Strain identifier

BacDive ID: 134216

Type strain: Yes

Species: Komagataeibacter kombuchae

Strain Designation: RG3

NCBI tax ID(s): 436 (species)

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General

@ref: 31910

BacDive-ID: 134216

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

description: Komagataeibacter kombuchae RG3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from plant endophyte.

NCBI tax id

  • NCBI tax id: 436
  • Matching level: species

doi: 10.13145/bacdive134216.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Komagataeibacter
  • species: Komagataeibacter kombuchae
  • full scientific name: Komagataeibacter kombuchae (Dutta and Gachhui 2007) Yamada et al. 2013

  • synonyms

    @refsynonym
    20215Komagatabacter kombuchae
    20215Gluconacetobacter kombuchae

@ref: 31910

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Acetobacteraceae

genus: Komagataeibacter

species: Komagataeibacter hansenii

strain designation: RG3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31910negative2.0-3.0 µm0.1-0.2 µmrod-shapedyes
69480negative99.99

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31910positivegrowth30-37mesophilic
31910positiveoptimum33.5mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31910
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3191016449alanine+carbon source
3191022599arabinose+carbon source
3191028885butanol+carbon source
3191017754glycerol+carbon source
3191029864mannitol+carbon source
3191030911sorbitol+carbon source
3191026986threonine+carbon source

enzymes

  • @ref: 31910
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 31910
  • sample type: plant endophyte

isolation source categories

Cat1Cat2
#Host#Other
#Host#Plants

taxonmaps

  • @ref: 69479
  • File name: preview.99_1535.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_64;97_67;98_72;99_1535&stattab=map
  • Last taxonomy: Komagataeibacter
  • 16S sequence: AY688433
  • Sequence Identity:
  • Total samples: 810
  • soil counts: 119
  • aquatic counts: 106
  • animal counts: 397
  • plant counts: 188

Sequence information

16S sequences

  • @ref: 31910
  • description: Komagataeibacter hansenii strain RG3 16S ribosomal RNA gene, partial sequence
  • accession: AY688433
  • length: 1442
  • database: nuccore
  • NCBI tax ID: 436

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novacetimonas hansenii LMG 23726GCA_003207935contigncbi436
66792Novacetimonas hansenii LMG 23726GCA_001938755scaffoldncbi436
66792Komagataeibacter hansenii strain LMG 23726436.9wgspatric436
66792Komagataeibacter hansenii strain LMG 23726436.15wgspatric436
66792Komagataeibacter hansenii LMG 237262849443596draftimg436

GC content

  • @ref: 31910
  • GC-content: 55.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.26no
gram-positiveno96.003yes
anaerobicno98.342yes
halophileno89.632no
spore-formingno94.684no
glucose-utilyes86.765no
aerobicyes81.452yes
thermophileno94.55yes
motileno81.378yes
glucose-fermentno86.651no

External links

@ref: 31910

culture collection no.: LMG 23726, MTCC 6913

straininfo link

  • @ref: 91811
  • straininfo: 389481

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267978Nitrogen-fixing and cellulose-producing Gluconacetobacter kombuchae sp. nov., isolated from Kombucha tea.Dutta D, Gachhui RInt J Syst Evol Microbiol10.1099/ijs.0.64638-02007Amino Acids/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cellulose/biosynthesis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Food Microbiology, Genes, rRNA, Gluconacetobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nitrogen Fixation, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Tea/*microbiologyMetabolism
Phylogeny19542117Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting: Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii.Cleenwerck I, De Wachter M, Gonzalez A, De Vuyst L, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.005157-02009Acetobacteraceae/*classification/genetics/isolation & purification, *Amplified Fragment Length Polymorphism Analysis, *Bacterial Typing Techniques, DNA Fingerprinting/*methods, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Deoxyribonucleases, Type II Site-Specific/metabolism, Food Microbiology, Genes, rRNA, Genotype, Gluconacetobacter/*classification/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Genetics28408680Complete Genome Sequence of Komagataeibacter hansenii LMG 23726(T).Pfeffer S, Santos R, Ebels M, Bordbar D, Brown RM JrGenome Announc10.1128/genomeA.00168-172017

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
31910Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172816728776041
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
91811Reimer, 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-ID389481.1