Strain identifier
BacDive ID: 162844
Type strain: 
Species: Gluconobacter oxydans
Strain history: IAM 1821 <-- T. Asai G-11 ("Gluconobacter melanogenus") <-- IFO 3293 <-- K. Kondo 25.
NCBI tax ID(s): 1315969 (strain), 442 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162844
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Gluconobacter oxydans JCM 20282 is a mesophilic, Gram-negative bacterium that was isolated from Dried persimmon.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1315969 | strain |
| 442 | species |
strain history
- @ref: 67770
- history: IAM 1821 <-- T. Asai G-11 ("Gluconobacter melanogenus") <-- IFO 3293 <-- K. Kondo 25.
doi: 10.13145/bacdive162844.20250331.9.3
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 oxydans
- full scientific name: Gluconobacter oxydans (Henneberg 1897) De Ley 1961 (Approved Lists 1980)
synonyms
@ref synonym 20215 Acetobacter suboxydans 20215 Gluconobacter industrius 20215 Acetobacter melanogenus 20215 Bacterium industrium 20215 Gluconobacter oxydans subsp. suboxydans 20215 Acetomonas suboxydans 20215 Bacterium oxydans 20215 Gluconobacter suboxydans 20215 Gluconobacter uchimurae 20215 Gluconobacter oxydans subsp. industrius 20215 Gluconobacter oxydans subsp. melanogenes
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodospirillales
family: Acetobacteraceae
genus: Gluconobacter
species: Gluconobacter oxydans
full scientific name: Gluconobacter oxydans (Henneberg 1897) De Ley 1961
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 97.333 |
| 125439 | negative | 99.4 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 93.9
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 90.169 |
| 125439 | no | 92.9 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Dried persimmon
taxonmaps
- @ref: 69479
- File name: preview.99_530.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_336;97_374;98_430;99_530&stattab=map
- Last taxonomy: Gluconobacter
- 16S sequence: AB178423
- Sequence Identity:
- Total samples: 4981
- soil counts: 721
- aquatic counts: 546
- animal counts: 2856
- plant counts: 858
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Gluconobacter oxydans gene for 16S rRNA, partial sequence, strain:NBRC 3293 | AB178423 | 1409 | nuccore | 442 |
| 124043 | Gluconobacter oxydans DNA, 16S-23S rRNA internal transcribed spacer, strain:NBRC 3293. | AB163859 | 676 | nuccore | 442 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gluconobacter oxydans NBRC 3293 | 1315969.3 | wgs | patric | 1315969 |
| 66792 | Gluconobacter oxydans NBRC 3293 | 2895238798 | draft | img | 442 |
| 66792 | Gluconobacter oxydans NBRC 3293 | GCA_011766445 | contig | ncbi | 1315969 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.333 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 84.496 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.169 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.634 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 95.765 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 63.272 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 92.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 78.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 93.9 |
External links
@ref: 67770
culture collection no.: JCM 20282, IAM 1821, IFO 3293, LMG 1385, NBRC 3293
straininfo link
- @ref: 113648
- straininfo: 2900
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 7574579 | Cloning and nucleotide sequencing of the membrane-bound L-sorbosone dehydrogenase gene of Acetobacter liquefaciens IFO 12258 and its expression in Gluconobacter oxydans. | Shinjoh M, Tomiyama N, Asakura A, Hoshino T | Appl Environ Microbiol | 10.1128/aem.61.2.413-420.1995 | 1995 | Acetobacter/*enzymology/*genetics, Acetobacteraceae/*genetics, Aldehyde Oxidoreductases/*genetics, Amino Acid Sequence, Base Sequence, Cloning, Molecular, Conjugation, Genetic, DNA, Bacterial/genetics, Gene Expression, *Genes, Bacterial, Membranes/enzymology, Molecular Sequence Data, Restriction Mapping, Sorbitol/metabolism, Sorbose/analogs & derivatives/metabolism, Sugar Acids/metabolism | Metabolism |
| Metabolism | 7765162 | Characterisation of plasmids from diketogluconic acid producing strains of Gluconobacter oxydans. | Verma V, Felder M, Cullum J, Qazi GN | J Biotechnol | 10.1016/0168-1656(94)90026-4 | 1994 | Base Sequence, Gluconates/*metabolism, Molecular Sequence Data, *Plasmids, Pseudomonadaceae/*genetics/metabolism | Genetics |
| Metabolism | 11111029 | The pyrroloquinoline quinone synthesis genes of Gluconobacter oxydans. | Felder M, Gupta A, Verma V, Kumar A, Qazi GN, Cullum J | FEMS Microbiol Lett | 10.1111/j.1574-6968.2000.tb09429.x | 2000 | Bacterial Proteins/*genetics/metabolism, Cloning, Molecular, DNA Transposable Elements, *Genes, Bacterial, Genetic Complementation Test, Gluconobacter oxydans/*genetics/metabolism, Glucose Dehydrogenases/genetics, Multigene Family, Mutagenesis, Insertional, PQQ Cofactor, Quinolones/*metabolism, Quinones/*metabolism, Sequence Analysis, DNA | Enzymology |
| Metabolism | 19844074 | Glycerol conversion to D-xylulose by a two-stage microbial reaction using Candida parapsilosis and Gluconobacter oxydans. | Habe H, Fukuoka T, Kitamoto D, Sakaki K | J Oleo Sci | 10.5650/jos.58.595 | 2009 | *Candida/chemistry/metabolism, *Fermentation, *Gluconobacter oxydans/chemistry/metabolism, Glycerol/*chemistry/metabolism, Phylogeny, Xylulose/*chemistry/metabolism | Phylogeny |
| 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 |
| Metabolism | 33127815 | The Auxiliary NADH Dehydrogenase Plays a Crucial Role in Redox Homeostasis of Nicotinamide Cofactors in the Absence of the Periplasmic Oxidation System in Gluconobacter oxydans NBRC3293. | Sriherfyna FH, Matsutani M, Hirano K, Koike H, Kataoka N, Yamashita T, Nakamaru-Ogiso E, Matsushita K, Yakushi T | Appl Environ Microbiol | 10.1128/AEM.02155-20 | 2021 | Gluconobacter oxydans/*enzymology/genetics/metabolism, Homeostasis, NAD/*metabolism, NADH Dehydrogenase/*metabolism, NADP/*metabolism, Niacinamide/metabolism, Oxidation-Reduction, Periplasm/metabolism | 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 |
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/ | |
| 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/ |
| 113648 | 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-ID2900.1 |
| 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 |