Strain identifier

BacDive ID: 20

Type strain: Yes

Species: Acetobacter nitrogenifigens

Strain Designation: RG1

Strain history: NRIC 0976 <-- NBRC 105050 <-- LMG 23498 <-- R. Gachhui; Jadavpur Univ., India; RG1 <-- D. Dutta; Jadavpur Univ., India.

NCBI tax ID(s): 1120919 (strain), 285268 (species)

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General

@ref: 17427

BacDive-ID: 20

DSM-Number: 23921

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

description: Acetobacter nitrogenifigens RG1 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Kombucha tea.

NCBI tax id

NCBI tax idMatching level
1120919strain
285268species

strain history

@refhistory
17427<- R. Gachhui, Jadavpur Univ., Kolkata, India; RG1 <- D. Dutta
67770NRIC 0976 <-- NBRC 105050 <-- LMG 23498 <-- R. Gachhui; Jadavpur Univ., India; RG1 <-- D. Dutta; Jadavpur Univ., India.

doi: 10.13145/bacdive20.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Acetobacter
  • species: Acetobacter nitrogenifigens
  • full scientific name: Acetobacter nitrogenifigens Dutta and Gachhui 2006

@ref: 17427

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Acetobacter

species: Acetobacter nitrogenifigens

full scientific name: Acetobacter nitrogenifigens Dutta and Gachhui 2006

strain designation: RG1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23235negative1.5-2.0 µm0.1-0.2 µmrod-shapedyespolar
69480negative99.998

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
232352-3 mmtransparentcircular5 daysnitrogen-free LGI
23235dark yellowLGI agar
23235light brownpotato agar

Culture and growth conditions

culture medium

@refnamegrowthcomposition
23235LGI agaryessupplemented with 0.001% bromothymol blue
23235nitrogen-free LGIyes
23235potato agaryes

culture temp

  • @ref: 67770
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

tolerance

@refcompoundpercentage
23235Sucrose30
23235Glucose30
23235Ethanol10

oxygen tolerance

  • @ref: 23235
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2323517790methanol-assimilation
2323516857L-threonine-carbon source
2323516857L-threonine-nitrogen source
2323517632nitrate-reduction
2323517108D-arabinose+carbon source
2323515824D-fructose+carbon source
2323512936D-galactose+carbon source
2323516899D-mannitol+carbon source
2323517924D-sorbitol+carbon source
2323565327D-xylose+carbon source
2323516977L-alanine+carbon source
2323517561L-cysteine+carbon source
2323517295L-phenylalanine+carbon source
2323528938ammonium+growth
2323516236ethanol+oxidation

metabolite production

@refChebi-IDmetaboliteproduction
2323516016dihydroxyacetoneyes
23235379664h-pyran-4-oneyes

enzymes

@refvalueactivityec
23235catalase+1.11.1.6
23235cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17427Kombucha teaIndiaINDAsia
67770Kombucha tea

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_2615.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_152;97_827;98_2025;99_2615&stattab=map
  • Last taxonomy: Acetobacter
  • 16S sequence: HG424425
  • Sequence Identity:
  • Total samples: 888
  • soil counts: 133
  • aquatic counts: 132
  • animal counts: 499
  • plant counts: 124

Safety information

risk assessment

  • @ref: 17427
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acetobacter nitrogenifigens partial 16S rRNA gene, strain LMG 23498HG4244251421ena1120919
17427Acetobacter nitrogenifigens strain RG1 16S ribosomal RNA gene, partial sequenceAY6695131451ena1120919
67770Acetobacter nitrogenifigens gene for 16S rRNA, partial sequence, strain: NBRC 105050AB6822351415ena1120919

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acetobacter nitrogenifigens DSM 239211120919.3wgspatric1120919
66792Acetobacter nitrogenifigens DSM 23921 = LMG 23498 strain NBRC 1050501120919.6wgspatric1120919
66792Acetobacter nitrogenifigens NBRC 1050502927201423draftimg1120919
66792Acetobacter nitrogenifigens DSM 239212522572157draftimg1120919
67770Acetobacter nitrogenifigens DSM 23921 = NBRC 105050GCA_000429165scaffoldncbi1120919
67770Acetobacter nitrogenifigens DSM 23921 = NBRC 105050GCA_007991375contigncbi1120919

GC content

@refGC-content
1742764.1
2323564.10

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.34yes
flagellatedno61.275yes
gram-positiveno96.859yes
anaerobicno98.463yes
aerobicyes91.734yes
halophileno93.203no
spore-formingno93.111no
thermophileno96.89yes
glucose-utilyes89.517no
glucose-fermentno91.273no

External links

@ref: 17427

culture collection no.: DSM 23921, LMG 23498, MTCC 6912, JCM 33644, BCC 33377, BCRC 80095, NBRC 105050, NRIC 0976, TBRC 15

straininfo link

  • @ref: 69704
  • straininfo: 290409

literature

  • topic: Phylogeny
  • Pubmed-ID: 16902028
  • title: Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha tea.
  • authors: Dutta D, Gachhui R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64101-0
  • year: 2006
  • mesh: Acetobacter/chemistry/*classification/isolation & purification/physiology, Base Composition, Carbohydrates, Culture Media, DNA, Bacterial/chemistry/genetics, Dihydroxyacetone/metabolism, Ethanol, *Food Microbiology, Molecular Sequence Data, Nitrogen/metabolism, Nitrogen Fixation, Nucleic Acid Hybridization, Pyrones/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Tea/*microbiology, Ubiquinone/analysis
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17427Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23921)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23921
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
23235Debasree Dutta, Ratan Gachhui10.1099/ijs.0.64101-0Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha teaIJSEM 56: 1899-1903 200616902028
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
69704Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290409.1StrainInfo: A central database for resolving microbial strain identifiers