Are Environmental Toxins Disrupting Your Gut Bacteria?


  1. The top 5 toxins that disrupt the gut microbiome

  2. How to protect your gut bacteria from environmental toxins

  3. My Toxin-Free Shopping List

The human gut microbiome is home to more than 1000 species of microbes that perform many vital functions; they help us metabolize food, regulate our immunity, and protect us from pathogenic microorganisms. However, despite the powerful roles gut microbes play in our bodies, they are quite vulnerable to harm from external influences such as environmental toxins. Exposure of gut microbes to environmental toxins disrupts their important metabolic activities and subsequently has a detrimental impact on our own health. Over time, gut microbiome disruption may even lead to chronic diseases such as autoimmune disease, diabetes, obesity, allergies, and gastrointestinal disorders. To keep our bodies in a state of optimal health, it is crucial that we protect our gut microbes by avoiding toxic environmental exposures.

The top 5 toxins that disrupt the gut microbiome

A rapidly-growing body of research indicates that chemicals used in industry, agriculture, consumer goods, and medications harm gut microbes and have adverse downstream effects on our health. The top five groups of environmental toxins that disrupt gut bacteria include triclosan, pesticides, plasticizers (such as BPA and phthalates), heavy metals, and pharmaceutical drugs.


Triclosan is a synthetic antibacterial chemical found in personal care products such as soap, mouthwash, toothpaste, hand sanitizer, and deodorant, is easily absorbed through the skin and gastrointestinal tract and rapidly alters the microbial composition of the gastrointestinal tract. (1)(2) This rapid restructuring of the gut microbiome impairs the immune system-regulating activities of gut microbes. In fact, the frequent use of antibacterial products has been associated with an increased risk of food sensitivities, seasonal allergies, and asthma! (3)(4)


A staggering 1 billion pounds of pesticides are used per year in the United States, and 5.6 billion pounds are used worldwide. Unfortunately, pesticides don’t just kill insects in crop fields and on our lawns; they also kill beneficial bacteria in the gut! Animal studies indicate that pesticides decimate beneficial gut bacteria; this may ultimately increase the risk of intestinal dysbiosis and immune system disorders, among many other chronic health issues. (5)


Plasticizers are chemicals that confer flexibility or rigidity to plastic products. These chemicals are highly prevalent in our environment and have a significant impact on gut bacteria. Bisphenol-A (BPA), found in plastic water bottles, receipts, and the lining of canned foods, alters the normal gut flora and disrupts the body’s hormonal system by mimicking the hormone estrogen. (6) While often marketed as safe alternatives to BPA, “BPA-free” plastic alternatives may be equally, if not more, harmful to our gut microbes. Bisphenol-S and bisphenol-F demonstrate endocrine-disrupting effects comparable to that of BPA. These adverse effects may extend to the gut microbiome. (7) Phthalates, another class of endocrine-disrupting plasticizers used as solvents in personal care products and vinyl plastic, also reduce levels of beneficial gut bacteria. (8)

Heavy metals

Heavy metals, such as cadmium, lead, and arsenic, reduce levels of beneficial bacteria in the gut that protect against intestinal inflammation and may, therefore, promote inflammatory gastrointestinal disorders. (9)(10) Heavy metals are common contaminants in soil and drinking water due to industrial pollution.

Pharmaceutical drugs

It is common knowledge that antibiotics disrupt the gut microbiome. However, they are not the only pharmaceuticals that promote an imbalance in gut bacteria. The synthetic form of estrogen (ethinyl estradiol) in the birth control pill also detrimentally alters gut flora, as do proton pump inhibitors (PPIs). (11)(12) I recommend finding alternatives to these drugs if you want to maintain a healthy gut microbiome.

How to protect your gut bacteria from environmental toxins

While the abundance of toxins in our environment can feel overwhelming, the good news is that there are steps we can take to reduce our exposure and protect our gut health. Here are my top six tips for reducing your exposure to microbiome-disrupting toxins:

  1. Instead of using conventional cleaning products, which often contain triclosan, switch to a plant-based brand such as Seventh Generation. Better yet, try making your own cleaning products at home! Check out Environmental Working Group’s Guide to Healthy Cleaning website for more information on non-toxic cleaning products.

  2. Avoid commercial body care products, as these are a significant source of triclosan, phthalates, and parabens.[G1] Absorption of these chemicals through your skin may ultimately affect your gut microbes. To find natural, healthy body care products that don’t contain microbiome-disrupting chemicals, check out Environmental Working Group’s Skin Deep Cosmetics Database.

  3. Eat organic produce. Conventionally-grown fruits and vegetables are a major source of microbiome-disrupting pesticide exposure. Research indicates that consuming organic produce can significantly lower your body burden of pesticides, thus protecting your gut microbes. For a list of which types of fruits and vegetables it is best to buy organic, look at Environmental Working Group’s 2017 Shopper’s Guide to Pesticides in Produce.

  4. Reduce your use of plastics and limit your consumption of canned foods to reduce your exposure to BPA and BPA alternatives. Use glass or stainless-steel water bottles and storage dishes instead of plastic, and opt for fresh food instead of canned! Check out my toxin-free shopping list below to see the products I use and recommend!

  5. Filter your drinking and bathing water. Unfortunately, tap water is rife with pesticide residues, heavy metals, plasticizers, and pharmaceutical drug residues. Consider investing in a high-quality water filter that can remove these substances from your drinking water. I have personally used a Berkey water filter for the past 5 years, and am confident that it is one of the best water filters out there! It removes many heavy metals, pesticide residues, industrial pollutants, and harmful bacteria.

  6. Support your gut microbiome by consuming prebiotics and probiotics. Probiotics add beneficial bacteria to your gut and may even help in the metabolism of toxins! Prebiotics, a form of indigestible dietary fiber, feeds probiotics and help to support their growth and proliferation in the gastrointestinal tract.

My Toxin-Free Shopping List

Glass Pyrex Storage Dishes

Lifefactory Glass Water Bottle

Berkey Water Filtration System 

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