Strain identifier
BacDive ID: 1967
Type strain:
Species: Paraburkholderia phenoliruptrix
Strain Designation: AC1100
Strain history: CIP <- 2004, CCUG <- 2003, LMG <- 2003, T. Coenye, Ghent Univ., Ghent, Belgium <- 1999, D. Henry, British Columbia Univ., Vancouver, Canada: strain AC1100
NCBI tax ID(s): 252970 (species)
General
@ref: 7177
BacDive-ID: 1967
DSM-Number: 17773
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Paraburkholderia phenoliruptrix AC1100 is an aerobe, mesophilic, motile bacterium that was isolated from chemostat with 2,4,5-trichlorophenoxyacetic acid.
NCBI tax id
- NCBI tax id: 252970
- Matching level: species
strain history
@ref | history |
---|---|
7177 | <- CCUG <- LMG <- T. Coenye, Gent <- D. Henry, Univ. British Columbia, Vancouver, Canada |
121796 | CIP <- 2004, CCUG <- 2003, LMG <- 2003, T. Coenye, Ghent Univ., Ghent, Belgium <- 1999, D. Henry, British Columbia Univ., Vancouver, Canada: strain AC1100 |
doi: 10.13145/bacdive1967.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiaceae
- genus: Paraburkholderia
- species: Paraburkholderia phenoliruptrix
- full scientific name: Paraburkholderia phenoliruptrix (Coenye et al. 2005) Sawana et al. 2015
synonyms
- @ref: 20215
- synonym: Burkholderia phenoliruptrix
@ref: 7177
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Paraburkholderia
species: Paraburkholderia phenoliruptrix
full scientific name: Paraburkholderia phenoliruptrix (Coenye et al. 2005) Sawana et al. 2015
strain designation: AC1100
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 95.781 | ||
69480 | 99.965 | negative | ||
121796 | no | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7177 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
7177 | MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) | yes | https://mediadive.dsmz.de/medium/457 | Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water |
41977 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
121796 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7177 | positive | growth | 28 | mesophilic |
41977 | positive | growth | 30 | mesophilic |
58230 | positive | growth | 30 | mesophilic |
121796 | positive | growth | 25-37 | mesophilic |
121796 | no | growth | 5 | psychrophilic |
121796 | no | growth | 10 | psychrophilic |
121796 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
58230 | aerobe |
121796 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.987 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121796 | NaCl | positive | growth | 0-2 % |
121796 | NaCl | no | growth | 4 % |
121796 | NaCl | no | growth | 6 % |
121796 | NaCl | no | growth | 8 % |
121796 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | 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 |
121796 | 4853 | esculin | - | hydrolysis |
121796 | 17632 | nitrate | - | reduction |
121796 | 16301 | nitrite | - | reduction |
121796 | 17632 | nitrate | - | respiration |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121796 | 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 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
121796 | oxidase | + | |
121796 | beta-galactosidase | + | 3.2.1.23 |
121796 | alcohol dehydrogenase | - | 1.1.1.1 |
121796 | gelatinase | - | |
121796 | amylase | + | |
121796 | DNase | - | |
121796 | caseinase | - | 3.4.21.50 |
121796 | catalase | + | 1.11.1.6 |
121796 | tween esterase | - | |
121796 | lecithinase | - | |
121796 | lipase | - | |
121796 | lysine decarboxylase | - | 4.1.1.18 |
121796 | ornithine decarboxylase | - | 4.1.1.17 |
121796 | protease | - | |
121796 | tryptophan deaminase | - | |
121796 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121796 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7177 | - | - | - | - | - | - | - | + | + | + | + | + | + | - | + | +/- | +/- | + | + | + | +/- |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121796 | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | - | + | + | - | - | - | - | + | - | - | - | + | - | - | + | + | + | - | + | - | + | + | - | - | - | - | - | - | - | - | + | + | - | + | - | - | - | - | - | + | - | - | - | - | - | + | - | + | + | - | - | - | - | + | - | - | + | + | - | - | - | - | - | - | - | + | + | - | + | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7177 | chemostat with 2,4,5-trichlorophenoxyacetic acid | Illionis | USA | USA | North America |
58230 | Chemostat grown with 2,4,5-trichlorophenoxyacetic | Vancouver | Canada | CAN | North America |
121796 | Chemostat grown with 2 4 5-trichlorophenoxyacetic | Vancouver | Canada | CAN | North America |
isolation source categories
- Cat1: #Engineered
- Cat2: #Bioreactor
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7177 | 1 | Risk group (German classification) |
121796 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Burkholderia phenoliruptrix strain LMG 22037 16S ribosomal RNA gene, partial sequence | HQ849094 | 1126 | ena | 252970 |
7177 | Burkholderia sp. AC1100 16S ribosomal RNA gene, partial sequence | AY435213 | 1485 | ena | 252970 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paraburkholderia phenoliruptrix LMG 22037 | GCA_902833655 | contig | ncbi | 252970 |
66792 | Paraburkholderia phenoliruptrix LMG 22037 | GCA_902859825 | contig | ncbi | 252970 |
66792 | Paraburkholderia phenoliruptrix AC1100 | GCA_000416445 | contig | ncbi | 1337996 |
66792 | Paraburkholderia phenoliruptrix strain LMG 22037 | 252970.3 | wgs | patric | 252970 |
66792 | Paraburkholderia phenoliruptrix strain LMG 22037 | 252970.5 | wgs | patric | 252970 |
66792 | Paraburkholderia phenoliruptrix AC1100 | 2554235175 | draft | img | 1337996 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 88.86 | no |
gram-positive | no | 98.098 | no |
anaerobic | no | 98.799 | no |
aerobic | yes | 86.958 | yes |
halophile | no | 95.061 | no |
spore-forming | no | 92.72 | no |
glucose-util | yes | 89.84 | yes |
flagellated | no | 85.166 | no |
thermophile | no | 99.425 | yes |
glucose-ferment | no | 89.958 | yes |
External links
@ref: 7177
culture collection no.: DSM 17773, CCUG 48558, CIP 108591, LMG 22037
straininfo link
- @ref: 71612
- straininfo: 43466
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15612618 | Burkholderia phenoliruptrix sp. nov., to accommodate the 2,4,5-trichlorophenoxyacetic acid and halophenol-degrading strain AC1100. | Coenye T, Henry D, Speert DP, Vandamme P | Syst Appl Microbiol | 10.1078/0723202042369992 | 2004 | 2,4,5-Trichlorophenoxyacetic Acid/*metabolism, Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, Burkholderia/*classification/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenols/*metabolism, Phylogeny, Proteome/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Xenobiotics/metabolism | Metabolism |
Genetics | 23929488 | Genome Sequence of the 2,4,5-Trichlorophenoxyacetate-Degrading Bacterium Burkholderia phenoliruptrix Strain AC1100. | Xu P, Yu H, Chakrabarty AM, Xun L | Genome Announc | 10.1128/genomeA.00600-13 | 2013 | ||
Metabolism | 23955343 | Catalytic mechanism of 5-chlorohydroxyhydroquinone dehydrochlorinase from the YCII superfamily of largely unknown function. | Hayes RP, Lewis KM, Xun L, Kang C | J Biol Chem | 10.1074/jbc.M113.499368 | 2013 | Amino Acid Sequence, *Biocatalysis, Burkholderia/*enzymology, Catalytic Domain, Circular Dichroism, Crystallography, X-Ray, Hydroquinones/chemistry/*metabolism, Ligands, Lyases/chemistry/*metabolism, Models, Molecular, Molecular Sequence Data, *Multigene Family, Mutant Proteins/chemistry/metabolism, Mutation/genetics, Protein Structure, Quaternary, Quantum Theory, Sequence Alignment, Solutions, Substrate Specificity | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7177 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17773) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17773 | |||
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 | |
41977 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6236 | ||||
58230 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 48558) | https://www.ccug.se/strain?id=48558 | |||
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 | |||
71612 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43466.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121796 | Curators of the CIP | Collection of Institut Pasteur (CIP 108591) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108591 |