How Toxins Affect The Microbiome & Overall Health

October 01, 2023 4 min read

How Toxins Affect The Microbiome & Overall Health

In the last article we covered what the microbiome is, a colony of trillions of bacteria in our colon, and how it affects every aspect of our health, our hormones, our longevity and the ability to build muscle and stay fit. 

These bacteria also produce or help to produce neurotransmitters in our body, such as Serotonin and GABA, which calm and relax us, de-stress us and allow us to fall asleep.

Some of these bacteria eat the foods coming in such as amino acids, vitamins and other nutrients, and some actually produce amino acids, or vitamins, or other nutrients that the body can use or that other bacteria feed off of.

It’s actually a miniature circle of life down there with whole food chains or bacteria consuming food and then making food for other bacteria, producing neurotransmitters for the body to use and even consuming them when too much are produced.

So keeping these in balance is very important, and knowing what harms them, so we can prevent that, is even more important.

In this article we’re going to cover how the number of toxins coming into our body, which increases every year, affects these bacteria.


Glyphosate, the chemical in the Herbicide Roundup which is used on all major food crops, micro-plastics, and heavy metals are all neurotoxins and hormone disruptors. A neurotoxin is something that poisons the nerves. It can cause them to speed up or slow down or even stop your heart, if concentrated enough.

They’re also antibiotics in that they kill bacteria — including the bacteria in your microbiome that you need.

When nerve channels are slowed we can get brain fog, become less alert, and have a harder time figuring things out.

When they’re sped up we can become hyperactive, aggressive, or have a crawling in our skin feeling.

And when they get too messed up in different areas, speeding up or slowing down along channels that were meant to operate at incredibly fast speeds, or when we have actual nerve death from poisoning by these factors, we get things like autism or Alzheimer's.

And this all relates to the health of our gut bacteria, because while this is part a poisoning of the actual nerve cells, it’s also a poisoning of the bacteria that produce the neurotransmitters that allow for communication between the nerve cells.


When we look at children with autism we see seizures, sensory sensitivities, anxiety, intestinal disturbances, and lowered immunity.

These are all related to the nervous system and the gut, which we now know are inextricably intertwined. In fact, when a child is growing, their microbiome and nervous system form parallel to one another.

When we look at Glyphosate, an herbicide used on all major crops these days and which is in almost all processed foods and meats, we’re looking at an antibiotic — something that kills bacteria.

So if you’re consuming food with glyphosate this will kill off some of these bacteria that are necessary to the production of neurotransmitters.

We also have heavy metals and PFAS (so called forever chemicals) in our food and water supplies. These can either kill off these helpful bacteria, or the bacteria can take the toxins into themselves, holding them so they don’t harm you at the time, but slowly poisoning the bacteria, only to be released again when the bacteria dies.

This is part of the flu-like symptoms we experience during detoxes, candida diets, and even just weight loss diets or “going Keto”. This is these bacteria being either killed by the detox or starved by a new diet, and so dying and releasing the toxins they’ve held onto which then make us feel terrible.

Then there are antibiotics that we take for an infection. Antibiotics work by preventing bacteria from reproducing, both the destructive bacteria, but also the good bacteria.

Just to give you an example, there is a statistic where about 20% of people who take a course of antibiotics suffer depression for the next couple of months. And when we up that to two courses that percentage rises to about 40%.

This is these bacteria being killed off and so lessening the production of GABA, serotonin, and other major neurotransmitters.

That’s why it’s very important to take probiotics and amino acids after a course of antibiotics, to build these back and feed them so they can thrive once more.

So it’s very important to eat organic food, or if not possible then to follow the Clean 15 foods and stay away from the Dirty Dozen.

It’s also smart to get a reverse-osmosis filtration system for your drinking water to prevent these toxins from coming into your body.

And make sure you’re taking your probiotics, Greens, and PerfectAmino to help rebuild these bacteria and feed them what they thrive on.

I hope this helps.

And, if you haven't seen the Gut Health Protocol & 30-Day Challenge, I highly recommend you check it out! It's very possibly the most important program we have for overall health.

Just use the code GUTHEALTH for 10% off the Gut Health Collection.

And make sure to join our PerfectAmino VIP Group if you haven’t already, where you can ask all of your questions and we can help you with anything you need.

*These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any disease.