Pandoraea pnomenusa R140 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from cystic fibrosis patient.
Gram-negative motile obligate aerobe genome sequence 16S sequence Bacteria| @ref 20215 |
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| Domain Bacteria |
| Phylum Pseudomonadota |
| Class Betaproteobacteria |
| Order Burkholderiales |
| Family Burkholderiaceae |
| Genus Pandoraea |
| Species Pandoraea pnomenusa |
| Full scientific name Pandoraea pnomenusa Coenye et al. 2000 |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 6474 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | Medium recipe at MediaDive | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water | ||
| 42009 | MEDIUM 72- for trypto casein soja agar | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |||
| 121915 | CIP Medium 72 | Medium recipe at CIP |
| @ref | Chebi-ID | Metabolite | Utilization activity | Kind of utilization tested | |
|---|---|---|---|---|---|
| 23367 | 17128 ChEBI | adipate | - | growth | |
| 68369 | 17128 ChEBI | adipate | - | assimilation | from API 20NE |
| 68369 | 29016 ChEBI | arginine | - | hydrolysis | from API 20NE |
| 23367 | 16947 ChEBI | citrate | + | growth | |
| 121915 | 16947 ChEBI | citrate | + | carbon source | |
| 23367 | 17634 ChEBI | D-glucose | - | growth | |
| 68369 | 17634 ChEBI | D-glucose | - | assimilation | from API 20NE |
| 68369 | 17634 ChEBI | D-glucose | - | fermentation | from API 20NE |
| 68369 | 16899 ChEBI | D-mannitol | - | assimilation | from API 20NE |
| 68369 | 16024 ChEBI | D-mannose | - | assimilation | from API 20NE |
| 23367 | 27689 ChEBI | decanoate | + | growth | |
| 68369 | 27689 ChEBI | decanoate | + | assimilation | from API 20NE |
| 23367 | 4853 ChEBI | esculin | - | hydrolysis | |
| 121915 | 4853 ChEBI | esculin | - | hydrolysis | |
| 68369 | 4853 ChEBI | esculin | - | hydrolysis | from API 20NE |
| 68369 | 5291 ChEBI | gelatin | - | hydrolysis | from API 20NE |
| 68369 | 24265 ChEBI | gluconate | + | assimilation | from API 20NE |
| 68369 | 30849 ChEBI | L-arabinose | - | assimilation | from API 20NE |
| 23367 | 24996 ChEBI | lactate | + | growth | |
| 68369 | 25115 ChEBI | malate | - | assimilation | from API 20NE |
| 23367 | 17306 ChEBI | maltose | - | growth | |
| 68369 | 17306 ChEBI | maltose | + | assimilation | from API 20NE |
| 68369 | 59640 ChEBI | N-acetylglucosamine | - | assimilation | from API 20NE |
| 121915 | 17632 ChEBI | nitrate | + | reduction | |
| 121915 | 17632 ChEBI | nitrate | - | respiration | |
| 68369 | 17632 ChEBI | nitrate | + | reduction | from API 20NE |
| 23367 | 16301 ChEBI | nitrite | - | reduction | |
| 121915 | 16301 ChEBI | nitrite | - | reduction | |
| 23367 | 17992 ChEBI | sucrose | - | growth | |
| 23367 | 27897 ChEBI | tryptophan | - | energy source | |
| 68369 | 27897 ChEBI | tryptophan | - | energy source | from API 20NE |
| 23367 | 53426 ChEBI | tween 80 | - | hydrolysis | |
| 68369 | 16199 ChEBI | urea | - | hydrolysis | from API 20NE |
| @ref | Value | Activity | Ec | |
|---|---|---|---|---|
| 68382 | acid phosphatase | + | 3.1.3.2 | from API zym |
| 121915 | alcohol dehydrogenase | - | 1.1.1.1 | |
| 68382 | alkaline phosphatase | - | 3.1.3.1 | from API zym |
| 68382 | alpha-chymotrypsin | - | 3.4.21.1 | from API zym |
| 68382 | alpha-fucosidase | - | 3.2.1.51 | from API zym |
| 68382 | alpha-galactosidase | - | 3.2.1.22 | from API zym |
| 68382 | alpha-glucosidase | - | 3.2.1.20 | from API zym |
| 68382 | alpha-mannosidase | - | 3.2.1.24 | from API zym |
| 121915 | amylase | - | ||
| 68369 | arginine dihydrolase | - | 3.5.3.6 | from API 20NE |
| 68382 | beta-galactosidase | - | 3.2.1.23 | from API zym |
| 121915 | beta-galactosidase | - | 3.2.1.23 | |
| 68382 | beta-glucosidase | - | 3.2.1.21 | from API zym |
| 68369 | beta-glucosidase | - | 3.2.1.21 | from API 20NE |
| 68382 | beta-glucuronidase | - | 3.2.1.31 | from API zym |
| 121915 | caseinase | - | 3.4.21.50 | |
| 121915 | catalase | + | 1.11.1.6 | |
| 68382 | cystine arylamidase | - | 3.4.11.3 | from API zym |
| 68369 | cytochrome oxidase | - | 1.9.3.1 | from API 20NE |
| 23367 | DNase | - | ||
| 121915 | DNase | - | ||
| 68382 | esterase (C 4) | + | from API zym | |
| 68382 | esterase lipase (C 8) | + | from API zym | |
| 121915 | gelatinase | - | ||
| 68369 | gelatinase | - | from API 20NE | |
| 121915 | lecithinase | - | ||
| 68382 | leucine arylamidase | + | 3.4.11.1 | from API zym |
| 121915 | lipase | - | ||
| 68382 | lipase (C 14) | - | from API zym | |
| 121915 | lysine decarboxylase | - | 4.1.1.18 | |
| 68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 | from API zym |
| 68382 | naphthol-AS-BI-phosphohydrolase | + | from API zym | |
| 121915 | ornithine decarboxylase | - | 4.1.1.17 | |
| 121915 | oxidase | + | ||
| 121915 | protease | - | ||
| 68382 | trypsin | - | 3.4.21.4 | from API zym |
| 23367 | tryptophan deaminase | - | 4.1.99.1 | |
| 121915 | tryptophan deaminase | - | ||
| 121915 | tween esterase | - | ||
| 23367 | urease | + | 3.5.1.5 | |
| 121915 | urease | + | 3.5.1.5 | |
| 68369 | urease | - | 3.5.1.5 | from API 20NE |
| 68382 | valine arylamidase | - | from API zym |
Global distribution of 16S sequence AY268170 (>99% sequence identity) for Pandoraea from Microbeatlas ![]()
| @ref | Description | Assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | Score | |
|---|---|---|---|---|---|---|---|---|
| 66792 | ASM76761v3 assembly for Pandoraea pnomenusa DSM 16536 | complete | 93220 | 98.3 |
| @ref | Description | Accession | Length | Database | NCBI tax ID | |
|---|---|---|---|---|---|---|
| 20218 | Pandoraea pnomenusa strain CCUG 38742 16S ribosomal RNA gene, partial sequence | AY268170 | 1461 | 93220 | ||
| 6474 | Pandoraea pnomenusa 16S ribosomal RNA gene, partial sequence | AF139174 | 1474 | 93220 | ||
| 124043 | Burkholderia thailandensis strain 2002721643 16S ribosomal RNA gene, partial sequence. | AY268168 | 1461 | 93220 |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125439 | spore_formation | BacteriaNetⓘ | no | 75.20 | no |
| 125439 | motility | BacteriaNetⓘ | yes | 51.70 | no |
| 125439 | gram_stain | BacteriaNetⓘ | positive | 63.80 | no |
| 125439 | oxygen_tolerance | BacteriaNetⓘ | obligate aerobe | 97.40 | no |
| @ref | Trait | Model | Prediction | Confidence in % | In training data |
|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positiveⓘ | no | 99.00 | yes |
| 125438 | anaerobic | anaerobicⓘ | no | 98.49 | yes |
| 125438 | aerobic | aerobicⓘ | yes | 85.25 | yes |
| 125438 | spore-forming | spore-formingⓘ | no | 91.03 | yes |
| 125438 | thermophilic | thermophileⓘ | no | 97.50 | no |
| 125438 | flagellated | motile2+ⓘ | yes | 83.33 | no |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Genetics | Complete Genome Sequence Analysis of Pandoraea pnomenusa Type Strain DSM 16536(T) Isolated from a Cystic Fibrosis Patient. | Lim YL, Ee R, Yong D, Yu CY, Ang GY, Tee KK, Yin WF, Chan KG. | Front Microbiol | 10.3389/fmicb.2016.00109 | 2016 | |
| Transcriptome | Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting. | McDermott JE, Cort JR, Nakayasu ES, Pruneda JN, Overall C, Adkins JN. | PeerJ | 10.7717/peerj.7055 | 2019 | |
| Metabolism | Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil. | Uhlik O, Wald J, Strejcek M, Musilova L, Ridl J, Hroudova M, Vlcek C, Cardenas E, Mackova M, Macek T. | PLoS One | 10.1371/journal.pone.0040653 | 2012 | |
| Phylogeny | Use of 16S rRNA gene sequencing for rapid identification and differentiation of Burkholderia pseudomallei and B. mallei. | Gee JE, Sacchi CT, Glass MB, De BK, Weyant RS, Levett PN, Whitney AM, Hoffmaster AR, Popovic T. | J Clin Microbiol | 10.1128/jcm.41.10.4647-4654.2003 | 2003 | |
| Pathogenicity | Intrinsic carbapenem-hydrolyzing oxacillinases from members of the genus Pandoraea. | Schneider I, Bauernfeind A. | Antimicrob Agents Chemother | 10.1128/aac.01112-15 | 2015 | |
| Epidemic spread of Pandoraea pulmonicola in a cystic fibrosis center. | Degand N, Lotte R, Deconde Le Butor C, Segonds C, Thouverez M, Ferroni A, Vallier C, Mely L, Carrere J. | BMC Infect Dis | 10.1186/s12879-015-1327-8 | 2015 | ||
| Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei. | Woods DE, Jeddeloh JA, Fritz DL, DeShazer D. | J Bacteriol | 10.1128/jb.184.14.4003-4017.2002 | 2002 | ||
| Phylogeny | Genomic diversity of Burkholderia pseudomallei clinical isolates: subtractive hybridization reveals a Burkholderia mallei-specific prophage in B. pseudomallei 1026b. | DeShazer D. | J Bacteriol | 10.1128/jb.186.12.3938-3950.2004 | 2004 | |
| Phylogeny | Pandoraea terrae sp. nov., isolated from forest soil, and emended description of the genus Pandoraea Coenye et al. 2000. | Jeong SE, Lee HJ, Jia B, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001229 | 2016 | |
| Phylogeny | Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.). | Anandham R, Indiragandhi P, Kwon SW, Sa TM, Jeon CO, Kim YK, Jee HJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.012823-0 | 2009 | |
| Phylogeny | Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov. | Coenye T, Falsen E, Hoste B, Ohlen M, Goris J, Govan JR, Gillis M, Vandamme P | Int J Syst Evol Microbiol | 10.1099/00207713-50-2-887 | 2000 |
| #6474 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16536 |
| #20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 ) |
| #20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 ) |
| #23367 | T Coenye, E Falsen, B Hoste, M Ohlén, J Goris, J R Govan, M Gillis, P Vandamme: Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov.. IJSEM 50: 887 - 899 2000 ( DOI 10.1099/00207713-50-2-887 , PubMed 10758901 ) |
| #42009 | ; Curators of the CIP; |
| #54431 | Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38742 |
| #66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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 . |
| #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.: MicrobeAtlas 1.0 beta . |
| #121915 | Collection of Institut Pasteur ; Curators of the CIP; CIP 106626 |
| #124043 | Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy . |
| #125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 ) |
| #125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 . |
| #126262 | A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 ) |
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