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How to Support the Gut, Part 1: Intestinal Flora

Posted by cleanteam

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Over the next few weeks, I’ll take you on a journey through the gut system. The image above shows you the different parts of the gut that I will be talking about. You’ll see what they do, how they get damaged and what we can do to repair them.

Today we’ll start with the fascinating intestinal flora.

We’ll be doing some basic physiology which I think will give you a good picture of how important the gut is and how gut repair can really aid our health.

The Intestinal Flora

The day and age of probiotics and intestinal flora has arrived. What was once a strange and “weird” topic in the health and medical fields is now center-stage.

More and more we are seeing the important connections made between our intestinal flora and the quality of our digestion, mood, skin, and immune system. Yet, we have hardly begun to crack the surface of this fascinating topic.

Think of your intestinal flora as your body’s tenants and collaborators. The giant folded area that lines the wall of your intestines is prime real estate for these microorganisms to take up residence. They love it there. It’s warm and cozy, humid, protected from the elements, and food falls from the skies. It is bacteria heaven.

Throughout our natural evolution, we have become friendly with a number of them. We give them lodging and food. They pay us back by handling a heavy workload.

Our gut is filled with hundreds of different species of good bacteria. In fact, there are more of them in a healthy gut than there are cells in the entire body.

These microorganisms perform many important functions. Though the good bacteria of the intestinal flora don’t share your DNA, they can—and should— be considered some of your own tissues, or even organs, given everything they do on your body’s behalf.

They are the first things other organisms encounter in the digestive tube, and they fight to protect their territory and prevent other organisms from taking hold. In this way, the intestinal flora helps the immune system fight invaders.

Digestion, B-vitamins and Detoxification

The intestinal flora does many other things as well. They digest part of our food for us. Certain nutrients, such as the B vitamins, have to be predigested by bacteria before the body can absorb them.

Bacteria in general have different digestive systems from ours and can do certain chemical tricks with food that our bodies can’t. Some of the digestive processes that the good bacteria perform are very useful to us. A healthy gut acts like a fermentation tank inside you.

The intestinal flora is also a key contributor in detoxification, ridding the body of 40 percent of the toxins in food. In this sense, they serve as a satellite liver.

Put another way, if the gut didn’t have the intestinal flora, the liver would have to work almost twice as hard.    

We are really just starting to fully understand what goes on in a healthy gut and, even more recently, how opportunistic micro-organisms in our gut—such as viruses, parasites, yeast, and pathogenic bacteria—or the lack of good bacteria, are associated with many more problems than we ever thought.

Yet our understanding of our micro-flora and the environment they live in is pretty basic and our understanding of how to repopulate the gut with good bacteria is even less complete. Nobody really knows what combination of species is the ideal one for an individual. What is unquestionable, however, is that they are beneficial.

How our intestinal flora is destroyed

Today our intestinal flora is constantly under attack. It is the first part of the gut that suffers the most from the unnatural conditions we are living in.

From C-sections, antibiotics, chlorinated water, chemicals and food preservatives, to opportunistic organisms like yeast fungus and parasites, our intestinal flora need all the support and help they can get. Knowing where the damage comes from is half the battle.


Let’s start with C-sections. While often absolutely necessary, today, too many women are induced. This leads to C-sections that would not have been necessary if the natural process of labor had been respected and allowed to proceed without disruption.

A baby in the womb is sterile, but when passing through the birth canal, it is exposed to bacteria, mouth first. These bacteria are supposed to colonize the gut, nature’s first vaccination of sorts. This does not happen during a C-Section.

I see a correlation between many of patients who are chronically ill and C-section births. Right from the beginning, their intestinal flora was not given the chance to flourish.


Antibiotics are the second problem the intestinal flora often face. While our culture is beginning to become aware of our over-prescribing of antibiotics, it is still often the case that children are given antibiotics for every kind of infection—throat, ear, sinus, etc.

In fact, because this antibiotic regime starts early, far too many of us have always lived with compromised intestinal flora and have never been truly healthy.

I see more and more of this in my practice every year. It is my experience that chronically ill people, who often present with an elusive diagnosis, have a long history of consuming antibiotics. The earlier they started, the more complicated their symptoms are later in their lives and the harder it is for doctors to find a diagnosis.

A single-course of antibiotics   

Health-related problems, however, often pop up regardless of the number of antibiotic courses taken during a lifetime. Some of my patients suffer greatly after a single course of antibiotics, even if the antibiotics were absolutely necessary.

Let me be clear here: I am not saying that we shouldn’t use antibiotics when needed. Antibiotics saved my life when I was drowning with double pneumonia.

But we currently use antibiotics excessively and irresponsibly. We are wiping the population of good bacteria from the face of the earth, and we may not be able to live healthy lives without them. The medical profession—myself included—needs to be more prudent and vigilant about prescribing antibiotics so promptly.

Chemicals in our food  

The chemicals found in our food is the most common way that we make trouble for our intestinal flora on a day-to-day basis. Some of the same antibiotics doctors prescribe to human patients are administered to livestock by the food industry.These antibiotics kill your good bacteria as well.

We also have to be aware of chemicals the food industry adds to any processed food that comes in a box, jar, bag, tube, or bottle. These chemicals are added to food during processing to kill any bacteria or funguses that would shorten a product’s shelf life.

The food industry calls them preservatives, but in essence they act as antibiotics.

Other chemicals, such as coloring agents, texture, odor, and flavor chemicals, also make it hard for good bacteria to thrive. How else would something edible last for years without decomposing?

Next time you shop the aisles of a supermarket, remember: the longer the shelf life of what you are eating, the shorter the lifespan of your intestinal flora.

Opportunistic organisms and parasites 

Opportunistic organisms are constantly traveling down the digestive tube. Despite their constant trips down there, they only take up residence when the good bacteria are not there to keep them out.

Once introduced, these dangerous new occupants compete with us for valuable nutrients. They gorge on and thrive on all the garbage food we consume. Parasites then attack our weakened cells and tissues, essentially eating them for lunch. Viruses can take over your cells’ DNA and make your own cells manufacture more viruses.

When this happens, it prevents the body from absorbing valuable nutrients, which the body needs to manufacture things such as hormones, neurotransmitters, and other cells that participate in the body’s molecular activities.

The consequences can be devastating. An unhealthy population of organisms in the gut is a condition known as dysbiosis. Several studies suggest that changes in the composition of gut bacteria are linked to such varied diseases as obesity, inflammatory bowel disease, asthma, mental disorders, and many others.

Chlorinated Water

Tap water and shower water are two places that can cause problems for our intestinal flora. The water we shower with is absorbed through the skin and ends up in our circulatory systems, just like the water we drink.

Most city-supplied water has some amount of chlorine, which was used upstream to prevent bacteria from growing. It makes for a bacteria-free shower, but contributes to bacterial genocide in the intestines.

Recent reports reveal that your shower and tap water may contain increasingly detectable levels of most of the popular prescription medications such as antidepressants, antibiotics, hormones, and immunosuppressants, all serious problems for the good bacteria in our gut.


One of the most fascinating areas of study is how stress affects the gut and the intestinal flora. Research is beginning to suggest that stress itself can cause significant changes to the diversity, composition and number of gut microorgansims.

During chronic stress, communities of bacteria become less diverse and have greater numbers of pathogenic bacteria.¹ When the pathogenic bacteria were removed, results indicated that the negative effects of stress on the immune system were avoided.

Stress has been linked to a variety of gut conditions such as food allergies, GERD, and IBS.² Stress has also been shown to slow bowel transit time, which encourages the growth of bad bacteria and plays a role in leaky gut and small intestinal bowel overgrowth, also known as SIBO.

5 ways to support your intestinal flora

I’ve given you the most common ways that our intestinal flora is damaged. Many of these ways, such as food chemicals, chlorinated water, and stress are within our control. With awareness and action, we can support our intestinal flora and lay the groundwork for feeling great.

1. Eat chemical-free whole foods and use chemical-free products. You have heard this before and we’ll repeat this until the cows come home: Look for whole foods free of preservatives, conservatives, and coloring agents. Use chemical-free makeup, body-care and cleaning products.

2. Take a multi-strain probiotic. The truth is we are still learning about which probiotics are the most useful and in what quantities. But we do know that probiotics support the intestinal flora. I recommend rotating your probiotics to include different strains and different amounts.

3. Get a shower and water filter. Keep chlorine and other chemicals from being absorbed and damaging your microflora by using a shower and drinking water filter. Use the water-filter buying guide from the Environmental Working Group to help you find a filter that’s a good fit for you.

4. Reduce stress. There are many strategies to help reduce stress. Find one that works for you and use it. Some of the easiest ways to do this are: don’t under-eat, refrain from over-exercising, eat after exercising and get plenty of sleep.

5. Do the Clean Gut Cleanse. We are all walking around with some degree of gut dysfunction. This is all-in-one 21-day program to give our gut the love it needs. I recommend doing some kind of gut repair program at least once a year.


Topics: Clean Life

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