Strain identifier
BacDive ID: 14107
Type strain:
Species: Pedobacter metabolipauper
Strain Designation: WB2.3-71
Strain history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-71
NCBI tax ID(s): 425513 (species)
General
@ref: 7854
BacDive-ID: 14107
DSM-Number: 19035
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Pedobacter metabolipauper WB2.3-71 is a mesophilic, Gram-negative, motile bacterium that was isolated from stream water.
NCBI tax id
- NCBI tax id: 425513
- Matching level: species
strain history
- @ref: 7854
- history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-71
doi: 10.13145/bacdive14107.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter metabolipauper
- full scientific name: Pedobacter metabolipauper Muurholm et al. 2007
@ref: 7854
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter metabolipauper
full scientific name: Pedobacter metabolipauper Muurholm et al. 2007
strain designation: WB2.3-71
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32230 | negative | 2.2 µm | 0.83 µm | rod-shaped | yes | |
69480 | no | 90.154 | ||||
69480 | negative | 99.982 |
pigmentation
- @ref: 32230
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7854 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
33301 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7854 | positive | growth | 25 | mesophilic |
32230 | positive | growth | 08-31 | |
32230 | positive | optimum | 25 | mesophilic |
33301 | positive | growth | 15 | psychrophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32230 | positive | growth | 5.9-8.0 |
32230 | positive | optimum | 6.95 |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
32230 | no | |
69481 | no | 100 |
69480 | no | 99.979 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32230 | NaCl | positive | growth | <4 % |
32230 | NaCl | positive | optimum | 2 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32230 | 17057 | cellobiose | + | carbon source |
32230 | 17234 | glucose | + | carbon source |
32230 | 17716 | lactose | + | carbon source |
32230 | 17306 | maltose | + | carbon source |
32230 | 37684 | mannose | + | carbon source |
32230 | 28053 | melibiose | + | carbon source |
32230 | 17992 | sucrose | + | carbon source |
32230 | 27082 | trehalose | + | carbon source |
32230 | 53426 | tween 80 | + | carbon source |
32230 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32230 | alkaline phosphatase | + | 3.1.3.1 |
32230 | catalase | + | 1.11.1.6 |
32230 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 7854
- sample type: stream water
- geographic location: Lower Saxony, Westhöfer Bach
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #River (Creek)
Safety information
risk assessment
- @ref: 7854
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 32230
- description: Pedobacter metabolipauper partial 16S rRNA gene, type strain WB2.3-71T
- accession: AM491370
- length: 1505
- database: nuccore
- NCBI tax ID: 425513
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pedobacter metabolipauper DSM 19035 | GCA_004362715 | scaffold | ncbi | 425513 |
66792 | Pedobacter metabolipauper strain DSM 19035 | 425513.4 | wgs | patric | 425513 |
66792 | Pedobacter metabolipauper DSM 19035 | 2636416080 | draft | img | 425513 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 85.677 | yes |
flagellated | no | 96.598 | no |
gram-positive | no | 97.931 | yes |
anaerobic | no | 99.172 | no |
aerobic | yes | 87.6 | no |
halophile | no | 96.604 | no |
spore-forming | no | 95.979 | yes |
glucose-util | yes | 90.182 | yes |
thermophile | no | 99.28 | yes |
glucose-ferment | no | 90.896 | no |
External links
@ref: 7854
culture collection no.: DSM 19035
straininfo link
- @ref: 83274
- straininfo: 310980
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17911287 | Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet. | Muurholm S, Cousin S, Pauker O, Brambilla E, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.65166-0 | 2007 | Animals, Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Germany, Molecular Sequence Data, Organic Chemicals/metabolism, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid | Genetics |
Phylogeny | 24659428 | Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field. | Ngo HT, Son HM, Park SY, Kim KY, Yi TH | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0154-z | 2014 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Phylogeny | 25520261 | Pedobacter bambusae sp. nov., isolated from soil of a bamboo plantation. | Won KH, Kook M, Yi TH | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0352-8 | 2014 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Poaceae/growth & development, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7854 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19035) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19035 | ||||
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 | ||||
32230 | 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 | 28472 | 28776041 | ||
33301 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7228 | |||||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
83274 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID310980.1 | StrainInfo: A central database for resolving microbial strain identifiers |