In a Nutshell:

  • Many serious health concerns have now been linked to disruption of the human microbiome, especially the gut microbiome.
  • Many environmental chemicals can disrupt the human microbiome. These include endocrine disrupting chemicals (like BPA and phthalates), persistent organic pollutants (such as flame retardants), heavy metals (like arsenic), and pesticides.
  • There are a lot of things you can do to reduce your exposure to MDCs, such as buying phthalate-free personal care products, eating organic food when you can, and filtering your air and water when you’re at home.

Microbes living on and in your body play a huge role in keeping you healthy. Microbiome disrupting chemicals disturb their delicate balance and can put your health at risk.

Would you believe that certain chemicals you encounter in your daily routine could be the reason you experience digestive issues or skin problems? A bad mood or brain fog could be due to these environmental chemicals, too.

But which one(s)? Could it be the:

  • Pesticide or antibiotic residue on the apple you had for lunch
  • Antimicrobial soap in the restroom you used
  • PFAS in the non-stick pan you fried an egg on
  • Chemicals in your sunscreen or lipstick applied a minute ago
  • BPA in the grocery store receipt you were handed

In all of these cases—and so, so many more—environmental chemicals upset your microbiome and cause health problems for you.

An obvious way to restore microbiome balance is to steer clear of microbiome disrupting chemicals. But doing that in the 21st century is easier said than done. 

But being aware of major types of chemicals that can disrupt your microbiome and evading them as best as you can is essential to this reset. 

Here you’ll discover what microbiome disrupting chemicals are and how you’re exposed to them. Then you’ll be in a better place to remedy your microbiome if it’s out of balance. We offer a few ways to get the healing process started.

This article contains affiliate links, which means we may earn commission if you decide to make a purchase.

First of All, What Is a Microbiome?

Many of us have heard of “the microbiome” at this point, as it’s become quite trendy in the past several years. In its broadest sense, a microbiome is the collection of microbes in an ecosystem. All microorganisms—including bacteria, viruses, fungi, and protozoa—are included. The ecosystem could be a forest, wetland, or desert. It could also be your body.

Your body is home to more microbes than the number of human cells you have—almost 40 trillion microbes vs. 30 trillion cells. Surprisingly, it’s only in the past few decades that scientists have begun to study the human microbiome and understand its role in human health and disease.

When someone talks about the “human microbiome,” they could be referring to the body’s microbiome as a whole, or they could be referencing the microbiome on a specific part of the body. For example, you probably know about the gut microbiome, but there’s also a microbiome in your mouth, on your skin, etc.

The microbiome begins at birth as a baby passes through the birth canal and acquires their parent’s microbiome. The number of types and species of microbes in a human’s microbiome grows over time. Greater diversity of species in the microbiome is associated with better health.

The microbiome constantly changes in response to diet, antibiotic treatments, and exposure to environmental chemicals.

An adult may have several hundred species in their microbiome dominated by two bacterial phyla: Firmicutes and Bacteroidetes. The ratio between these two—called the F/B ratio—determines the health status of your intestinal microbiome. When Firmicutes dominate, you’re prone to obesity. When there’s more Bacteroidetes, irritable bowel syndrome could trouble you.  

The Functions of the Human Microbiome

Some of the functions of the human microbiome include:

  • Nutrient metabolism
  • Drug and chemical metabolism
  • Vitamin synthesis
  • Maintenance of the gut mucosal lining
  • Immune system regulation
  • Protection against pathogens
  • Positive mood
  • Cognition function
  • Healthy skin
  • Normal aging

When a person encounters certain environmental chemicals, some of these functions are disrupted, resulting in microbiome dysbiosis.

What Is Microbiome Dysbiosis?

Microbiome dysbiosis occurs when the fragile balance of microorganisms in your microbiome is upset. Any number of negative symptoms is possible depending on which part of the microbiome is affected (gut, skin, or respiratory). These include:

  • Diarrhea
  • Cramping
  • Constipation
  • Bloating
  • Flatulence 
  • Indigestion
  • Food allergies 
  • Chronic bad breath
  • Breathing difficulties
  • Insomnia
  • Depression
  • Anxiety
  • Slow wound healing
  • Eczema
  • Acne

What Are Microbiome Disrupting Chemicals?

Microbiome disrupting chemicals (MDCs) are chemicals found in the soil, air, water, food, dust, and consumer products that upset the normal equilibrium among the trillions of microorganisms that reside in and on your body, causing dysbiosis. 

Unfortunately, most people are constantly exposed to several of these chemicals daily through ingestion, inhalation, or dermal absorption (through the skin). MDCs take a long time (months, years, or even longer) to break down and exit the body. Their breakdown products (metabolites) may also disturb the microbiome. 

Some MDCs, however, are known to build up in the body and never leave. The per- and polyfluoroalkyl substances (PFAS)— known as forever chemicals for this reason—are one example.

how environmental chemicals can disrupt the microbiome

Is There a List of Microbiome Disrupting Chemicals?

As part of its National Biomonitoring Program, the Centers for Disease Control and Prevention have documented over 400 environmental chemicals in human biological samples (urine, blood, serum, breast milk, and meconium). All of the MDCs that scientists know about are on this list. They include:

  • Benzophenone-3
  • Bisphenol A
  • Triclosan
  • Arsenic
  • Cadmium
  • Lead
  • Mercury
  • Insecticides
  • Pesticides
  • Parabens
  • Phthalates
  • Polybrominated diphenyl ethers (PBDEs) 
  • Polybrominated biphenyls (PBBs)
  • Polycyclic aromatic hydrocarbons (PAHs)
  • Benzene
  • Styrene

It’s possible to group most of the listed chemicals into four broad categories for ease of discussion: endocrine disruptors, pesticides, persistent organic pollutants (POPs), and heavy metals.

(Note, however, that the latter three categories can ALSO have endocrine-disrupting characteristics too.)

In most cases, what we know about the impact of MDCs on the microbiome derives from animal studies.

1. Endocrine disrupting chemicals (EDCs)

Bisphenol A (BPA), phthalates, fluorochemicals, and related compounds create perturbations in the human endocrine systems and microbiomes.

In mice and rabbits, BPA exposure led to a reduction in gut microbial diversity with a decrease in protective bacteria. As a result, the animals showed chronic intestinal, liver inflammation, and metabolic disorder.

Observational studies on human babies undergoing intravenous infusions with tubing containing phthalates revealed altered gut microbiota commonly associated with a lowered response to vaccines.

In animals, phthalate exposure has also led to abnormal lipid metabolism.

2. Persistent organic pollutants (POPs)

Persistent organic pollutants (POPs) are carbon-containing chemicals that can be carried long distances through the air and water. Since they resist environmental degradation, POPs and their metabolites build up in the ecosystem.

Dioxins and furans, such as 2,3,7,8-tetrachlorodibenzofuran (TCDF), are common POPs released through fossil fuel and wood burning. When human intestinal cells were exposed to TCDF, there was increased production of interleukin-8, a pro-inflammatory substance. This suggested TCDF exposure is linked to gut inflammation.

PBDEs, another kind of POP, are commonly used as flame retardants in building materials and electronics. (Until recently, they were widely used in furniture and bedding as well, but that’s begun to change). Exposure to PBDEs in mice led to impaired carbohydrate and protein metabolism. It also reduced the diversity of gut microbial species. 

3. Heavy metals

As chemical elements, heavy metals are naturally present in the Earth. Humans become further exposed to them through air pollution created by the burning of fossil fuels.

In mice, lead exposure reduced the diversity of gut microbial species. It also negatively affected the metabolism of vitamin E, bile acids, and nitrogen.

An observational human study in Bangladesh reported that arsenic exposure through contaminated water resulted in an overproduction of gut microbes from the genus Citrobacter. These microbes can create a wide variety of health problems such as urinary tract infections, respiratory conditions, or inflammation in the gastrointestinal tract. 

Analysis of arterial thickness revealed people with greater numbers of Citrobacter in their gut have thicker arteries, meaning their risk of developing cardiovascular diseases, specifically atherosclerosis, is higher.

4. Pesticides

Pesticides include insecticides, fungicides, and herbicides. There are a lot of different kinds of pesticides on the market, and the potential negative health effects vary depending on the specific product. In general, though, pesticides are associated with things like altered lipid metabolism, inflammation, and oxidative stress.

The most commonly used herbicide in the world, glyphosate (Roundup), breaks down quickly in the environment. For this reason, its manufacturer claims glyphosate is not harmful to humans. However, there are many studies showing it is not the breakdown products of glyphosate—but, rather, glyphosate itself, that causes abnormalities in the gut.

(If you want to take a very scienc-y deep dive into the mechanisms by which glyphosate/Roundup may cause problems for human health, you might want to check out the book Toxic Legacy by Stephanie Seneff.)

what are microbiome disrupting chemicals

Health Effects from Exposure to Microbiome Disrupting Chemicals

Some of the adverse health outcomes associated with microbiome disrupting chemical exposure as established in animal studies and in vitro studies using human cells are:

  • Oxidative stress
  • Type 2 diabetes
  • Cardiovascular dysfunction
  • Liver disease
  • Obesity
  • Thyroid disorders
  • Immune dysfunction 
  • Cancer 
  • Neurobehavioral disorders
  • Reproductive abnormalities

How Can I Reduce My Exposure to Microbiome Disrupting Chemicals?

To reduce your exposure to microbiome disrupting chemicals (MDCs), adopting healthy lifestyle habits can help keep them at bay. For example:

  • Choose cosmetics, personal care products, and cleaning products that do not contain MDCs.
  • DIY face masks with probiotic yogurt or raw honey to encourage a healthy microbiome.
  • Take daily probiotics. We like Seed and Ritual.
  • Consume high-fiber, organic food to feed your microbes (and you!) well and reduce your body burden of pesticides.
  • Remove pollutants from your home airspace with an effective air purifier
  • Use a reverse osmosis water filter or a water distiller, which will separate out harmful contaminants from water and help reduce your exposure to MDCs.

TL;DR on Microbiome Disrupting Chemicals

The estimated 40 trillion microbes living on and in your body play a major role in keeping you healthy—both physically and mentally. The skin has its own unique set of microbes making up the first line of defense against pathogens. The microbes in your gut—where 80% of your immune system resides—serve as their backup support.

Besides this critical function, your gut microbiome aids in:

  • Nutrient metabolism
  • Drug and chemical metabolism
  • Vitamin production
  • Immune system regulation
  • Maintenance of the gut mucosal lining

Chemical insults to your skin and gut microbiomes include:

  • Endocrine disrupting chemicals (EDCs)
  • Persistent organic pollutants (POPs)
  • Heavy metals
  • Pesticides

You can avoid these microbiome disrupting chemicals in several ways such as:

  • Choosing cosmetics, personal care, and cleaning products that do not contain EDCs
  • Using an air purifier and water filter at home
  • Eating organic foods

Chemical onslaughts to your microbiome destroy their natural balance needed to maintain your physical and mental health. By choosing a healthy lifestyle, you can avoid many of them. Keeping up with healthy habits is a never-ending process, but the rewards of optimal health are worth it.

About Jeanne

Jeanne Yacoubou, MS is an experienced researcher and writer passionate about all things environmental. She's written extensively on renewable energy, sustainability, the environmental impacts of diet, and toxic chemicals in food, water, air, and consumer products. When she’s not tending her organic garden or hanging out with her three teens, Jeanne is blogging about the latest scientific reports on our climate crisis. Jeanne holds master’s degrees in chemistry, ethics, and education. In between her graduate work, Jeanne served as a high school science teacher in Benin, West Africa as a Peace Corps volunteer for over three years.

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