Strain identifier
BacDive ID: 13131
Type strain:
Species: Pseudomonas borbori
Strain Designation: R-20821
Strain history: CIP <- 2006, DSMZ <- B. Vanparys, Ghent Univ., Ghent, Belgium: strain R-20821
NCBI tax ID(s): 289003 (species)
General
@ref: 7205
BacDive-ID: 13131
DSM-Number: 17834
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Pseudomonas borbori R-20821 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from nitrifying starting culture for the detoxification of aquaculture ponds and aquaria.
NCBI tax id
- NCBI tax id: 289003
- Matching level: species
strain history
@ref | history |
---|---|
7205 | <- B. Vanparys; R-20821 |
116841 | CIP <- 2006, DSMZ <- B. Vanparys, Ghent Univ., Ghent, Belgium: strain R-20821 |
doi: 10.13145/bacdive13131.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas borbori
- full scientific name: Pseudomonas borbori Vanparys et al. 2006
@ref: 7205
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas borbori
full scientific name: Pseudomonas borbori Vanparys et al. 2006
strain designation: R-20821
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31765 | negative | 02-03 µm | 1 µm | rod-shaped | yes | |
69480 | yes | 98.273 | ||||
69480 | negative | 99.995 | ||||
116841 | negative | rod-shaped | yes |
pigmentation
- @ref: 31765
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7205 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
37533 | MEDIUM 328- for nutrient agar | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g) | |
116841 | CIP Medium 328 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7205 | positive | growth | 28 | mesophilic |
31765 | positive | growth | 22-28 | |
31765 | positive | optimum | 22-28 | |
37533 | positive | growth | 30 | mesophilic |
60007 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31765 | positive | growth | 7 |
31765 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31765 | aerobe |
60007 | aerobe |
116841 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31765 | no | |
69481 | no | 100 |
69480 | no | 99.993 |
observation
- @ref: 31765
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31765 | 24265 | gluconate | + | carbon source |
31765 | 17234 | glucose | + | carbon source |
31765 | 17306 | maltose | + | carbon source |
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 |
116841 | 17632 | nitrate | + | reduction |
116841 | 16301 | nitrite | + | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
116841 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
31765 | catalase | + | 1.11.1.6 |
31765 | cytochrome oxidase | + | 1.9.3.1 |
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 |
116841 | oxidase | + | |
116841 | catalase | + | 1.11.1.6 |
116841 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116841 | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7205 | + | - | - | - | - | - | - | - | + | - | - | - | - | + | + | + | - | + | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7205 | nitrifying starting culture for the detoxification of aquaculture ponds and aquaria | Gent | Belgium | BEL | Europe |
60007 | A nitrifying inoculum | ||||
116841 | Nitrifying inoculum | Ghent | Belgium | BEL | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Aquaculture |
#Engineered | #Laboratory | #Lab enrichment |
#Environmental | #Aquatic | #Pond (small) |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7205 | 1 | Risk group (German classification) |
116841 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7205
- description: Pseudomonas borbori partial 16S rRNA gene, type strain R-20821T
- accession: AM114527
- length: 1494
- database: ena
- NCBI tax ID: 289003
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas borbori DSM 17834 | GCA_900115555 | scaffold | ncbi | 289003 |
66792 | Pseudomonas borbori strain DSM 17834 | 289003.4 | wgs | patric | 289003 |
66792 | Pseudomonas borbori LMG 23199 | 2671180032 | draft | img | 289003 |
GC content
- @ref: 31765
- GC-content: 60.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.991 | yes |
flagellated | yes | 81.167 | no |
gram-positive | no | 98.705 | yes |
anaerobic | no | 98.186 | no |
aerobic | yes | 90.031 | no |
halophile | no | 63.103 | no |
spore-forming | no | 96.521 | no |
glucose-ferment | no | 91.475 | no |
thermophile | no | 99.564 | yes |
glucose-util | yes | 88.078 | yes |
External links
@ref: 7205
culture collection no.: CCUG 53773, DSM 17834, LMG 23199, CIP 109375
straininfo link
- @ref: 82339
- straininfo: 94088
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16902024 | Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum. | Vanparys B, Heylen K, Lebbe L, De Vos P | Int J Syst Evol Microbiol | 10.1099/ijs.0.64224-0 | 2006 | *Aquaculture, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nitrites/*metabolism, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/chemistry/*classification/isolation & purification/physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, *Water Microbiology | Genetics |
Phylogeny | 18319482 | Pseudomonas marincola sp. nov., isolated from marine environments. | Romanenko LA, Uchino M, Tebo BM, Tanaka N, Frolova GM, Mikhailov VV | Int J Syst Evol Microbiol | 10.1099/ijs.0.65406-0 | 2008 | Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Echinodermata/*microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 21278410 | Pseudomonas composti sp. nov., isolated from compost samples. | Gibello A, Vela AI, Martin M, Mengs G, Alonso PZ, Garbi C, Fernandez-Garayzabal JF | Int J Syst Evol Microbiol | 10.1099/ijs.0.027086-0 | 2011 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Metabolism |
Phylogeny | 35396979 | Pseudomonas tumuqii sp. nov., isolated from greenhouse soil. | Kong D, Li Q, Zhou Y, Wang Y, Jiang X, Wang Z, Ruan Z | Arch Microbiol | 10.1007/s00203-022-02869-y | 2022 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, *Pseudomonas, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7205 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17834) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17834 | |||
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 | |||
31765 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28038 | 28776041 | |
37533 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7109 | ||||
60007 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 53773) | https://www.ccug.se/strain?id=53773 | |||
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 | |||
82339 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID94088.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116841 | Curators of the CIP | Collection of Institut Pasteur (CIP 109375) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109375 |