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The Microbiology And Making Of Milk Kefir


Staff member
Dec 14, 2023
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Only recently I discovered the delight of fermenting my own foods at home. Before getting started, I took some time to research fermented foods and talk to some experts, which turned into a really fun blog post series on fermented foods. My first fermented food adventure was with kombucha—I made some from a store-bought jar. That turned out poorly, but it didn’t matter, because I was hooked. Next, I made sauerkraut and bought a kombucha scoby from Amazon and made some delicious kombucha.

Here, I’m going to share about my latest fermented food adventure: milk kefir. This post will serve as a guide for anyone who would like to make milk kefir but also wants to know about the microbiology behind it.

I’ll cover the following questions:

  • What is milk kefir?
  • What microbes are in milk kefir?
  • What are the benefits of drinking milk kefir?
  • How do you make milk kefir?

Then, I’ll conclude with my personal experience with making milk kefir and my favorite milk kefir recipe.

What is milk kefir?​

Milk kefir is a fermented milk beverage with the consistency of a very thin yogurt, except it has many more species of bacteria than yogurt and also contains yeast species.

The Microbiology And Making Of Milk Kefir | Joyful Microbe

Milk Kefir. Photo by Justine Dees.

The taste of milk kefir was described in a paper as having “a refreshing, yeasty taste and a ‘sparkling’ mouthfeel.” I like that description, but I would add that it is slightly sour. The beauty of fermented foods is that they are customizable—you can let kefir ferment for a longer or shorter amount of time, and the flavors and mouthfeel will change. It’s fun to experiment and decide what you prefer.

The Microbiology And Making Of Milk Kefir | Joyful Microbe

Milk kefir grains. Photo by Justine Dees.
The Microbiology And Making Of Milk Kefir | Joyful Microbe

Strained milk kefir grains. Photo by Justine Dees.

To start making your own milk kefir, you have to have a starter culture called milk kefir grains. The name is a bit misleading because these are not literally “grains” like the seeds we eat and grow plants from; however, they are a way to “seed” and grow a microbial community in milk. Milk kefir grains are full of microbes, specifically bacteria and yeast.

The kefir grains have a gummy-like consistency because the microbes create a matrix of lipids, proteins, and polysaccharides. And they resemble cauliflower or cottage cheese.

The microbes in kefir grains grow in a symbiotic relationship, so they are a type of scoby (symbiotic community of bacteria and yeast). The word scoby is most often used to refer to a kombucha scoby. Still, it applies here because these grains are a symbiotic community of microbes, just like kombucha, except they live and grow in a different environment (milk rather than sweet tea) and are composed of different microbes.

One thing to note is that another type of kefir exists. Water kefir is made from sugar or fruit in water. But water and milk kefir grains are composed of different organisms and are held together by a different matrix.

What microbes are in milk kefir?​

Bacteria: The number of bacterial species in milk kefir varies but can be anywhere between 22 to 61 based on a study that assessed the number of species in 23 different milk kefir samples. The kefir grains have a similar number of species, between 24 to 56.

The bacterial genera in kefir milk and grains can include Lactobacillus, Lactococcus, Streptococcus, Leuconostoc, Oenococcus, Acetobacter, Bifidobacterium.

Yeast: Milk kefir can contain between 10-42 and yeast species, whereas the grains can have between 4-37 species based on the study mentioned above that identified microbial species in milk kefir.

The yeast genera Saccharomyces, Kluyveromyces, and Candida usually dominate the yeast population in kefir milk and grains.

Kefir grains and kefir milk have different communities of microbes with some overlapping species. Because of this difference, though, you cannot use kefir milk to start a new batch of kefir. You must inoculate the milk with kefir grains.

Store-bought milk kefir is often produced using a starter culture of specific species derived from kefir grains. But, as a result, these store-bought products will likely not contain as many species of bacteria and yeast.

What are the benefits of drinking milk kefir?​

Kefir contains live microorganisms. And it is beneficial for us to encounter a variety of harmless and potentially good microbes, whether or not they actually take residence in our bodies and become a part of our microbiome. (To learn more about your microbiome, check out Sarah’s Little World blog post series on the microbiome.)

Some of the species in kefir are considered probiotics, meaning that they confer a health benefit when they are at sufficient numbers. Scientific studies—many of which were done in vitro or in animal models and have not been validated in humans—have shown that kefir and the species in kefir can improve gastrointestinal health, reduce cholesterol, modulate the immune system, have anti-tumor and anti-allergenic effects.

Sounds like a miracle, right? Well, not so fast. As I said, many of these studies, all of which are exciting, were not conducted in humans yet. So, we can’t rely on kefir for all of these health benefits. Kefir and fermented foods are not cure-alls. But kefir has a lot of potential to help and is considered safe, so why not drink it?

How do you make milk kefir?​

The whole process of making milk kefir only takes 24 hours. But this means it is a high-maintenance fermented beverage that requires daily attention.

You start by adding kefir grains to a cup of milk. The best kefir grain to milk ratio is between 1:30 to 1:50. So, if you have 1 cup of milk, you only need about ½ of a tablespoon of grains. But I have seen others recommend 1 tablespoon of grains for 1 cup of milk. If you have too many grains in the milk, the fermentation will proceed much faster and finish in less than 24 hours, which can produce a different flavor, possibly one you would or would not prefer. It’s an experiment, so see what is best for you.

Temperature also can affect fermentation speed—higher temperatures increase the speed. So, you can store your milk kefir in the refrigerator if you want to slow it down to take a break (everyone goes out of town sometimes).

So, how can you tell when it is done? You will begin to see the curds and whey (clear liquid) separating. The whey forms bubbles at the bottom of the bottle and separates slightly throughout. Also, the kefir grains float at the top in a mass with some of the curds. If you continue to ferment it, the whey will separate out completely.

The Microbiology And Making Of Milk Kefir | Joyful Microbe

Curds and whey separating. See whey at the bottom. Photo by Justine Dees.

My personal experience with making milk kefir​

The day my grains arrived, I followed the instructions that came with them, which was to strain them, rinse them with milk, and then place them in a new glass of milk with a cover that is not airtight. After a few hours, it began to smell a little yeasty, which I liked and meant it was proceeding as it should.

The next day, I strained the grains and tasted a small amount, maybe two tablespoons. Honestly, I didn’t know what to think. It was a little weird—it gave me the feeling I was drinking something I shouldn’t. I figured I needed to give it another round of fermentation and see what it was like the next day. Also, I wondered if it would taste better cold. So, I placed it in the refrigerator and tasted it again. It had a slightly sour but otherwise pleasant flavor.

It is best to gradually introduce your digestive system to milk kefir, which is why I only drank a few tablespoons of the first batch on the first day and put the rest in the refrigerator.

Yemoos, the company I bought the grains from, said that the grains may take a couple of batches to get used to their new environment. And that was true of my experience. The second batch tasted better (bready, sour, and buttery) and fermented quicker.

Now that I’ve had my kefir going for a few weeks, I’m hooked. It is delicious. The way I usually drink it is in a green smoothie. I highly recommend this combination. Here’s the recipe below.

Joyful Microbe Milk Kefir Green Smoothie​


  • 1 cup milk kefir
  • ½ cup spinach
  • ½ cup kale
  • ½ banana
  • 1 tsp. peanut butter


  1. Place all ingredients in a blender.
  2. Blend until smooth.

So, that’s my experience with milk kefir. If you have any questions about milk kefir, I’d be happy to answer them. If you’ve enjoyed kefir, it would be fun to hear about your experience. Feel free to share in the comments or on social media. I’m thrilled to be on this new fermented food adventure, and this certainly won’t be the last. I would love for you to join me.

Further Reading​

Kefir – a complex probiotic
High-throughput sequence-based analysis of the bacterial composition of kefir and an associated kefir grain
Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir
The Microbiota and Health Promoting Characteristics of the Fermented Beverage Kefir
YouTube video about the microbial strains in kefir and their associated flavors

The post The Microbiology And Making Of Milk Kefir appeared first on Joyful Microbe.
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