Strain identifier
BacDive ID: 11630
Type strain:
Species: Paenibacillus urinalis
Strain Designation: 5402403
Strain history: CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 5402403
NCBI tax ID(s): 521520 (species)
General
@ref: 16176
BacDive-ID: 11630
DSM-Number: 22281
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-negative, motile, rod-shaped, human pathogen
description: Paenibacillus urinalis 5402403 is a facultative anaerobe, spore-forming, mesophilic human pathogen that was isolated from Human urine, 36-yr-old woman.
NCBI tax id
- NCBI tax id: 521520
- Matching level: species
strain history
@ref | history |
---|---|
37526 | 2006, V. Roux, Timone Hosp., Marseille, France: strain 5402403 |
16176 | <- CCUG; CCUG 53521 <- V. Roux; Timone hospital, Marseille, France; 5402403 |
123753 | CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 5402403 |
doi: 10.13145/bacdive11630.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Paenibacillaceae
- genus: Paenibacillus
- species: Paenibacillus urinalis
- full scientific name: Paenibacillus urinalis Roux et al. 2008
@ref: 16176
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus urinalis
full scientific name: Paenibacillus urinalis Roux et al. 2008
strain designation: 5402403
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32267 | negative | 3.2 µm | 1 µm | rod-shaped | yes | |
69480 | yes | 96.573 | ||||
69480 | positive | 100 | ||||
123753 | positive | rod-shaped | yes |
pigmentation
- @ref: 32267
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16176 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water |
37526 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123753 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16176 | positive | growth | 35 | mesophilic |
32267 | positive | growth | 30-37 | mesophilic |
32267 | positive | optimum | 33.5 | mesophilic |
37526 | positive | growth | 37 | mesophilic |
59923 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32267 | facultative anaerobe |
59923 | aerobe |
123753 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
32267 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
halophily
- @ref: 32267
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 5 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32267 | 22599 | arabinose | + | carbon source |
32267 | 17234 | glucose | + | carbon source |
32267 | 17306 | maltose | + | carbon source |
32267 | 29864 | mannitol | + | carbon source |
32267 | 506227 | N-acetylglucosamine | + | carbon source |
32267 | 4853 | esculin | + | hydrolysis |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | + | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | + | builds acid from |
68371 | 16634 | raffinose | + | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | + | builds acid from |
68371 | 17716 | lactose | + | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 27613 | amygdalin | + | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 16899 | D-mannitol | + | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | + | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | + | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | + | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 30849 | L-arabinose | + | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
123753 | 17632 | nitrate | - | reduction |
123753 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 123753
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
32267 | catalase | + | 1.11.1.6 |
123753 | oxidase | - | |
123753 | catalase | + | 1.11.1.6 |
123753 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123753 | - | - | + | + | - | + | - | - | - | + | - | + | + | + | - | - | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123753 | - | - | - | + | + | + | - | - | + | + | + | + | + | - | + | - | - | + | +/- | +/- | +/- | + | + | + | + | + | + | + | + | + | + | +/- | - | +/- | + | + | - | - | +/- | +/- | - | - | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
16176 | Human urine, 36-yr-old woman | Timone hospital, Marseille | France | FRA | Europe | ||
59923 | Human urine,36-yr-old woman | Marseille,Timone hospital | France | FRA | Europe | 2005-11-01 | |
123753 | Human, Urine | Marseille | France | FRA | Europe | 2005 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | #Female |
#Host Body Product | #Fluids | #Urine |
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
16176 | yes, in single cases | 1 | Risk group (German classification) |
123753 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 16176
- description: Paenibacillus urinalis strain 5402403 16S ribosomal RNA gene, partial sequence
- accession: EF212892
- length: 1403
- database: ena
- NCBI tax ID: 1204727
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paenibacillus urinalis strain DSM 22281 | 521520.3 | wgs | patric | 521520 |
66792 | Paenibacillus urinalis DSM 22281 | 2901084651 | draft | img | 521520 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 76.149 | yes |
anaerobic | no | 98.85 | no |
halophile | no | 78.42 | no |
spore-forming | yes | 94.926 | no |
glucose-util | yes | 92.626 | yes |
aerobic | yes | 92.161 | no |
thermophile | no | 98.19 | yes |
flagellated | yes | 88.35 | no |
motile | yes | 91.883 | no |
glucose-ferment | no | 87.125 | no |
External links
@ref: 16176
culture collection no.: DSM 22281, CCUG 53521, CIP 109357, CCUG 53521T
straininfo link
- @ref: 80855
- straininfo: 343460
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18319478 | Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine. | Roux V, Fenner L, Raoult D | Int J Syst Evol Microbiol | 10.1099/ijs.0.65228-0 | 2008 | Adult, Bacterial Typing Techniques, Cerebrospinal Fluid/*microbiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Female, Genes, rRNA, Genotype, Gram-Negative Bacteria/*classification/genetics/*isolation & purification, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Urine/*microbiology | Genetics |
Phylogeny | 26310301 | Paenibacillus insulae sp. nov., isolated from soil. | Cho SJ, Cho SH, Kim TS, Park SH, Kim SB, Lee GH | J Microbiol | 10.1007/s12275-015-4610-x | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Genome, Bacterial, Nucleic Acid Hybridization, Paenibacillus/chemistry/*genetics/growth & development/*isolation & purification, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Phylogeny | 29134934 | Paenibacillus shunpengii sp. nov., isolated from farmland soil. | Yang YJ, Zhang YT, Chen GQ, Cheng D, Qiu JG, He Q, He J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002484 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16176 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22281) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22281 | |||
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 | |||
32267 | 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 | 28508 | 28776041 | |
37526 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7089 | ||||
59923 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 53521) | https://www.ccug.se/strain?id=53521 | |||
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 | |||||
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 | |||
80855 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID343460.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123753 | Curators of the CIP | Collection of Institut Pasteur (CIP 109357) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109357 |