Gut Microbiome Dysbiosis: Symptoms, Causes, and Natural Strategies to Restore Balance

TL;DR

The gut microbiome influences digestion, immunity, metabolism, and brain function
Dysbiosis (imbalance) is linked to IBS, autoimmune disease, obesity, and depression
Diet is the foundation—supplements are secondary
A simple rotation of Saccharomyces boulardii and berberine can help rebalance gut flora
Improving digestion and healing the intestinal lining are essential for long-term results

Category 4: Microbial Issues in the GI/Dysbiosis

If this is one of your SymptomQuiz high scores, the information in this article may help you improve your Wellness Score. This is not treatment. It is a way to improve your Wellness Score over the next 30 days.

There are many ways to improve the microbiome. Presenting a complete list with the literature references may be a bit unwieldy. There are many different approaches and many different products. First, follow the Roadmap to Health diet. Supplementation should be secondary.

Quick cookbook: Follow the Roadmap to Health diet. Give 1 capsule of Saccharomyces boulardii, 2x/day for 2 weeks. For the following two weeks, stop taking the Saccharomyces and take 2 capsules of Berberine for 3x/day. Repeat this pattern for 60 days (this is the exception to our 30-day program).

Why the Microbiome Matters for Overall Health

Chemical byproducts from intestinal bacteria have a powerful effect on health. Plus, over 70% of the immune system is associated with the GI tract. A high score in this category means that balancing the bowel ecology may be a good strategy to improve your Wellness Score.

If you have dysbiosis, you can follow the program for more than 60 days. An improved diet and improving the health of the intestinal lining will create a more desirable environment for good bowel flora. The improvements in health can become permanent.

Other Antimicrobial Substances

There are a lot of natural substances that will kill undesirable flora. These include emulsified oregano oil, olive leaf extract, garlic, artemisia, black walnut hulls, cloves, caprylic acid, and many others. There is a learning curve if you need to kill a parasite, for example. Some of these substances will kill normal flora as well. The quick cookbook approach will help most people; just realize that some people will need a more sophisticated approach. Get professional help.

What Is the Microbiome?

The intestines are an ecosystem. You have between 3-6 pounds of bacteria (called bowel flora) in your colon. There are more bacterial cells in the colon than there are cells in your entire body (bacteria cells are much smaller than your other cells). When describing this system, the word “microbiome” is frequently used.

Bacteria are like little chemical factories. Good flora produce vitamins, heal the intestinal lining, break down toxins, and suppress bad flora. Bad flora produce toxins, irritate the intestinal lining, and suppress good flora. There is a connection between bowel flora and allergy. A group of scientists measured the composition of microbes in the stool of infants from Estonia and Sweden. They found that children who developed allergies by the time they turned 2 years of age had different amounts of certain bacteria in their guts than those without allergies [1].

It is fairly obvious that GI symptoms would be caused by bowel flora imbalance. Studies have shown this to be true [2-4]. Addressing the microbiome can also be helpful in liver disease [5].

The Microbiome and Chronic Disease

Bacterial byproducts are linked to toxicity, nutrient status, the immune system, and general biochemistry. The makeup of the bowel flora can affect organs and systems beyond the GI tract. Also, the GI symptoms may not be severe or obvious in people with bowel flora imbalance or leaky gut.

The Microbiome Affects Type 2 Diabetes, Obesity, and Metabolic Syndrome

Several studies link insulin insensitivity and diabetes to the makeup of the bowel flora [6-9]. The makeup of the bowel flora is also linked to obesity [10,11]. Fat people generally have different bowel flora than skinny people.

Berberine and its benefit to insulin insensitivity and type 2 diabetes has been extensively studied. Berberine also kills certain microbes and affects the bowel flora. Studies have shown that this may be the reason berberine is beneficial to diabetics [12,13].

Cardiovascular Health and the Microbiome

There are a few studies that show cradiovascular benefit by addressing the microbiome [14]. High cholesterol has been linked to imbalance of the bowel flora [15,16].

The Microbiome Affects the Brain and Nervous System

Research has shown that gut bacteria can affect the brain [17]. Bowel flora may also be involved with neurodegenerative diseases, like Parkinson’s [18].

Depression: New research is showing a strong connection between bowel ecology and depression [19-22]. There is a lot of excitement about this; addressing the makeup of bowel flora and the accompanying inflammation may be the way to help severely depressed individuals.

Immunity and the Microbiome

Since so much of the immune system is associated with the GI tract, problems with bowel flora and leaky gut have a strong effect. The makeup of the microbiome has a profound effect on the immune system in general. There are also studies that show GI involvement with allergies and with autoimmune diseases.

General Immunity and the Microbiome

The makeup of the microbiome can affect your resistance to viral and bacterial infection. There are several studies that support this. Most of them show that probiotic supplementation (good flora) can support the immune system [23-25].

Allergies and the Microbiome

Both leaky gut and bowel flora imbalance are linked to allergies. Studies show that leaky gut is linked to allergy [26-30]. The connection to allergies and liver was mentioned in the Allergy category. Addressing the microbiome can also be helpful in liver disease [31-33].

One interesting way that allergy/microbiome connection has been tested is with fecal transplant. Fecal transplant, which is moving the bowel flora from one individual to another, is one way to see if bowel flora have an effect on allergies. There are a few studies where fecal transplant improved atopic dermatitis [34,35]. (this is just research; we are not suggesting it as a treatment). Something as simple as taking probiotics has benefited people with allergies [36].

One study even found bifidobacterial supplementation for mothers and newborns reduced the incidence of allergy [37]. There is other evidence that taking probiotics during pregnancy affects the microbiome of the newborn [38]. It may give us a way to prevent asthma. Infants with delayed development of the microbiome are prone to asthma, and that issue can be addressed with probiotic supplementation [39].

Autoimmune Disease and the Microbiome

Addressing the microbiome and leaky gut may be the best way to help people with autoimmune diseases. According to studies, there is a connection between the severity of the disease and the makeup of the microbiome and the integrity of the intestinal lining.

People with psoriasis and psoriatic arthritis have a distinct bowel flora makeup, according to studies [40,41]. In rheumatoid arthritis, changes in the microbiome can reduce symptoms [42,43]. Interestingly, the changes in the microbiome and the symptomatic improvements were brought about by changes in the diet.

There may be a link between inflammatory bowel disease and autoimmune disease [44]. Inflammatory bowel disease seems to have both immune and autoimmune components [45].

IBS, SIBO, and IBD

SIBO & IBS

It is appropriate to discuss SIBO (small intestine bacterial overgrowth) and IBS (irritable bowel syndrome) at the same time. For one thing, SIBO is likely to be responsible for most cases of IBS [46,47]. Even if that is not the case, bacteria and the makeup of the microbiome is strongly linked to irritable bowel syndrome [48-55]. Fecal transplant has been used to successfully treat IBS [56-58]. That, combined with the fact that many cases of IBS begin as a gastrointestinal infection [59], indicate involvement of the microbiome with IBS.

IBD (Inflammatory Bowel Disease)

IBD includes Crohn’s disease and ulcerative colitis. There is much evidence that the microbiota plays a role in these diseases. Fecal transplant has consistently gotten ulcerative colitis patients to go into remission [60-62]. (There are many more studies, just a few are listed here). One study even identified problem bacteria [61].

Fecal transplant in patients with Crohn’s disease has also been successful in some studies. Success is less pronounced than it is for ulcerative colitis. This makes sense because Crohn’s disease occurs mainly in the small intestine, and bacteria do not belong there. Specific bacteria have been identified and linked to symptoms of Crohn’s disease.

Saccharomyces Boulardii is a yeast that displaces other flora. It is used to get rid of undesirable bowel flora. Studies have shown it to be an effective treatment for inflammatory bowel disease [63,64]. Once you stop taking Saccharomyces Boulardii, it goes away.

The microbiome may play a role in Crohn’s disease. Enteral feeding will produce remission in 80-90% of patients. The authors of one study believe that the improvement is due to changes in the microbiome and a reduction in bacterial toxins [65]. They state, “A significant change occurs in the production of microbial metabolites after enteral feeding in both healthy volunteers and patients with CD [Crohn’s disease]. Many of those detected in CD are toxic and may feasibly lead to the immunological attack on the gut microbiota, which is characteristic of inflammatory bowel disease. The reduction in the production of such metabolites after enteral feeding may be the reason for its effectiveness in CD.”

The specific carbohydrate diet was developed by Dr. Sydney Haas in the 1940s. It was made popular by Elaine Gottschall in her book, Ending the Vicious Cycle. It presents a reasonable mechanism for at least some cases of Crohn’s disease and ulcerative colitis. Many practitioners have found that this approach helps with other digestive issues, like IBS, SIBO, GERD etc. The diet has been well-studied and found to be effective in many cases of inflammatory bowel disease as well as cases of IBS and SIBO [66-68].

The mechanism that leads to digestive problems that Gottschall suggests is as follows.

Incomplete digestion –> Growth of improper GI flora –>Irritation of the SI mucosa –>Decreased production of enzymes from the SI (disaccharidases) –>Incomplete digestion–>More improper flora, etc.

Poor digestion can cause inappropriate bowel flora to grow. Complex carbohydrates, in general, seem to have the potential to disrupt the microbiome. This may explain the popularity of ketogenic and Paleo diets.

What Disrupts the Microbiome?

Drug therapy, especially acid suppressing medications and antibiotics can alter it. Diet, especially refined foods, and chemical additives can disrupt it as well. There is some indication that gluten and dairy are often problematic. Eating food that is not well digested grows inappropriate flora, which is why the specific carbohydrate diet is so effective. Food that is not digested rots and disrupts the ecology of the intestines.

STRATEGIES TO IMPROVE THE MICROBIOME AND HEAL LEAKY GUT

Probiotics: Taking the right kind of bacteria has become a way to improve the intestinal ecology. As more research is being done, we are finding the importance of specific strains. Bifidobacterium, for example, is often beneficial to allergy patients. Increasing floral diversity has been one way to improve the health of IBD patients. This is another example of the use of probiotics for health.

The environment is more important: Many who take probiotic supplements find that they have to keep taking them. The good bacteria do not colonize because of poor living conditions. It is a lot like dropping polar bears off in the jungle or leaving tropical birds in Antarctica. They do not survive. You need to create an environment that is friendly to the new bacteria. Diet, chewing your food thoroughly, and addressing the initial phase of digestion need to be addressed if you want the desirable bowel flora to survive.

Diet and the Microbiome: What you eat and how you eat affects the content of the microbiome. Gluten, for example, has been shown to create problems with the microbiome in many patients (not just those with Celiac disease) [69]. Avoiding chemical additives, GMOs, and refined foods is vital.

Getting plenty of vegetables in the diet is important. Vegetables contain polyphenols (powerful antioxidants), and fiber, both of which help healthy flora to grow [70-72]. Studies have shown that healthy diets, like the Mediterranean diet, help balance the microbiome [73].

The Specific Carbohydrate Diet: Avoiding complex carbohydrates seems to be an effective way to help balance the microbiome. Avoid starches (like corn, rice, potatoes), and disaccharides (like table sugar, lactose [dairy]).

Healing Leaky Gut: There are supplements, like glycine, that can help heal the intestinal lining. Balancing the bowel flora is one way to help heal the intestinal lining. You can also make and drink bone broth. Making fresh green vegetable juice provides polyphenols, which will protect and heal the lining. Dr. George Goodheart advocated making a large, chopped salad twice each day. Many have found this to be effective because it nourishes healthy bacteria as well as heals. Making and drinking bone broth is also a good strategy.

The Initial Phase of Digestion: This starts with thoroughly chewing your food and mixing it with salivary amylase, helping to ensure that it is well digested.

Stomach HCl: In a study that looked at the effect HCl production had on the microbiome, researchers concluded, “in those cases where acidity is reduced, the gut is more likely to be colonized by pathogens.” [74]
Pancreatic Enzymes: Unlike hypochlorhydria, medicine recognizes the possibility of the pancreas not producing adequate enzymes for digestion.
Biliary Insufficiency: People with biliary stasis may experience pain over the eyes, pain when pressure is applied to the webbing between the right thumb and forefinger, and pain between the shoulder blades. Biliary stasis can progress to the formation of gallstones. People with this issue do not digest fats well.

Natural Antimicrobials for Dysbiosis

Killing microbes: Since the growth of inappropriate flora is the cause of SIBO and the likely cause of IBS, killing undesirable bacteria is a common approach. Natural substances, unlike antibiotic drugs, tend to not further disrupt the microbiome. Here are a few natural antimicrobials:

Saccharomyces Boulardii has been used to treat inflammatory bowel disease and other intestinal infections [75,76]. It is a microbe that will crowd out all other microbes in the GI tract and disappear when supplementation is discontinued.

Olive Leaf not only kills bacteria, but supports the immune system [77,78].

Berberine will not only kill undesirable bacteria, but it will also support normal bowel bacteria and reduce intestinal inflammation. It has also been used to treat colitis [79,80,81,90].

Emulsified Organic Oregano Oil is one of the most powerful natural substances that kill undesirable bacteria [82-85].