Strain identifier
BacDive ID: 140303
Type strain:
Species: Rodentibacter trehalosifermentans
Strain Designation: H1987082031
Strain history: <- H. Christensen, University of Copenhagen, Frederiksberg, DENMARK; H1987082031 <-W. Nicklas, German Cancer Research Centre, Heidelberg, Germany
NCBI tax ID(s): 1908263 (species)
General
@ref: 42910
BacDive-ID: 140303
DSM-Number: 104075
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, colony-forming, animal pathogen
description: Rodentibacter trehalosifermentans H1987082031 is a microaerophile, mesophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from laboratory rat, trachea.
NCBI tax id
- NCBI tax id: 1908263
- Matching level: species
strain history
- @ref: 42910
- history: <- H. Christensen, University of Copenhagen, Frederiksberg, DENMARK; H1987082031 <-W. Nicklas, German Cancer Research Centre, Heidelberg, Germany
doi: 10.13145/bacdive140303.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pasteurellales
- family: Pasteurellaceae
- genus: Rodentibacter
- species: Rodentibacter trehalosifermentans
- full scientific name: Rodentibacter trehalosifermentans Adhikary et al. 2017
@ref: 42910
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pasteurellales
family: Pasteurellaceae
genus: Rodentibacter
species: Rodentibacter trehalosifermentans
full scientific name: Rodentibacter trehalosifermentans Adhikary et al. 2017
strain designation: H1987082031
type strain: yes
Morphology
cell morphology
- @ref: 43243
- gram stain: negative
- motility: no
colony morphology
- @ref: 43243
- type of hemolysis: gamma
- colony size: 1-2 mm
- colony shape: circular
- incubation period: 1 day
- medium used: Bovine blood agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43243 | Bovine blood agar | yes | ||
42910 | CHOCOLATE AGAR (DSMZ Medium 429b) | yes | https://mediadive.dsmz.de/medium/429b | Name: CHOCOLATE AGAR (DSMZ Medium 429b) Composition: Horse blood 100.0 g/l Sheep blood 100.0 g/l Columbia agar base |
42910 | BHI/3 MEDIUM (DSMZ Medium 218) | yes | https://mediadive.dsmz.de/medium/218 | Name: BHI/3 MEDIUM (DSMZ Medium 218) Composition: Brain heart infusion 37.0 g/l Casein hydrolysate 10.0 g/l Starch 1.0 g/l Distilled water |
42910 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
63643 | positive | growth | 37 | mesophilic |
42910 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 63643
- oxygen tolerance: microaerophile
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43243 | 13389 | nad | + | required for growth |
43243 | 17234 | glucose | - | fermentation |
43243 | 16537 | galactarate | + | builds acid from |
43243 | 15792 | malonate | + | builds base from |
43243 | 15226 | tetrathionate | - | reduction |
43243 | 53424 | tween 20 | - | hydrolysis |
43243 | 48095 | (-)-D-fructose | + | builds acid from |
43243 | 12936 | D-galactose | + | builds acid from |
43243 | 17306 | maltose | + | builds acid from |
43243 | 17634 | (+)-D-glucose | + | builds acid from |
43243 | 48095 | (-)-D-fructose | - | builds gas from |
43243 | 12936 | D-galactose | - | builds gas from |
43243 | 17306 | maltose | - | builds gas from |
43243 | 17634 | (+)-D-glucose | - | builds gas from |
43243 | 17113 | erythritol | - | builds acid from |
43243 | 15963 | ribitol | - | builds acid from |
43243 | 17151 | xylitol | - | builds acid from |
43243 | 18333 | (+)-D-arabitol | - | builds acid from |
43243 | 65328 | (-)-L-xylose | - | builds acid from |
43243 | 16813 | galactitol | - | builds acid from |
43243 | 17924 | D-sorbitol | + | builds acid from |
43243 | 28847 | (+)-D-fucose | - | builds acid from |
43243 | 62345 | L-rhamnose | - | builds acid from |
43243 | 17266 | (-)-L-sorbose | - | builds acid from |
43243 | 17057 | cellobiose | - | builds acid from |
43243 | 6731 | melezitose | - | builds acid from |
43243 | (+)-D-glycogen | - | builds acid from | |
43243 | 15443 | inulin | - | builds acid from |
43243 | 4853 | esculin | - | builds acid from |
43243 | 27613 | amygdalin | - | builds acid from |
43243 | 18305 | arbutin | - | builds acid from |
43243 | 28066 | gentiobiose | - | builds acid from |
43243 | 17814 | salicin | - | builds acid from |
43243 | 32528 | turanose | - | builds acid from |
43243 | 30849 | L-arabinose | - | builds acid from |
43243 | 16988 | (-)-D-ribose | +/- | builds acid from |
43243 | 65327 | D-xylose | - | builds acid from |
43243 | 17268 | myo-inositol | - | builds acid from |
43243 | 16899 | D-mannitol | + | builds acid from |
43243 | 16024 | D-mannose | + | builds acid from |
43243 | 17716 | lactose | - | builds acid from |
43243 | 17992 | sucrose | + | builds acid from |
43243 | 27082 | trehalose | + | builds acid from |
43243 | 23652 | dextrin | + | builds acid from |
43243 | 28053 | melibiose | + | builds acid from |
43243 | 16634 | raffinose | + | builds acid from |
metabolite production
- @ref: 43243
- Chebi-ID: 15688
- metabolite: acetoin
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | methylred-test | voges-proskauer-test |
---|---|---|---|---|
43243 | 17234 | glucose | - | |
43243 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43243 | catalase | + | 1.11.1.6 |
43243 | cytochrome oxidase | + | 1.9.3.1 |
43243 | urease | + | 3.5.1.5 |
43243 | alkaline phosphatase | + | 3.1.3.1 |
43243 | arginine dihydrolase | - | 3.5.3.6 |
43243 | phenylalanine deaminase | - | 4.3.1.5 |
43243 | gelatinase | - | |
43243 | beta-glucosidase | - | 3.2.1.21 |
43243 | alpha-fucosidase | - | 3.2.1.51 |
43243 | beta-xylosidase | - | |
43243 | alpha-mannosidase | - | 3.2.1.24 |
43243 | lysine decarboxylase | - | 4.1.1.18 |
43243 | ornithine decarboxylase | - | 4.1.1.17 |
43243 | beta-galactosidase | + | 3.2.1.23 |
43243 | alpha-glucosidase | + | 3.2.1.20 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
42910 | laboratory rat, trachea | Germany | DEU | Europe |
43243 | rats samples | |||
63643 | Laboratory rat,trachea |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Laboratory | |
#Host | #Mammals | #Muridae (Mouse/Rat) |
#Host Body-Site | #Oral cavity and airways | #Trachea |
Safety information
risk assessment
- @ref: 42910
- pathogenicity animal: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 42910
- description: Rodentibacter trehalosifermentans strain H1987082031 16S ribosomal RNA gene, partial sequence
- accession: KX858172
- length: 1428
- database: ena
- NCBI tax ID: 1908263
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rodentibacter trehalosifermentans H1987082031 | GCA_002000545 | contig | ncbi | 1908263 |
66792 | Rodentibacter trehalosifermentans H1987082031 | 2791354947 | draft | img | 1908263 |
GC content
@ref | GC-content | method |
---|---|---|
43243 | 40.9 | |
42910 | 40.9 | sequence analysis |
External links
@ref: 42910
culture collection no.: DSM 104075, CCUG 69668
straininfo link
- @ref: 96608
- straininfo: 407757
literature
- topic: Phylogeny
- Pubmed-ID: 28629498
- title: Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies.
- authors: Adhikary S, Nicklas W, Bisgaard M, Boot R, Kuhnert P, Waberschek T, Aalbaek B, Korczak B, Christensen H
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001866
- year: 2017
- mesh: Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Nucleic Acid Hybridization, Pasteurellaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rodentia/*microbiology, Sequence Analysis, DNA
- topic2: Transcriptome
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 | |||
42910 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104075 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104075) | |||
43243 | Sadhana Adhikary, Werner Nicklas, Magne Bisgaard, Ron Boot, Peter Kuhnert, Torsten Waberschek, Bent Aalbaek, Bozena Korczak and Henrik Christensen | Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies | 10.1099/ijsem.0.001866 | IJSEM 67: 1793-1806 2017 | 28629498 | |
63643 | Curators of the CCUG | https://www.ccug.se/strain?id=69668 | Culture Collection University of Gothenburg (CCUG) (CCUG 69668) | |||
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 | |
96608 | 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-ID407757.1 |