Environmental Factors That Affect the Microbiome

Natural Medicine Journal Podcast

The gut microbiota has a tremendous impact on immunity. In a recent interview, Editor-in-Chief Tina Kaczor, ND, FABNO, had the opportunity to talk with immunologist and Natural Medicine Journal Editorial Board Member Heather Zwickey, PhD, about environmental factors that affect the gut microbiota. They discussed pesticides, herbicides, and petroleum chemicals and the impacts they can have on the 100 trillion–plus microorganisms that reside in the human gut.

About the Expert

Heather Zwickey, PhD, is a professor of immunology and chair of the Department of Health Sciences at the National University of Natural Medicine in Portland, Oregon. She launched the Helfgott Research Institute, which advances the science of natural medicine. Zwickey founded the school of graduate studies and developed masters programs in research, nutrition, and global health. Zwickey has received the Champion of Naturopathic Medicine Award from the American Association of Naturopathic Physicians. She currently leads a National Institutes of Health–funded clinical research training program focused on integrative medicine research and studies the gut-brain axis in neuroinflammation.

Abbreviated Transcript

Tina Kaczor, ND, FABNO: What do you think is the most pressing topic that people need to know about as far as environmental factors that influence the gut?

Heather Zwickey, PhD: I think that as we start to discuss gut microbiota, it has such a profound impact on the immune system. And the immune system has really been my focus—neuroimmunomodulation. So when we think about the gut microbiota, we're often thinking about the obvious things that have an effect on it, like antibiotics. But we don't often consider some of the less obvious things that have an effect on microbiota, like pesticides we find in the environment and in our food.

Kaczor: When you say pesticides, so you're talking about Roundup, glyphosate, that kind of thing?

Zwickey: Sure. Roundup (or glyphosate) is one of the more common pesticides that we find in the environment. There have been studies that detect it in urine. So we are getting measurable levels of glyphosate in our diet. That might come from eating foods that are not organic, or if you live out in the country, it could come from places like your well water, where glyphosate has been sprayed on crops around you and has leached into the well water. The reason that we worry about that is that glyphosate actually has an effect on an enzyme that affects all bacteria. In fact, it affects everything except mammals. So insects like bees that are going to pollinate our fruits and vegetables can be killed by glyphosate.

But when we think about glyphosate with respect to humans, we have to remember that we have this microbial community within us, and it is susceptible to glyphosate. Some really recent data has shown that not all microbes in our gut are responsive to glyphosate. Many microbes can use tryptophan and other ring-based amino acids without needing the shikimate pathway, which is what glyphosate blocks. But Lactobacillus and Bifidobacterium, 2 of the big ones, require the shikimate pathway, and glyphosate can kill them.

Kaczor: In our world of clinical medicine, we always have outliers who can't seem to hold the Lactobacillus population in their gut. They'll go through courses of probiotics, we'll change brands a few times, and it just keeps going back down to nothing. We probably should be looking more closely at their glyphosate exposure in their urine.

Zwickey: Absolutely. You can actually measure their consumption and keep in mind that for most probiotics they're not going to become commensals. So what we need to be doing is addressing the metabolites that make our endogenous Lactobacillus and our endogenous Bifidobacterium grow. And for that, we're really looking at short-chain, fatty acids. Thinking about the metabolites might give us a different direction to go therapeutically. You might want to use a postbiotic or a prebiotic, as opposed to a probiotic.

Kaczor: You mentioned bees earlier. Can you talk a bit about how some of the compounds that are used in bee farming can affect the gut.

Zwickey: We know about the problem with the bees, and we've targeted a particular pesticide, the neonicotinoids, as one of the culprits for killing off our bee population. But glyphosate is clearly involved in this one as well. When you kill the bees’ microbiota, they get infectious disease—usually mites and viruses. A study came out a few years ago out of Boston on giving probiotics to the bees. They're actually putting Lactobacillus plantarum into the hives. And guess what? The bees recover.

Kaczor: I'm out in the country, and I would love it if they would spray Lactobacillus on the plants instead of manure.

Zwickey: Yeah, no kidding. But the issue around the neonicotinoids gets even more interesting when we start looking at how neonicotinoids are being administered onto plants these days. Historically we would spray pesticides on the plants, but apple growers and other fruit growers noticed that they were still getting worms in their apples. And more recently, trees are either injected with the pesticide or the pesticide is sprayed at the bottom of the tree so that it goes into the root system. And that way you don't have any worms in your apples, but that also means that you can't wash pesticide off of those fruits.

In another study out of Boston, researchers went to the grocery stores, took apples off the shelves, blended them up like you would for a smoothie, and then measured pesticide content. And what they discovered was that apples that were not organic had 300-fold more neonicotinoids. When we encourage people to eat apples, we need to encourage them to eat organic apples, because you can't get the pesticides out of there. And neonicotinoids affect the human gut microbiome as well.

Kaczor: Can you talk about environmental influences on the gut during pregnancy?

Zwickey: So one of the things that I have studied for a long time is vaccinations. People worry about vaccinations with respect to ADHD, autism, and neurodevelopment. And we're starting to discover that it's probably not related to vaccinations. It's probably related more to antibiotic exposure. There's great data now looking at antibiotic exposure in the first year of life for a child, but now they've gone backward and they've looked at maternal antibiotic exposure, and 80% of women are exposed to antibiotics during pregnancy. That's a huge number. If a woman is exposed to an antibiotic during pregnancy, we look at the fetal microbiome and then the microbiome of the offspring when the infant is born, and we see that within 60 days, we can get it back to 89% of normal, but it never reaches 100%.

That's interesting because one of the things we notice in kids with autism and kids with neurodevelopmental delay is that they're missing certain species of microbes. Are they missing species of microbes because mom was on an antibiotic? Are they missing species of microbes because mom was on some other medication? There's now data showing that when moms are on antidepressants, it can have an effect on their microbiome. And there's a great Nature paper that came out a couple of years ago, 2018, that showed that nonantibiotic drugs are absolutely able to influence microbiome. Some of them kill off different species of microbes, and some of them make different species of microbes overgrow.

So here we are with some might call a health emergency when we look at incidence of autism at 1 in 60 for males these days, and we know that there's a microbiome relationship, but we're not paying attention to all the various things that have an effect on the microbiome, especially of a developing child.

Kaczor: What can you tell us about preservatives in food?

Zwickey: A preservative is designed specifically to kill microbes, and that's good. We don't want necessarily pathogenic microbes in our food supply. But if it's designed to kill microbes, it is probably going to kill off some of your gut microbes as well. So again, there's so much that has an effect on our gut microbes—BPAs, plastics, diesel—all of these things have an effect on the microbial community. And what we need to remember is that we're never going to be able to control everything that has an effect on your gut microbes. So instead we have to be thinking about how we can constantly be doing things that make them happy. Making them happy is eating plant-based foods, plant-based fibers.

There was some really interesting research that came out of University of California, San Diego, that showed that 30 plant-based fibers per week is important for maintaining the diversity, the alpha diversity of our gut microbiome. And 30 is a lot. That's not 30 servings, that's 30 different fibers. We need the diversity of the fibers to feed the diversity of our microbiome. So if you're only eating tomatoes as your vegetable, for example, you need to add some more different varieties of plant-based fibers in order to truly maintain that healthy gut microbiome.

A lot of times people in the exercise industry promote the goal of 10,000 steps a day. Well, in the nutrition industry, maybe the goal should be “get your 30 different plant-based foods.” That includes nuts, spices, and all these things that we don't necessarily consider when we think of plant-based foods

Kaczor: I tell people, "Tend your culture.” You’ve got a culture in your gut, and you need to tend it.

Zwickey: Yeah. You say tend the culture, I say, feed the beast. You've got this little beast in your gut, and it gets mad if you don't feed it.

Kaczor: The concept is that the microbiome is an entity unto itself. And actually we should treat it like we treat any organ. You wouldn't consciously take in chemical compounds that are toxic to your heart, right?

Zwickey: Exactly.