Strain identifier

BacDive ID: 6701

Type strain: Yes

Species: Lacticaseibacillus saniviri

Strain history: K. Oki YIT 12363.

NCBI tax ID(s): 931533 (species)

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

@ref: 17626

BacDive-ID: 6701

DSM-Number: 24301

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

description: Lacticaseibacillus saniviri DSM 24301 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from feces of a Japanese healthy adult male.

NCBI tax id

  • NCBI tax id: 931533
  • Matching level: species

strain history

@refhistory
17626<- K. Oki, Yakult Central Inst. Microbiol. Res., Kunitachi, Japan; YIT 12363 <- K. Watanabe
67770K. Oki YIT 12363.

doi: 10.13145/bacdive6701.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lacticaseibacillus
  • species: Lacticaseibacillus saniviri
  • full scientific name: Lacticaseibacillus saniviri (Oki et al. 2012) Zheng et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus saniviri

@ref: 17626

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lacticaseibacillus

species: Lacticaseibacillus saniviri

full scientific name: Lacticaseibacillus saniviri (Oki et al. 2012) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30248positive1.5-3.0 µm1 µmrod-shapedno
69480no97.246
69480positive100

pigmentation

  • @ref: 30248
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17626
  • 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
17626positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

  • @ref: 30248
  • ability: positive
  • type: growth
  • pH: 4.0-8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
17626microaerophile
30248facultative anaerobe

spore formation

@refspore formationconfidence
30248no
69481no100
69480no99.987

halophily

  • @ref: 30248
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 5 %

murein

  • @ref: 17626
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3024817754glycerol+carbon source
3024828053melibiose+carbon source
3024816634raffinose+carbon source
3024833942ribose+carbon source
3024817814salicin+carbon source
3024817992sucrose+carbon source
68371Potassium 5-ketogluconate-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
6837132528turanose-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
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
17626-+---+----++++----+---+++++++--++--+---+--+-------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17626feces of a Japanese healthy adult maleJapanJPNAsia
67770Feces of a healthy Japanese male

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_7550.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1783;97_4323;98_5534;99_7550&stattab=map
  • Last taxonomy: Lacticaseibacillus saniviri subclade
  • 16S sequence: LC519994
  • Sequence Identity:
  • Total samples: 1527
  • soil counts: 107
  • aquatic counts: 132
  • animal counts: 1244
  • plant counts: 44

Safety information

risk assessment

  • @ref: 17626
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus saniviri strain DSM 24301 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceJN6447562250ena1293598
17626Lactobacillus saniviri gene for 16S rRNA, partial sequenceAB6025691558ena1293598
67770Lactobacillus saniviri JCM 17471 gene for 16S rRNA, partial sequenceLC5199941502ena1293598

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus saniviri JCM 17471 = DSM 243011293598.4wgspatric1293598
66792Lactobacillus saniviri JCM 17471 = DSM 243011293598.3wgspatric1293598
66792Lacticaseibacillus saniviri DSM 243012663763364draftimg1293598
66792Lacticaseibacillus saniviri JCM 174712728369696draftimg1293598
67770Lacticaseibacillus saniviri JCM 17471 = DSM 24301GCA_001311785contigncbi1293598
67770Lacticaseibacillus saniviri JCM 17471 = DSM 24301GCA_001437465scaffoldncbi1293598

GC content

@refGC-contentmethod
1762648.1high performance liquid chromatography (HPLC)
3024848.7
6777047.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.367yes
gram-positiveyes96.194yes
anaerobicno94.688yes
aerobicno95.111no
halophileyes83.367no
spore-formingno93.32yes
thermophileno98.15no
glucose-utilyes92.163no
flagellatedno97.44yes
glucose-fermentyes85.138no

External links

@ref: 17626

culture collection no.: DSM 24301, JCM 17471, YIT 12363

straininfo link

  • @ref: 76175
  • straininfo: 398599

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21515698Lactobacillus saniviri sp. nov. and Lactobacillus senioris sp. nov., isolated from human faeces.Oki K, Kudo Y, Watanabe KInt J Syst Evol Microbiol10.1099/ijs.0.031658-02011Aerobiosis, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Feces/*microbiology, Humans, Lactobacillus/*classification/genetics/*isolation & purification/physiology, Locomotion, Molecular Sequence Data, Phenylalanine-tRNA Ligase/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny22021580Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis).Volokhov DV, Amselle M, Beck BJ, Popham DL, Whittaker P, Wang H, Kerrigan E, Chizhikov VEInt J Syst Evol Microbiol10.1099/ijs.0.033852-02011Animals, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/analysis, Feces/microbiology, Geese/*microbiology, Genes, Bacterial, Genotype, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
17626Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24301)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24301
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
30248Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126590
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76175Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398599.1StrainInfo: A central database for resolving microbial strain identifiers