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)

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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/bacdive24141.20250331.9.3

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 stainconfidencemotility
67771rod-shaped
67771positive
125439positive92.2
12543893no
125438positive94.304

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

@refgrowthtypetemperature
21001positivegrowth37
67771positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
21001microaerophile
67771anaerobe
125439microaerophile94.7

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 90.463

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371D-galactose-builds acid from12936
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
68371N-acetylglucosamine-builds acid from59640
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
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: nuccore
  • 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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes94.304yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no69.461no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no95.883yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.463no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno93no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno76.1
125439BacteriaNetmotilityAbility to perform movementno82.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive92.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile94.7

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG