Cite this strain

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

Links

Name and taxonomic classification

Gluconobacter oxydans JCM 20282 is a mesophilic, Gram-negative bacterium that was isolated from Dried persimmon.

Gram-negative mesophilic genome sequence 16S sequence Bacteria

SI-ID 2900

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

Last LPSN update 2024-12-09 10:52:35

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)

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

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

Spore formation

@ref	Spore formation	Confidence
125438		90.169
125439		92.9

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93.9

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

Safety information

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		442
124043	Gluconobacter oxydans DNA, 16S-23S rRNA internal transcribed spacer, strain:NBRC 3293.	AB163859	676		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	JGI IMG/M	442
66792	Gluconobacter oxydans NBRC 3293	GCA_011766445	contig		1315969

Genome-based predictions

Predictions

Predictions from Diaspora project 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 Diaspora project 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

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
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

Straininfo Link

@ref	Straininfo	Culture collections
113648	2900	LMG 1385, IAM 1821, IFO 3293, KCTC 2875, NBRC 3293, KCTC 12319, JCM 20282

Culture collection no.

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

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 .
#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 . ( DOI 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. 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 .

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