Friends In The Belly: how probiotics support health

I think it was Walt Whitman who said “I am large, I contain multitudes”. I’m pretty sure he wasn’t talking about probiotics, the beneficial bacteria that line our digestive tract, but he could have been. It has been estimated that bacteria in our G.I. tracts outnumber the cells that make up our bodies. Why are they there? What good, or harm, do they do us and does taking probiotic supplements or eating yogurt really do us any good?

Bacteria are everywhere. They have been found in the polar ice caps and in the deepest reaches of the ocean. They live in our bellies, on our skin, on our counter tops, in our toothbrushes, in the soil and pretty much anywhere else you can think of. If this scares you or grosses you out, please read on.

Since the invention of antibiotics we have been taught that bacteria are harmful and that we need to destroy them, avoid them and defend ourselves against them. The reality, however, is that throughout the history of our existence we have lived with them — and for the most part peaceably.

The number of bacterial species that are known to cause human disease is quite a small percentage of the total number of species in existence. Most types of bacteria could care less about us, some bacteria can harm us under certain circumstances (a topic for another blog) and some bacteria can be helpful to us. In fact, it is likely that if our bodies were completely sterilized we could not survive and it is certain that without beneficial bacteria health is impossible.

What I am talking about here is the concept of symbiosis; the idea that certain species benefit from or are dependent on other species for health and survival. We humans do not live in a vacuum. We have evolved in relationship to other species and cannot exist in the absence of those relationships. Disturbing — or cool, depending on your point of view.

Throughout the history of human existence, we have come into contact with thousands of bacterial species. Some of them have found our bodies to be desirable real estate and have set up shop on our skin and in our digestive, respiratory and urinary tracts. A small portion of those, simply by going about their usual business, have benefited us and thus helped us survive, thrive and carry on our species.

Our prehistoric ancestors ate many raw plants which were (and still are)  covered with potentially symbiotic bacteria. Our more recent ancestors discovered that fermented foods such as cheese, yogurt and sauerkraut not only helped to preserve food, but benefited health as well. In fact, most traditional cultures consume fermented foods as a part of their regular diet.

Our first contact with bacteria occurs at birth. Babies are inoculated with their mother’s vaginal flora as they pass through the birth canal and then via contact with her skin and through breast feeding. Not surprisingly, the two primary types of bacteria necessary for health of the digestive system, Lactobacillus and Bifidobacterium species,  comprise the dominant species of a healthy vaginal environment (Lactobacillus) and of the skin in the region of the breasts (Bifidobacterium). In fact, it has been shown that vaginal levels of Lactobacillus bacteria actually increase during the final months of pregnancy.

Infants born via cesarean section have low levels of Lactobacillus bacteria in their G.I. tracts and tend instead to be colonized with Staphylococcus and Enterococcus species. Similarly, infants who only receive bottle feeding tend to be low in Bifidobacterium species and are colonized instead with E. coli and Serratia species. None of these bacterial species are symbiotic and all of them are potentially pathogenic.

How Probiotics Benefit Us

Probiotic bacteria interact with the immune system in complex ways that support balanced and optimized function.

At birth, the immune system is imbalanced and not yet mature. As a result, during the first year of life, we are quite vulnerable to the development of allergies which, in addition to being troublesome in their own right, can predispose us towards the development of other health conditions such as asthma, eczema and hives. The presence of probiotic bacteria in the intestinal tract modulates immune function in a way that reduces this allergic predisposition. This can be seen in the fact that infants born by C-section have significantly higher rates of allergies than children born vaginally.

In addition, a healthy balance of probiotic bacteria has been shown to increase immune factors related to anti-cancer and anti-viral activity. In the elderly, regular intake of Lactobacillus acidophilus supports increased activity of antigen presenting cells and natural killer cells, both of which are specialized immune cells central to the identification and destruction of cancer cells.

When levels of probiotic bacteria such as Lactobacillus acidophilus and Bifidobacterium bifidum are deficient, other species of bacteria and yeasts such as E. coli, Clostridium difficile and Candida albicans tend to dominate the intestinal environment. This condition is referred to as dysbiosis.

Although many dysbiotic species can cause outright disease, often they do not but instead cause low levels of inflammation in the G.I. tract and produce waste products that can adversely effect health.

One of the common effects of this inflammation and irritation is a breakdown in the ability of the gut to distinguish between health-giving nutrients and potentially harmful toxins. As a result, incompletely digested food particles and toxins from dysbiotic bacteria and yeasts are absorbed and stimulate harmful immune reactions and other toxic effects. This condition is referred to as “leaky gut syndrome”.

It is well documented, for instance, that systemically absorbed bacterial toxins are a causative factor in rheumatoid arthritis and ankylosing spondylitis, two very serious autoimmune diseases. In addition, the absorption of incompletely digested milk proteins is associated with the development of type I diabetes in children. Other autoimmune diseases, such as ulcerative colitis and Crohn’s disease are strongly associated with dysbiosis and leaky gut syndrome as well.

Maintaining an abundance of health promoting bacteria in the gut can significantly decrease our chances of contracting many immune-related disorders and replenishment of probiotic bacteria can help to reverse dysbiosis and leaky gut if they exist (although there will probably be other factors that need addressing as well).

Non-Immune Effects of Dysbiosis

Dysbiosis can significantly effect the absorption of nutrients from our food, leading to certain nutritional deficiencies.  It can also alter the movement of food through the gut, leading to chronic diarrhea or constipation.

The toxins produced by dysbiotic bacteria can have a number of effects as well, potentially causing fatigue, bad breath and even altered mental function. Dysbiosis is strongly associated with autism, irritable bowel syndrome and to a lesser extent with migraine headaches and menstrual symptoms. It has even been recently discovered that dysbiotic bacteria within the esophagus produce toxins which abnormally relax the valve (sphincter) between the esophagus and the stomach, leading to esophageal reflux, or GERD.

Antibiotics and dysbiosis

There are many factors which can harm the balance of beneficial bacteria in our G.I. tracts (and other places within the body as well). Some of these have already been discussed: cesarean birth, lack of breast feeding, diets that lack adequate fresh, raw foods or high quality fermented foods.

One of the principle factors affecting probiotic balance is the use of antibiotics. Antibiotics, for those who may not know, are medications that kill bacteria. They make no distinction between the beneficial bacteria that we need for health and invasive organisms that are doing us harm. They are often used inappropriately, such as being prescribed for infections which show every evidence of being caused by a virus rather than a bacteria.

The primary bacterial species which should dominate our G.I. tracts, Acidophilus and Bifidobacterium, are highly sensitive to antibiotics and will often be affected much more strongly than many of the potentially problematic bacteria in our guts.  A healthy gut flora is all about balance. There may be hundreds of species of bacteria and tens of species of yeasts present in the gut. As long as beneficial species predominate, potentially harmful species can not reach sufficient numbers to cause us trouble.

Even a single course of antibiotics can greatly reduce the number of beneficial bacteria, while potentially harmful bacteria are harmed to a far lesser degree. Without the good guys dominating the real estate, dysbiotic bacteria can flourish and increase their numbers dramatically in a short period of time. If the change in balance is not corrected it can persist indefinitely and worsen over time.

As an example, every doctor knows that giving antibiotics, particularly to elderly patients, can result in an infection with a troublesome bug called Clostridium difficile. Clostridium is a species that is commonly found in the gut and in small amounts does no harm. If beneficial bacteria are wiped out with antibiotics Clostridium, which tends to be much more antibiotic resistant, can (and often does) take over and cause potentially life threatening diarrhea.

There are many reasons to avoid the use of antibiotics whenever possible, and this is certainly one of them. Having said that, infections can be dangerous and I am not suggesting that use of antibiotics is never appropriate. We recommend that you consult with a qualified health practitioner (preferably a Naturopathic Doctor) if you have any serious infectious illness. There are many natural alternatives to antibiotics and some of them are very effective against pathogenic bacteria without appreciably harming beneficial flora.

If you must take antibiotics, taking a good probiotic supplement during your course of antibiotics and for at least 30 to 60 days afterwards can greatly reduce any ill effects.

Supporting the good guys

Nature has provided many ways for us to populate ourselves with beneficial bacteria. Birth and breast feeding themselves accomplish this beautifully if we follow nature’s plan. Many traditional diets and life in close contact with nature also offer daily re-inoculations with beneficial bacteria.

Modern life frequently fails to provide the opportunities that we need to establish and maintain beneficial bacteria populations. For example, in many hospitals, the rate of C-section is about one out of every three births.

There is much about the way we currently eat that also limits our exposure to beneficial bacteria: diets without much produce, diets of mostly cooked foods, consumption of chemically treated crops (many agricultural chemicals are toxic to probiotic bacteria in the soil and on plants), the irradiation of foods and the pasteurization of fermented foods (pasteurization kills the bacteria that caused the fermentation).

For these reasons, it is important to consciously insure that we and our children are receiving adequate probiotic intake.

Perhaps the most elegant way to accomplish this is to adopt dietary habits that give us plenty of opportunities to establish and repopulate our beneficial flora. Diets of whole foods, low in sugars, with a moderate to abundant amounts of fresh, chemical free and non-irradiated produce. Perhaps most important is the regular inclusion of unpasteurized fermented foods rich in beneficial bacteria.

Traditional preparations of vegetable fermentations, such as sauerkraut, the Korean condiment kimchee and various traditional pickle dishes are rich in probiotic species, as long as they are allowed to ferment naturally and not heated or pasteurized.

Yogurt is another excellent source of probiotic bacteria if it is fermented naturally and not heated or pasteurized. Commercial yogurt products are pasteurized after fermentation which kills all of the beneficial bacteria. A small amount of culture is added after pasteurization (so the label can say “contains live cultures”), but they are present in relatively small amounts.

If made properly, a modest portion of homemade yogurt, say 1/2 cup, can have far more probiotic bacteria than any commercially available supplement. Yogurt takes a certain amount of work and care to make, but there are home yogurt makers that make the process nearly fool proof if you’re willing to put in the effort. It should be noted that many people have adverse reactions to dairy products (or at least cow dairy products). For these people alternative yogurts, such as goat’s milk, coconut milk or nut milk yogurts can work as well.

If making your own sauerkraut or yogurt is not feasible, probiotic supplements can also work very well, however, they are not a sure thing. We often run intestinal bacterial cultures to check for both pathogenic and beneficial bacteria in the G.I. tracts of our patients. Sometimes patients who have been taking probiotic supplements for a long time are still deficient in one or all of the principle beneficial bacteria needed for health.

One issue is that people often simply do not take enough to replenish their intestinal flora. In other cases the quality of the supplement itself may be sub par. Some probiotic strains used in supplements simply do not colonize the intestinal tract very well. As a result they are quickly washed out or do not survive. In other cases manufacturing and quality control practices may be poor and the probiotic organisms may be diminished or no longer alive by the time they put into capsules. They may also die or be greatly diminished in shipping and storage. Finally, some probiotic supplements have been found to be contaminated with microorganisms that should not be in them at all — an unsettling thought.

If you are going to take a probiotic supplement, I recommend doing your research. Make sure the supplement you are taking emphasizes strains of bacteria known to build G.I. and immune system health that are not capable of causing illness, such as the Lactobacillus and Bifidobacterium species. It is also important to make sure you are taking enough. It is difficult to put a number on this because there are so many strains and manufacturing processes in use. The formulas we use in our clinic range from about 20 billion organisms per day to about 100 billion organisms per day. Using a product that has a strong history of clinical success and taking it as directed is one way to insure you are getting enough.

Also, freedom from contamination and consistency from bottle to bottle is important. We only use products for which every batch is tested by an independent lab for potency and purity. This information is rarely listed on the bottle. A call to the manufacturer can get this question answered. Finally, more expensive does not necessarily mean better (thankfully). There are some very expensive probiotic supplements out there. Many of the best products are actually quite reasonably priced.

Here is a related article that might be of interest:

Lacto-Fermentation (traditional pickling of fruits and vegetables)


  1. Kelly says

    Thanks so much for this post! I have been wondering about probiotics for myself and my son’s skin problems. I love how your blog posts give lots of good information in terms anyone can understand!
    P.S. The link for the article is not working… I’ll try to google the article and see if I can find it.

    • Dr. Sandro says

      Thanks Kelly, I appreciate the feedback. My intention is exactly what you say: to give useful health information in a way that people can understand. I have repaired the link at the end of the blog if you haven’t been able to find the article through a search.

  2. Nancy Lee Harper says

    Very interesting blog. Thank you! However, the link was not downloadable for some reason.

  3. Matt Ellis says

    Thanks Dr. Sandro! I enjoyed this article because it caused me to reflect on the way our modern culture promotes anti-bacterial products as if all bacteria are bad. I think instead that there is a very delicate, beautiful balance needed in life. Now if you will excuse me, I need to go wash my hands. :)

  4. Hasnain Walji. Ph.D. says

    Thank you Dr Sandro. Great article and discussion on the choice of probiotic supplements. With your permission we would like to share this on our Facebook page.

  5. Dan Cohen says

    I think I’m one of those rare individuals who survives without any bacteria whatsoever. I have been told that they are repelled by my personality. Still, your post was extremely helpful (as always), and serves, among other purposes, as a caution against taking antibiotics when there are natural alternatives. Thanks, Dr. Sandro!!

  6. says

    Hi Dr. Sandro
    Thanks for Sharing! There is a lot of hype surrounding pro-biotic bacteria today. Supplements have been increasing in popularity because of the growing interest in natural health and wellness. This Article is a Great Discussion on pro-biotic. Thank you Dr. Sandro and your helpers for all the research and information. 😀

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