Strain identifier

BacDive ID: 24141

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
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

@refcell shapegram stainmotilityconfidence
67771rod-shaped
67771positive
69480no98.164
69480positive100

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

@refgrowthtypetemperaturerange
21001positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
21001microaerophile
67771anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
21001-----+/------+++-----------+/---+--+/-------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
21001colon of a wild mouse Mus musculus)Mus musculusCentral Bohemia, JeseticeCzech RepublicCZEEurope
67771From colon of a wild mouse, `Mus musculus`Central Bohemia, JeseticeCzech RepublicCZEEurope

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus rodentium DSM 24759GCA_003423665scaffoldncbi947835
66792Lactobacillus rodentium strain DSM 24759947835.3wgspatric947835
66792Lactobacillus rodentium DSM 247592916469829draftimg947835
66792Lactobacillus rodentium DSM 24759GCA_024622425contigncbi947835

GC content

@refGC-contentmethod
2100143.7high performance liquid chromatography (HPLC)
6777143.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.815no
flagellatedno98.564no
gram-positiveyes96.925yes
anaerobicno54.43no
aerobicno97.201yes
halophileyes88.463no
spore-formingno97.375no
glucose-utilyes91.392no
thermophileno99.548yes
glucose-fermentyes90.371no

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

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
21001Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24759Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24759)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88099Reimer, 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 identifiers10.60712/SI-ID397556.1