Strain identifier
BacDive ID: 140609
Type strain:
Species: Rodentibacter heylii
Strain Designation: P309, C57
Strain history: <- CCUG; CCUG 998 <- K. Bövre, Natl. Vet. Inst., Oslo, Norway; C57
NCBI tax ID(s): 1906744 (species)
General
@ref: 67678
BacDive-ID: 140609
DSM-Number: 112292
keywords: genome sequence, Bacteria, mesophilic, Gram-negative, colony-forming
description: Rodentibacter heylii P309 is a mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from mouse.
NCBI tax id
- NCBI tax id: 1906744
- Matching level: species
strain history
- @ref: 67678
- history: <- CCUG; CCUG 998 <- K. Bövre, Natl. Vet. Inst., Oslo, Norway; C57
doi: 10.13145/bacdive140609.20230509.8.1
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 heylii
- full scientific name: Rodentibacter heylii Adhikary et al. 2017
@ref: 67678
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pasteurellales
family: Pasteurellaceae
genus: Rodentibacter
species: Rodentibacter heylii
full scientific name: Rodentibacter heylii Adhikary et al. 2017
strain designation: P309, C57
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 | ||
43243 | MacConkey agar | no | ||
67678 | 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: 67678
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43243 | 17234 | glucose | + | fermentation |
43243 | 17632 | nitrate | + | reduction |
43243 | 16947 | citrate | - | carbon source |
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 | 53426 | tween 80 | - | hydrolysis |
43243 | 17108 | D-arabinose | - | 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 | 18287 | L-fucose | + | 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 | 17634 | (-)-D-glucose | + | builds acid from |
43243 | 17754 | glycerol | - | builds acid from |
43243 | 28053 | melibiose | + | builds acid from |
43243 | 16634 | raffinose | + | builds acid from |
68377 | 17634 | D-glucose | + | builds acid from |
68377 | 16199 | urea | + | hydrolysis |
68381 | 29016 | arginine | - | hydrolysis |
68381 | 16988 | D-ribose | - | builds acid from |
68381 | 16899 | D-mannitol | - | builds acid from |
68381 | 30911 | sorbitol | - | builds acid from |
68381 | 17716 | lactose | - | builds acid from |
68381 | 27082 | trehalose | - | builds acid from |
68381 | 16634 | raffinose | - | builds acid from |
68381 | 17992 | sucrose | - | builds acid from |
68381 | 30849 | L-arabinose | - | builds acid from |
68381 | 18333 | D-arabitol | - | builds acid from |
68381 | 40585 | alpha-cyclodextrin | - | builds acid from |
68381 | 606565 | hippurate | - | hydrolysis |
68381 | 28087 | glycogen | - | builds acid from |
68381 | 27941 | pullulan | - | builds acid from |
68381 | 17306 | maltose | - | builds acid from |
68381 | 28053 | melibiose | - | builds acid from |
68381 | 6731 | melezitose | - | builds acid from |
68381 | 320055 | methyl beta-D-glucopyranoside | - | builds acid from |
68381 | 16443 | D-tagatose | - | builds acid from |
68381 | 16199 | urea | + | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43243 | 8337 | porphyrin | yes |
43243 | 15688 | acetoin | no |
68381 | 15688 | acetoin | no |
metabolite tests
@ref | Chebi-ID | metabolite | methylred-test | voges-proskauer-test |
---|---|---|---|---|
43243 | 17234 | glucose | - | |
43243 | 15688 | acetoin | - | |
68381 | 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 |
43243 | alpha-galactosidase | + | 3.2.1.22 |
68381 | urease | + | 3.5.1.5 |
68381 | beta-mannosidase | - | 3.2.1.25 |
68381 | glycyl tryptophan arylamidase | - | |
68381 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68381 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68381 | beta-galactosidase | + | 3.2.1.23 |
68381 | Alanyl-Phenylalanyl-Proline arylamidase | - | |
68381 | alkaline phosphatase | + | 3.1.3.1 |
68381 | alpha-galactosidase | + | 3.2.1.22 |
68381 | beta-glucuronidase | - | 3.2.1.31 |
68381 | beta-glucosidase | - | 3.2.1.21 |
68381 | arginine dihydrolase | - | 3.5.3.6 |
68377 | gamma-glutamyltransferase | + | 2.3.2.2 |
68377 | proline-arylamidase | - | 3.4.11.5 |
68377 | beta-galactosidase | + | 3.2.1.23 |
68377 | alkaline phosphatase | + | 3.1.3.1 |
68377 | lipase | - | |
68377 | urease | + | 3.5.1.5 |
68377 | beta-lactamase | - | 3.5.2.6 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
65643 | - | + | - | - | - | + | - | - | - | - | + | + | + | + | - | + | - | - | - | - |
API NH
@ref | PEN | GLU | FRU | MAL | SAC | ODC | URE | LIP | PAL | beta GAL | ProA | GGT | IND |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
67678 | - | + | - | +/- | +/- | - | + | - | + | + | - | + | + |
65643 | - | + | + | + | + | + | + | - | + | + | - | + | - |
API rID32STR
@ref | ADH Arg | beta GLU | beta GAR | beta GUR | alpha GAL | PAL | RIB | MAN | SOR | LAC | TRE | RAF | SAC | LARA | DARL | CDEX | VP | APPA | beta GAL | PyrA | beta NAG | GTA | HIP | GLYG | PUL | MAL | MEL | MLZ | Mbeta DG | TAG | beta MAN | URE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
65643 | - | - | + | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
43243 | mouse | Australia | Australia | AUS | Australia and Oceania |
67678 | mouse | Australia | AUS | Australia and Oceania |
isolation source categories
- Cat1: #Host
- Cat2: #Mammals
- Cat3: #Muridae (Mouse/Rat)
Safety information
risk assessment
- @ref: 67678
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rodentibacter heylii ATCC 12555 | GCA_001019715 | contig | ncbi | 1906744 |
66792 | [Pasteurella] pneumotropica strain ATCC 12555 | 758.15 | wgs | patric | 758 |
66792 | Rodentibacter heylii ATCC 12555 | 2651869757 | draft | img | 1906744 |
GC content
- @ref: 43243
- GC-content: 40.2
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 88.873 | yes |
flagellated | no | 93.087 | no |
gram-positive | no | 98.067 | yes |
anaerobic | no | 96.288 | no |
aerobic | no | 83.944 | no |
halophile | no | 52.086 | no |
spore-forming | no | 98.709 | no |
glucose-util | no | 51.287 | no |
thermophile | no | 98.517 | no |
glucose-ferment | yes | 66.232 | no |
External links
@ref: 67678
culture collection no.: MCCM 237, RGWyllie C57, HIM 1014-1, CCUG 998, ATCC 12555, DSM 112292
straininfo link
- @ref: 96755
- straininfo: 35605
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 | journal | pubmed | catalogue |
---|---|---|---|---|---|---|
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 | |||
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 | |
65643 | Curators of the CCUG | https://www.ccug.se/strain?id=998 | Culture Collection University of Gothenburg (CCUG) (CCUG 998) | |||
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 | |
67678 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-112292 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 112292) | |||
68377 | Automatically annotated from API NH | |||||
68381 | Automatically annotated from API rID32STR | |||||
68382 | Automatically annotated from API zym | |||||
96755 | 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-ID35605.1 |