The Difference Between Water Kefir and Kombucha; Which One is Healthier?

by Kaitlynn Fenley

The main difference between kombucha and water kefir is the microorganisms in the starter cultures. Kombucha SCOBYs contain more yeast, and acetic acid bacteria are the dominant bacterial species. Water kefir grains contain less yeast, and lactic acid bacteria are the most dominant types of bacteria. Read the blog to learn more!

It’s not that one is more beneficial than the other…

The two beverages are just very different and involve completely unique fermentation processes. Let’s compare the two.


  • SCOBYs
  • Acetic acid fermentation
  • Acetic acid bacteria form the symbiotic colony structure (the SCOBY)
  • Yeasts carbonate in secondary fermentation
  • Health benefits from postbiotic compounds
  • Usually contains more yeast than bacteria
  • About two weeks for primary and secondary fermentation

Water Kefir

  • Kefir Grains
  • Lactic acid fermentation (and sometimes acetic acid fermentation)
  • Lactic acid bacteria create the symbiotic colony structure (the grains)
  • Leuconostoc bacteria produce most of the carbonation in secondary fermentation
  • Health benefits from probiotic bacteria and postbiotic compounds
  • Usually contains more bacteria than yeast
  • About four days for primary and secondary fermentation
dark red grape water kefir in a small glass with a lot of carbonation bubbles.

Water Kefir Microbiome

Tibicos (aka water kefir grains) are symbiotic colonies of bacteria and yeast, but these colonies contain vastly different microbes than kombucha SCOBYs. Water kefir has postbiotic benefits and also includes microorganisms that are considered probiotics. Most water kefir grains include bacterial species in the genera Lactobacillus, Bifidobacterium, Pediococcus, and Leuconostoc.

The water kefir microbiome also includes beneficial postbiotic compounds. The microorganisms in water kefir grains produce beneficial compounds like glucuronic acid, vitamins and minerals, antioxidant polyphenols, exopolysaccharides, organic acids, and bioactive peptides during fermentation. These benefits in tandem with the probiotic benefits make water kefir one of the best-fermented drinks.

Peach kombucha being poured from a bottle into a glass cup with large cubes of ice and peach slices

Kombucha Microbiome

A SCOBY is a symbiotic colony of bacteria and yeast living in a polysaccharide matrix synthesized by acetic acid bacteria. I cannot give the exact microbial composition of kombucha because it varies for every SCOBY. Most SCOBYs include Pediococcus, Acetobacter, Saccharomyces, Gluconacetobacter and Brettanomyces.

The microorganisms found in kombucha are not “verified probiotics” (except for maybe the yeast Saccharomyces). That does not mean much to me because I do not think there needs to be a clinical trial on kombucha microbes to verify that it has benefits. It’s a drink that has been around since about 130 B.C. Through microbial fermentation, kombucha contains glucuronic acid, vitamins and minerals, antioxidant polyphenols, exopolysaccharides, organic acids, and bioactive peptides. It may not be “probiotic,” but it is definitely a healthy and beneficial drink.

The Difference Between Kefir and Kombucha

The main differences are brewing practices, fermentation timeline, microbial composition, and flavor. In summary, both kombucha and water kefir are beneficial and can be part of a healthy diet. Here are some recipes you might like to try:

For more in-depth fermentation science on water kefir and kombucha join us in our online course!

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Leave a Comment


A Real Address January 1, 2022 - 10:58 am


I wondered if, as an interested scientist, you could answer this one for me?

I read on Happy Gut Pro a claim that their water kefir (WK) is “concentrated with b12, b6, and b1”. I challenged them on this & by reply they sent a paper referring to milk kefir. Now, obviously, milk already has B12 in it, so I presume that is the source. Have you ever seen any evidence that WK can produce B12? By reading of the list of bacteria is that there are no B12 producing bacteria in it, & where would they get the cobalt to do so?

I’m also interested in the actually level of micronutrients (concentrated reads as awfully misleading to me) but also their nutritional requirements. Beyond just dropping a fig in now & again, could we/should we been feeding them more than just sugar? Could that increase their nutritional value & health?

On the other hand, I’d be interested to know if it was possible to add B12 bacteria to the culture. It would be a real game changer for the vegan movement if you could “home brew” your own B12. For example, B12 producing endosymbiotic bacteria have recently been discovered in some plant sources.

Sorry to be so verbose but I find the lack of serious discussion about these beyond the hype on the internet to be very frustrating. Even the relatively few academic papers really don’t seem to say much beyond “more study required”.

Cheap, alternative fizzy pop aside, do we even know if or how good drinking it is on a long term basis?

Lastly, have you ever done any alcohol level testing on yours?

Thank you

Kaitlynn Fenley January 2, 2022 - 8:18 am

Hi there,

First, mostly all acedemic studies end with “more studies are required”. That’s the nature of science. There’s always more to know, and more to find out. Not all fermented foods and drinks are created equally. There are a lot of vriables that impact fermentation and what microbially syntesized byproducts are in fermented foods and drinks. This makes it hard for studies to draw “blaket” conclusions about specific fermented products. For instance, my water kefir and sauerkraut are vastly different from any others.

I do not fact check or validate fermentation information provided by others, so let’s just move straight to discussing bacteria that produce B12…

Water kefir grains and milk kefir grains do contain similar microorganisms, but there are a few species differences. Species in water kefir grains vary, depending on the source and how they are cared for. Yes, I have read in a few studies that the Lactobacillus species in water kefir can produce B12. Some of these microbes have a B12‐dependent metabolic pathway that converts glycerol (glycerol is produced by Leuconostoc bacteria via heterolactic fermentation) into propanediol, which allows LAB to synthesize B12. It happens in sauerkraut and other fermented vegetables too, but conditions and fermentation parameters like salt concentration and fermentation time have to be right.

I feed our water kefir with molasses, sea salt and sugar to provide nutrients. So yes, I think they should be fed more than just sugar. The molasses provides manganese, magnesium, copper, vitamin B6, selenium, iron and calcium.

Yes, drinking water kefir is wonderfully healthy in moderation. 6 ounces a day is enough and it provides vitamins, enzymes and probiotic species of microbes. But again, the health attributes and safety all depend on how it is made, ingredients used, fermentation time, source of grains etc.

No need to do alcohol testing, as I fully understand the microbial metabolism that happens with my grains. I do not use more than 5% sugar, so there’s never more than about 0.2% alcohol in my water kefir.

A Real Address January 1, 2022 - 11:00 am

* (I tried making a ‘long term brew’ entire in the fridge a few times, & it came up with a really nice, sharp & clear taste, which I put down to a higher alcohol level. No sweetness, but no vinegary flavor at all).