Strain identifier
BacDive ID: 24141
Type strain:
Species: Lactobacillus rodentium
Strain Designation: MYMRS/TLU1
Strain history: <- DSM <- J Killer, Inst Animal Physiol and Genetics, Czech Acad Sci, Prague, MYMRS-TLU1
NCBI tax ID(s): 947835 (species)
General
@ref: 21001
BacDive-ID: 24141
DSM-Number: 24759
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, rod-shaped
description: Lactobacillus rodentium MYMRS/TLU1 is a microaerophile, mesophilic, rod-shaped bacterium that was isolated from colon of a wild mouse Mus musculus).
NCBI tax id
- NCBI tax id: 947835
- Matching level: species
strain history
@ref | history |
---|---|
21001 | <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; MYMRS-TLU1 |
67771 | <- DSM <- J Killer, Inst Animal Physiol and Genetics, Czech Acad Sci, Prague, MYMRS-TLU1 |
doi: 10.13145/bacdive24141.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Lactobacillaceae
- genus: Lactobacillus
- species: Lactobacillus rodentium
- full scientific name: Lactobacillus rodentium Killer et al. 2014
@ref: 21001
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Lactobacillus
species: Lactobacillus rodentium
full scientific name: Lactobacillus rodentium Killer et al. 2014
strain designation: MYMRS/TLU1
type strain: yes
Morphology
cell morphology
@ref | cell shape | gram stain | motility | confidence |
---|---|---|---|---|
67771 | rod-shaped | |||
67771 | positive | |||
69480 | no | 98.164 | ||
69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 21001
- name: MRS MEDIUM (DSMZ Medium 11)
- growth: yes
- link: https://mediadive.dsmz.de/medium/11
- composition: Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
21001 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
21001 | microaerophile |
67771 | anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
API 50CHac
@ref | Q | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
21001 | - | - | - | - | - | +/- | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | + | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
21001 | colon of a wild mouse Mus musculus) | Mus musculus | Central Bohemia, Jesetice | Czech Republic | CZE | Europe |
67771 | From colon of a wild mouse, `Mus musculus` | Central Bohemia, Jesetice | Czech Republic | CZE | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Muridae (Mouse/Rat) |
#Host Body-Site | #Gastrointestinal tract | #Large intestine |
Safety information
risk assessment
- @ref: 21001
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21001
- description: Lactobacillus rodentium strain MYMRS/TLU1 16S ribosomal RNA gene, partial sequence
- accession: HQ851022
- length: 1436
- database: ena
- NCBI tax ID: 947835
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactobacillus rodentium DSM 24759 | GCA_003423665 | scaffold | ncbi | 947835 |
66792 | Lactobacillus rodentium strain DSM 24759 | 947835.3 | wgs | patric | 947835 |
66792 | Lactobacillus rodentium DSM 24759 | 2916469829 | draft | img | 947835 |
66792 | Lactobacillus rodentium DSM 24759 | GCA_024622425 | contig | ncbi | 947835 |
GC content
@ref | GC-content | method |
---|---|---|
21001 | 43.7 | high performance liquid chromatography (HPLC) |
67771 | 43.7 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 96.815 | no |
flagellated | no | 98.564 | no |
gram-positive | yes | 96.925 | yes |
anaerobic | no | 54.43 | no |
aerobic | no | 97.201 | yes |
halophile | yes | 88.463 | no |
spore-forming | no | 97.375 | no |
glucose-util | yes | 91.392 | no |
thermophile | no | 99.548 | yes |
glucose-ferment | yes | 90.371 | no |
External links
@ref: 21001
culture collection no.: DSM 24759, CCM 7945, KCTC 21049
straininfo link
- @ref: 88099
- straininfo: 397556
literature
- topic: Phylogeny
- Pubmed-ID: 24478214
- title: Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents.
- authors: Killer J, Havlik J, Vlkova E, Rada V, Pechar R, Benada O, Kopecny J, Kofronova O, Sechovcova H
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.054924-0
- year: 2014
- mesh: Animals, Bacterial Typing Techniques, Base Composition, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Genes, Bacterial, Intestine, Small/*microbiology, Lactobacillus/*classification/genetics/isolation & purification, Mice/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rectum/microbiology, Sequence Analysis, DNA
- topic2: Genetics
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 | |||
21001 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24759 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24759) | |||
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 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
88099 | 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-ID397556.1 |