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A cuddly-looking ball of a crocheted microbe with big eyes.

Could most of the microorganisms found our digestive systems be as friendly as this guy? Photo and microbe by Stacey Trock of

What’s living in your gut? Are the microorganisms in there good for you? And how does your diet influence them? These are interesting questions for fans of living, fermented foods, and science is just beginning to answer them as it investigates the microbiome. The fact that we’re asking them at all is pretty cool.

The diversity of bacteria that live on the body is staggering. The Human Microbiome Project claims there are about 10,000 spices altogether, found everywhere from our mouths to our bellybuttons and that they outnumber human cells ten to one. In our digestive systems, it’s possible that we have “enterotypes” in the same way we have blood types. And it’s possible that different people have different populations depending on their diet, or where they grew up. Right now, anybody can find out what they’ve got inside by joining the American Gut campaign, which is wrapping up in a few days.

Why care? Maintaining and even cultivating our digestive diversity could be healthy, and learning how our microbiome works and reacts could open a whole new area of disease treatments, something that’s covered in depth in this excellent article in the New Yorker. As that article makes clear, we’re still really early in understanding the ins and outs of our bodies’ relationships to the many microorganisms they host.

One thing is becoming more clear, though: We need healthy microbiomes, which means we should carefully consider the use of antibiotics. It’s starting to look like taking them is akin to swallowing a grenade that can blow up a lot of beneficial bystanders at the same time that it hits the bad guys. If many of the microbes we harbor contribute to our health, then wiping them out by mistake with drugs could allow other harmful microbes to take root, produce autoimmune disorders, or trigger other problems. It’s possible that digestive bacteria protect against celiac disease, for example. They could help determine body weight. And, in some studies, fecal transplants have cured the diarrhea caused by Clostridium difficile infections, showing that changing the population in the gut can bring about health results.

I’m looking forward to the news that comes in the next few years, but I’m especially curious to learn how our diets, especially oes that include fermented foods and lots of live microorganisms, influence the microbiome and our health. Is there a change in our guts if we load up on kraut and yogurt every day? And do those little beasts stick around inside us and do good things? I can’t wait to find out.

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kefir grains

An article in yesterday’s New York Times raises the question, are probiotics just hype? The answer, according to the article, is no. But the author points out that there are many kinds of potentially beneficial bacteria in unpasteurized fermented foods such as yogurt, and not all of them are beneficial in the same way. Indeed, even a particular bacterium has different strains that may or may not offer particular health boosts.

How are you supposed to know which probiotics are helpful and which aren’t? The author recommends searching the abstracts of studies at, which can be both enlightening and confusing. It would be nice to have a source or a number of sources that gather scientific data together into a kind of guide to probiotics. Does anybody out there know of any?

Meanwhile, I’m not about to stop eating live foods just because each and every bacteria that populate them has yet to be profiled. Eating yogurt or homemade kefir daily, along with turmeric paste, has helped me stop heartburn. More on how to do that later! Up above are my kefir grains, a little colony of bacteria and yeast that turn milk into kefir yogurt for me. And a strawberry-melon-mint kefir shake like the one below is a particularly tasty way to get a stomach full of helpful probiotics.

kefir shake

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