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

Abstract

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.

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

“…Comparing to Kombucha samples analyzed in other studies, the Turkish Kombucha samples have relatively lower microbial diversity in the sampling days which could be caused by previous long periods of fermentation or DNA isolation method. When we compared our taxonomic analysis results with previously reported NGS‐based Kombucha studies (Chakravorty et al., ; Coton et al., ; De Filippis et al., ; Marsh et al., ; Reva et al., 2015), we observed a high concordance with Marsh et al. () which applied a very similar DNA isolation method and found ≥90% Gluconacetobacter , which formerly included Komagataeibacter (Yamada et al., ), and ≥95% Zygosaccharomyces at day 3 and day 10.…”

“…Due to its claimed positive effects on human health, a number of research studies have been conducted on the biochemical characteristics, microbiology, toxicity, cellulose production, and fermentation dynamics of this beverage (Greenwalt, Steinkraus, & Ledford, 2000;Jayabalan et al, 2014;Rosma, Karim, & Bhat, 2012;Sreeramulu, Zhu, & Knol, 2000). Until recently, studies on the microbial ecology of Kombucha have determined the bacterial and fungal diversity through culture-based methods or sequencing of the phylogenetic marker genes (Chakravorty et al, 2016;Coton et al, 2017;De Filippis, Troise, Vitaglione, & Ercolini, 2018;Marsh, O'Sullivan, Hill, Ross, & Cotter, 2014;Reva et al, 2015).…”

Fermented Foods as a Dietary Source of Live Organisms

“…Bacteria commonly found in kombucha include the acetic acid bacteria belonging to the genera, Acetobacter, Gluconacetobacter , and Gluconobacter , as well as LAB. Most of the yeasts associated with kombucha are species of Saccharomyces , although other yeast genera may also be present (Teoh et al, 2004; Coton et al, 2017). While this product is now widely consumed, and manufacturers promote the presence of live microorganisms on product labels, there are few published data on the levels of microbes present in retail products.…”

“…While this product is now widely consumed, and manufacturers promote the presence of live microorganisms on product labels, there are few published data on the levels of microbes present in retail products. One recent study reported both bacterial and yeast counts for two kombucha products that were produced under industrial manufacturing conditions (Coton et al, 2017). In general, acetic acid bacteria levels ranged from 10 6 to 10 7 cfu/mL at the end of the fermentation, and similar counts were reported for LAB and total aerobic bacteria.…”

Adaptation of two groups ofOenococcus oenistrains to red and white wines: the role of acidity and phenolic compounds

“…Oenococcus oeni is the predominant species in wine and in apple cider and it was also recently reported in kombucha fermentation (Coton et al . ), but it is rarely detected in other environments. Multilocus sequence typing analyses have shown that the species comprises two major lineages, named groups A and B, and probably at least one additional group C (Bilhere et al .…”