Strain identifier
BacDive ID: 6701
Type strain:
Species: Lacticaseibacillus saniviri
Strain history: K. Oki YIT 12363.
NCBI tax ID(s): 931533 (species)
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
@ref | history |
---|---|
17626 | <- K. Oki, Yakult Central Inst. Microbiol. Res., Kunitachi, Japan; YIT 12363 <- K. Watanabe |
67770 | K. 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30248 | positive | 1.5-3.0 µm | 1 µm | rod-shaped | no | |
69480 | no | 97.246 | ||||
69480 | positive | 100 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
17626 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
- @ref: 30248
- ability: positive
- type: growth
- pH: 4.0-8.5
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
17626 | microaerophile |
30248 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
30248 | no | |
69481 | no | 100 |
69480 | no | 99.987 |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30248 | 17754 | glycerol | + | carbon source |
30248 | 28053 | melibiose | + | carbon source |
30248 | 16634 | raffinose | + | carbon source |
30248 | 33942 | ribose | + | carbon source |
30248 | 17814 | salicin | + | carbon source |
30248 | 17992 | sucrose | + | carbon source |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | + | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | + | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | + | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | + | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 27613 | amygdalin | + | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | + | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | + | builds acid from |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
17626 | - | + | - | - | - | + | - | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | + | + | + | + | + | + | + | - | - | + | + | - | - | + | - | - | - | + | - | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
17626 | feces of a Japanese healthy adult male | Japan | JPN | Asia |
67770 | Feces of a healthy Japanese male |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Lactobacillus saniviri strain DSM 24301 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | JN644756 | 2250 | ena | 1293598 |
17626 | Lactobacillus saniviri gene for 16S rRNA, partial sequence | AB602569 | 1558 | ena | 1293598 |
67770 | Lactobacillus saniviri JCM 17471 gene for 16S rRNA, partial sequence | LC519994 | 1502 | ena | 1293598 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactobacillus saniviri JCM 17471 = DSM 24301 | 1293598.4 | wgs | patric | 1293598 |
66792 | Lactobacillus saniviri JCM 17471 = DSM 24301 | 1293598.3 | wgs | patric | 1293598 |
66792 | Lacticaseibacillus saniviri DSM 24301 | 2663763364 | draft | img | 1293598 |
66792 | Lacticaseibacillus saniviri JCM 17471 | 2728369696 | draft | img | 1293598 |
67770 | Lacticaseibacillus saniviri JCM 17471 = DSM 24301 | GCA_001311785 | contig | ncbi | 1293598 |
67770 | Lacticaseibacillus saniviri JCM 17471 = DSM 24301 | GCA_001437465 | scaffold | ncbi | 1293598 |
GC content
@ref | GC-content | method |
---|---|---|
17626 | 48.1 | high performance liquid chromatography (HPLC) |
30248 | 48.7 | |
67770 | 47.7 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 94.367 | yes |
gram-positive | yes | 96.194 | yes |
anaerobic | no | 94.688 | yes |
aerobic | no | 95.111 | no |
halophile | yes | 83.367 | no |
spore-forming | no | 93.32 | yes |
thermophile | no | 98.15 | no |
glucose-util | yes | 92.163 | no |
flagellated | no | 97.44 | yes |
glucose-ferment | yes | 85.138 | no |
External links
@ref: 17626
culture collection no.: DSM 24301, JCM 17471, YIT 12363
straininfo link
- @ref: 76175
- straininfo: 398599
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21515698 | Lactobacillus saniviri sp. nov. and Lactobacillus senioris sp. nov., isolated from human faeces. | Oki K, Kudo Y, Watanabe K | Int J Syst Evol Microbiol | 10.1099/ijs.0.031658-0 | 2011 | Aerobiosis, 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, DNA | Pathogenicity |
Phylogeny | 22021580 | Lactobacillus 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 VE | Int J Syst Evol Microbiol | 10.1099/ijs.0.033852-0 | 2011 | Animals, 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 Specificity | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
17626 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24301) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24301 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
30248 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 26590 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68371 | Automatically annotated from API 50CH acid | ||||||
69479 | João 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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
76175 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398599.1 | StrainInfo: A central database for resolving microbial strain identifiers |