Metabolome-microbiome signatures in the fermented beverage, Kombucha

Int J Food Microbiol. 2020 Nov 16:333:108778. doi: 10.1016/j.ijfoodmicro.2020.108778. Epub 2020 Jul 9.


Kombucha is a fermented tea. Here we investigate the fermentation kinetics, metabolite production, microbiome and potential health promoting properties of three different kombucha consortia. Shotgun metagenomic sequencing revealed several dominant bacterial genera such as Komagataeibacter, Gluconacetobacter and Gluconobacter. Brettanomyces and Schizosaccharomyces were the most dominant yeasts identified. Species distribution reflected different patterns of sugar consumption, with S. pombe being present in samples with the highest sugar conversion. Liquid-liquid extractions were performed with organic solvents in order to obtain dried extracts, which were later characterized. HPLC-DAD and GC-MS analysis revealed differences in the production of organic acids, sugars, alcohols and phenolic compounds, where the presence of caffeine, propanoic acid and 2,3 butanediol differ greatly across the three kombuchas. Metabolomic analysis exhibited a link between the microbiota and the production of bioactive compounds in kombucha fermentation. In vitro assays were carried out in order to evaluate potential health-promoting features of the fermented teas, with notable outcomes including antioxidant ability against DPPH radical and against the 15-lipoxygenase enzyme, indicating a potential anti-inflammatory activity. These investigations considerably enhance our understanding of the relationship between the microbiota and metabolites as well as health promoting potential of kombucha and have the potential for the development of future generations of kombucha products in which these relationships are optimized.

Keywords: Chemical profile; Fermentation; Kombucha bioactivity; Shotgun sequencing.

MeSH terms

  • Antioxidants / analysis
  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Chromatography, High Pressure Liquid
  • Fermentation / physiology*
  • Gas Chromatography-Mass Spectrometry
  • Kombucha Tea / analysis*
  • Kombucha Tea / microbiology*
  • Metabolome / physiology
  • Metagenome / genetics
  • Microbiota / physiology
  • Phytochemicals / analysis*
  • Yeasts / classification
  • Yeasts / genetics
  • Yeasts / isolation & purification


  • Antioxidants
  • Kombucha Tea
  • Phytochemicals