Understand why healthy bacteria in your gut is essential for health

March 27, 2016 Dr. Martin Gleixner, MSc, ND

Understand why healthy bacteria in your gut is essential for health

By Dr. Martin Gleixner, MSc, ND

Optimizing your digestive system (especially the microbes that inhabit there) is a great approach to improving our overall health.

Who knew…

  • there are approximately 100 trillion bacteria colonized in our gut?
  • one prescription of antibiotics could wipe out good bacteria in the digestive system?
  • a diet low in complex fibers, high in additives and processed foods leads to a decline in our microbiota as well?
  • beneficial bacteria protect the body from ‘bad’ microbes that may otherwise take hold in the body?
  • such ‘good’ bacteria are helpers in maintaining the health of our digestive lining? and
  • they also play a role in helping our bodies manufacture certain vitamins and preventing inflammatory conditions such as rheumatoid arthritis?

Our gut flora apparently helps the body in more ways than we even knew possible.

In the past, scientists were mainly interested in ‘bad’ microbes that have the potential to cause life-threatening infections. In more recent years, scientists have shifted their research to focus also on ‘good’ microbes that inhabit the human body. The American Gut project for example and other similar microbiome projects worldwide have the aim to map out the human microbiota genome.  Such projects were discussed by my favourite author on nutrition, Michael Pollan, in his article entitled “Some of My Best Friends Are Germs” (The New York Times Magazine, May 15th 2013).

As it turns out, our skin, every orifice or openings of our body and the entire length of our digestive system are colonized by beneficial microbes include certain species of bacteria and yeast. Scientists are observing that our modern day lifestyle is creating significant changes in these populations. Such microbial imbalances in our digestive tract also know as ‘gut dysbiosis’ can include the lack of normal ‘healthy’ bacteria or yeast; and/or presence of ‘bad’ microbes such as bacteria, yeast and parasites.

In a previous column, I discussed how gut dysbiosis, along with what I call the top 5 ‘silent imbalancers’ were among the most important, yet often undiagnosed causes of disease:

  1. dysbiosis (especially gut dysbiosis);
  2. food sensitivities;
  3. dysfunctional lymphatic system;
  4. toxicity; and
  5. subconscious stress.

I proposed that addressing such ‘silent problems’ was as important as improving lifestyle basics such as diet, exercise and sleep. I called these causes ‘silent’ since they:

  • are particularly problematic because they affect most people with chronic health problems and diseases;
  • tend to influence bodily functions 24 hours per day (therefore they can impact the body in negative ways 24-hours a day!); and
  • for some, they often go undetected because certain advanced medical tests are not conducted by our local hospitals.

Let’s review how we benefit from a balanced profile of microbes in the gut and how we can test for it to determine if it’s a problem:



Provides defence

Beneficial bacteria protect the gut from pathogenic (or ‘bad’) microbes that are trying to take hold. In doing so they may decrease one’s risk of acquiring the stomach flu (aka gastroenteritis) caused by the introduction of ‘bad’ species of bacteria, viruses or parasites. This likely explains why some people are more prone to food poisoning while others can eat the same meal without any symptoms.

Oral doses of known ‘good’ gut microbes as prescribed by Naturopathic Doctors and can help top up the defences in the digestive tract. Recent studies indicate that the prophylactic use of probiotics in hospitals have decreased the risk of acquiring opportunistic infection such as C. difficile.



Keeps our gut lining healthy while making vitamins

Adequate populations of ‘good’ microbes are helpers in maintaining the health of our digestive lining. This lining, called the epithelium, is the interface between the outside world and the inside world (all the organs inside our bodies).  A healthy lining creates an important protection against any harmful invaders and is specialized in digestion and absorbing our foods properly. Some ‘good’ bacteria can directly improve its function while others create nutritional substances that epithelial cells use to stay healthy. For example, ‘good’ gut bacteria in the colon produce short-chain fatty acids (SCFAs) derived from a byproduct of fermented plant fibres. The formation of certain nutrients (otherwise unavailable in our foods) such as vitamin K is also dependent on adequate levels of good bacteria in the gut.



Better detoxification of certain waste products and toxins

The digestive system and the liver work in tandem to detoxify. The liver packages toxins and our body’s waste products (e.g unwanted hormones, excess cholesterol, etc…) and excrete them from the body via the digestive tract (this is done by the liver’s production of bile). Once in the gut, these waste metabolites are usually evacuated via our bowel movements. ‘Bad’ gut bacteria, however, appear to release enzymes that can lead to the re-circulation of these wastes. If this occurs, our body may continue to store and circulate too many toxins and cholesterol molecules.

As a more specific example, if the gut reabsorbs unwanted estrogenic compounds, hormonal imbalances can occur which contribute to a host of conditions such as PMS, irregular menstrual cycles, changes in libido, etc…



Prevents inflammation & improper immune activity

Good bacteria in our gut also have an important immune function.

By keeping the gut lining healthy and merely by their presence, ‘good’ gut bacteria appear to be involved in helping to control inflammation and even regulate allergic responses. Likewise, in the event of a ‘leaky gut’ (a lay man’s term for what is known in medical research as ‘increased intestinal permeability’), the epithelial lining of the gut becomes compromised and therefore more permeable. The barrier is breached.

In this situation, byproducts and improperly digested foods (especially proteins that react with the immune system) can slip into the bloodstream. If bad bacteria are present in the gut, they can produce endotoxins that can also bypass our intestinal barrier.

Research has linked leaky gut and alterations in the intestinal microflora with inflammatory conditions such as allergies, irritable bowel syndrome (IBS), inflammatory bowel disease (Crohn’s disease and ulcerative colitis), rheumatoid arthritis, and ankylosing spondylitis; just to name a few.

In due time, I suspect that scientists will discover that changes in our gut flora may play an important role in the increased rates of allergies (e.g. peanut allergies in children), food sensitivities/intolerances and autoimmune diseases that we are witnessing today.

Since our gut flora apparently helps the body in more ways than we even knew possible, how do we know it’s a problem?



Advanced lab testing for digestive health

At the moment, our hospital labs only have certain tests available; those include: 1) checking the blood for certain antibodies (e.g. for the H. pylori bacteria that is related to peptic ulcers); 2) checking the stool for parasites; and 3) checking the stool of only a selective group of ‘bad’ microbes that are mainly linked to acute digestive conditions. This later test is helpful to diagnose severe cases of diarrhea (aka acute gastroenteritis) for example, especially for bacterial infections caused by ingesting a contaminated food or while travelling in foreign countries. While such bad microbes such as E. coli, C. difficile, Giardia, Cryptosporidium are important to diagnose for an acute case of diarrhea, such tests are rarely helpful for understanding the cause of chronic digestive problems and diseases associated with poor digestive health.

Although our present health care system is often slow to integrate new diagnostic tools, as Naturopathic Doctors, we provide many diagnostic tests that fill any gaps in our ability to understand health conditions. For gastrointestinal conditions such as chronic constipation, irritable bowel syndrome (IBS), heartburn/reflux (known as GERD), inflammatory conditions (e.g. gastritis, ulcerative colitis, Crohn’s disease, etc), we recognize the need to verify and diagnose the cause of these conditions.  IgG food sensitivity blood tests, small intestinal bacterial overgrowth (SIBO) breath tests and specialized stool testing are available at the Moncton Naturopathic Medical Clinic. It is now possible to assess for the presence of ‘bad’ microbes (yeast, bacteria, parasites) and verify if there is sufficient 'good’ bacteria in the digestive system. The value of such tests is becoming known in Moncton, as certain MDs are actively referring to the Moncton Naturopathic Medical Clinic for these tests (note: such tests are available to everyone; via referrals or simply by directly making an appointment).

Once gut dysbiosis is diagnosed, the correct treatments can be prescribed. A team approach is often used, such that your Naturopathic Doctor will work with your family GP or gastroenterologist. Depending which strains of ‘good’ bacteria are missing, effective probiotics formulations can be prescribed by your Naturopathic Doctor to correct this problem. Likewise, if certain species of bad bacteria are found, therapeutic dosages of naturopathic botanical formulations can be used to eradicate them.



Published by Dr. Gleixner on Tuesday, January 28th, 2014 in Times & Transcript. Modified December 23rd 2019.


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