Strain identifier

BacDive ID: 48

Type strain: Yes

Species: Gluconobacter oxydans

Strain Designation: I, 1

Variant: Isotype of BacDive ID 49 & 23496

Strain history: CIP <- 1984, ATCC <- NCIB, Acetomonas oxydans <- J.G. Carr: strain 1

NCBI tax ID(s): 442 (species)

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General

@ref: 1399

BacDive-ID: 48

DSM-Number: 3503

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Gluconobacter oxydans I is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from Beer.

NCBI tax id

  • NCBI tax id: 442
  • Matching level: species

strain history

@refhistory
1399<- ATCC <- NCIB (Acetomonas oxydans) <- J.G. Carr, I
67770NCIB 9013 <-- J. G. Carr 1.
121484CIP <- 1984, ATCC <- NCIB, Acetomonas oxydans <- J.G. Carr: strain 1

doi: 10.13145/bacdive48.20230509.8.1

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 oxydans
  • full scientific name: Gluconobacter oxydans (Henneberg 1897) De Ley 1961 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Gluconobacter oxydans subsp. suboxydans
    20215Acetomonas suboxydans
    20215Gluconobacter industrius
    20215Bacterium oxydans
    20215Gluconobacter suboxydans
    20215Gluconobacter uchimurae
    20215Bacterium industrium
    20215Gluconobacter oxydans subsp. industrius
    20215Gluconobacter oxydans subsp. melanogenes
    20215Acetobacter suboxydans
    20215Acetobacter melanogenus

@ref: 1399

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Gluconobacter

species: Gluconobacter oxydans

full scientific name: Gluconobacter oxydans (Henneberg 1897) De Ley 1961 emend. Mason and Claus 1989

strain designation: I, 1

variant: Isotype of BacDive ID 49 & 23496

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23244negativerod-shaped
69480yes94.427
69480negative99.998

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1399GLUCONOBACTER OXYDANS MEDIUM (DSMZ Medium 105)yeshttps://mediadive.dsmz.de/medium/105Name: GLUCONOBACTER OXYDANS MEDIUM (DSMZ Medium 105) Composition: Glucose 100.0 g/l CaCO3 20.0 g/l Agar 15.0 g/l Yeast extract 10.0 g/l Distilled water
1399YPM MEDIUM (DSMZ Medium 360)yeshttps://mediadive.dsmz.de/medium/360Name: YPM MEDIUM (DSMZ Medium 360) Composition: Mannitol 25.0 g/l Agar 12.0 g/l Yeast extract 5.0 g/l Peptone 3.0 g/l Distilled water
40524MEDIUM 1 - for Acetobacter, Azotobacter, Gluconobacter, Gluconacetobacter, Mesorhizodium ciceri and Pseudomonas doudoroffiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (5.000 g);Peptone (3.000 g);Mannitol (25.000 g)
121484CIP Medium 1yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=1

culture temp

@refgrowthtypetemperaturerange
1399positivegrowth26mesophilic
23244inconsistentgrowth33mesophilic
23244inconsistentgrowth34mesophilic
23244nogrowth35mesophilic
23244nogrowth37mesophilic
40524positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

tolerance

  • @ref: 23244
  • compound: Glucose
  • percentage: 10

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
23244NaClpositivegrowth0.5 %
23244NaClpositivegrowth0.75 %
23244NaClpositivegrowth1 %
23244NaClinconsistentgrowth1.2 %
23244NaClinconsistentgrowth1.4 %
23244NaClnogrowth1.5 %
23244NaClnogrowth2 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2324417268myo-inositol-growth
2324417992sucrose-growth
2324417151xylitol-growth
2324427856acetamide-hydrolysis
232444853esculin-hydrolysis
2324416199urea-hydrolysis
2324417234glucose+builds acid from
2324417716lactose+builds acid from
2324417306maltose+builds acid from
2324429864mannitol+builds acid from
2324417268myo-inositol+builds acid from
2324415963ribitol+builds acid from
2324430911sorbitol+builds acid from
2324418222xylose+builds acid from
2324417234glucose+/-growth

metabolite production

  • @ref: 23244
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
23244acid phosphatase+3.1.3.2
23244alkaline phosphatase-3.1.3.1
23244alpha-chymotrypsin+3.4.21.1
23244alpha-fucosidase-3.2.1.51
23244alpha-galactosidase-3.2.1.22
23244alpha-glucosidase+/-3.2.1.20
23244alpha-mannosidase-3.2.1.24
23244beta-galactosidase-3.2.1.23
23244beta-glucosidase-3.2.1.21
23244beta-glucuronidase-3.2.1.31
23244cystine arylamidase+3.4.11.3
23244Dnase-
23244esterase+/-
23244esterase lipase (C 8)+
23244leucine arylamidase+3.4.11.1
23244lipase-
23244N-acetyl-beta-glucosaminidase+3.2.1.52
23244phosphatidate phosphatase+3.1.3.4
23244trypsin+3.4.21.4
23244valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample type
67770Beer
121484Food, Beer

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: JF794027
  • Sequence Identity:
  • Total samples: 4981
  • soil counts: 721
  • aquatic counts: 546
  • animal counts: 2856
  • plant counts: 858

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
13991Risk group (German classification)
1214841Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gluconobacter oxydans strain DSM 3503 16S ribosomal RNA gene, partial sequenceJF7940271355ena442
20218Gluconobacter oxydans genes for 16S rRNA, 16S-23S rRNA internal transcribed spacer and 23S rRNA, partial and complete sequenceAB1621151162ena442
20218Gluconobacter oxydans strain LMG 1408 16S ribosomal RNA gene, partial sequenceJF7940261347ena442
20218Gluconobacter oxydans DNA, 16S-23S rRNA ITS region. strain:NBRC 14819AB111901805ena442
20218Gluconobacter oxydans DNA, 16S-23S rRNA internal transcribed spacer, strain:NBRC 14819AB163869676ena442
20218Gluconobacter oxydans gene for 16S rRNA, partial sequence, strain:NBRC 14819AB1784331409ena442
20218Gluconobacter oxydans 16S rRNA, partial sequenceAB003953155ena442
20591Gluconobacter oxydans gene for 16S rRNAX738201476ena442

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gluconobacter oxydans LMG1408GCA_015244575contigncbi442
66792Gluconobacter oxydans strain DSM 3503442.16wgspatric442
66792Gluconobacter oxydans strain LMG1408442.42wgspatric442
66792Gluconobacter oxydans strain NBRC 14819442.19wgspatric442
66792Gluconobacter oxydans DSM 35032784746773draftimg442
67770Gluconobacter oxydans NBRC 14819GCA_006539685contigncbi442
67770Gluconobacter oxydans DSM 3503GCA_004346605contigncbi442

GC content

@refGC-contentmethod
2291953-55
6777060.6thermal denaturation, midpoint method (Tm)
6777057.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno95.763yes
anaerobicno99.071no
halophileno85.664yes
spore-formingno95.64no
glucose-utilyes85.2no
aerobicyes78.179no
flagellatedno79.341no
thermophileno94.032no
motileyes71.827no
glucose-fermentno85.961no

External links

@ref: 1399

culture collection no.: DSM 3503, ATCC 19357, DSM 4494, IAM 14436, NCIB 9013, JCM 7642, CCM 3607, CCUG 18132, CIP 103106, DSM 7145, IFO 14819, LMG 1408, LMG 1589, NBRC 14819, NCIMB 9013, NRIC 1843

straininfo link

  • @ref: 69733
  • straininfo: 311027

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology7751271Biochemical characterization and sequence analysis of the gluconate:NADP 5-oxidoreductase gene from Gluconobacter oxydans.Klasen R, Bringer-Meyer S, Sahm HJ Bacteriol10.1128/jb.177.10.2637-2643.19951995Amino Acid Sequence, *Bacterial Proteins, Base Sequence, Cell Compartmentation, Cloning, Molecular, Escherichia coli/genetics, Genes, Bacterial/*genetics, Gluconates/*metabolism, Gram-Negative Aerobic Bacteria/enzymology/*genetics, Molecular Sequence Data, Molecular Weight, NADP/metabolism, Oxidoreductases/biosynthesis/*genetics/isolation & purification, Protein Conformation, Recombinant Proteins/biosynthesis, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Substrate SpecificityTranscriptome
Phylogeny12361267Gluconobacter asaii Mason and Claus 1989 is a junior subjective synonym of Gluconobacter cerinus Yamada and Akita 1984.Katsura K, Yamada Y, Uchimura T, Komagata KInt J Syst Evol Microbiol10.1099/00207713-52-5-16352002Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Gluconobacter/*classification/genetics/growth & development/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicGenetics
Phylogeny15057706Identification of strains assigned to the genus Gluconobacter Asai 1935 based on the sequence and the restriction analyses of the 16S-23S rDNA internal transcribed spacer regions.Yukphan P, Potacharoen W, Nakagawa Y, Tanticharoen M, Yamada YJ Gen Appl Microbiol10.2323/jgam.50.92004Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/*genetics, Deoxyribonucleases, Type II Site-Specific/metabolism, Gluconobacter/classification/*genetics/metabolism, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Sequence Alignment, Sequence Analysis, DNAMetabolism
18601061Incapability of Gluconobacter oxydans to produce tartaric acid.Klasen R, Bringer-Meyer S, Sahm HBiotechnol Bioeng10.1002/bit.2604001261992
Metabolism20223802Characterization and inactivation of the membrane-bound polyol dehydrogenase in Gluconobacter oxydans DSM 7145 reveals a role in meso-erythritol oxidation.Voss J, Ehrenreich A, Liebl WMicrobiology (Reading)10.1099/mic.0.037598-02010Erythritol/*metabolism, Gluconates/metabolism, Gluconobacter oxydans/*enzymology/*genetics/metabolism, Glucose/metabolism, L-Iditol 2-Dehydrogenase/genetics/*metabolism, Oxidation-Reduction, Substrate Specificity, Tetroses/metabolismEnzymology
Phylogeny32584749Gluconobacter aidae sp. nov., an acetic acid bacterium isolated from tropical fruits in Thailand.Yukphan P, Charoenyingcharoen P, Malimas S, Muramatsu Y, Nakagawa Y, Tanasupawat S, Yamada YInt J Syst Evol Microbiol10.1099/ijsem.0.0042922020Acetic Acid, Ananas/microbiology, Bacterial Typing Techniques, Base Composition, Citrullus/microbiology, DNA, Bacterial/genetics, Fruit/*microbiology, Gluconobacter/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, ThailandTranscriptome
Biotechnology34454960Dihydroxyacetone production via heterogeneous biotransformations of crude glycerol.Ripoll M, Jackson E, Trelles JA, Betancor LJ Biotechnol10.1016/j.jbiotec.2021.08.0112021Biotransformation, *Dihydroxyacetone, *Gluconobacter oxydans, Glycerol

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1399Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3503)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3503
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
20591Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4494)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4494
22919L E Fuentes-Ramírez, R Bustillos-Cristales, A Tapia-Hernández, T Jiménez-Salgado, E T Wang, E Martínez-Romero, J Caballero-Mellado10.1099/00207713-51-4-1305Novel nitrogen-fixing acetic acid bacteria, Gluconacetobacter johannae sp. nov. and Gluconacetobacter azotocaptans sp. nov., associated with coffee plants.IJSEM 51: 1305-1314 200111491326
23244Lori M. Mason, G. William Claus10.1099/00207713-39-2-174Phenotypic Characteristics Correlated with Deoxyribonucleic Acid Sequence Similarities for Three Species of Gluconobacter: G. oxydans (Henneberg 1897) De Ley 1961, G. frateurii sp. nov., and G. asaii sp. nov.IJSEM 39: 174-184 1989
40524Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14865
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
69733Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID311027.1StrainInfo: A central database for resolving microbial strain identifiers
121484Curators of the CIPCollection of Institut Pasteur (CIP 103106)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103106