Strain identifier
BacDive ID: 160959
Type strain: 
Species: Ligilactobacillus salivarius
Strain history: T. Mitsuoka PNF-7-6.
NCBI tax ID(s): 1624 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 160959
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Ligilactobacillus salivarius JCM 1046 is a mesophilic, Gram-positive bacterium that was isolated from Swine intestine.
NCBI tax id
- NCBI tax id: 1624
- Matching level: species
strain history
- @ref: 67770
- history: T. Mitsuoka PNF-7-6.
doi: 10.13145/bacdive160959.20250331.9.3
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 salivarius
- full scientific name: Ligilactobacillus salivarius (Rogosa et al. 1953) Zheng et al. 2020
synonyms
@ref synonym 20215 Lactobacillus salivarius 20215 Lactobacillus salivarius subsp. salicinius
@ref: 67770
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Ligilactobacillus
species: Ligilactobacillus salivarius
full scientific name: Ligilactobacillus salivarius (Rogosa et al. 1953) Zheng et al. 2020
type strain: no
Morphology
cell morphology
- @ref: 125438
- gram stain: positive
- confidence: 91.965
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: microaerophile
- confidence: 94.9
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Swine intestine
Sequence information
16S sequences
- @ref: 124043
- description: Lactobacillus salivarius subsp. salicinius strain JCM 1046 16S ribosomal RNA gene, partial sequence.
- accession: AY137587
- length: 1489
- database: nuccore
- NCBI tax ID: 1624
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ligilactobacillus salivarius JCM1046 | GCA_000758365 | complete | ncbi | 1624 |
| 66792 | Lactobacillus salivarius JCM1046 | 1624.19 | complete | patric | 1624 |
| 66792 | Lactobacillus salivarius strain JCM1046 | 1624.118 | plasmid | patric | 1624 |
| 66792 | Lactobacillus salivarius strain JCM1046 | 1624.117 | plasmid | patric | 1624 |
| 66792 | Lactobacillus salivarius strain JCM1046 | 1624.115 | plasmid | patric | 1624 |
| 66792 | Lactobacillus salivarius strain JCM1046 | 1624.116 | plasmid | patric | 1624 |
| 66792 | Ligilactobacillus salivarius JCM 1046 | 2630968332 | complete | img | 1624 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 91.965 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 78.351 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 93.382 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.981 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 94.028 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 88 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 54.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 56.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 74 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | microaerophile | 94.9 |
External links
@ref: 67770
culture collection no.: JCM 1046, KCTC 3156
straininfo link
- @ref: 113123
- straininfo: 63142
literature
- topic: Genetics
- Pubmed-ID: 25201645
- title: Unusual genome complexity in Lactobacillus salivarius JCM1046.
- authors: Raftis EJ, Forde BM, Claesson MJ, O'Toole PW
- journal: BMC Genomics
- DOI: 10.1186/1471-2164-15-771
- year: 2014
- mesh: Bacteriophages/genetics, Clustered Regularly Interspaced Short Palindromic Repeats/genetics, Conjugation, Genetic, DNA Transposable Elements, DNA, Bacterial/genetics, Gene Order, Genetic Variation, *Genome, Bacterial, *Genomics, Lactobacillus/*genetics/virology, Molecular Sequence Data, Phenotype, Plasmids/genetics, Replicon, Transposases/genetics/metabolism
- topic2: Phenotype
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 113123 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID63142.1 |
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |