Strain identifier
BacDive ID: 1566
Type strain:
Species: Psychrobacillus psychrodurans
Strain Designation: 68E3, 68000
Strain history: CIP <- 2008, DSMZ <- H.A. Abd El-Rahman, Egypt: strain 68E3
NCBI tax ID(s): 126157 (species)
General
@ref: 4453
BacDive-ID: 1566
DSM-Number: 11713
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, motile
description: Psychrobacillus psychrodurans 68E3 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.
NCBI tax id
- NCBI tax id: 126157
- Matching level: species
strain history
@ref | history |
---|---|
4453 | <- H. A. Abd El-Rahman; 68E3 |
122016 | CIP <- 2008, DSMZ <- H.A. Abd El-Rahman, Egypt: strain 68E3 |
doi: 10.13145/bacdive1566.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Caryophanaceae
- genus: Psychrobacillus
- species: Psychrobacillus psychrodurans
- full scientific name: Psychrobacillus psychrodurans (Abd El-Rahman et al. 2002) Krishnamurthi et al. 2011
synonyms
- @ref: 20215
- synonym: Bacillus psychrodurans
@ref: 4453
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Caryophanaceae
genus: Psychrobacillus
species: Psychrobacillus psychrodurans
full scientific name: Psychrobacillus psychrodurans (Abd El-Rahman et al. 2002) Krishnamurthi et al. 2011
strain designation: 68E3, 68000
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 98.72 | ||
69480 | 100 | positive | ||
122016 | yes | positive | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4453 | 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 |
38231 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122016 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4453 | positive | growth | 25 | mesophilic |
38231 | positive | growth | 25 | mesophilic |
122016 | positive | growth | 22-45 | |
122016 | no | growth | 10 | psychrophilic |
122016 | no | growth | 55 | thermophilic |
culture pH
- @ref: 122016
- ability: positive
- type: growth
- pH: 6
Physiology and metabolism
oxygen tolerance
- @ref: 122016
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
122016 | yes |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
122016 | NaCl | positive | growth | 0-6 % |
122016 | NaCl | no | growth | 8 % |
122016 | NaCl | no | growth | 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 | 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 | 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 |
122016 | citrate | - | carbon source | 16947 |
122016 | esculin | - | hydrolysis | 4853 |
122016 | hippurate | + | hydrolysis | 606565 |
122016 | nitrate | + | reduction | 17632 |
122016 | nitrite | - | reduction | 16301 |
122016 | nitrate | - | respiration | 17632 |
antibiotic resistance
- @ref: 122016
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
- @ref: 122016
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
122016 | 15688 | acetoin | - | |
122016 | 17234 | glucose | - |
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 |
122016 | oxidase | + | |
122016 | beta-galactosidase | - | 3.2.1.23 |
122016 | alcohol dehydrogenase | - | 1.1.1.1 |
122016 | gelatinase | - | |
122016 | amylase | - | |
122016 | DNase | - | |
122016 | caseinase | + | 3.4.21.50 |
122016 | catalase | + | 1.11.1.6 |
122016 | tween esterase | + | |
122016 | gamma-glutamyltransferase | + | 2.3.2.2 |
122016 | lecithinase | - | |
122016 | lipase | - | |
122016 | lysine decarboxylase | - | 4.1.1.18 |
122016 | ornithine decarboxylase | - | 4.1.1.17 |
122016 | protease | - | |
122016 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122016 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122016 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122016 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
4453 | garden soil | El-Kanater | Egypt | EGY | Africa |
122016 | Environment, Soil | El Kanater | Egypt | EGY | Africa |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Engineered | #Agriculture | #Garden |
taxonmaps
- @ref: 69479
- File name: preview.99_15779.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_221;97_240;98_269;99_15779&stattab=map
- Last taxonomy: Psychrobacillus
- 16S sequence: AJ277984
- Sequence Identity:
- Total samples: 8478
- soil counts: 5352
- aquatic counts: 817
- animal counts: 1751
- plant counts: 558
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
4453 | 1 | Risk group (German classification) |
122016 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bacillus psychrodurans partial 16S rRNA gene, isolate OS-64.c | AM237365 | 956 | ena | 126157 |
4453 | Bacillus psychrodurans 16S rRNA gene, strain DSM 11713 | AJ277984 | 1486 | ena | 126157 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Psychrobacillus psychrodurans DSM 11713 | GCA_900114885 | contig | ncbi | 126157 |
66792 | Psychrobacillus psychrodurans strain DSM 11713 | 126157.3 | wgs | patric | 126157 |
66792 | Psychrobacillus psychrodurans DSM 11713 | 2675903167 | draft | img | 126157 |
66792 | Psychrobacillus psychrodurans DSM 11713 | GCA_027563345 | scaffold | ncbi | 126157 |
GC content
- @ref: 4453
- GC-content: 36.3
- method: Buoyant density centrifugation (BD)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 90.755 | no |
gram-positive | yes | 93.728 | no |
anaerobic | no | 98.37 | no |
aerobic | yes | 91.416 | no |
halophile | no | 60.764 | no |
spore-forming | yes | 92.719 | no |
thermophile | no | 99.239 | yes |
glucose-util | yes | 87.142 | no |
flagellated | yes | 86.674 | no |
glucose-ferment | no | 87.126 | no |
External links
@ref: 4453
culture collection no.: DSM 11713, ATCC BAA 796, CIP 107791, NCIMB 13837
straininfo link
- @ref: 71211
- straininfo: 87967
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12508879 | Two novel psychrotolerant species, Bacillus psychrotolerans sp. nov. and Bacillus psychrodurans sp. nov., which contain ornithine in their cell walls. | Abd El-Rahman HA, Fritze D, Sproer C, Claus D | Int J Syst Evol Microbiol | 10.1099/00207713-52-6-2127 | 2002 | Bacillus/*classification/genetics/*metabolism, Base Composition, Cell Wall/metabolism, Cold Temperature, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Ornithine/*metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as Topic | Metabolism |
Phylogeny | 20650590 | Psychrobacillus gen. nov. and proposal for reclassification of Bacillus insolitus Larkin & Stokes, 1967, B. psychrotolerans Abd-El Rahman et al., 2002 and B. psychrodurans Abd-El Rahman et al., 2002 as Psychrobacillus insolitus comb. nov., Psychrobacillus psychrotolerans comb. nov. and Psychrobacillus psychrodurans comb. nov. | Krishnamurthi S, Ruckmani A, Pukall R, Chakrabarti T | Syst Appl Microbiol | 10.1016/j.syapm.2010.06.003 | 2010 | Bacillus/*classification/cytology/genetics/physiology, *Bacterial Typing Techniques, Base Composition, Base Sequence, Carbohydrates/chemistry, Chemotaxis, Cold Temperature, DNA, Bacterial/genetics, *Gram-Positive Endospore-Forming Rods/classification/cytology/genetics/physiology, Lipids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, RNA, Species Specificity, Terpenes/chemistry | Genetics |
Phylogeny | 28933325 | Psychrobacillus lasiicapitis sp. nov., isolated from the head of an ant (Lasius fuliginosus). | Shen Y, Fu Y, Yu Y, Zhao J, Li J, Li Y, Wang X, Zhang J, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002315 | 2017 | Animals, Ants/*microbiology, Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 31985396 | Psychrobacillus glaciei sp. nov., a psychrotolerant species isolated from an Antarctic iceberg. | Choi JY, Lee PC | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003998 | 2020 | Antarctic Regions, Bacillaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4453 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11713) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11713 | |||
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 | |
38231 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5265 | ||||
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 | |||
71211 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87967.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122016 | Curators of the CIP | Collection of Institut Pasteur (CIP 107791) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107791 |