• Kristyn Emmer

6 Ways You're Killing Your Microbiome (And you don’t even know it)

We’re finally starting to understand that we humans are far less human DNA than we imagined. Turns out, we aren’t the center of the universe.

Microbes are.

As science has evolved, researchers have discovered that we are far more microbial DNA than we are human DNA. What that means is that these tiny microscopic friends are the key drivers behind our mood, our outlook on life, our energy, relationships, thought patterns and the list goes on.

And because these microbes’ roles are so key to our experience as humans, it’s important to take care of them well. Unfortunately, though, so much of our modern world is at odds with the microbiome. Toxins, chemicals, food supply issues. In fact, even our language is against these microbes with our obsession with killing germs, winning wars against viruses, and smothering ourselves in antibacterial everything.

Remind me, again. What exactly is the microbiome?

I’m glad you asked. The microbiome is the connection of life among you, all of the microbiomes of many kinds that journey with you as your experience on earth. The most common is our gut microbiome, but we also have trillions of microscopic friends that make up the microbiomes all over every part of your body -- your eyes, your mouth, your skin, your breast tissue and vagina. They shift and move to help us navigate the world around us, and although they are mighty, they are quite fragile.

So what are the daily choices we are making every day that wreak havoc on our microbiome?

A diet of corn, soy, & sugar

Why these? Here are your top genetically modified foods (GMO’s), and what makes GMO’s so special is that they grow best when they are paired with chemicals. Glyphosate, one of the most common agrochemicals, is rampant in our food supply. It’s a water-soluble antibiotic, which means it is not only on your food, but it’s also IN your food, wreaking havoc on the diversity within your microbiome. In fact, 94% of soybeans and 89% of corn grown in the US are grown from RoundUp Ready seeds.

These three culprits also happen to be the most common ingredients in our most highly processed foods, which we know lead to acidosis in the body and a shift in the gut microbiome, making a ripe environment for illness and disease.


Even the smallest changes in your stress level can alter the composition of your gut microbiome. This can be a frustrating reality because in today’s world, stress is worn like a badge of honor. We don’t have great ways of combating it and still show up for our modern lives.

While scientists are still trying to understand the exact mechanism for how stress changes the microbiome, the cascade of hormone responses in the body tell the gut microbiome to shift, creating an unhappy, and perhaps even hostile environment within your gut. And because of our gut-brain axis thanks to the connection of our vagus nerve, this stress state can further alter our mood and therefore our gut microbiome.


Antibiotics, birth control, antidepressants, ibuprofen. And the list goes on. Every medication taken has side effects that alter the state of your microbiome. While I’m not suggesting you never take another medication again, it’s important to know what you’re signing up for when you’re seeking to get rid of your headache or relief from that menstrual cycle.

Depending on the medication, you’ll be depleting important nutrients in the body as well as taking a hit to the important receptors for serotonin and your immune system that find their origins in your gut microbiome. For example, in one clinical trial in Sweden, researchers found that participants had compromised microbiomes an entire year later after only a week of taking antibiotics. And some hormonal contraceptives impact the function of your immune system.

Tap Water

The sad reality is that no matter where you go these days, “the tap water is just fine” is a false statement. It isn’t fine. Today’s tap water is not just the H2O you learned about in school. It’s also chlorine, fluoride, medications, birth control, pesticides and herbicides, and so much more. I bet you didn’t think you were filling your glass with antibiotics and estrogen when you went to quench your thirst? And as we have already discussed, medication, antibiotics, and agrochemicals can decimate the diversity within the microbiome.

If you’re curious about the state of the water in your own area, use the Environmental Working Group’s tap water tester to see how you score.

Eating the same thing over and over again

Our microbiome works best for us when it is diverse. Eating the same foods over and over again means that your body is taking in the same kinds of information and microbes over and over again. In agriculture, we call this monocropping. It can damage the richest soil, leeching important vitamins and minerals from the ground causing disease, weeds, and illness among our crops. The same thing happens in our body. When we get caught in a food rut reaching for the same foods, we end up monocropping our microbiome, limiting the incredible power it has to keep us healthy, happy, and healing. I would recommend trying to eat 40 different types of food in one week to keep your microbiome thriving.

Your bedtime and wake up routine

What you do in your bathroom before you go to bed and when you wake up can significantly alter the health of this widespread microbiome. According to the Environmental Working Group, women apply 168 unique chemicals to their body every single day. This is in our makeup, our soaps and moisturizers, our toothpaste and our hand wash. Our mouthwash is destroying our the microbiome of our mouth and the antibacterial soaps are stripping important “germs” from the surface of our skin.

So what can you do to protect your gut microbiome?

  1. Shop locally and in season where possible.

  2. Make sure you’re feeding yourself diverse nutrients, vitamins, and minerals every day. Here’s a great way to make sure you’re actually doing that.

  3. Get some help for your gut and detoxify glyphosate from your body.

  4. Switch out at least one toxic product in your home today. Use an app called Think Dirty to help you decide what your stay and what should go.

  5. Filter your water! A charcoal stick is a great start, but you might also try a more comprehensive option where possible.

  6. Choose herbal medicine first and find options pharmaceutical free wherever possible.

  7. Buy organic (or even better, regenerative organic) wherever possible. If you’re tight on a budget, take a look at Environmental Working Group’s Clean 15 and Dirty Dozen.

Remember, a healthy and diverse microbiome is the key to health and regeneration. Caring for it is one of the most noble and courageous acts for your health and your family's health in the modern lifestyle we live.

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