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
285268species
1120919strain

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/bacdive20.20250331.9.3

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
125438negative96.333
125439negative99.5

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

Physiology and metabolism

tolerance

@refcompoundpercentage
23235Sucrose30
23235Glucose30
23235Ethanol10

oxygen tolerance

@refoxygen toleranceconfidence
23235aerobe
125439obligate aerobe91.1

spore formation

@refspore formationconfidence
125438no91.758
125439no99.3

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 23498HG4244251421nuccore1120919
17427Acetobacter nitrogenifigens strain RG1 16S ribosomal RNA gene, partial sequenceAY6695131451nuccore1120919
67770Acetobacter nitrogenifigens gene for 16S rRNA, partial sequence, strain: NBRC 105050AB6822351415nuccore1120919

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe91.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.5
125439BacteriaNetmotilityAbility to perform movementyes89.9
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.3
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.333yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.745yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.758no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.367yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.977yes
125438motile2+flagellatedAbility to perform flagellated movementyes77.575yes

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1