Unraveling microbial ecology of industrial-scale Kombucha fermentations by metabarcoding and culture-based methods

FEMS Microbiol Ecol. 2017 May 1;93(5). doi: 10.1093/femsec/fix048.


Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites produced by its microbiome. Despite its long history of production, microbial richness and dynamics have not been fully unraveled, especially at an industrial scale. Moreover, the impact of tea type (green or black) on microbial ecology was not studied. Here, we compared microbial communities from industrial-scale black and green tea fermentations, still traditionally carried out by a microbial biofilm, using culture-dependent and metabarcoding approaches. Dominant bacterial species belonged to Acetobacteraceae and to a lesser extent Lactobacteriaceae, while the main identified yeasts corresponded to Dekkera, Hanseniaspora and Zygosaccharomyces during all fermentations. Species richness decreased over the 8-day fermentation. Among acetic acid bacteria, Gluconacetobacter europaeus, Gluconobacter oxydans, G. saccharivorans and Acetobacter peroxydans emerged as dominant species. The main lactic acid bacteria, Oenococcus oeni, was strongly associated with green tea fermentations. Tea type did not influence yeast community, with Dekkera bruxellensis, D. anomala, Zygosaccharomyces bailii and Hanseniaspora valbyensis as most dominant. This study unraveled a distinctive core microbial community which is essential for fermentation control and could lead to Kombucha quality standardization.

Keywords: Fermented tea; Kombucha; metabarcoding, bacteria, yeast; microbial ecology.

MeSH terms

  • Acetic Acid / metabolism
  • Acetobacter / classification
  • Acetobacter / genetics
  • Acetobacter / isolation & purification
  • Bacterial Typing Techniques
  • Biofilms / growth & development
  • Dekkera / classification
  • Dekkera / genetics
  • Dekkera / isolation & purification
  • Fermentation / physiology*
  • Hanseniaspora / classification
  • Hanseniaspora / genetics
  • Hanseniaspora / isolation & purification
  • Kombucha Tea / microbiology*
  • Lactic Acid / metabolism
  • Microbiota / genetics*
  • Mycological Typing Techniques
  • Oenococcus / classification
  • Oenococcus / genetics
  • Oenococcus / isolation & purification
  • Saccharomyces cerevisiae / classification
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / isolation & purification
  • Zygosaccharomyces / classification
  • Zygosaccharomyces / genetics
  • Zygosaccharomyces / isolation & purification


  • Kombucha Tea
  • Lactic Acid
  • Acetic Acid