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 41 comments on this article

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

    Reply to this comment
  • 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.

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    • 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 …

      Reply to this comment
    • Theodore Dixon says:

      One study with proper methodology is worth more than all the anecdotal evidence in the world. Please share the methodology and data behind the claims you make, otherwise it comes across sounding like “I’ve been doin’ it this way for years, it was good enough for Grandpa, it’s good enough for you, I don’t need no high-falutin’ scientists tellin’ me what to believe”.

      Reply to this comment
    • Elaine Olsthoorn says:

      Jamba,Thanks, for your knowledge sharing!

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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.

        Reply to this comment
  • 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?

    Reply to this comment
    • debra bourne says:

      Dear Amber

      I have thoroughly enjoyed reading the above thread. It feels like alive ferment of expertise.
      Although I’ve had an organic diet, including some ferments for over twenty-five years, I’ve never made my own. I’ve been slightly nervous about being keen, but unknowledgable and cultivating ‘bad ‘ bacteria.

      However, I’ve decided to start. I want to begin with sauerkraut and fermented tea.

      I imagine the origin of the scoby is key. Is there a trusted source that you would direct a total beginner like me to go for both the starter and instruction, in order to create a bacterially potent brew.

      I would like to end up with a 5L ongoing supply, so I can drink one glass a day. I began taking probiotics about 7 years ago to support recovery from auto-immune type symptons and would love to maintain my health in this way.

      Many thanks in advance for any help



      Reply to this comment
  • Stan says:

    What I’ve been trying to discover (and what lead me to this article is): if yeasts use the sugars to produce alcohol and the alcohol is consumed by the bacteria to produce acetic acid to create the finished kombucha, other than as a “flavoring agent”, what role does the (black, green or other) “tea” play?
    Does the bacteria or yeast feed on the tea?

    Does it merely provide acidity in the form of tannins?

    Some claim to have made, with no or with a minimal amount of tea, kombucha tea that, in most ways, appears very similar to typical kombucha tea.

    Though I enjoy tea as well as its health benefits

    Tea drinking also has plenty of negative side effects, for example, from the fluoride and tannins. Tannin …slow the absorption of several important minerals, such as zinc, calcium, and iron, can cause constipation, and may contribute to iron deficiency. It has been suggested that tannin increases the risk of nasal and esophageal cancer.

    So, the role of the sugar(s) is clear but what is the relationship between the “tea” and the microbes / bacteria / yeast?

    Reply to this comment
  • […] with a bacteria and yeasts culture. Kombucha contains a variety of minerals, vitamins, and enzymes (1). The taste of this drink can vary depending on the type of the tea, from a sparkling apple cider […]

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  • I brew beer and make yoghurt as well as making our own family ginger kombucha so I know the tricks. Tea is expensive, water isn’t. Keeping complex probiotics is complicated while adding dry yeast is easy. Even if you have a good probiotic base the yeast element will easily take over and brewing from batch to batch is easy without the need for a solid scoby. Bottom line is I believe most commercial kombucha drinks are fermented sugar water plus flavorings. Our own family ginger beer is made from a long established “ginger beer plant” and tastes just like the more expensive ginger kombuchas I buy in Trader Joe’s. And this explains the high percentage of yeast and lactic acid as opposed to true probiotics as found in yoghurt.

    Reply to this comment
  • TrayPo says:

    Microbiologist here. I’ve attended a handful of recent seminars regarding Kombucha microbial population studies. I don’t have the research to referance at my disposal. My take away, albeit second hand paraphrasing, is:
    The population of Kombucha microbial community varies greatly.
    The list of a single SCOBY could contain dozens of different microbes.
    Regional SCOBY ‘s have regional profiles.
    There are many of the usual suspects of recognized “Probiotics.”
    The dynamics of population competition for resources prohibits a consistent population profile.
    I hypothesize individual recipe/processes wold produce great variability.
    I am going to start brewing my own today.
    I prefer not to have the acetic acid bacteria prominent.
    Any suggestions?
    Thanks for renewing the thread!

    Reply to this comment
    • Hi TrayPo –
      Great summary!
      Acetic acid are necessary for a traditional ferment. Without them, you’ll just have alcoholic tea (just alcohol production). You might be able to get lactic acid bacteria to be happy with the yeast, but I am not aware of anyone that has tried that.

      Reply to this comment
    • My husband and I have been brewing our own Kombucha for Years. He likes the acetic taste, I don’t. I prefer about a 14 day brew…we were advised to start tasting at 10 days, to decide your favorite result. It was also easiest at 14 days to choose a day of the week to pour and start a new batch routinely. We sanitize with boiling water for the tea (10 minutes), and cleaning used gallon bottles with hottest tap water, no soap to leave residues that would adversely affect the scobey. We bought our first scobey from a culturing company. We have branches into Kefir and water kefir, and dabbled with pounded cabbage and beets sauerkraut. We cover with unbleached coffee filters and rubber bands. We created an elaborate brewing room in the basement only to find it was a lousey place to try to brew…too cold, etc.so we had to switch to an inside closet shelf.

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  • Douglas Skites says:

    Hey TryPo:

    Why the aversion to acetic acid bacteria?


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  • […] Research has not yet proven the efficacy of Kombucha as a supplement for improving our gut health. Although Kombucha is a source of potentially healthy microorganisms, the drink’s long-term benefits on gut flora diversity have yet to be examined. […]

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  • […] There are two most dominate bacterias present in Kombucha, Acetobacter and Gluconacetobacter. These two bacterias produce acetic acid which is responsible for providing that vinegar taste in Kombucha. (4)  […]

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  • thanks for the information

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  • […] of multiple kombucha (tea fungus) samples či jeho čtivějšího a předžvýkaného excerpta Microbial diversity of kombucha, což je docela moderní poznatek, který interpretuje data z DNA sekvenceru. O chemii […]

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  • Robert Segraves says:

    IN light of VERY recent studies of dietary intake influence on COVID-19 severity and death rates, we need to crank up a study of the potential (or lack thereof) kombucha consumption on the effects of the virus.

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  • Jerry says:

    This is a fantastic article. There is widespread misconception online on what the “SCOBY” actually is. This post does an excellent job at educating people that microbes are responsible for the fermentation and not the pellicle itself.

    Reply to this comment
  • Andrew McCallister says:

    Thanks for the great artcile and the photo is awesome! How can I get permission to use it on my slides?

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  • […] was a common way to brew it a decade ago, but this flora-diverse and fizzy drink has come a long way since then. Now, we have […]

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  • […] conditions, it does behave differently due to the fact that its a probiotic. Kombucha is made from living bacteria that can react to its environment. It serves as a preservative which can make it last longer since […]

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