How kefir changes the microbiome

If you follow the microbiome at all, you’ll eventually discover the benefits of kefir. Google the phrase “one of the most potent probiotic foods available” and you’ll find kefir in all the top results. A recent BBC documentary that tested people after consuming different types of “gut-friendly” foods found that kefir had by far the biggest effect. My interest piqued when, after my disappointment with kombucha, I spoke with a man who happened to mention his good luck with kefir as a solution to his many gut issues. On a doctor’s recommendation, he tried kefir for a number of years with limited success, until — frustrated with the $3/day expense of buying it at Trader Joe’s — he began making it himself at home. "What a difference!” he claimed.

Let’s jump to the conclusion: I tried it myself and it’s true. I found a very noticeable change in my gut microbiome — the most significant I’ve seen among my many experiments. Look at my levels of Lactococcus, the main genus of microbe known to be found in kefir:

You’ll note that I had none of this microbe until late January, when I started to drink kefir. The two dips after that, one in mid-March and another in early-April, coincide with trips out of town when I was not able to drink my kefir regularly.

So it apparently has a big effect on the microbiome. What is this stuff anyway?

The first thing to know about kefir is the pronunciation. Say “Keh-FEAR”, with the accent on the second syllable, not “KEE-fur” or “kEH-fir”. The Russian origin of the term is a reminder of a time in the distant past when — it’s unclear exactly where or how — the first batch was prepared and then passed along, its microbial components shared from person to person until it reached today’s status as a popular drink you can buy in most grocery stores.

Making it at home brings more benefits than just saving money. Commercially-purchased drinks are subject to unavoidable regulatory, shelf-life, and consistency contraints that are important for business. But more than that, if you believe like I do that microbes are highly-customized to our environments, making at home will ensure that the kefir is well-adapted to your own personal microbial environment. The batch that survives and thrives in your kitchen will, by definition, have proven its ability to withstand whatever whatever conditions you face there.

Making it yourself is surprisingly easy. It begins with a bundle of the component microbes, a cauliflower-shaped substance usually called the “grain” or “seed”. Instruction books often tell you to be careful how you handle the grains, but I find them robust enough that I pick them up with my bare fingers. I drop them into a glass of milk left sitting on the counter overnight and — voila! — twenty four hours later, the liquid has turned into kefir. Pull out the kefir grains from that glass, plop it into another, and you’re all set for tomorrow’s batch. Unlike yogurt, which requires heating and a stable temperature, kefir doesn’t appear to care about how it's handled, so long as you keep it at room temperature and can wait for twenty four hours. The reaction might vary by a few hours if the room is a bit colder or warmer, but otherwise I find it surprisingly consistent. Just set and forget.

The ease with which the kefir fermentation happens today begs the question of how the very first kefir grains were created. Nobody knows exactly, but there are people who make them from scratch. I haven’t tried this myself, but apparently a goat-hide bag filled with pasteurized milk and the intestinal flora of a sheep will do, so long as you shake every hour and maintain a constant temperature.

Even without going the goat-hide route, I found that getting started was the only hard part of the process. You can order some starter grains online for under $25, but to survive shipping the manufacturers generally give them to you in a freeze-dried form that requires a week or so of preparation before the microbes are fully alive and kicking out drinkable quantities of kefir.

I got mine by asking around until I found a neighbor who had been brewing his own. Anyone who makes homemade kefir will be happy to give you some extra grains. The fermentation process causes the grains to multiply, and you will find yourself throwing them out regularly.

The grains themselves contain a combination of lactic acid bacteria (Lactobacillus, Lactococcus, Leuconostoc), acetic acid bacteria, and yeast, clumped together with casein (milk proteins) and complex sugars in a matrix of a unique polysaccharide called Kefiran. The nutritional content apparently varies depending on fermentation time and other factors, but there’s a lot of good stuff in there. One study shows the following:

A rigorous microbial analysis by an Irish lab recently showed precisely which microbes are present in kefir, at various stages in the fermentation process. This chart shows the composition of ordinary pasteurized milk as it changes from before adding kefir grains (time 0 at the bottom) until 24 hours have passed (top) and the milk has been transformed into just Acetobacter, Lactobacillus, and Leuconostoc.

The uBiome test looks only at the 16S ribosomal gene, which unfortunately can’t detect yeasts, so I don’t have an easy way to track the yeasts in the kefir.

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