Strain identifier
BacDive ID: 8180
Type strain:
Species: Psychrobacter frigidicola
Strain history: CIP <- 1997, ACAM <- Jeremy Austin
NCBI tax ID(s): 45611 (species)
General
@ref: 4548
BacDive-ID: 8180
DSM-Number: 12411
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative
description: Psychrobacter frigidicola DSM 12411 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from ornithogenic soil.
NCBI tax id
- NCBI tax id: 45611
- Matching level: species
strain history
@ref | history |
---|---|
4548 | <- ACAM <- J. P. Bowman <- J. Austin |
119462 | CIP <- 1997, ACAM <- Jeremy Austin |
doi: 10.13145/bacdive8180.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Moraxellaceae
- genus: Psychrobacter
- species: Psychrobacter frigidicola
- full scientific name: Psychrobacter frigidicola Bowman et al. 1996
@ref: 4548
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Moraxellaceae
genus: Psychrobacter
species: Psychrobacter frigidicola
full scientific name: Psychrobacter frigidicola Bowman et al. 1996
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.999 | ||
119462 | negative | coccus-shaped | no |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4548 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
41492 | MEDIUM 118 - for Pasteurella, Actinobacillus and Psychrobacter frigidicola | yes | Distilled water make up to (1000.000 ml);Yeast extract (1.000 g);Tryptocasein soy agar (40.000 g) | |
119462 | CIP Medium 118-b | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=118-b |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4548 | positive | growth | 10 | psychrophilic |
41492 | positive | growth | 10 | psychrophilic |
52069 | positive | growth | 10-15 | psychrophilic |
119462 | positive | growth | 5-30 | |
119462 | no | growth | 37 | mesophilic |
119462 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
52069 | aerobe |
119462 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
halophily
- @ref: 119462
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-10 %
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | - | builds acid from | 16024 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | - | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
119462 | citrate | - | carbon source | 16947 |
119462 | esculin | - | hydrolysis | 4853 |
119462 | glucose | - | fermentation | 17234 |
119462 | lactose | - | fermentation | 17716 |
119462 | nitrate | - | reduction | 17632 |
119462 | nitrite | - | reduction | 16301 |
119462 | sodium thiosulfate | - | builds gas from | 132112 |
119462 | glucose | - | degradation | 17234 |
119462 | nitrate | - | respiration | 17632 |
antibiotic resistance
- @ref: 119462
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 119462
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
119462 | 15688 | acetoin | - | |
119462 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
119462 | oxidase | + | |
119462 | beta-galactosidase | - | 3.2.1.23 |
119462 | alcohol dehydrogenase | - | 1.1.1.1 |
119462 | gelatinase | - | |
119462 | amylase | - | |
119462 | DNase | - | |
119462 | caseinase | - | 3.4.21.50 |
119462 | catalase | + | 1.11.1.6 |
119462 | tween esterase | - | |
119462 | gamma-glutamyltransferase | + | 2.3.2.2 |
119462 | lecithinase | - | |
119462 | lipase | - | |
119462 | lysine decarboxylase | - | 4.1.1.18 |
119462 | ornithine decarboxylase | - | 4.1.1.17 |
119462 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
119462 | tryptophan deaminase | - | |
119462 | 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 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 52069 C9:0 0.5 9 52069 C10:0 3.5 10 52069 C16:0 1.3 16 52069 C18:0 0.6 18 52069 C12:0 3OH 2.6 13.455 52069 C14:0 3OH/C16:1 ISO I 1.2 15.485 52069 C15:0 ISO 3OH 4.8 16.135 52069 C16:1 ω11c 0.4 15.757 52069 C16:1 ω7c 21.1 15.819 52069 C17:0 iso 0.5 16.629 52069 C17:1 ω9c 2.5 16.773 52069 C18:1 ω9c 27.2 17.769 52069 C18:2 ω6,9c/C18:0 ANTE 1.5 17.724 52069 Unidentified 18.1 9.143 52069 Unidentified 2.5 9.432 52069 Unidentified 1.5 10.239 52069 Unidentified 1.9 12.672 52069 Unidentified 0.6 16.289 52069 Unidentified 0.6 17.109 52069 Unidentified 7.3 18.093 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119462 | - | - | + | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119462 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119462 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | continent | latitude | longitude | sampling date | country | origin.country | isolation date |
---|---|---|---|---|---|---|---|---|---|
4548 | ornithogenic soil | S68°32'30" E77°54'30", Magnetic Island, Vest fold Hills | Australia and Oceania | -68.5417 | 77.9083 | ||||
52069 | Soil,ornithogenic | Antarctic coast,Magnetic Island | Australia and Oceania | 1991-12-01 | Antarctica | ATA | |||
119462 | Environment, Ornithogenic soil | Antarctica | Antarctica | ATA | 1990 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Host | #Birds | |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_275.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_209;98_234;99_275&stattab=map
- Last taxonomy: Psychrobacter
- 16S sequence: AJ609556
- Sequence Identity:
- Total samples: 2913
- soil counts: 306
- aquatic counts: 1127
- animal counts: 1430
- plant counts: 50
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
4548 | 1 | Risk group (German classification) |
119462 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Psychrobacter frigidicola ACAM 304 16S ribosomal RNA gene | U46143 | 1484 | ena | 45611 |
4548 | Psychrobacter frigidicola 16S rRNA gene, type strain DSM 12411T | AJ609556 | 1528 | ena | 45611 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Psychrobacter frigidicola Psychrobacter frigidicola ACAM304 | GCA_904845925 | contig | ncbi | 45611 |
66792 | Psychrobacter frigidicola ACAM 304 | GCA_007997305 | contig | ncbi | 45611 |
66792 | Psychrobacter frigidicola strain ACAM 304 | 45611.3 | wgs | patric | 45611 |
66792 | Psychrobacter frigidicola strain Psychrobacter frigidicola ACAM304 | 45611.4 | wgs | patric | 45611 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.614 | no |
anaerobic | no | 98.678 | yes |
halophile | yes | 71.801 | no |
spore-forming | no | 96.982 | no |
glucose-util | no | 63.418 | no |
aerobic | yes | 78.08 | no |
flagellated | no | 92.924 | no |
thermophile | no | 99.525 | yes |
motile | no | 90.186 | no |
glucose-ferment | no | 93.713 | no |
External links
@ref: 4548
culture collection no.: DSM 12411, ACAM 304, ATCC 700361, CCUG 34377, CIP 10501, CIP 105101
straininfo link
- @ref: 77583
- straininfo: 46959
literature
- topic: Pathogenicity
- Pubmed-ID: 8863407
- title: Novel Psychrobacter species from Antarctic ornithogenic soils.
- authors: Bowman JP, Cavanagh J, Austin JJ, Sanderson K
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-46-4-841
- year: 1996
- mesh: Antarctic Regions, Base Composition, Base Sequence, DNA, Ribosomal/chemistry, Humans, Lipids/analysis, Molecular Sequence Data, Moraxella/chemistry/*classification/genetics, Phenotype, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4548 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12411) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12411 | |||
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 | |
41492 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17082 | ||||
52069 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 34377) | https://www.ccug.se/strain?id=34377 | |||
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) | |||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
77583 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46959.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119462 | Curators of the CIP | Collection of Institut Pasteur (CIP 105101) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105101 |