Strain identifier

BacDive ID: 6510

Type strain: Yes

Species: Ligilactobacillus ruminis

Strain Designation: RFl, RF 1

Strain history: CIP <- 1988, NCFB <- 1973, M.J. Lathan: strain RF 1

NCBI tax ID(s): 1623 (species)

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General

@ref: 8789

BacDive-ID: 6510

DSM-Number: 20403

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Ligilactobacillus ruminis RFl is an anaerobe, mesophilic bacterium that was isolated from bovine rumen.

NCBI tax id

  • NCBI tax id: 1623
  • Matching level: species

strain history

@refhistory
8789<- M.E. Sharpe, RFl
67770ATCC 27780 <-- M. E. Sharpe RF1.
122313CIP <- 1988, NCFB <- 1973, M.J. Lathan: strain RF 1

doi: 10.13145/bacdive6510.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Ligilactobacillus
  • species: Ligilactobacillus ruminis
  • full scientific name: Ligilactobacillus ruminis (Sharpe et al. 1973) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus ruminis

@ref: 8789

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus ruminis

full scientific name: Ligilactobacillus ruminis (Sharpe et al. 1973) Zheng et al. 2020

strain designation: RFl, RF 1

type strain: yes

Morphology

colony morphology

  • @ref: 54804
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8789MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232)yeshttps://mediadive.dsmz.de/medium/232Name: MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232) 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)2 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
40544MEDIUM 43 - for Lactobacillus hamsteri and Lactobacillus ruminisyesDistilled water make up to (900.000 ml);Man Rogosa Sharp broth (55.000 g);Cysteine hydrochloride 5 % solution - M0172 (100.000 ml)
122313CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperaturerange
8789positivegrowth37mesophilic
40544positivegrowth37mesophilic
54804positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8789anaerobe
54804anaerobe
54804microaerophile

murein

  • @ref: 8789
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

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
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
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
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
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8789----------++++--------++++++++++---+--------------
8789----------++++--------++++++++++---+---+----------

Isolation, sampling and environmental information

isolation

@refsample type
8789bovine rumen
54804Bovine rumen
67770Bovine rumen
122313Animal, Cattle, rumen

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_1998.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1108;97_1298;98_1563;99_1998&stattab=map
  • Last taxonomy: Ligilactobacillus ruminis subclade
  • 16S sequence: LC064897
  • Sequence Identity:
  • Total samples: 120412
  • soil counts: 2943
  • aquatic counts: 6299
  • animal counts: 110193
  • plant counts: 977

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87891Risk group (German classification)
1223131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus ruminis 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer region, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF080103533ena1623
20218Lactobacillus ruminus 16S ribosomal RNAM588281567ena1623
20218Lactobacillus ruminis gene for 16S rRNA, partial sequence, strain: JCM 1152AB289286659ena1623
20218Lactobacillus ruminis gene for 16S rRNA, partial sequence, strain: NBRC 102161AB3263541488ena1623
67770Lactobacillus ruminis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1152LC0648971465ena1623

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus ruminis DSM 20403 = NBRC 1021611423798.3wgspatric1423798
66792Lactobacillus ruminis DSM 20403 = NBRC 1021611423798.4wgspatric1423798
66792Lactobacillus ruminis DSM 20403 = NBRC 1021611423798.5wgspatric1423798
66792Lactobacillus ruminis strain ATCC 277801623.10wgspatric1623
66792Ligilactobacillus ruminis DSM 204032667527649draftimg1423798
66792Ligilactobacillus ruminis ATCC 277802627853909draftimg1623
66792Ligilactobacillus ruminis NBRC 1021612731957672draftimg1423798
66792Ligilactobacillus ruminis DSM 204032593339155draftimg1423798
67770Ligilactobacillus ruminis DSM 20403 = NBRC 102161GCA_001436475contigncbi1423798
67770Ligilactobacillus ruminis DSM 20403 = NBRC 102161GCA_001591905contigncbi1423798
67770Ligilactobacillus ruminis DSM 20403 = NBRC 102161GCA_900113455scaffoldncbi1423798
67770Ligilactobacillus ruminis ATCC 27780GCA_001008755contigncbi1623

GC content

@refGC-contentmethod
878943.8
6777043.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes56.35no
gram-positiveyes92.73no
anaerobicyes54.233no
halophileyes68.721no
spore-formingno88.618no
glucose-utilyes92.239no
thermophileno90.158no
aerobicno98.358yes
flagellatedno82.86no
glucose-fermentyes90.317no

External links

@ref: 8789

culture collection no.: DSM 20403, ATCC 27780, CCUG 39465, JCM 1152, LMG 10756, CIP 103153, BCRC 14620, CECT 4061, KCTC 3601, NBRC 102161, NCFB 2029, NCIMB 702029, NRIC 1689, NRRL B-14853, VTT E-97852, NCDO 2029

straininfo link

  • @ref: 75982
  • straininfo: 3363

literature

  • topic: Pathogenicity
  • Pubmed-ID: 28450859
  • title: A Comparative Characterization of Different Host-sourced Lactobacillus ruminis Strains and Their Adhesive, Inhibitory, and Immunomodulating Functions.
  • authors: Yu X, Avall-Jaaskelainen S, Koort J, Lindholm A, Rintahaka J, von Ossowski I, Palva A, Hynonen U
  • journal: Front Microbiol
  • DOI: 10.3389/fmicb.2017.00657
  • year: 2017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8789Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20403)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20403
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
40544Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14919
54804Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39465)https://www.ccug.se/strain?id=39465
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
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75982Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3363.1StrainInfo: A central database for resolving microbial strain identifiers
122313Curators of the CIPCollection of Institut Pasteur (CIP 103153)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103153