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Throughout our series of articles, we emphasized the importance of the gut microbiome and the number of factors that impact its composition.

Generally speaking, the gut microbiome does a great job at getting rid of toxins and waste products, especially if you are eating a balanced diet rich in fiber, probiotics and prebiotics.

However, if the microbes grow out of control, you could be subject to severe complications, involving small intestine bacterial overgrowth (SIBO) and leaky gut syndrome.

In this article, we will cover the effects of toxicity on your gut microbiome to shed some light on the importance of diet and healthy bacteria.

The effects of toxic substances on your gut microbiome

Ever since the surge of microbiome research, scientists provided a lot of information about the factors that alter the composition of your gut microbiota.

Some of these factors include genetics, diet, and daily habits. However, environmental chemicals and contaminants in food are major influencers on the diversity of your gut microbiome.

Additionally, researchers found a link between exposure to environmental chemicals and several health problems (e.g., obesity, type 2 diabetes, cancer, immune dysfunction, reproductive system disorders).

The scientific literature indicates that gut microbes are effective at metabolizing azoreductases, nitroreductases, β-glucuronidases, sulfatases, and β-lyases.

However, when these microbes are incapable of handling large amounts of toxins, you are bound to take a hit that may present in a variety of ways.

Here is a list of the chemical families with the most impacts on the gut microbiome:

  • Bisphenols
  • Phthalates
  • Persistent organic pollutants
  • Heavy metals
  • Pesticides

The complications of gut microbiome toxicity

The primary complication of gut microbiome toxicity is SIBO.

This condition occurs when bacteria start growing out of control in the small intestines. As a result, symptoms of disrupted digestion, such as diarrhea, constipation, bloating, gas, and abdominal pain, arise.

The mechanisms involved in SIBO are poorly understood; however, and aside from toxin accumulation, there are some documented risk factors that may trigger this disease, including:

  • Infection (e.g., gastroenteritis)
  • Celiac disease
  • Crohn’s disease
  • Gastroparesis
  • Cirrhosis
  • Portal hypertension
  • Irritable bowel syndrome
  • Gastric bypass

Your physician will ask you multiple questions to collect a clear history of your disease. He/she will then conduct a proper physical examination. Finally, some blood and fecal tests might get ordered to confirm the diagnosis.

How to treat SIBO?

Usually, SIBO is treated with antibiotics to stop the bacteria from growing and causing damage. The most commonly prescribed antibiotics include ciprofloxacin, metronidazole, and rifaximin.

By killing the extra bacteria, antibiotics are able to reset the balance of your microbiome.

However, physicians are starting to sway more toward probiotics to treat SIBO.

Here are the treatment options for gut microbiome toxicity:


Probiotics are dietary supplements rich in microorganisms that will reestablish the healthy competition for food between all the microbes. As a result, opportunistic species will halt their growth, and the intestinal flora will restore its physiological balance.

In a 2010 study, researchers found that probiotics might be more effective in treating SIBO than antibiotics

The best way to replenish the healthy bacteria of your gut flora is by taking daily doses of probiotics.

Reduce your carbohydrate intake

Reducing sugar intake can have major benefits on your health, including a risk reduction of developing chronic diseases such as diabetes, coronary artery disease, and blood hypertension.

Carbs are also used as a primary fuel source for harmful microbes, which may boost their growth and worsen your symptoms.

Disclaimer: if you suspect that you have chronic exposure to toxins, you may want to speak with your doctor before trying alternative detoxifying methods.

Takeaway message

Having too many toxins in your gut will inadvertently surpass your microbiome’s cleansing properties. Additionally, the composition of your gut microbiome will shift toward unhealthy bacteria, precipitating SIBO.

Colon hydrotherapy, or colonics is a fantastic procedure that works in harmony with your colon to cleanse it from all the toxins and waste products.

Hopefully, this article helped introduce colon cleanse and how it helps with digestive disorders by detoxing harmful agents, including bacteria. If you still have any questions, feel free to contact our Wellness Center for more information by calling us at (212) 719-3611 or emailing to