Strain identifier

BacDive ID: 6484

Type strain: Yes

Species: Ligilactobacillus murinus

Strain Designation: 313

Strain history: CIP <- 1996, JCM <- D. Hemme: strain 313

NCBI tax ID(s): 1622 (species)

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General

@ref: 8824

BacDive-ID: 6484

DSM-Number: 20452

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped

description: Ligilactobacillus murinus 313 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from intestine of rat.

NCBI tax id

  • NCBI tax id: 1622
  • Matching level: species

strain history

@refhistory
8824<- D. Hemme, 313
67770D. Hemme 313.
121197CIP <- 1996, JCM <- D. Hemme: strain 313

doi: 10.13145/bacdive6484.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Ligilactobacillus
  • species: Ligilactobacillus murinus
  • full scientific name: Ligilactobacillus murinus (Hemme et al. 1982) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus murinus

@ref: 8824

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus murinus

full scientific name: Ligilactobacillus murinus (Hemme et al. 1982) Zheng et al. 2020

strain designation: 313

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121197positiverod-shapedno
125438positive92.275

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8824MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: 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
39105MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121197CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
8824positivegrowth37
39105positivegrowth37
67770positivegrowth37
121197positivegrowth22-45
121197nogrowth10
121197nogrowth15

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
51811anaerobe
51811microaerophile
121197facultative anaerobe
125439microaerophile96.7

murein

  • @ref: 8824
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12119717632nitrate-reduction
12119716301nitrite-reduction
12119717632nitrate+respiration
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

antibiotic resistance

  • @ref: 121197
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 121197
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
121197oxidase-
121197alcohol dehydrogenase-1.1.1.1
121197catalase-1.11.1.6
121197lysine decarboxylase-4.1.1.18
121197ornithine decarboxylase-4.1.1.17
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121197-+---+----++++------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8824----------++++----+---+-++++++++---+---+----------
121197---++/-----++++--------+-++++++++---+---++--------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121197---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
8824intestine of rat
51811Rat digestive tract
67770Rat intestine
121197Animal, Rat, intestine

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Gastrointestinal tract

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88241Risk group (German classification)
1211971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus murinus 16S ribosomal RNAM588261514nuccore1622
20218Lactobacillus murinus genes for 16S-23S intergenic spacer region, 23S ribosomal RNA, strain:JCM 1717AB1587642934nuccore1622
20218Lactobacillus murinus gene for 16S rRNA, partial sequence, strain: JCM 1717AB289205624nuccore1622
20218Lactobacillus murinus partial 16S rRNA gene, strain LMG 14189TAJ6215541459nuccore1622
20218Lactobacillus murinus gene for 16S rRNA, partial sequence, strain: NBRC 14221AB3263491489nuccore1622
67770Lactobacillus murinus gene for 16S ribosomal RNA, partial sequence, strain: JCM 1717LC0718091455nuccore1622

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ligilactobacillus murinus DSM 20452 = NBRC 14221GCA_001591685contigncbi1423772
66792Lactobacillus murinus DSM 20452 = NBRC 142211423772.3wgspatric1423772
66792Lactobacillus murinus DSM 20452 = NBRC 142211423772.4wgspatric1423772
66792Ligilactobacillus murinus NBRC 142212731957662draftimg1423772
66792Ligilactobacillus murinus DSM 204522663762947draftimg1423772
67770Ligilactobacillus murinus DSM 20452 = NBRC 14221GCA_001436015scaffoldncbi1423772

GC content

@refGC-contentmethod
882443.7
6777040.1genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes92.275no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no83.136no
125438spore-formingspore-formingAbility to form endo- or exosporesno86.39no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.417yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.5no
125438motile2+flagellatedAbility to perform flagellated movementno89no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno54.9
125439BacteriaNetmotilityAbility to perform movementno59.9
125439BacteriaNetgram_stainReaction to gram-stainingvariable73.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile96.7

External links

@ref: 8824

culture collection no.: DSM 20452, ATCC 35020, CNRZ 220, CCUG 33904, LMG 14189, CIP 104818, JCM 1717, BCRC 14020, CECT 4135, CGMCC 1.2626, IFO 14221, KCTC 3546, LMG 18317, LMG 9475, NBRC 14221, NCFB 2808, NCIMB 702808

straininfo link

  • @ref: 75957
  • straininfo: 125684

literature

  • topic: Pathogenicity
  • Pubmed-ID: 2632048
  • title: Superoxide dismutase activity in some strains of lactobacilli: induction by manganese.
  • authors: Gonzalez SN, Apella MC, Romero N, Pesce de Ruiz Holgado AA, Oliver G
  • journal: Chem Pharm Bull (Tokyo)
  • DOI: 10.1248/cpb.37.3026
  • year: 1989
  • mesh: Enzyme Induction/drug effects, Lactobacillus/*enzymology, Manganese/*pharmacology, Superoxide Dismutase/*biosynthesis
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8824Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20452)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20452
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39105Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16769
51811Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33904)https://www.ccug.se/strain?id=33904
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
75957Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125684.1StrainInfo: A central database for resolving microbial strain identifiers
121197Curators of the CIPCollection of Institut Pasteur (CIP 104818)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104818
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1