Gluconobacter oxydans (NBRC 3293, LMG 1385, IFO 3293)

Name: Gluconobacter oxydans (NBRC 3293, LMG 1385, IFO 3293)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 162844

Type strain

Culture col. no. NBRC 3293 LMG 1385 IFO 3293 IAM 1821 JCM 20282

NCBI tax ID(s) 1315969 442

Special Collections JCM

History IAM 1821 <-- T. Asai G-11 ("Gluconobacter melanogenus") <-- IFO 3293 <-- K. Kondo 25.

Links

Gluconobacter oxydans JCM 20282 is a mesophilic prokaryote that was isolated from Dried persimmon.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 2900

LMG 1385,IAM 1821,IFO 3293,KCTC 2875,NBRC 3293,KCTC 12319,JCM 20282

@ref 20215

Last LPSN update 2026-02-09 11:39:29

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 (11)

Gluconobacter oxydans subsp. suboxydans
"Gluconobacter industrius"
Gluconobacter oxydans subsp. melanogenes
"Acetomonas suboxydans"
"Bacterium oxydans"
"Gluconobacter suboxydans"
Gluconobacter uchimurae
Gluconobacter oxydans subsp. industrius
"Acetobacter suboxydans"
"Acetobacter melanogenus"
"Bacterium industrium"

BacDive ID	Other strains from **Gluconobacter oxydans** (23)	Type strain
48	G. oxydans I, 1, DSM 3503, ATCC 19357, DSM 4494, IAM ... (type strain)
46	G. oxydans DSM 2343, ATCC 621H, NCIB 8036, CIP 104215, ...
47	G. oxydans B 4099, DSM 2003, CN 1221
49	G. oxydans DSM 7145, ATCC 19357, NCIB 9013
50	G. oxydans DSM 46615, ATCC 12303, CCM 1804, IFO 3262, ...
51	G. oxydans No 27, Porges 27, DSM 46616, ATCC 9844, CCM ...
52	G. oxydans DSM 50049, ATCC 621, CIP 104737, NCIB 7069, ...
23496	G. oxydans DSM 4494, ATCC 19357, NCIB 9013
139194	G. oxydans CIP 104736, ATCC 9324, IFO 3171, NCTC 4739, ...
143264	G. oxydans CCUG 18134, ATCC 33447, LMG 1581
143265	G. oxydans CCUG 18136, ATCC 33446, LMG 1674
152146	G. oxydans CCUG 45891
155021	G. oxydans CCUG 56122
155022	G. oxydans CCUG 56123
162845	G. oxydans JCM 20283, BCRC 10384, IAM 1822, IFO 3294, ...
162851	G. oxydans JCM 20294, IAM 1839
162852	G. oxydans JCM 20295, IAM 1841
162853	G. oxydans JCM 20296, IAM 1842, LMG 1425
162920	G. oxydans JCM 20430, IAM 12138, IFO 3010, NBRC 3010
163101	G. oxydans JCM 21178, ATCC 11894, CCM 1769, IAM 14365, ...
163102	G. oxydans JCM 21179, ATCC 23772, IAM 14366, LMG 1399, ...
163103	G. oxydans JCM 21180, ATCC 23755, CCM 1795, IAM 14367, ...
163111	G. oxydans JCM 21218, ATCC 15164, IAM 14435, IFO 3243, ...

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.333
125439	negative	99.4

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93.9

Spore formation

@ref	Spore formation	Confidence
125438		90.169
125439		92.9

Isolation, sampling and environmental information

Isolation

67770

Sample typeDried persimmon

Taxonmaps

69479

Global distribution of 16S sequence AB178423 (>99% sequence identity) for Gluconobacter from Microbeatlas

Aquatic Samples	546
Soil Samples	721
Animal Samples	2856
Plant Samples	858
Total Samples	4981

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1176644v1 assembly for Gluconobacter oxydans NBRC 3293	contig	GCA_011766445	1315969.3	2895238798	1315969	71.12

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Gluconobacter oxydans gene for 16S rRNA, partial sequence, strain:NBRC 3293	AB178423	1409		442
124043	Gluconobacter oxydans DNA, 16S-23S rRNA internal transcribed spacer, strain:NBRC 3293.	AB163859	676		442

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gluconobacter oxydans NBRC 3293
NCBI: GCA_011766445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.90	no
125439	motility	BacteriaNetⓘ	yes	78.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gluconobacter oxydans NBRC 3293
PATRIC: 1315969.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.33	no
125438	anaerobic	anaerobicⓘ	no	84.50	no
125438	spore-forming	spore-formingⓘ	no	90.17	no
125438	aerobic	aerobicⓘ	yes	81.63	no
125438	thermophilic	thermophileⓘ	no	95.77	yes
125438	flagellated	motile2+ⓘ	yes	63.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Dihydroxyacetone production via heterogeneous biotransformations of crude glycerol.	Ripoll M, Jackson E, Trelles JA, Betancor L.	J Biotechnol	10.1016/j.jbiotec.2021.08.011	2021
Metabolism	Efficient glycerol transformation by resting Gluconobacter cells.	Jackson E, Ripoll M, Betancor L.	Microbiologyopen	10.1002/mbo3.926	2019
Metabolism	A single membrane-bound enzyme catalyzes the conversion of 2,5-diketo-d-gluconate to 4-keto-d-arabonate in d-glucose oxidative fermentation by Gluconobacter oxydans NBRC 3292.	Tazoe M, Oishi H, Kobayashi S, Hoshino T.	Biosci Biotechnol Biochem	10.1080/09168451.2016.1164584	2016
Enzymology	2,5-Diketo-D-Gluconate Hyperproducing Gluconobacter sphaericus SJF2-1 with Reporting Multiple Genes Encoding the Membrane-Associated Flavoprotein-Cytochrome c Complexed Dehydrogenases.	Son H, Han SU, Lee K.	Microorganisms	10.3390/microorganisms10112130	2022
	Determination of Dehydrogenase Activities Involved in D-Glucose Oxidation in Gluconobacter and Acetobacter Strains.	Sainz F, Jesus Torija M, Matsutani M, Kataoka N, Yakushi T, Matsushita K, Mas A.	Front Microbiol	10.3389/fmicb.2016.01358	2016
Cultivation	High-Yield Production of Dihydroxyacetone from Crude Glycerol in Fed-Batch Cultures of Gluconobacter oxydans.	Gorska K, Garncarek Z.	Molecules	10.3390/molecules29122932	2024
Enzymology	High-Throughput Screening of a 2-Keto-L-Gulonic Acid-Producing Gluconobacter oxydans Strain Based on Related Dehydrogenases.	Chen Y, Liu L, Shan X, Du G, Zhou J, Chen J.	Front Bioeng Biotechnol	10.3389/fbioe.2019.00385	2019
	On the way toward regulatable expression systems in acetic acid bacteria: target gene expression and use cases.	Fricke PM, Klemm A, Bott M, Polen T.	Appl Microbiol Biotechnol	10.1007/s00253-021-11269-z	2021
Metabolism	Metabolic engineering of Gluconobacter oxydans for improved growth rate and growth yield on glucose by elimination of gluconate formation.	Krajewski V, Simic P, Mouncey NJ, Bringer S, Sahm H, Bott M.	Appl Environ Microbiol	10.1128/aem.03022-09	2010
Metabolism	Knockout and overexpression of pyrroloquinoline quinone biosynthetic genes in Gluconobacter oxydans 621H.	Holscher T, Gorisch H.	J Bacteriol	10.1128/jb.01009-06	2006
Metabolism	NADPH-dependent L-sorbose reductase is responsible for L-sorbose assimilation in Gluconobacter suboxydans IFO 3291.	Shinjoh M, Tazoe M, Hoshino T.	J Bacteriol	10.1128/jb.184.3.861-863.2002	2002
Enzymology	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
Metabolism	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
Metabolism	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
Metabolism	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
Metabolism	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
Enzymology	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
Metabolism	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

References

#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. IJSEM ( DOI 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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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. 2024 ( DOI 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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Gluconobacter oxydans (NBRC 3293, LMG 1385, IFO 3293)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_011766445

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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