The problem with our vanishing bacteria

I’ve seen thousands of patients over the years who give me a confused look when I tell them we need to work on their bacteria.

Now, with the trend of probiotics and fermented foods like sauerkraut and kombucha, it’s becoming easier to understand what a beneficial impact certain types of bacteria can have on our health.

That goes for viruses and fungi, too, as the three collectively up make up our microbiome—the microbes that live in and on us and influence everything from our immune system and digestion to our ability to focus and have a clear complexion, plus so much more.

And while it’s wonderful that the microbiome is finally getting some of the attention it deserves, there’s a pretty big problem: we’re starting to see a disappearance of microbes from our bodies.

Within developed countries, each new generation is found to have less and less of our native microbes. And while we know that certain imbalances lead to specific problems—for example, low levels of Bifidobacterium and high levels of the fungi Candida are related to eczema and allergies—we can’t quite predict what could happen if certain varieties of our native microbes become extinct.

There are many reasons for this microbial decline, some of which we can work on with our daily diet and lifestyle choices.

You won’t be surprised to hear me talk about food first; a high-fiber diet supports microbial diversity, while one of refined carbs and starches (very high in the Standard American Diet) does not. Microbes need to eat just like we do, prebiotic fiber is the best way to feed our internal probiotics.

Then there is our obsession with cleanliness, leading to the use of hand sanitizers that do kill bad bacteria but take the good bacteria with it. And of course, antibiotics are a major part of this conversation, as they do the same thing on a larger scale—wipe out bad microbes and take the beneficial ones too. The aftermath of antibiotics can linger long after use, can support the spread of opportunistic bacteria, and can also lead to antibiotic resistance due to widespread overuse. Antibiotics were definitely a breakthrough in medicine, we are just using them entirely too much and often without looking at alternative options as our first line of defense.

Another link to our changing microbiome may surprise you—dirt. Or, to be more specific, the soil we are growing our crops in. Conventional farming practices like pesticides, heavy tillage, and a failure to add organic matter back to the soil have depleted the soil microbiome that our own microbes coevolved with, affecting both our food and our health.

For more on the topic of soil and the microbiome, be sure to check out my latest episode of The Doctor’s Farmacy with Dr. Daphne Miller, where we discuss how healthy dirt leads to a healthier food system and healthier body. I hope you’ll tune in to gain a better understanding of soil microbes and how they impact us.