The Microbiology of Milk Kefir [Plus, How to Make Kefir at Home]

Originally published Jan 20, 2017. Updated May 22, 2022.

We can thank microbes for the tangy flavor and the effervescent creamy texture of kefir. If you’re new to kefir, it’s similar to yogurt. Both are made by fermenting milk. To my taste buds, kefir is like an intensified form of yogurt, effervescent and wonderfully tart and tangy. Kefir is thinner than yogurt so it is easier to drink on the go.

Kefir relies on dozens of bacteria and yeasts to convert the lactose and other compounds found in milk to small molecules that contribute to the taste and texture of kefir. Thank you microbes! In this blog post, I’ll cover the history of kefir, some of the microbiology behind it, and how I make kefir at home.

Kefir’s History

Kefir has a rich history dating back thousands of years and is thought to have originated in the northern Caucasus, the region between the Black Sea and the Caspian Sea. The name kefir is believed to be derived from “kef,” a Turkish word meaning “good feeling.” Kefir has become a prized possession in the Caucasus and was initially kept secret from the rest of the world. Throughout time, many have believed that this concoction holds special powers: a gift from the gods, an elixir of life, a miracle drink.

Even Elie Metchnikoff, who was awarded the 1908 Nobel Prize in Physiology or Medicine for the discovery of phagocytosis, had theories about fermented milk. He wondered about the beneficial effects of lactic acid bacteria and attempted to alter his own intestinal microbiota by drinking fermented milk he prepared himself from lactobacilli isolates. Metchnikoff noticed health benefits from drinking kefir and documented his work in The prolongation of life; optimistic studies. For a deeper discussion on Elie Metchnikoff’s life and work (and to get a glimpse of late 19th-early 20th century science), check out R. B. Vaughan’s The Romantic Rationalist: A Study of Elie Metchnikoff.

Kefir Microbiology and Chemistry

While yogurt is fermented with just bacteria, kefir is fermented with a more diverse community of bacteria and yeast. As a result the chemistry between the two products differ and contribute to the differences in taste and texture.

Microbes and How They Affect The Flavor of Kefir

To investigate the microbes behind the tangy goodness, scientists from University College Cork sought to address such questions by analyzing kefir grains (the mini-cauliflower shaped globs of bacteria and yeast that perform the fermentation) and their fermentation products. The group obtained kefir grains from three distinct geographical locations (France, Ireland, and the United Kingdom) and began to ferment milk in the lab.

The scientists first identified the microbes present in the kefir grains. In all three grains, more than 92% of the microbes were Lactobacillus (lactic acid producing bacteria). Since the kefir grains disperse microbes into the milk during fermentation, the team also characterize the microbes in the milk at different stages of the fermentation process. They sampled the kefir at 0 hours, 8 hours, and 24 hours after fermentation was initiated. Despite the different origins of the kefir grains, microbes from all three kefir samples followed the same pattern of microbial succession: Lactobacillus dominated at the early stages of fermentation but as fermentation progressed, Leuconostoc and Aceobacter (acetic acid producing bacteria) took over.

From these samples, the scientists also identified what genes were expressed at different times and the volatile compounds in the kefir that could contribute to its flavors. Armed with information about the microbial species present, genes expressed, and volatile compounds in the kefir, the team could correlate the volatile compounds produced with the microbes in the kefir.

The researchers saw the following correlations between microbe and flavor:

A. pasteurianus: vinegar flavors
L. kefiranofaciens: cheesy flavors
L. mesenteroides: buttery flavors
L. kefiranofaciens and S. cerevisiae: fruity flavors

Does Kefir Contain Lactose or Alcohol?

Almost all of the lactose in the milk is metabolized to lactic acid by the lactic acid bacteria that dominate kefir making it possible for lactose intolerant individuals to drink kefir without ill effects. Lactose is also broken down into kefiran, a water-soluble polysaccharide that contributes to kefir’s creamy texture.

Towards the end of the fermentation process, yeasts break lactose down to ethanol and carbon dioxide giving kefir its bubbly characteristic. You can’t get drunk on kefir however; the alcohol concentration in kefir is usually approximately 0.2-0.3 percent.

Equipment for Making Kefir at Home

When I started my kefir making journey in 2017, I was surprised how quickly the fermentation process takes: only 12-24 hours! After doing some reading, the first step was to acquire some equipment and kefir grains.

Note: As an Amazon Associate I may earn commissions from qualifying purchases from links in this post (affiliate disclosure).

Kefir Grains

I ordered kefir grains from Fusion Teas and when they arrived in the mail, the first thing you had to do was to “reactivate them.” Since they’ve been in transit, subject to temperature changes, and without a fresh source of milk, it could take a few days to revive. To revive the grains, you’d place them in fresh milk and leave it out at room temperature. The next day, fish out the grains and transfer to fresh milk. You’ll do this for a few days until the grains start to grow.

These grains contain bacteria and yeast that are encased in a matrix of protein, lipids and sugars. Making kefir is pretty simple: obtain grains, drop them in milk, and let it sit at room temperature for 12-24 hours. After this incubation is complete, the grains can be transferred to fresh milk to make the next batch or grains can be covered in a little milk for storage in the fridge. Kefir grains will grow in size as they are propagated from batch to batch making it easy to share or keep an extra stash of grains incase of mess-ups.

Strainer

The strainer is a big help to remove the grains from the kefir. I opted for a plastic fine mesh strainer as I didn’t want the metal interfering with the kefir growth.

Jar for Fermentation

You’ll use a jar to hold your fermenting kefir. I prefer to use glass as it is nonreactive and easier to clean than plastic. It’s best to get a screw top lid so you can keep it loose to vent. If you have an airtight lid, pressure will build up in the jar and depending how much pressure there is, it could pop the lid off and leave you with a bit of a mess.

Kefirko (Optional)

At some point, I acquired a Kefirko, which is basically a glass jar with a strainer built in. I found that the Kefirko is best if you want to make a large batch of kefir at once. Since I was the only kefir drinker in the household, it was easier for me to use a one pint container.

How to Make Kefir at Home, Step-by-step

Place about a teaspoon of revived milk kefir grains into a jar.
Add one cup of milk into the jar. I’ve used anything from 1% to whole milk.
Cover the jar with a loose lid or a towel secured over the top of the jar with a rubber band or hair tie.
Leave out at room temperature for about 24 hours. Overtime, you can see the top layer of the milk thicken up.
The kefir is done when it is thick. You’ll want to catch this before the curds completely separate from the whey. Now, you’ll strain the kefir over a new container to place in the fridge. Pour the kefir over the strainer and use a spoon to push down the kefir through the strainer and into your container. The grains will remain on the strainer and can be used for the next round of fermentation (go back to step 1).

How Temperature Affects the Kefir Fermentation Time

One of the trickiest parts of making kefir for me is that the fermentation time depends on both how many grains you are using relative to the amount of milk and the temperature in the room. At warmer temperatures, the kefir will ferment faster while at cooler temperatures, the kefir will ferment slower. And, using more grains will ferment the milk faster than if you use fewer grains. I found myself adjusting to using fewer grains in the summertime or else the fermentation was done in 12 hours or so. When you accumulate too many grains, you can give away the extras to kefir enthusiasts you may know or blend them in a smoothie.

Store Bought vs. Homemade Kefir

I had read about how it’s difficult to make kefir using store bought kefir. Prolonged storage and low temperatures can kill off many of the microbes in kefir and limit the diversity of microbes making subsequent batches diverge away from the ideal kefir microbial communities. Furthermore, store bought kefir is made with about 10 strains of bacteria and yeasts whereas homemade kefir contains approximately 50 strains! I haven’t tried using store bought kefir as a “starter” but if you do, I’ll be interested to hear how it turned out.

If you’re looking for more kitchen fermentation microbiology + step-by-step recipe, check out this post all about yogurt making.

The Microbiology of Milk Kefir [Plus, How to Make Kefir at Home]

Kefir’s History

Kefir Microbiology and Chemistry