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Microbial diversity of kombucha

In the most comprehensive study of kombucha microbial diversity to date, a team of scientists recently uncovered new microbial dimensions of this popular fermented tea. In this Science Digested, I provide a summary of what you need to know from this exciting new work and how it may change our understanding of how kombucha is produced.

Kombucha is fermented tea. To make kombucha, tea is brewed, sugar is added to the tea, and then a microbial community is added to the tea. This community is usually a giant slimy blob that goes by many names: mother, SCOBY (for symbiotic community of bacteria and yeast), and pellicle. I think pellicle is the most scientific, so I’ll use that throughout the rest of this piece. This microbial community is a perfect example of a microbial biofilm, a dense microbial mat fused together by substances that the microbes secrete. In this case, it’s cellulose that is produced by the bacteria that is primarily responsible for the glued together community.

A SCOBY of kombucha under the microscope. This 400X magnification shows both the larger yeast cells as well the smaller bacterial cells that coexist in a typical kombucha microbial community.

A pellicle (more commonly called SCOBY or mother) of kombucha under the microscope. This 400X magnification shows both the larger yeast cells as well the smaller bacterial cells that coexist in a typical kombucha microbial community. Photo by Benjamin Wolfe.

Yeasts living in the biofilm use the sugars in the tea to produce alcohol. This alcohol is then consumed by neighboring bacteria to produce acetic acid (vinegar). The resulting kombucha tea is an earthy and slightly sweet (depending on the length of fermentation) beverage with hints of vinegar. When bottled and stored, carbon dioxide is trapped making the kombucha bubbly. Some find kombucha to be refreshing and delightful. Others run away in fear and disgust (to be fair, it’s one of the ugliest fermented foods I’ve ever seen!).

Previous studies had identified the yeasts and bacteria present in a few kombucha SCOBYs. Most of these studies just focused on one kombucha tea made in one place. But kombucha is now made around the world. Kombucha brewers pass their pellicle from one location to the next to help friends inoculate new batches. How have the microbial communities changed as people have passed them along? Do the kombucha microbial communities in one part of the world look similar to another? By sampling kombucha communities made in several different regions (the UK, Ireland, Canada, and the United States) this new paper by Alan Marsh and colleagues attempts to broadly define the typical community within kombucha.

The microbiologists in this paper were the first to use high-throughput (sometimes called next-generation) DNA sequencing techniques to analyze kombucha microbial diversity. This type of DNA sequencing approach allows for rare types of microbes that might be missed with other techniques that can’t sample as ‘deeply.’  Another important aspect of this paper is that the scientists studied both the bacteria and the fungi (yeasts in this case). Often these two microbial groups are studied separately and therefore the view of microbial diversity becomes disconnected. Finally, the study examined the microbial diversity of both the solid mass of the pellicle, but also the microbes in the liquid tea to see how the two environments compared.

Several important findings from this work refine our understanding of kombucha microbiology. First, the bacterial component of the community was dominated by two bacterial genera, Acetobacter and Gluconacetobacter. These are both genera of bacteria that can produce acetic acid and are responsible for the vinegar flavor that comes through in a lot of kombuchas. Previous studies had considered Acetobacter to dominate kombucha communities, but Gluconacetobacter was most abundant in this paper. Interestingly, the authors suggest that some of the most abundant types of Gluconacetobacter could be poorly characterized strains. The authors are careful to note that changes in bacterial taxonomy are shaking up our classification of Acetobacter and Gluconacetobacterand these changes may account for how their results contrast with previous studies.

One surprisingly finding from the bacterial portion of this study was the large abundance of lactic acid bacteria in some of the kombucha pellicles. Generally, these bacteria, which are more abundant in lactic fermented foods such as yogurt, cheese, and salame, are rarely detected in kombucha. Lactic acid bacteria were most abundant in the pellicle from Ireland, making up over 30% of the bacterial community. Previous studies may have missed these bacteria because they require specific types of media not normally used in studies of kombucha microbial diversity.

In the fungal part of these microbial communities, one type of yeast, Zygosaccharomyces, dominated both the pellicle and liquid of the kombucha. In almost all samples, it made up greater than 90% of the community composition. This wasn’t a huge surprise because previous studies had also observed dominance by Zygosaccharomyces in other samples.

What might this new research mean for the production of kombucha? The finding of lactic acid bacteria at high abundance suggests a potentially under-appreciated component of kombucha microbiology. What are these lactic acid bacteria contributing to the fermentation? Are their impacts desirable? Why are they present in some samples and not others? The finding that not all komnucha samples are the same also suggests that each producer, whether a home or professional fermenter, can develop unique microbial communities. Future work can experimentally tease apart why these unique communities develop and how the differences in microbial composition translate to differences in kombucha flavors.


For more details on this study, please check out the full article here:

Marsh, Alan J., et al. “Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples.” Food Microbiology 38 (2014): 171-178.  http://www.sciencedirect.com/science/article/pii/S0740002013001846


Post written by Benjamin Wolfe. Header photo by Adam Detour/Catrine Kelty.




There are 20 comments on this article

  • Great article! Looking forward to more studies about Kombucha – its a fascinating culture =)

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  • I am the founder of Rowdy Mermaid Kombucha, located in Boulder, Colorado so I’m always interested in new research and information about fermentation. Granted, I’ve not yet had a moment to read the original research paper, just several summaries of the research, but this particular study struck me for several reasons.

    The issue with drawing conclusions based on the sequencing of just five different ferments is that the outcome of a kombucha batch is the result of a plethora of factors, including brewing and flavor trends, sugar source, tea origin, recipe, cleaning and sanitizing practices, brewing temperature, fermenting time, fermenting temperature, container size, container covering, starter origin, ventilation, batch cooling procedures and steeping practices, to name a few.

    To accurately understand even one factor, such as the dominance of Zygosaccharomyces, a yeast which most professional brewers already understand, one would need to begin by understanding their sugar source. Zygosaccharomyces, being a spoilage yeast, favors conditions where sweet fructose predominates. Beet sugar, sucrose high in fructose or sucrose dumped into an acidic starter which cleaves the negative electron of the covalent bond to flood the tank with fructose make for perfect conditions for Zygosaccharomyces, especially if sugar is introduced into the tank and allowed to cool before the yeast and bacteria is added. Since it’s a wild yeast, just a single cell of Zygosaccharomyces can colonize and overrun a ferment before the addition of pure strain yeast.

    Many companies that sell kombucha culture kits, and some of the national kombucha brands which brewers purchase and raise to make their batches–if they don’t purchase “pure” strains from a lab–contain lacto. Certain areas where there is a lot of dairy production will also be richer in malolactic bacteria. Such bacteria are sometimes used as a soil conditioner, and these can be airborne. If the brewing trend is to allow kombucha wort containing sugar to naturally cool there is a good chance a range of malolactic bacteria will enter the ferment, if it’s not part of the starter culture already.

    As a kombucha brewer, I am always aware of the relationship between ingredients, methodology and outcome. Reading the research at hand is surprising to me only because of the narrow interpretation, but not because of the results. I know these results almost aesthetically through working with these cultures, and the results of each of the ferments studied is like a reverse engineering window into the best practices that resulted in the findings in the first place.

    For instance, if a brewer uses vinegar as a cleaner or additive, or if they received their starter from a brewer who does use vinegar, and some large breweries do, then they should expect Gluconacetobacter since industrial acetic acid is most often the result of several strains of Gluconacetobacter. And since this is a low acid and high heat loving bacteria, I would venture a guess that the brewers don’t properly cool their batches before pitching.

    It’s also worth mentioning there are literally dozens of ways to make kombucha, not all producers even use a SCOBY, and many of us use control methods (such as introducing pure strains of yeast and bacteria) or brewing with different sugars to control our populations.

    Reply to this comment
    • Thanks so much for point out all of these important nuances, Jamba! This is great stuff and it’s wonderful to hear all these important details from a producer. I think this type of study is really just the beginning. It is by far one of the most comprehensive, but you are right – there are so many ways to make kombucha and 5 different kombucha samples can’t really even begin to capture that diversity. I suspect there will be larger studies of this nature in the future.

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    • Mary Ann says:

      thanks for such a brilliantly phrased tutorial…you are indeed a Master… And as an amature brewer I can use any info at all …

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  • Sounds like a great study – would love to find out what conclusion this study revealed in terms of the health benefits of Kombucha. Is it good or bad?

    Reply to this comment
    • Hi Martin –

      The authors weren’t looking at health benefits – just diversity of the microbes. It’s difficult to infer whether the microbes can do anything good or bad by just knowing what species are present. We’ll be writing a post in the future on the scientific evidence for probiotic effects of fermented foods. Keep your eyes open for that. And thanks for checking out MicrobialFoods.org!

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  • yvonne says:

    I’ve been loving my kombucha – second fermenting with organic orange peel or ginger and it tastes bedtter than beer! However, I’ve learned to “burp” my bottles on the second ferment as I had two glass bottles which exploded even though I’d left an air gap in the neck of the bottle. Thankfully despite being very messy, nobody was hurt! :)

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  • Benjamin,

    Thank you so much for the reply.

    Like you, I’m extremely excited about the recent scientific research into fermentation and probiotics. We have to start somewhere, and the study at hand is a good example of what is possible with modern machines and methodologies.

    Gaining a clearer understanding of the field will require a multiplicity of perspectives and experiences. Microbialfoods is the perfect place for such discussions to take place. I look forward to learning together.

    Thank you!

    Reply to this comment
  • Lisa Klieger says:

    Comment Thank you for helping make this research available and understandable. I am currently working on some research involving Kombucha and the use of Medical Qi-gong Energetic Emissions in the fermentation process. I must agree with Jamba that there are many nuances in the creation of the beverage. Using traditional practices of Chinese medical Qi manipulation I am getting some dramatic result differences between my sample and my control using the same culture, in the same environment using the same batches of tea/sucrose. So the differences may go even beyond the scientifically measurable factors. Since I lack the equipment necessary to measure all the factors, I have mostly been using the fished weight of the SCOBY. I have been getting typically 20% larger SCOBY from the treated Kombucha, than from the non treated Kombucha. The flavor of the two batches are subtly different as well. Thanks again for helping to get this information out so that we all may foster each other in this learning process.

    Reply to this comment
    • Gizelle says:

      You have given me a great idea! I am going to consciously send my kombucha brew some love every day and see what happens. I love drinking it anyway but sending it some positive energy while it is growing can’t hurt.

      Reply to this comment
    • wow, cool work….. is there any way to follow your results?
      i would love to learn about your experience with this…
      and i do know that at least one commercial brewer always works some love and ceremony of their intentions for their brew into every batch.

      Reply to this comment
  • lance says:

    Great article, and I am fascinated by how the location is a key component into which yeasts and bacterias come from. I have about 200 scobys in Phnom Penh, Cambodia. They are being fermented, and some are being dried and used as paper or canvas, and i turned about 20 of them into a fake UFC championship belt. I really really want to get a good microscope to compare my 10 month old strains that have replicated dozens of times and see if my microorganisms very in any way from the local settings of South East Asia. As much as I love drinking kombucha, it is these great articles that enthrall me, knowing that more answers lead to more questions. and im excited to be part of such an amazing group who follow this closely. A lot of us think there are some seriously amazing finds waiting to be found. The cellulose production alone is at its basics as far as textiles go, and just like 3d printing, we are at a stage where the imagination of our combined interests will drive us further to researching all aspects of its potential uses.

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  • Edith Attreed says:

    It is good to know the analysis in Kombucha but what about the transformation in our system when we drink Kombucha?

    Reply to this comment
    • Hi Edith –

      As far as I am aware, there haven’t been any studies of the probiotic potential of kombucha for the human gut microbiome (the microbes that live in our guts). Hopefully we’ll see some research on that soon.


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  • Always good to learn of new research done on Kombucha!

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  • […] You can get a taste for that in the abstract and introduction of this study, but there are many other […]

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  • Kei says:

    I wish people would stop calling it “kombucha”, since the Japanese drink kombucha (昆布茶) is actually tea made from kelp (kombu). The drink people call kombucha is actually the Japanese drink koucha-kinoko (紅茶キノコ). Somewhere along the line someone confused the two drinks and for some reason the name stuck, even though it’s incorrect.

    Reply to this comment
    • Thanks for the note, Kei! I agree that the naming of this fermented tea beverage has a confusing history. The culture alone has a multitude of names (SCOBY, mother, mushroom, pellicle). It would be interesting to know how the confusion came about.

      Reply to this comment
      • Kei says:

        Interesting to hear that the culture is sometimes referred to as the “mushroom” as the literal translation of the Japanese name for the drink (koucha-kinoko) is “tea mushroom”. Personally I think people should just call it “fermented tea”, but that doesn’t sound nearly as exotic so I doubt it will catch on.

        P.S. The site is great. I love how it’s science based and contains real data, unlike many sites out there dedicated to fermentation/bacteria.

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  • Amber says:

    Thank you so much for sharing & for summarizing the study! I work in a Microbiology Lab and I brew Kombucha, so I find this fascinating!

    I’ve been wanting to culture my Kombucha to see what strains of bacteria and fungi predominant it. Unfortunately not all bacteria grow on the standard media that we would use for culture, so I find the results from this next generation DNA sequencing study very interesting.

    I am a bit confused by the statement that Lactobacillus species were often missed in previous studies. In my experience Lactobacillus grow on routine BAP and Chocolate media, which is likely what the researchers are using because these are standard less selective medias. Perhaps the other species in the culture overgrew the slower growing Lacto, causing them to be missed in some studies?

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