Strain identifier
BacDive ID: 24133
Type strain:
Species: Secundilactobacillus oryzae
Strain history: CIP <- 2013, JCM
NCBI tax ID(s): 1202668 (species)
General
@ref: 20993
BacDive-ID: 24133
DSM-Number: 26518
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped
description: Secundilactobacillus oryzae DSM 26518 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from fermented rice grains.
NCBI tax id
- NCBI tax id: 1202668
- Matching level: species
strain history
@ref | history |
---|---|
33558 | 2013, JCM |
20993 | <- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; SG293 |
67770 | M. Tohno SG293. |
67771 | <- DSM <- M Tohno, National Agriculture and Food Res Org (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan, SG293 |
121454 | CIP <- 2013, JCM |
doi: 10.13145/bacdive24133.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Lactobacillaceae
- genus: Secundilactobacillus
- species: Secundilactobacillus oryzae
- full scientific name: Secundilactobacillus oryzae (Tohno et al. 2013) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus oryzae
@ref: 20993
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Secundilactobacillus
species: Secundilactobacillus oryzae
full scientific name: Secundilactobacillus oryzae (Tohno et al. 2013) Zheng et al. 2020
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30984 | positive | 5 µm | 1 µm | rod-shaped | no | |
67771 | rod-shaped | no | ||||
67771 | positive | |||||
69480 | no | 94.64 | ||||
69480 | positive | 100 | ||||
121454 | positive | rod-shaped | no |
pigmentation
- @ref: 30984
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
33558 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
20993 | MRS MEDIUM (DSMZ Medium 11) | yes | 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 | https://mediadive.dsmz.de/medium/11 |
121454 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20993 | positive | growth | 30 | mesophilic |
30984 | positive | growth | 04-45 | |
30984 | positive | optimum | 30 | mesophilic |
33558 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 30984
- ability: positive
- type: growth
- pH: 5.0-8.0
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
20993 | microaerophile |
30984 | facultative anaerobe |
67771 | microaerophile |
spore formation
@ref | spore formation | confidence |
---|---|---|
30984 | no | |
67771 | no | |
69481 | no | 100 |
69480 | no | 99.992 |
halophily
- @ref: 30984
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 04-08 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30984 | 16808 | 2-dehydro-D-gluconate | + | carbon source |
30984 | 24265 | gluconate | + | carbon source |
30984 | 17234 | glucose | + | carbon source |
30984 | 17306 | maltose | + | carbon source |
30984 | 506227 | N-acetylglucosamine | + | carbon source |
30984 | 33942 | ribose | + | 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 |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30984 | acid phosphatase | + | 3.1.3.2 |
30984 | alkaline phosphatase | + | 3.1.3.1 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20993 | - | - | - | - | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | host species |
---|---|---|---|---|---|---|
20993 | fermented rice grains | Tochigi, Ohtawara | Japan | JPN | Asia | |
67770 | Fermented rice grain (Oryza sativa L. subsp. japonica) | Ohtawara, Tochigi | Japan | JPN | Asia | Oryza sativa L. subsp. japonica |
67771 | From fermented rice grains | Tochigi, Ohtawara | Japan | JPN | Asia | |
121454 | Fermented rice grain, Oryza sativa Lactobacillus japonica | Tochigi, Japan | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Vegetable (incl. Grains) |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Engineered | #Food production | #Fermented |
taxonmaps
- @ref: 69479
- File name: preview.99_94879.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_936;97_1089;98_1299;99_94879&stattab=map
- Last taxonomy: Secundilactobacillus oryzae
- 16S sequence: LC521992
- Sequence Identity:
- Total samples: 330
- soil counts: 32
- aquatic counts: 42
- animal counts: 224
- plant counts: 32
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
20993 | 1 | Risk group (German classification) |
121454 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20993 | Lactobacillus oryzae gene for 16S ribosomal RNA, partial sequence, strain: SG293 | AB731660 | 1488 | ena | 1291743 |
67770 | Lactobacillus oryzae JCM 18671 gene for 16S rRNA, partial sequence | LC521992 | 1502 | ena | 1291743 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Secundilactobacillus oryzae JCM 18671 | GCA_001311525 | contig | ncbi | 1291743 |
66792 | Lactobacillus oryzae JCM 18671 | 1291743.4 | wgs | patric | 1291743 |
66792 | Lactobacillus oryzae JCM 18671 | 1291743.3 | wgs | patric | 1291743 |
66792 | Secundilactobacillus oryzae JCM 18671 | 2728369689 | draft | img | 1291743 |
67771 | Secundilactobacillus oryzae JCM 18671 SG293 | GCA_000740055 | contig | ncbi | 1291743 |
GC content
@ref | GC-content | method |
---|---|---|
20993 | 43.4 | high performance liquid chromatography (HPLC) |
30984 | 43.4 | |
67770 | 42.8 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 95.611 | no |
gram-positive | yes | 94.422 | yes |
anaerobic | no | 92.819 | yes |
aerobic | no | 96.309 | yes |
halophile | yes | 91.997 | no |
spore-forming | no | 96.811 | no |
glucose-util | yes | 91.89 | yes |
flagellated | no | 98.886 | yes |
thermophile | no | 99.054 | yes |
glucose-ferment | yes | 84.391 | no |
External links
@ref: 20993
culture collection no.: DSM 26518, JCM 18671, KCTC 21047, SG 293, CIP 110586
straininfo link
- @ref: 88091
- straininfo: 390384
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23378109 | Lactobacillus oryzae sp. nov., isolated from fermented rice grain (Oryza sativa L. subsp. japonica). | Tohno M, Kitahara M, Irisawa T, Inoue H, Uegaki R, Ohkuma M, Tajima K | Int J Syst Evol Microbiol | 10.1099/ijs.0.048918-0 | 2013 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Fermentation, Food Microbiology, Japan, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Biotechnology |
Genetics | 25169865 | Draft Genome Sequence of Lactobacillus oryzae Strain SG293T. | Tanizawa Y, Fujisawa T, Mochizuki T, Kaminuma E, Nakamura Y, Tohno M | Genome Announc | 10.1128/genomeA.00861-14 | 2014 |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
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 | ||||
20993 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26518 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26518) | ||||
30984 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27314 | 28776041 | ||
33558 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/30383 | |||||
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 | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
88091 | 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-ID390384.1 | ||||
121454 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110586 | Collection of Institut Pasteur (CIP 110586) |