Meet your microbiome: understanding your risk for dysbiosis.

Meet your microbiome: understanding your risk for dysbiosis.

Our bodies are home to a flourishing world of microorganisms that assist with all the important functions and processes that keep us alive: the microbiome. The microbiome starts to become populated with microorganisms at birth, and it develops and changes with us throughout our lives. 

These are some common risk factors that can make the microbiome sick, or dysbiotic. 

BUT, keep in mind that simple lifestyle changes can re-establish a healthy microbiome in the midst of environmental stressors.

Birth Method

The microbes that colonize your gut are shaped by method of birth--vaginal delivery or C-section. Babies born vaginally are colonized by the healthy bacteria found in their mother’s birth canal; those born by C-sections are instead exposed to powerful antibiotics and colonized by microbes commonly found around the operation room as well as potentially harmful skin bacterias.

There are times when C-sections are necessary and even life-saving, but elective C-sections are on the rise in the U.S.  Their effects on the budding microbiome can be life-altering, dramatically increasing the risk of children developing ADHD, allergies, autism, celiac disease, obesity, and type-1 diabetes, among other things.

Breast Feeding

Early-life nutritional experiences are instrumental in the development of the microbiome. Breast-fed babies are exposed to the nutrients and good bacteria necessary to developing a healthy microbiome, but their formula-fed peers develop microbiomes that are far less diverse, predisposing them to a host of life-altering conditions like diabetes, autoimmune disorders, and obesity--to name a few.

Fortunately, for those who can’t or choose not to breast-feed, there are many strategies that can support the developing microbiome and therefore make it less likely that these conditions will develop.


When the body encounters any type of stress, whether it be from true danger, or from everyday stressors, it reacts the same way: it revs the body up for a fight or flight response. This response is critical to human survival, but the chemicals released during times of stress--adrenaline, cortisol, and inflammatory cytokines--are damaging to the body over time.

Our classic definition of stress doesn’t encompass all the ways our body perceives stress. Biological stress occurs when we’re exposed to toxins, which meet and damage the microbiome by triggering immune and stress reactivity.

Toxins are practically unavoidable in our environment, so this near constant immune and stress response leads to inflammation in the body, which in turn leads to disease and degeneration. Protecting and supporting the microbiome in the face of an environment full of toxins can reduce the risk of developing chronic diseases like autoimmune disorders, Parkinson’s, depression, multiple sclerosis, inflammatory bowel diseases, dementia, and cancer.

The Western Diet

What we eat is of vital importance in supporting a healthy microbiome, but the Western diet is high in toxins and low in microbiota-accessible carbohydrates (MACs)--food for the microorganisms in the gut. Researchers accurately refer to the Western Diet as a way of “starving the microbial self.”

Lacking the nutritional value to support a healthy, diverse microbiome, and favoring the propagation of harmful microorganisms over health promoting ones, the Western diet contributes to a dysbiotic microbiome, which triggers inflammation and damages the body. It is implicated in the development of all sorts of chronic, “Western” diseases, like obesity, diabetes, autoimmune disorders, celiac disease, and dementia--to name a few.

Modern Sanitation

In modern societies that emphasize sanitation, diverse microbial ecosystems are rapidly disappearing, leaving behind a “Westernized” microbiome with microorganisms selected by human forces, rather than those selected by millions of years of evolution.

Researchers are beginning to uncover the link between this new “Western” microbiome and modern illnesses like heart disease, cancer, autoimmune disorders, and dementia. Leading researchers on this subject speculate that “it is possible that the Western [microbiome] is actually dysbiotic and predisposes individuals to a variety of diseases.”--Sonnenburg & Sonnenburg 2014


Antibiotics have revolutionized modern medicine and saved countless people from life-threatening illnesses, but there is a dangerous side to antibiotics that isn’t properly accounted for: their impact on the microbiome.

Antibiotics work by killing the microorganisms that are making us sick, but they don’t stop there; they wipe out the health promoting microorganisms that live in the gut too, creating a dysbiotic microbiome and leading to disease and degeneration if not corrected. They are especially dangerous for the developing microbiomes of babies and children: “Antibiotics are like a fire in the forest. The baby is forming a forest. If you have a fire in a forest that is new, you get extinction.” --Dr. Dominguez-Bello

Antibiotics can be difficult to avoid due to issues with the way they are prescribed--frequently, indiscriminately, and without proper consideration for microbial health--as well as their presence in our meats, poultry, and dairy products. However, limiting exposure to antibiotics, and supporting the microbiome when they are necessary can help protect from their negative effects.


Found in fruit and most processed foods, fructose is exceedingly common in the Western diet. The way the body processes this calorie packed substance affects metabolic regulation and leads to long-term changes in the body’s physiology. Researchers are beginning to understand that these problems begin with how fructose is broken down in the microbiome. 

Microorganisms in the gut love to eat fructose, and when they do, fructose fermentation occurs, producing short-chain fatty acids and biologically active gases. These byproducts disrupt digestion, impede colon activity, and damage the intestinal lining. When the intestinal lining is damaged, it’s much easier for bacteria and harmful substances to get into the bloodstream, inciting the immune system and damaging other organs.

A diet high in fructose also promotes the growth of sugar-loving microbial populations, not health-promoting microbes. This microbial imbalance triggers sugar-cravings and, in turn, increased sugar consumption. High sugar consumption is linked to impaired glucose tolerance, insulin resistance, high blood fats, and hypertension, which over time can lead to diabetes, obesity, and liver damage. 


Dr. David Perlmutter, an expert on gluten sensitivity, describes gluten as one of the “most inflammatory ingredients of the modern era,” yet it’s practically ubiquitous in our society--not only found in wheat based foods, but also in most processed food and even added to cosmetics.

When gluten interacts with the microbiome, it interrupts the breakdown and absorption of nutrients and tells the immune system to send out inflammatory chemicals. These chemicals quickly damage the delicate intestinal lining, making it easier for harmful substances to make their way into the bloodstream and triggering continued inflammation.

This inflammatory chain of events wreaks havoc on the entire body, especially the brain. Gluten exposure can set into motion cancerous cellular growth, autoimmune diseases, and neurological dysfunction, among other things.

The Pill

The Pill is an incredibly popular form of birth control that employs synthetic hormones to stop the body from ovulating. With long term use, these hormonal changes take their toll on the body, depleting thyroid hormone, testosterone levels, and certain vitamins, minerals, and antioxidants.

The Pill keeps the microorganisms in the gut from getting the components they need to build the body’s chemical messengers. For example, women who take birth control long term often end up with chronically inadequate supplies of Vitamin B6, which is essential for the construction of serotonin and GABA--two neurotransmitters that are vital to brain health. It’s therefore unsurprising that two of the pill’s most commonly reported side effects are mood and anxiety disorders.

It’s also associated with increased insulin resistance, oxidative stress, and inflammatory markers. It may even be a risk factor for the development of inflammatory bowel diseases, especially Crohn’s disease. Since it’s taken daily and often long-term, even small effects can begin to add up over time and stress the microbiome. It’s definitely worth exploring less risky, non-hormonal birth control options.

RoundUp Ready GMOs

Research hasn’t caught up with the effects of genetic modification on human health in general, but at least one form of genetic modification is inarguably damaging: making crops RoundupⓇ Ready.

When a crop is RoundUpⓇ Ready, it’s resistant to glyphosate (RoundUpⓇ)--an herbicide--that kills surrounding weeds. While it makes crops hardier and yields larger, it also means that humans are ingesting large amounts of glyphosate, as an estimated 80% of conventional processed food contains GMOs.

RoundUpⓇ wreaks havoc on the microbiome and therefore the entire body, compromising detoxification processes, impairing brain functioning, and depleting mineral supplies. It has also been linked to the rise in Celiac Disease and likely plays a role in many other modern illnesses. That’s why eating organic and GMO free whenever possible is very important to a healthy microbiome.

Environmental Chemicals

The synthetic chemicals we encounter in our environment are largely unregulated, and therefore are not thoroughly analyzed for their effects on the human body. These chemicals may have the ability to influence our hormones and overload the liver with damaging toxins. Things like chlorine and pesticides--both chemicals found in abundance in the food we eat and the water we drink--are specifically known for their toxic effect on the microorganisms in the gut.

While we can change some of our habits to mitigate exposure to some chemicals, it is difficult to truly control what pollutants we come in contact with, and being at the top of the food chain exposes us to large amounts of toxins through bioaccumulation; the food we eat contains traces of the chemicals our food has been exposed to.

Balancing your microbiome

If you’re looking at this list and noticing that you have many of these risk factors, there’s so many things you can do to bring your microbiome back into balance. Limiting your exposure to toxins and processed foods, eating a balanced diet, and starting a whole food supplement regimen will encourage health promoting microorganism populations to flourish, while starving off damaging populations.  The microbiome is an ever-changing environment that’s very responsive to lifestyle and dietary changes!



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