Strain identifier
BacDive ID: 2059
Type strain:
Species: Pandoraea apista
Strain history: CIP <- 2000, CCUG <- 1997, P. Vandamme, LMG, Ghent, Belgium <- N. Höiby, Denmark
NCBI tax ID(s): 93218 (species)
General
@ref: 6473
BacDive-ID: 2059
DSM-Number: 16535
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile
description: Pandoraea apista DSM 16535 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from sputum from cystic fibrosis patient.
NCBI tax id
- NCBI tax id: 93218
- Matching level: species
strain history
@ref | history |
---|---|
6473 | <- CCM <- CCUG <- P. Vandamme <- N. Hoiby |
116422 | CIP <- 2000, CCUG <- 1997, P. Vandamme, LMG, Ghent, Belgium <- N. Höiby, Denmark |
doi: 10.13145/bacdive2059.20230509.8.1
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 apista
- full scientific name: Pandoraea apista Coenye et al. 2000
@ref: 6473
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Pandoraea
species: Pandoraea apista
full scientific name: Pandoraea apista Coenye et al. 2000
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | motility | confidence | cell shape |
---|---|---|---|---|---|---|
23367 | negative | 1.5-4.0 µm | 0.5-0.7 µm | yes | ||
69480 | yes | 92.695 | ||||
69480 | negative | 99.988 | ||||
116422 | negative | yes | rod-shaped |
pigmentation
- @ref: 116422
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6473 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | 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 |
42011 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
116422 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6473 | positive | growth | 37 | mesophilic |
23367 | positive | growth | 30-37 | mesophilic |
42011 | positive | growth | 37 | mesophilic |
116422 | positive | growth | 25-41 | |
116422 | no | growth | 5 | psychrophilic |
116422 | no | growth | 10 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 116422
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
23367 | no | |
69481 | no | 100 |
69480 | no | 99.994 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116422 | NaCl | positive | growth | 0-4 % |
116422 | NaCl | no | growth | 6 % |
116422 | NaCl | no | growth | 8 % |
116422 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
23367 | 27897 | tryptophan | - | energy source |
23367 | 17306 | maltose | - | growth |
23367 | 17992 | sucrose | - | growth |
23367 | 4853 | esculin | - | hydrolysis |
23367 | 53426 | tween 80 | - | hydrolysis |
23367 | 16301 | nitrite | - | reduction |
23367 | 27689 | decanoate | + | growth |
23367 | 16947 | citrate | + | growth |
23367 | 24996 | lactate | + | growth |
68369 | 25115 | malate | + | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | 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 |
116422 | 16947 | citrate | + | carbon source |
116422 | 4853 | esculin | - | hydrolysis |
116422 | 17632 | nitrate | - | reduction |
116422 | 16301 | nitrite | - | reduction |
116422 | 17632 | nitrate | - | respiration |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
23367 | 35581 | indole | no |
68369 | 35581 | indole | no |
116422 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
23367 | 35581 | indole | - |
68369 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
23367 | amylase | + | |
23367 | arginine dihydrolase | + | 3.5.3.6 |
23367 | beta-galactosidase | - | 3.2.1.23 |
23367 | catalase | + | 1.11.1.6 |
23367 | DNase | - | |
23367 | esterase lipase (C 8) | + | |
23367 | phosphoamidase | + | 3.9.1.1 |
23367 | tryptophan deaminase | - | 4.1.99.1 |
23367 | 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 |
116422 | oxidase | + | |
116422 | beta-galactosidase | - | 3.2.1.23 |
116422 | alcohol dehydrogenase | - | 1.1.1.1 |
116422 | gelatinase | - | |
116422 | amylase | - | |
116422 | DNase | - | |
116422 | caseinase | - | 3.4.21.50 |
116422 | catalase | + | 1.11.1.6 |
116422 | tween esterase | - | |
116422 | lecithinase | - | |
116422 | lipase | - | |
116422 | lysine decarboxylase | - | 4.1.1.18 |
116422 | ornithine decarboxylase | - | 4.1.1.17 |
116422 | protease | - | |
116422 | tryptophan deaminase | - | |
116422 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116422 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6473 | - | - | - | - | - | - | - | - | + | + | + | + | + | + | + | + | + | + | + | + | - |
6473 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | + | + | + | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116422 | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | + | + | + | + | + | + | + | - | - | + | - | + | + | + | + | - | + | + | + | + | + | - | - | - | - | - | + | + | - | + | + | + | + | + | - | - | - | - | - | + | + | + | + | + | + | + | - | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
6473 | sputum from cystic fibrosis patient | Denmark | DNK | Europe |
54244 | Human sputum,cystic fibrosis | Denmark | DNK | Europe |
116422 | Human, Sputum | Denmark | DNK | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Disease | #Cystic fibrosis |
#Infection | #Patient | |
#Host Body Product | #Fluids | #Sputum |
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: AY268172
- Sequence Identity:
- Total samples: 20583
- soil counts: 6943
- aquatic counts: 4192
- animal counts: 3605
- plant counts: 5843
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6473 | 2 | Risk group (German classification) |
116422 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pandoraea apista strain CCUG 38412 16S ribosomal RNA gene, partial sequence | AY268172 | 1461 | ena | 93218 |
6473 | Pandoraea apista strain LMG 16407 16S ribosomal RNA gene, partial sequence | AF139173 | 1485 | ena | 93218 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pandoraea apista DSM 16535 | GCA_001465595 | complete | ncbi | 93218 |
66792 | Pandoraea apista LMG16407 | GCA_001049515 | contig | ncbi | 93218 |
66792 | Pandoraea apista strain DSM 16535 | 93218.12 | complete | patric | 93218 |
66792 | Pandoraea apista strain DSM 16535 | 93218.21 | plasmid | patric | 93218 |
66792 | Pandoraea apista strain LMG16407 | 93218.9 | wgs | patric | 93218 |
66792 | Pandoraea apista LMG16407 | 2698536526 | draft | img | 93218 |
66792 | Pandoraea apista DSM 16535 | 2684623145 | complete | img | 93218 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 63.138 | no |
flagellated | no | 63.138 | no |
gram-positive | no | 98.924 | yes |
gram-positive | no | 98.924 | yes |
anaerobic | no | 99.215 | no |
anaerobic | no | 99.215 | no |
aerobic | yes | 93.209 | no |
aerobic | yes | 93.209 | no |
halophile | no | 93.797 | no |
halophile | no | 93.797 | no |
spore-forming | no | 95.681 | yes |
spore-forming | no | 95.681 | yes |
glucose-util | yes | 60.109 | no |
glucose-util | yes | 60.109 | no |
motile | yes | 91.004 | yes |
motile | yes | 91.004 | yes |
thermophile | no | 99.086 | yes |
thermophile | no | 99.086 | yes |
glucose-ferment | no | 90.354 | yes |
glucose-ferment | no | 90.354 | yes |
External links
@ref: 6473
culture collection no.: DSM 16535, CCM 4976, CCUG 38412, CIP 106627, LMG 16407
straininfo link
- @ref: 71706
- straininfo: 12489
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10758901 | 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 | Base Composition, Betaproteobacteria/chemistry/*classification/genetics/physiology, Burkholderia/classification/genetics, Burkholderia Infections/microbiology, Cystic Fibrosis/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Electrophoresis, Polyacrylamide Gel, Fatty Acids/analysis, Genes, rRNA, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sputum/*microbiology | Enzymology |
Genetics | 26564037 | Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain. | Millard AD, Westblade LF, LiPuma JJ, Vavikolanu K, Read TD, Pallen MJ, Burd EM, Constantinidou CI | Genome Announc | 10.1128/genomeA.01300-15 | 2015 | ||
27790203 | Characterization and Comparative Overview of Complete Sequences of the First Plasmids of Pandoraea across Clinical and Non-clinical Strains. | Yong D, Tee KK, Yin WF, Chan KG | Front Microbiol | 10.3389/fmicb.2016.01606 | 2016 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6473 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16535) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16535 | |||
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 | |
23367 | T Coenye, E Falsen, B Hoste, M Ohlén, J Goris, J R Govan, M Gillis, P Vandamme | 10.1099/00207713-50-2-887 | 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 | 10758901 | |
42011 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18779 | ||||
54244 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 38412) | https://www.ccug.se/strain?id=38412 | |||
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 | |||||
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 | |||
71706 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID12489.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116422 | Curators of the CIP | Collection of Institut Pasteur (CIP 106627) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106627 |