Strain identifier

BacDive ID: 1236

Type strain: Yes

Species: Lederbergia ruris

Strain Designation: MB 1669, R-6760

Strain history: CIP <- 2005, DSMZ <- M. Heyndrickx, Cent. Agric. Res., Melle, Belgium <- P. Scheldeman, Cent. Agric. Res., Melle, Belgium: strain R-6760

NCBI tax ID(s): 217495 (species)

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General

@ref: 6726

BacDive-ID: 1236

DSM-Number: 17057

keywords: 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Lederbergia ruris MB 1669 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from raw milk.

NCBI tax id

  • NCBI tax id: 217495
  • Matching level: species

strain history

@refhistory
6726<- M. Heyndrickx; R-6760 <- P. Scheldeman
122317CIP <- 2005, DSMZ <- M. Heyndrickx, Cent. Agric. Res., Melle, Belgium <- P. Scheldeman, Cent. Agric. Res., Melle, Belgium: strain R-6760

doi: 10.13145/bacdive1236.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Lederbergia
  • species: Lederbergia ruris
  • full scientific name: Lederbergia ruris (Heyndrickx et al. 2005) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus ruris

@ref: 6726

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Lederbergia

species: Lederbergia ruris

full scientific name: Lederbergia ruris (Heyndrickx et al. 2005) Gupta et al. 2020

strain designation: MB 1669, R-6760

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31563positive1.5 µm0.65 µmrod-shapedyes
122317positiverod-shapedyes

colony morphology

  • @ref: 122317

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6726CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
40099MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122317CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6726positivegrowth30mesophilic
31563positivegrowth30-40
31563positiveoptimum35mesophilic
40099positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31563positivegrowth06-11alkaliphile
31563positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31563facultative anaerobe
122317facultative anaerobe

spore formation

  • @ref: 31563
  • spore formation: yes

observation

  • @ref: 31563
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3156322599arabinose+carbon source
3156317057cellobiose+carbon source
3156328757fructose+carbon source
3156328260galactose+carbon source
3156317234glucose+carbon source
3156328087glycogen+carbon source
3156317716lactose+carbon source
3156317306maltose+carbon source
3156329864mannitol+carbon source
3156337684mannose+carbon source
3156328053melibiose+carbon source
3156337657methyl D-glucoside+carbon source
31563506227N-acetylglucosamine+carbon source
3156316634raffinose+carbon source
3156333942ribose+carbon source
3156317814salicin+carbon source
3156317992sucrose+carbon source
3156327082trehalose+carbon source
3156318222xylose+carbon source
315634853esculin+hydrolysis
3156317632nitrate+reduction
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837117151xylitol-builds acid from
683714853esculin+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12231717632nitrate+reduction
12231716301nitrite-reduction

metabolite production

  • @ref: 122317
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31563catalase+1.11.1.6
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
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
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
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122317oxidase+
122317alcohol dehydrogenase-1.1.1.1
122317catalase+1.11.1.6
122317lysine decarboxylase-4.1.1.18
122317ornithine decarboxylase-4.1.1.17
122317urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122317-+++-------+-+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122317+/---+/-+/-+/---+/-+/-+/-+/-+/--+/---+/-+/-+/-+/-+/-+/-+/-++/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+/-+/----+/---+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6726raw milkBelgiumBELEurope
122317Food, Raw milkBelgiumBELEurope

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Host#Mammals

taxonmaps

  • @ref: 69479
  • File name: preview.99_90688.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_357;97_1662;98_62558;99_90688&stattab=map
  • Last taxonomy: Lederbergia
  • 16S sequence: AJ535639
  • Sequence Identity:
  • Total samples: 57
  • soil counts: 35
  • aquatic counts: 2
  • animal counts: 13
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67261Risk group (German classification)
1223171Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6726
  • description: Bacillus ruris partial 16S rRNA gene, type strain R-6760
  • accession: AJ535639
  • length: 1423
  • database: ena
  • NCBI tax ID: 217495

GC content

  • @ref: 31563
  • GC-content: 39.2

External links

@ref: 6726

culture collection no.: DSM 17057, CIP 109042, LMG 22866

straininfo link

  • @ref: 70892
  • straininfo: 134674

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280525Bacillus ruris sp. nov., from dairy farms.Heyndrickx M, Scheldeman P, Forsyth G, Lebbe L, Rodriguez-Diaz M, Logan NA, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.63812-02005Animal Feed/*microbiology, Animals, Bacillus/classification/cytology/*isolation & purification/physiology, *Dairying, Milk/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNA, Spores, BacterialGenetics
Phylogeny20656804Bacillus graminis sp. nov., an endophyte isolated from a coastal dune plant.Bibi F, Chung EJ, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.023820-02010Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Elymus/*microbiology, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6726Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17057)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17057
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
31563Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2785328776041
40099Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6740
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
70892Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134674.1StrainInfo: A central database for resolving microbial strain identifiers
122317Curators of the CIPCollection of Institut Pasteur (CIP 109042)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109042