The Many Ways Probiotics Help Us

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Bacteria have a reputation as a health threat. Indeed, many are quite dangerous. Then again, many are quite helpful and required for good health. Over the past ten years there has been more ongoing research into how important good bacteria are for us.

In 2008, a scientific study called The Human Microbiome Project undertook the task of studying the genomes of the microbes that live in humans. The project took advantage of the latest computer analytics and gene sequencing technology to begin cataloging the hundreds of bacterial strains living on and inside the human body.  As a result of this study, a great deal of research was begun on the function of GI bacteria, known as the gut microbiota.

As we now know, these gut microbes affect much more than digestion. Dysbiosis, or an imbalance in an individual’s gut microbiome, may also harm the heart, immune system, and mental health. As science continues to track how different bacteria strains affect the body, more doctors are starting to treat dysbiosis through probiotic foods and supplements that contain helpful bacteria, as well as prebiotic foods that feed the helpful bacteria in the intestines.

                                     Some Fascinating Numbers!

The size of the gut microbiota is staggering. There are 10 times the number of bacterial cells living in the human body as there are human cells, and 100 times the number of bacterial genes to sequence in a person’s microbiome than genes in a human genome. Most of these bacteria live in the GI tract, where the number averages around 100 trillion!

Thanks to The Human Microbiome Project, we now have a greatly expanded understanding of the role these GI bacteria play in human health. Additionally, it changed long-held beliefs about the influence the GI tract has on the rest of the body. We are truly living in a symbiotic relationship with the bacteria we carry in our gut.  These GI bacteria feed on the food we eat and, in turn, they protect and nourish the body.

                                   What Good Bacteria Do For Us

Our gut microbiome begins to develop at birth. Infants pick up bacteria from the birth canal, from surfaces we touch in the hospital, and even  from breast milk.  In the first few years of life, we continually acquire bacteria which will help us digest food and fight disease.  It is now known that 70 percent of our immune system is located in the GI tract.  GI bacteria also help break down plant materials during digestion and create short chain fatty acids that are crucial to the body’s metabolism. GI bacteria also help prevent inflammation, help the body rid itself of harmful toxins, help metabolize xenobiotics, and create some essential vitamins.

Diet, medication, hygiene, and stress level can all impact which bacteria thrive and which do not. Infections and exposure to antibiotics can have lasting effects on our GI bacteria.

When the balance of bacterial strains in our GI tract is altered, it is possible that the gut microbiome can become harmful to us. In this case, instead of symbiosis, dysbiosis occurs. In my practice, this is frequently discovered through specialized stool testing. Examples of diseases influenced by GI dysbiosis include inflammatory GI diseases, asthma, eczema, and allergies.

Research into dysbiosis has been greatly advanced by metabolomics. This is a screening for metabolites – the substances produced when GI bacteria metabolize food – and match that metabolic activity to the correct strain of responsible bacteria. This testing allows for better identification of the bacteria present in an individual’s GI tract.

Research into metabolomics of GI bacteria can also help to identify bacterial function. As an example, some bacteria eat, metabolize, and activate compounds that are essential for our everyday physiological function. We may eat food with histadine, glutamate, and dietary fiber which are then bioactivated by GI bacteria in a way that helps maintain gut integrity, thereby reducing the chance of leaky gut syndrome. Physicians are beginning to realize how critical gut integrity is for normal immune function and the prevention of systemic inflammation. In irritable bowel syndrome (IBS) for example, GI bacteria are dysregulated and this dysbiosis will often impact the brain.

If dysbiosis exists in the GI tract, the biofilm which is produced can greatly affect the immune system. A healthy colon with good GI integrity and secretory IGA levels will have minimal inflammation. However, an individual with dysbiosis will experience a breakdown in the healthy barrier between the stool and the colon, which can result in increased inflammation and leaky gut syndrome.

An individual with healthy GI bacteria in the colon will have enough good bacteria to outcompete, and often kill, the pathogenic invading bacteria.  This symbiotic relationship is quite delicate. Taking antibiotics, for example, may deplete these good GI bacteria and create an opportunity for the small number of pathogens our GI tract deals with daily to take hold and disrupt GI integrity….which leads to systemic inflammation.

When the GI tract becomes compromised through dysbiosis, our whole body may feel the effects. Research into the systemic damage caused by dysbiosis and the mechanisms behind it are ongoing.

As an example, experiments conducted by Dr. Martin Blaser at New York University found that administering antibiotics to animals increased their fat mass, but not their lean muscle mass. Meat producers have known this for years, and now ongoing research has proven this correlation.

So, just how could this lead to obesity in humans? Antibiotics can lead to dysbiosis, which leads to inflammation. Inflammation can reduce insulin resistance and cause fat cells to store more fat molecules. Inflammation also decreases GI hormones that are protective against obesity, and decreases butyrate production which is essential to normal GI function.

Gastrointestinal conditions associated with dysbiosis include gallstones, colorectal cancer, gastric cancer, IBS, IBD and recurrent C. difficile infections.  Other systemic conditions that may be linked to dysbiosis include anxiety and depression, lymphoma, arthritis, asthma, autism, multiple sclerosis, chronic fatigue, fatty liver disease and cardiovascular problems.

Exactly how dysbiosis contributes to these conditions may depend on an individual’s diet.  For example, the connection between dysbiosis and accelerated vascular disease is likely connected to a Western diet. A diet rich in grain-fed red meat will load the body with phosphatidyl choline and carnitine, which will then be metabolized to TMA, or trimethyl amine. The liver will then oxidize TMA to TMAO. This blocks the transport of cholesterol from the coronary arteries back to the liver. At this point, the cholesterol remains in the arteries, thereby accelerating atherosclerosis.

Many factors that influence GI bacteria are outside the control of the individual. We have little choice over whether we were born by cesarean, whether we badly need antibiotics, or which foods we ate as a toddler. However, many other factors that have been shown to affect dysbiosis can be altered by an individual.

Some medications seem to be risky for inducing dysbiosis. For example, about half of the patients with IBS have a condition called small bowel overgrowth and the first line of treatment for IBS among many physicians is rifaximin (Xifaxan). There is evidence that rifaximin is useful for some immune-related disorders, such as Crohn’s Disease, because it alters immunity. However, for non-immune related IBS, there is the risk that the medication could cause some permanent, unintended effects on GI bacteria.

The proportion of nutrients in an individual’s diet may also affect GI bacteria. As an example, a high protein diet may overproduce hydrogen sulfide, which is very toxic to our body because it can destroy the epithelium and contribute to leaky gut syndrome.  Very high protein diets may work well in the short term, but in the long term there are some dangerous after effects, including increased cancer risk. On the other hand, fiber in the diet will be broken down by GI bacteria and result in more short chain fatty acids that can protect against cancer. A diet high in saturated fat will induce primary bile acids, and those bile acids can be both cancer causing and contribute to dysbiosis. This dysbiosis can make our body more inclined towards obesity.

Drinking alcohol in excess is another cause of GI dysbiosis. Alcohol can alter gut permeability and cause endotoxemia, which is one of the leading causes of liver disease. Animal studies have shown that taking therapeutic doses of probiotics can alter the dysbiosis effects of alcohol.

                                       My Approach To Evaluation

In my practice, when GI dysbiosis is suspected I recommend a comprehensive stool analysis with parasitology. This has been very helpful in confirming whether a patient has normal amounts of beneficial bacteria or whether they have pathogenic bacteria. Through this testing, patients are also evaluated for parasites, candida overgrowth, leaky gut syndrome, digestive issues, IBS and IBD.

If a problem is found, proper probiotics can be recommended as a treatment to inhibit the growth of the bad bacteria, help the growth of good bacteria, and alter the immunity and inflammatory conditions of the patient…all at the same time. If a patient is found to have pathogenic bacteria or small bowel overgrowth, I often prescribe antimicrobial herbs.

In my experience, about 50-75 percent of patients who have been diagnosed with IBS are actually suffering from an undiagnosed issue such as food sensitivity, dysbiosis, parasites, candida overgrowth, stress or neurotransmitter imbalances.

                                   How To Heal The GI Microbiome

It is quite possible to change the bacterial make-up of the GI tract by choosing food that nourishes healthy strains of bacteria as well as supplementing with healthy strains of bacteria.

According to a 2011 paper published in the journal Science, changes in a person’s microbiome composition were detectable within 24 hours of starting a controlled diet.  Researchers in the experiment gave participants either a high fat/low fiber diet, or a low fat/high fiber diet. Within 24 hours, this diet change resulted in small changes in the voluteers’ gut microbiome nearly overnight. The study also found that long-term diet habits, and not short-term changes, were more strongly associated with change in the GI bacteria. Specific diets known to alter the microbiome include the GAPS diet, and the paleo and ketogenic diets.

As our knowledge of what probiotic supplements do continues to grow, so does their popularity.  Probiotics have been defined as microorganisms that convey a specific health benefit. They are usually identified by strain, such as lactobacillus acidophilus, and can be quite genetically different from each other.

In my practice, I often recommend specific combinations and amounts for a given condition. For example, a frequent need is to restore good bacterial colonies in the GI tract following an infection that required treatment with antibiotics.  For this, I use Diamond Nutritionals’ Ultra Probiotic Formula (225 billion bacteria/6 probiotic strains), one packet daily for 4 weeks. After 4 weeks, Diamond Nutritionals’ Probiotic Formula (22 billion bacteria/6 probiotic strains), one capsule daily, is started for healthy GI maintenance.  

For children, I use Diamond Nutritionals’ Children’s Probiotic Formula (5 billion bacteria/7 probiotic strains) for healthy GI maintenance.

Happy Child

Probiotics play an important role in modulating the immune system and inflammation in the body. Probiotics are also crucial to the production of the B complex vitamins and vitamin K. They help to detoxify heavy metals from the body, including arsenic, lead, and mercury. Probiotics can shorten the duration of colds and flu as well as assist in the digestion of lactose in dairy. Research shows that probiotic strains move in and out of the GI tract within a few weeks. Therefore, it is very important to eat probiotic foods regularly along with proper probiotic supplementation.

Probiotic-rich foods include yogurt/kefir, natto, miso, sauerkraut, kim chee, raw pickles, olives, fermented vegetables, buttermilk, raw whey, raw vinegars, and sourdough.

It is also important to consider eating prebiotic foods. Prebiotic foods are primarily the plants that feed probiotic bacteria in the GI tract. Prebiotics help keep the gut microflora system balanced and they discourage the growth of C. difficile and other pathogenic organisms.  Most prebiotic foods have a low glycemic index, so they also help regulate blood sugar levels. Prebiotics also help lower ammonia levels in those who have liver illnesses such as cirrhosis.

Prebiotic-rich foods include onions, garlic, leeks, bananas, fruit, soybeans, asparagus, sugar maple, peas, yogur/kefir, cottage cheese, legumes, eggplant, beets, and honey.

When these foods are eaten, some of the starches go undigested into the lower GI tract where they are taken up by probiotic bacteria. The prebiotic fibers create short chain fatty acids to make butyric acid. This is used to maintain and renew every cell in the colon.


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