Strain identifier
BacDive ID: 24549
Type strain: 
Species: Pedobacter nutrimenti
Strain Designation: J22
Strain history: <- B. Derichs, Univ. Bonn, Germany; J22
NCBI tax ID(s): 1241337 (species)
version 9.1 (current version)
General
@ref: 20727
BacDive-ID: 24549
DSM-Number: 27372
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative
description: Pedobacter nutrimenti J22 is an aerobe, Gram-negative bacterium that was isolated from refrigerated fresh pasta filled with pork .
NCBI tax id
- NCBI tax id: 1241337
- Matching level: species
strain history
- @ref: 20727
- history: <- B. Derichs, Univ. Bonn, Germany; J22
doi: 10.13145/bacdive24549.20240916.9.1
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 nutrimenti
- full scientific name: Pedobacter nutrimenti Derichs et al. 2014
@ref: 20727
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter nutrimenti
full scientific name: Pedobacter nutrimenti Derichs et al. 2014
strain designation: J22
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.444
colony morphology
- @ref: 63124
- incubation period: 2 days
Culture and growth conditions
culture medium
- @ref: 20727
- name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
- growth: yes
- link: https://mediadive.dsmz.de/medium/545
- composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
culture temp
- @ref: 63124
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 63124
- oxygen tolerance: aerobe
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 20727 | refrigerated fresh pasta filled with pork (tortellini) | Bonn | Germany | DEU | Europe | |
| 63124 | Food,chilled | Bonn | Germany | DEU | Europe | 2010-03-15 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | #Food |
| #Engineered | #Food production | #Meat |
| #Host | #Mammals | #Suidae (Pig,Swine) |
Safety information
risk assessment
- @ref: 20727
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20727
- description: Pedobacter nutrimenti partial 16S rRNA gene, type strain J22T
- accession: HF536497
- length: 1457
- database: nuccore
- NCBI tax ID: 1241337
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pedobacter nutrimenti DSM 27372 | GCA_003208655 | scaffold | ncbi | 1241337 |
| 66792 | Pedobacter nutrimenti strain DSM 27372 | 1241337.3 | wgs | patric | 1241337 |
| 66792 | Pedobacter nutrimenti DSM 27372 | 2619619049 | draft | img | 1241337 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.444 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.445 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 84.929 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.01 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.847 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 84.5 | no |
External links
@ref: 20727
culture collection no.: DSM 27372, CCUG 64422
straininfo link
- @ref: 88404
- straininfo: 400780
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24425748 | Pedobacter nutrimenti sp. nov., isolated from chilled food. | Derichs J, Kampfer P, Lipski A | Int J Syst Evol Microbiol | 10.1099/ijs.0.058677-0 | 2014 | Animals, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Meat/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Swine, Vitamin K 2/analogs & derivatives/chemistry | Biotechnology |
| Phylogeny | 33502299 | Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana. | Qi SS, Cnockaert M, Carlier A, Vandamme P | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004667 | 2021 |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 20727 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27372 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27372) | |||
| 63124 | Curators of the CCUG | https://www.ccug.se/strain?id=64422 | Culture Collection University of Gothenburg (CCUG) (CCUG 64422) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 88404 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID400780.1 |