Strain identifier
version 8.1 (current version)
General
@ref: 29090
BacDive-ID: 133472
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped
description: Kosakonia oryzae LMG 24251 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from plant endophyte.
NCBI tax id
- NCBI tax id: 497725
- Matching level: species
doi: 10.13145/bacdive133472.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Enterobacteriaceae
- genus: Kosakonia
- species: Kosakonia oryzae
- full scientific name: Kosakonia oryzae (Peng et al. 2009) Brady et al. 2013
synonyms
- @ref: 20215
- synonym: Enterobacter oryzae
@ref: 29090
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacterales
family: Enterobacteriaceae
genus: Kosakonia
species: Kosakonia oryzae
type strain: yes
Morphology
cell morphology
- @ref: 29090
- gram stain: negative
- cell length: 1.7 µm
- cell width: 0.95 µm
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 29090 | positive | growth | 10-40 | |
| 29090 | positive | optimum | 32.5 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29090 | positive | growth | 3.5-10 | alkaliphile |
| 29090 | positive | optimum | 6.75 |
Physiology and metabolism
oxygen tolerance
- @ref: 29090
- oxygen tolerance: facultative anaerobe
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29090 | NaCl | positive | growth | <5 % |
| 29090 | NaCl | positive | optimum | <5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29090 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 29090 | 15963 | ribitol | + | carbon source |
| 29090 | 35391 | aspartate | + | carbon source |
| 29090 | 16947 | citrate | + | carbon source |
| 29090 | 28757 | fructose | + | carbon source |
| 29090 | 33984 | fucose | + | carbon source |
| 29090 | 25115 | malate | + | carbon source |
| 29090 | 17306 | maltose | + | carbon source |
| 29090 | 29864 | mannitol | + | carbon source |
| 29090 | 28053 | melibiose | + | carbon source |
| 29090 | 37657 | methyl D-glucoside | + | carbon source |
| 29090 | 30911 | sorbitol | + | carbon source |
| 29090 | 17992 | sucrose | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 29090
- sample type: plant endophyte
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Host | #Other |
| #Host | #Plants |
taxonmaps
- @ref: 69479
- File name: preview.99_1163.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_789;98_914;99_1163&stattab=map
- Last taxonomy: Enterobacteriaceae
- 16S sequence: EF488759
- Sequence Identity:
- Total samples: 5138
- soil counts: 222
- aquatic counts: 634
- animal counts: 3824
- plant counts: 458
Sequence information
16S sequences
- @ref: 29090
- description: Enterobacter oryzae strain Ola 51 16S ribosomal RNA gene, partial sequence
- accession: EF488759
- length: 1481
- database: nuccore
- NCBI tax ID: 497725
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Kosakonia oryzae CGMCC 1.7012 | GCA_900112145 | scaffold | ncbi | 497725 |
| 66792 | Kosakonia oryzae strain CGMCC 1.7012 | 497725.6 | wgs | patric | 497725 |
| 66792 | Kosakonia oryzae CGMCC 1.7012 | 2675902965 | draft | img | 497725 |
GC content
- @ref: 29090
- GC-content: 54.6-55.4
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 90.464 | yes |
| flagellated | no | 57.862 | no |
| gram-positive | no | 98.044 | yes |
| anaerobic | no | 95.563 | yes |
| aerobic | no | 70.369 | yes |
| halophile | no | 95.343 | no |
| spore-forming | no | 91.91 | no |
| glucose-ferment | yes | 91.656 | no |
| thermophile | no | 99.633 | yes |
| glucose-util | yes | 96.344 | no |
External links
@ref: 29090
culture collection no.: LMG 24251, CGMCC 1.7012, Ola 51
straininfo link
- @ref: 91455
- straininfo: 363406
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19578150 | Enterobacter oryzae sp. nov., a nitrogen-fixing bacterium isolated from the wild rice species Oryza latifolia. | Peng G, Zhang W, Luo H, Xie H, Lai W, Tan Z | Int J Syst Evol Microbiol | 10.1099/ijs.0.65484-0 | 2009 | Anti-Bacterial Agents/pharmacology, Bacterial Proteins/chemistry, Bacterial Typing Techniques, DNA, Bacterial/analysis, Drug Resistance, Bacterial, Enterobacter/*classification/genetics/isolation & purification/physiology, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, *Nitrogen Fixation, Oryza/*microbiology, Phenotype, Phylogeny, Plant Roots/microbiology, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
| Genetics | 28428833 | Complete genome sequence of Kosakonia oryzae type strain Ola 51(T). | Li Y, Li S, Chen M, Peng G, Tan Z, An Q | Stand Genomic Sci | 10.1186/s40793-017-0240-8 | 2017 |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 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 | ||
| 29090 | 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 | 25519 | 28776041 |
| 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 | ||
| 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/ | ||
| 91455 | 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-ID363406.1 |