Survival of Salmonella and Shiga Toxin-Producing Escherichia coli and Changes in Indigenous Microbiota during Fermentation of Home-Brewed Kombucha

Elevated abundance of Komagataeibacter results in a lower pH in kombucha production; insights from microbiomic and chemical analyses

Kombucha consumption has grown rapidly worldwide in the last decade, with production at both small- and large scales. The complex fermentation process involves both bacterial and yeast species, but little is known regarding the progression of microbial development during production. We explored the microbial diversity of multiple batches across two kombucha types, i. e commercial scale versus laboratory-made (hereafter "home") kombucha brew using metabarcoding to characterize both fungal and bacterial communities. We found the microbial community of the commercial kombucha brew to be more complex than that of the home brew. Furthermore, PERMANOVA uncovered significant compositional differences between the bacterial (F = 2.68, R2 = 0.23, p = 00.001) and fungal (F = 3.18, R2 = 0.26, p = 00.006) communities between batches. For the home brew, both alpha and beta diversity analyses revealed no significant differences between all batches and replicates. When the microbial diversity of the home and commercial kombucha types were directly compared, the former had higher proportions of Ammoniphilus and Komagataeibacter. The commercial kombucha on the other hand were high in Anoxybacillus, Methylobacterium and Sphingomonas. For the fungal communities, the most dominant fungal genera detected in both kombucha types were similar. Linear model revealed significant correlations between some microorganisms and the sugars and organic acids assayed in this study. For example, rising glucose levels correlated with an increase in the relative abundance of Komagataeibacter (F = 7.115, Adj. R2 = 0.44, p = 00.0003). We believe these results contribute towards achieving a better control of the kombucha fermentation process and may assist in targeted product diversification.

Microbial and Chemical Profiles of Commercial Kombucha Products

Kombucha is an increasingly popular functional beverage that has gained attention for its unique combination of phytochemicals, metabolites, and microbes. Previous chemical and microbial composition analyses of kombucha have mainly focused on understanding their changes during fermentation. Very limited information is available regarding nutrient profiles of final kombucha products in the market. In this study, we compared the major chemicals (tea polyphenols, caffeine), antioxidant properties, microbial and metabolomic profiles of nine commercial kombucha products using shotgun metagenomics, internal transcribed spacer sequencing, untargeted metabolomics, and targeted chemical assays. All of the nine kombucha products showed similar acidity but great differences in chemicals, metabolites, microbes, and antioxidant activities. Most kombucha products are dominated by the probiotic Bacillus coagulans or bacteria capable of fermentation including Lactobacillus nagelii, Gluconacetobacter, Gluconobacter, and Komagataeibacter species. We found that all nine kombuchas also contained varying levels of enteric bacteria including Bacteroides thetaiotamicron, Escherischia coli, Enterococcus faecalis, Bacteroides fragilis, Enterobacter cloacae complex, and Akkermansia muciniphila. The fungal composition of kombucha products was characterized by predominance of fermenting yeast including Brettanomyces species and Cyberlindnera jadinii. Kombucha varied widely in chemical content assessed by global untargeted metabolomics, with metabolomic variation being significantly associated with metagenomic profiles. Variation in tea bases, bacteria/yeast starter cultures, and duration of fermentation may all contribute to the observed large differences in the microbial and chemical profiles of final kombucha products.

Advances in Kombucha Tea Fermentation: A Review

Kombucha is a carbonated, slightly acidic beverage traditionally produced by the fermentation of sweetened tea by a symbiotic culture of bacteria and yeast (SCOBY). The microbial community of kombucha is a complex one, whose dynamics are still not fully understood; however, the emergence of culture-independent techniques has allowed a more comprehensive insight into kombucha microbiota. In recent times, advancements have been made towards the optimisation of the fermentation process, including the use of alternative substrates, defined starter cultures and the modification of fermentation parameters, with the aim of producing an innovative beverage that is improved in terms of its physiochemical, sensory and bioactive properties. The global kombucha market is rapidly increasing, with the rising popularity of the tea attributed in part to its purported health benefits, despite the lack of research in human subjects to substantiate such claims. Accordingly, the incidence of kombucha home-brewing has increased, meaning there is a requirement for individuals to recognise the potential hazards associated with fermentation and the relevant preventative measures to be undertaken to ensure the safe preparation of kombucha. The aim of this review is to provide an update regarding the current knowledge of kombucha production, microbiology, safety and marketing.