ||
59160 | Human wound,27-yr-old man,farming accident | Oklahoma | USA | USA | North America | 1973 | |
121408 | Human, Left thigh wound | Oklahoma | United States of America | USA | North America | 1973 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Patient | |
#Host | #Human | #Female |
#Host Body-Site | #Other | #Wound |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15939 | 2 | Risk group (German classification) |
121408 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Burkholderia oklahomensis strain LMG 23618 16S ribosomal RNA gene, partial sequence | HQ849092 | 1124 | ena | 342113 |
15939 | Burkholderia oklahomensis strain C6786 16S ribosomal RNA gene, partial sequence | DQ108388 | 1499 | ena | 441162 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Burkholderia oklahomensis C6786 | GCA_000959365 | complete | ncbi | 441162 |
66792 | Burkholderia oklahomensis C6786 | GCA_001522135 | complete | ncbi | 441162 |
66792 | Burkholderia oklahomensis LMG 23618 | GCA_900608545 | contig | ncbi | 342113 |
66792 | Burkholderia oklahomensis LMG 23618 | GCA_902829515 | scaffold | ncbi | 342113 |
66792 | Burkholderia oklahomensis C6786 | GCA_000170375 | contig | ncbi | 441162 |
66792 | Burkholderia oklahomensis C6786 | 441162.11 | complete | patric | 441162 |
66792 | Burkholderia oklahomensis C6786 | 441162.12 | wgs | patric | 441162 |
66792 | Burkholderia oklahomensis C6786 | 441162.10 | wgs | patric | 441162 |
66792 | Burkholderia oklahomensis strain LMG 23618 | 342113.5 | wgs | patric | 342113 |
66792 | Burkholderia oklahomensis strain LMG 23618 | 342113.7 | wgs | patric | 342113 |
66792 | Burkholderia oklahomensis C6786 | 641736121 | draft | img | 441162 |
66792 | Burkholderia oklahomensis C6786 | 2814123269 | complete | img | 441162 |
66792 | Burkholderia oklahomensis C6786 | 2627853643 | complete | img | 441162 |
GC content
- @ref: 23158
- GC-content: 66.0
- method: Thermal denaturation, fluorometry
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 96 | no |
motile | yes | 86.935 | yes |
flagellated | no | 82.31 | no |
gram-positive | no | 97.993 | no |
anaerobic | no | 98.015 | yes |
aerobic | yes | 85.561 | yes |
halophile | no | 92.115 | no |
spore-forming | no | 92.623 | no |
glucose-util | yes | 92.474 | yes |
thermophile | no | 99.661 | no |
glucose-ferment | no | 88.773 | yes |
External links
@ref: 15939
culture collection no.: DSM 21774, CCUG 51349, CIP 110344, LMG 23618, NCTC 13387, LMG 23678
straininfo link
- @ref: 71619
- straininfo: 297151
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16957116 | Burkholderia oklahomensis sp. nov., a Burkholderia pseudomallei-like species formerly known as the Oklahoma strain of Pseudomonas pseudomallei. | Glass MB, Steigerwalt AG, Jordan JG, Wilkins PP, Gee JE | Int J Syst Evol Microbiol | 10.1099/ijs.0.63991-0 | 2006 | Burkholderia/classification/genetics/isolation & purification, Burkholderia pseudomallei/*classification/genetics, DNA, Bacterial/analysis, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/*analysis/genetics | Pathogenicity |
Phylogeny | 29721827 | Burkholderia alba sp. nov., isolated from a soil sample on Halla mountain in Jeju island. | Lee JW, Kim YE, Park SJ | J Microbiol | 10.1007/s12275-018-8034-2 | 2018 | Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/growth & development/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial/genetics, Hydrogen-Ion Concentration, Islands, Nucleic Acid Hybridization, Phenotype, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride, Soil, *Soil Microbiology, Species Specificity, Temperature | Phenotype |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
15939 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21774) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21774 | |||
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 | |
23158 | Mindy B. Glass, Arnold G. Steigerwalt, Jean G. Jordan, Patricia P. Wilkins, Jay E. Gee | 10.1099/ijs.0.63991-0 | Burkholderia oklahomensis sp. nov., a Burkholderia pseudomallei-like species formerly known as the Oklahoma strain of Pseudomonas pseudomallei | IJSEM 56: 2171-2176 2006 | 16957116 | |
37596 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/8193 | ||||
59160 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 51349) | https://www.ccug.se/strain?id=51349 | |||
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) | |||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
71619 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297151.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121408 | Curators of the CIP | Collection of Institut Pasteur (CIP 110344) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110344 |