Strain identifier

BacDive ID: 134355

Type strain: Yes

Species: Gluconobacter japonicus

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
1307947strain
376620species

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

    @refsynonym
    20215Gluconobacter japonicus subsp. nephelii
    20215Gluconobacter nephelii

@ref: 32591

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Acetobacteraceae

genus: Gluconobacter

species: Gluconobacter japonicus

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32591negative1.0-2.0 µm0.8-1 µmrod-shapedyes
69480negative99.995

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32591positivegrowth25-35mesophilic
32591positiveoptimum25mesophilic

culture pH

@refabilitytypepHPH range
32591positivegrowth3.0-5.5acidophile
32591positiveoptimum5.5

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.98

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32591168082-dehydro-D-gluconate+carbon source
32591581435-dehydro-D-gluconate+carbon source
3259122599arabinose+carbon source
3259116236ethanol+carbon source
3259128757fructose+carbon source
3259128260galactose+carbon source
3259117234glucose+carbon source
3259117754glycerol+carbon source
3259129864mannitol+carbon source
3259137684mannose+carbon source
3259128053melibiose+carbon source
3259116634raffinose+carbon source
3259126546rhamnose+carbon source
3259130911sorbitol+carbon source
3259117992sucrose+carbon source
3259118222xylose+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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gluconobacter japonicus NBRC 3271GCA_002723975contigncbi376620
66792Gluconobacter japonicus strain NBRC 3271376620.10patric376620

GC content

  • @ref: 32591
  • GC-content: 55.1-56.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno74.547no
gram-positiveno95.955yes
anaerobicno99.224no
halophileno89.339no
spore-formingno94.548no
glucose-utilyes90.202yes
aerobicyes87.355no
motileyes76.97no
glucose-fermentno88.07no
thermophileno96.293no

External links

@ref: 32591

culture collection no.: BCC 14458, NBRC 3271

straininfo link

  • @ref: 91909
  • straininfo: 2866

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244423Gluconobacter 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 YInt J Syst Evol Microbiol10.1099/ijs.0.65740-02009Acetic 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 SpecificityGenetics
Metabolism25769838Efficient Production of 2,5-Diketo-d-Gluconate via Heterologous Expression of 2-Ketogluconate Dehydrogenase in Gluconobacter japonicus.Kataoka N, Matsutani M, Yakushi T, Matsushita KAppl Environ Microbiol10.1128/AEM.04176-142015Bacterial Proteins/*genetics/metabolism, Carbohydrate Dehydrogenases/*genetics/metabolism, *Gene Expression, Gluconates/*metabolism, Gluconobacter/classification/enzymology/genetics/*metabolism, Metabolic Engineering, Molecular Sequence DataEnzymology
Enzymology35150230Characterization 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 TBiosci Biotechnol Biochem10.1093/bbb/zbac0242022Gluconates/chemistry, *Gluconobacter/genetics, *Gluconobacter oxydans/genetics, OxidoreductasesBiotechnology
Metabolism36271931Development of efficient 5-ketogluconate production system by Gluconobacter japonicus.Kataoka N, Naoki K, Ano Y, Matsushita K, Yakushi TAppl Microbiol Biotechnol10.1007/s00253-022-12242-02022Calcium Chloride, *Gluconobacter, Gluconates/metabolism, PQQ Cofactor/metabolism, Glucose/metabolismBiotechnology

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
32591Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172880428776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91909Reimer, 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 identifiers10.60712/SI-ID2866.1