Study: Survey of Kombucha Microbial Communities
The journal FEMS Yeast Research, from the Federation of European Microbiological Societies, published an article by researchers at the University of Strasbourg on February 4, 2025, titled Comprehensive survey of kombucha microbial communities of diverse origins and fermentation practices. It addresses the functions of both “fractions” of the SCOBY–the pellicle and starter liquid–in fermentation.
Study Goals
This comprehensive survey was undertaken with the goal of advancing the understanding of the microbial ecology of kombucha. DNA analysis of a diverse collection of starters across successive cycles of fermentation identified a core microbiota of yeasts and bacteria that consistently underpins kombucha fermentation. It highlights the significant variability in the distribution and abundance of both core and accessory taxa across different fermentation stages and physical compartments, emphasizing the complex dynamics of these symbiotic consortia.
The authors note the uniqueness of kombucha compared to other fermented products:
Unlike many fermented products, where fermentation can be initiated by the spontaneous colonization of environmental microorganisms…kombucha fermentation relies entirely on human-driven conservation and propagation of SCOBYs that are passed from one fermentation cycle to the next as mandatory starters.
Findings
Commonality and diversity
The study identified a consistent core microbiota of yeasts (two Brettanomyces species: B. bruxellensis and B. anomalus) and bacteria (Komagataeibacter, Lactobacillus, and Acetobacteraceae, including the Acetobacter genus) across these diverse consortia.
A core microbiota of yeast and bacteria has been identified in these diverse kombucha symbiotic consortia, revealing consistent core taxa across symbiotic consortium of bacteria and yeasts from different starters.
The distribution of these core taxa varies between the liquid and biofilm (or pellicle) fractions (“mother” and “daughter”), as well as across successive fermentation cycles.
The biofilm fraction is known as the “mother.” During fermentation, a new cellulosic biofilm forms at the air–liquid interface, referred to as the “daughter.” For the next fermentation cycle, either biofilm can be used as part of the starter: when the original mother biofilm is reused, the process is called backslopping; when the daughter biofilm is used, it is known as repitching.
While a core microbiota exists, the overall microbial diversity within kombucha SCOBYs is relatively low, with a few accessory taxa also playing a role. This suggests that the fundamental microbial structure of kombucha, at a broad level, is consistent. However, on looking deeper into the specific makeup of the SCOBYs, even with a limited set of overall microbes, the relative abundances of key groups, particularly the core yeast species, can differ substantially:
Our analyses revealed distinct patterns of variation in SCOBY microbial compositions, reflecting the diversity of the initial starter communities. Yeast compositions, particularly the ratios of the core yeast species B. anomalus and B. bruxellensis, vary significantly between samples and may serve as a signature of SCOBY structural diversity especially when these ratios remain consistent within samples from the initial starter across at least three consecutive repitchings.
In other words, while the overall low diversity tells us that kombucha has a relatively simple microbial framework, the significant variations in yeast compositions suggest that there is considerable structural diversity within this framework.
Bacteria and yeast
The study highlights the consistent presence of B. anomalus in the core, whose functional role is less explored compared to B. bruxellensis. Notably, Lactobacillus is identified as part of the taxonomic core in this study, contrasting with some previous reports that found its presence inconsistent, possibly due to a focus on the solid biofilm fraction.
Analysis of yeast compositions across three successive repitchings showed that, for some starters, the compositions remained closely related. In contrast, others exhibited fluctuations, particularly in the ratio of B. anomalus and B. bruxellensis.
Komagataeibacter appears to prefer the biofilm, while Lactobacillus can dominate the liquid phase in some cases. Moreover:
…certain taxa do not permanently colonize the kombucha niche, but instead require recurrent reintroduction
Implications
- The identification of a consistent core microbiota provides a fundamental understanding of the microbial basis of kombucha fermentation.
- The observed variations in microbial composition across different starters and fermentation stages highlight the dynamic nature of kombucha SCOBYs and the influence of various factors, including the initial starter, brewing practices, and environmental conditions.
- The study suggests that the ratio of B. anomalus and B. bruxellensis could serve as a signature of SCOBY structural diversity.
- The findings regarding accessory taxa and their compartmentalization suggest that biofilms might act as reservoirs for these microorganisms, and their role in the overall fermentation process warrants further investigation.
- The influence of environmental factors and repitching strategies on SCOBY microbial diversity is underscored by the observation of fluctuating accessory taxa even under sterile repitching conditions.
Disclaimer
The content of this article is accurate to the best of our knowledge and is presented for general informational purposes only. The analysis was conducted with the help of NotebookLM. Please send corrections or questions to ian@boochnews.com. Comments are welcome.
Gary Spedding, Ph.D., Analytical Chemist at BDAS commented:
Several initial thoughts here.
A common core of microbiota (sum of all organisms in the matrix = Microbiome) for one specific SCOBY source location makes sense at first look. And a common set of key organisms between different SCOBY sources also makes sense. Of keen interest here, for a sour beverage, such as Kombucha is the presence of Brettanomyces species which are key to Belgian sour beer production. Other organisms listed can also be a source of (in this case unwanted) biofilms in the breweries and finished beer and malt-beverage products. The commonality of organisms in such a complex microbiome is instrumental to the defining of one style of beverage. Kombucha is kombucha as a defined beverage, not a clade of related beverages (at least as far as I understand it).
Different compositions of microbiota from different environmental/regional SCOBY origins potentially lead to some flavor profile differences (likely more subtle than fully distinct) . Ratios of the Brettanomyces species or other organisms can indeed be used to identify or characterize the different SCOBYs out there. Though the authors here state common taxa and additional microbes – accessory taxa. These seem to decline between serial re-pitching’s,’ so local microbes might still play a role from brewery to brewery. Even under pure culture pitching of fermentation organism many breweries and distilleries will always have an interplay with other indigenous (autochthonous) microbes involved to some extent. Whether that is important to consistent flavor profile – batch-to-batch production may depend on sanitary conditions in a brewhouse and good manufacturing practices. This may raise issues with respect to the statement that note “ Kombucha fermentation relies entirely on the propagation of SCOBY’s.” Careful sensory evaluations of one’s own products (or including competitor products) are important here as part of a Quality assurance/control program.
The presence of Lactobacillus organisms may give credence to the claims of Kombucha being probiotics – Acetobacter certainly do not (from the non-yeast perspective. I am unsure as to yeasts being generally characterized as probiotics directly.).
This is from just a preliminary look at the paper noted in the Post header here. A study of Belgian sour beer production might reveal some clues within big data or OMICS strategy thinking.
Based on the incredible consortia of organisms (Microbiota) and a simple or complex matrix (the Microbiome) – teas (Types), sugars, fruits, or other ingredients in a Kombucha formulation this is a wide-open world of possibilities for quality, consistency, and flavor profiling.