Strain identifier
BacDive ID: 14105
Type strain:
Species: Pedobacter hartonius
Strain Designation: WB3.3-3
Strain history: CIP <- 2007, DSMZ <- S. Muurholm, Weyhausen, Germany <- E. Brambilla <- O. Päuker: strain WB3.3-3
NCBI tax ID(s): 425514 (species)
General
@ref: 7852
BacDive-ID: 14105
DSM-Number: 19033
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Pedobacter hartonius WB3.3-3 is an obligate aerobe, psychrophilic, Gram-negative bacterium that was isolated from stream water.
NCBI tax id
- NCBI tax id: 425514
- Matching level: species
strain history
@ref | history |
---|---|
7852 | <- S. Muurholm <- E. Brambilla <- O. Päuker; |
119843 | CIP <- 2007, DSMZ <- S. Muurholm, Weyhausen, Germany <- E. Brambilla <- O. Päuker: strain WB3.3-3 |
doi: 10.13145/bacdive14105.20230509.8.1
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 hartonius
- full scientific name: Pedobacter hartonius Muurholm et al. 2007
@ref: 7852
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter hartonius
full scientific name: Pedobacter hartonius Muurholm et al. 2007
strain designation: WB3.3-3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32230 | negative | 2 µm | 0.73 µm | rod-shaped | yes | |
69480 | negative | 99.995 | ||||
119843 | negative | rod-shaped | no |
pigmentation
- @ref: 32230
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7852 | 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 |
37562 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
119843 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
119843 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7852 | positive | growth | 12 | psychrophilic |
32230 | positive | growth | 06-26 | |
32230 | positive | optimum | 14 | psychrophilic |
37562 | positive | growth | 15 | psychrophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32230 | positive | growth | 5.7-7.8 |
32230 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
- @ref: 119843
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32230 | no | |
69481 | no | 100 |
69480 | no | 99.988 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32230 | NaCl | positive | growth | 0-4 % |
32230 | NaCl | positive | optimum | 2 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32230 | 22599 | arabinose | + | carbon source |
32230 | 18403 | L-arabitol | + | carbon source |
32230 | 17057 | cellobiose | + | carbon source |
32230 | 23652 | dextrin | + | carbon source |
32230 | 28757 | fructose | + | carbon source |
32230 | 28260 | galactose | + | carbon source |
32230 | 5291 | gelatin | + | carbon source |
32230 | 17234 | glucose | + | carbon source |
32230 | 17716 | lactose | + | carbon source |
32230 | 17306 | maltose | + | carbon source |
32230 | 29864 | mannitol | + | carbon source |
32230 | 37684 | mannose | + | carbon source |
32230 | 28053 | melibiose | + | carbon source |
32230 | 37657 | methyl D-glucoside | + | carbon source |
32230 | 506227 | N-acetylglucosamine | + | carbon source |
32230 | 26546 | rhamnose | + | carbon source |
32230 | 17814 | salicin | + | carbon source |
32230 | 27082 | trehalose | + | carbon source |
32230 | 53426 | tween 80 | + | carbon source |
32230 | 18222 | xylose | + | carbon source |
32230 | 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 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | 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 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | 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 | 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 | 16988 | D-ribose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
119843 | 17632 | nitrate | - | reduction |
119843 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 119843
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
32230 | alkaline phosphatase | + | 3.1.3.1 |
32230 | catalase | + | 1.11.1.6 |
32230 | gelatinase | + | |
32230 | cytochrome oxidase | + | 1.9.3.1 |
119843 | oxidase | + | |
119843 | catalase | - | 1.11.1.6 |
119843 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119843 | - | + | + | + | - | + | - | - | - | - | + | + | - | + | - | - | + | + | + | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119843 | - | - | - | +/- | - | +/- | - | - | - | - | +/- | +/- | +/- | - | - | - | - | - | - | - | - | - | +/- | - | +/- | - | - | +/- | - | - | - | +/- | - | - | - | +/- | - | - | +/- | +/- | +/- | - | - | +/- | +/- | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
7852 | stream water | Lower Saxony, Westhöfer Bach | Germany | DEU | Europe | |
119843 | Environment, Fresh water | Westerhöfer Bach, Harz mountains | Germany | DEU | Europe | 2005 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #River (Creek)
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7852 | 1 | Risk group (German classification) |
119843 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 32230
- description: Pedobacter hartonius partial 16S rRNA gene, type strain WB3.3-3T
- accession: AM491371
- length: 1492
- database: nuccore
- NCBI tax ID: 425514
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pedobacter hartonius DSM 19033 | GCA_900107535 | scaffold | ncbi | 425514 |
66792 | Pedobacter hartonius strain DSM 19033 | 425514.7 | wgs | patric | 425514 |
66792 | Pedobacter hartonius DSM 19033 | 2693429882 | draft | img | 425514 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 83.323 | yes |
glucose-ferment | no | 87.98 | no |
flagellated | no | 97.247 | no |
gram-positive | no | 96.409 | yes |
anaerobic | no | 99.191 | no |
aerobic | yes | 85.532 | no |
halophile | no | 95.459 | no |
spore-forming | no | 93.05 | no |
thermophile | no | 99.6 | yes |
glucose-util | yes | 89.011 | yes |
External links
@ref: 7852
culture collection no.: DSM 19033, CIP 109468
straininfo link
- @ref: 83272
- straininfo: 310979
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 | 28109203 | Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine. | Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodriguez-Alcala LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001814 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sphingolipids, *Uranium, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7852 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19033) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19033 | ||||
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 | ||
37562 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7215 | |||||
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 | ||
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 | ||||
83272 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID310979.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
119843 | Curators of the CIP | Collection of Institut Pasteur (CIP 109468) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109468 |