Strain identifier
BacDive ID: 134355
Type strain:
Species: Gluconobacter japonicus
NCBI tax ID(s): 1307947 (strain), 376620 (species)
version 8.1 (current version)
General
@ref: 32591
BacDive-ID: 134355
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Gluconobacter japonicus BCC 14458 is a mesophilic, Gram-negative, motile bacterium of the family Acetobacteraceae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1307947 | strain |
376620 | species |
doi: 10.13145/bacdive134355.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Acetobacteraceae
- genus: Gluconobacter
- species: Gluconobacter japonicus
- full scientific name: Gluconobacter japonicus Malimas et al. 2009
synonyms
@ref synonym 20215 Gluconobacter japonicus subsp. nephelii 20215 Gluconobacter nephelii
@ref: 32591
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodospirillales
family: Acetobacteraceae
genus: Gluconobacter
species: Gluconobacter japonicus
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32591 | negative | 1.0-2.0 µm | 0.8-1 µm | rod-shaped | yes | |
69480 | negative | 99.995 |
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
32591 | positive | growth | 25-35 | mesophilic |
32591 | positive | optimum | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32591 | positive | growth | 3.0-5.5 | acidophile |
32591 | positive | optimum | 5.5 |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.98 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32591 | 16808 | 2-dehydro-D-gluconate | + | carbon source |
32591 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
32591 | 22599 | arabinose | + | carbon source |
32591 | 16236 | ethanol | + | carbon source |
32591 | 28757 | fructose | + | carbon source |
32591 | 28260 | galactose | + | carbon source |
32591 | 17234 | glucose | + | carbon source |
32591 | 17754 | glycerol | + | carbon source |
32591 | 29864 | mannitol | + | carbon source |
32591 | 37684 | mannose | + | carbon source |
32591 | 28053 | melibiose | + | carbon source |
32591 | 16634 | raffinose | + | carbon source |
32591 | 26546 | rhamnose | + | carbon source |
32591 | 30911 | sorbitol | + | carbon source |
32591 | 17992 | sucrose | + | carbon source |
32591 | 18222 | xylose | + | carbon source |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_1213.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_336;97_374;98_960;99_1213&stattab=map
- Last taxonomy: Gluconobacter
- 16S sequence: AB253435
- Sequence Identity:
- Total samples: 3822
- soil counts: 546
- aquatic counts: 376
- animal counts: 2369
- plant counts: 531
Sequence information
16S sequences
- @ref: 32591
- description: Gluconobacter japonicus gene for 16S rRNA, partial sequence, strain: NBRC 3271
- accession: AB253435
- length: 1406
- database: nuccore
- NCBI tax ID: 376620
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Gluconobacter japonicus NBRC 3271 | GCA_002723975 | contig | ncbi | 376620 |
66792 | Gluconobacter japonicus strain NBRC 3271 | 376620.10 | patric | 376620 |
GC content
- @ref: 32591
- GC-content: 55.1-56.4
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 74.547 | no |
gram-positive | no | 95.955 | yes |
anaerobic | no | 99.224 | no |
halophile | no | 89.339 | no |
spore-forming | no | 94.548 | no |
glucose-util | yes | 90.202 | yes |
aerobic | yes | 87.355 | no |
motile | yes | 76.97 | no |
glucose-ferment | no | 88.07 | no |
thermophile | no | 96.293 | no |
External links
@ref: 32591
culture collection no.: BCC 14458, NBRC 3271
straininfo link
- @ref: 91909
- straininfo: 2866
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19244423 | Gluconobacter japonicus sp. nov., an acetic acid bacterium in the Alphaproteobacteria. | Malimas T, Yukphan P, Takahashi M, Muramatsu Y, Kaneyasu M, Potacharoen W, Tanasupawat S, Nakagawa Y, Tanticharoen M, Yamada Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.65740-0 | 2009 | Acetic Acid/*metabolism, Alphaproteobacteria/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Genes, rRNA, Gluconobacter/chemistry/*classification/genetics/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
Metabolism | 25769838 | Efficient Production of 2,5-Diketo-d-Gluconate via Heterologous Expression of 2-Ketogluconate Dehydrogenase in Gluconobacter japonicus. | Kataoka N, Matsutani M, Yakushi T, Matsushita K | Appl Environ Microbiol | 10.1128/AEM.04176-14 | 2015 | Bacterial Proteins/*genetics/metabolism, Carbohydrate Dehydrogenases/*genetics/metabolism, *Gene Expression, Gluconates/*metabolism, Gluconobacter/classification/enzymology/genetics/*metabolism, Metabolic Engineering, Molecular Sequence Data | Enzymology |
Enzymology | 35150230 | Characterization of 3 phylogenetically distinct membrane-bound d-gluconate dehydrogenases of Gluconobacter spp. and their biotechnological application for efficient 2-keto-d-gluconate production. | Kataoka N, Saichana N, Matsutani M, Toyama H, Matsushita K, Yakushi T | Biosci Biotechnol Biochem | 10.1093/bbb/zbac024 | 2022 | Gluconates/chemistry, *Gluconobacter/genetics, *Gluconobacter oxydans/genetics, Oxidoreductases | Biotechnology |
Metabolism | 36271931 | Development of efficient 5-ketogluconate production system by Gluconobacter japonicus. | Kataoka N, Naoki K, Ano Y, Matsushita K, Yakushi T | Appl Microbiol Biotechnol | 10.1007/s00253-022-12242-0 | 2022 | Calcium Chloride, *Gluconobacter, Gluconates/metabolism, PQQ Cofactor/metabolism, Glucose/metabolism | Biotechnology |
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 | ||
32591 | 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 | 28804 | 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/ | ||
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 | ||
91909 | 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-ID2866.1 |