The joke in medicine is that our purpose in life as a human species is to carry around the vast amount of bacteria within our body. The composition of bacteria within our body impacts how we think, impacts the immune system, alters our susceptibility to triggering autoimmune diseases, implicated in causing mood disorders such as depression, facilitates metabolism and excretion of estrogens, implicated in triggering allergies that result in chronic asthma or eczema, can be a source for chronic inflammation that drives chronic diseases forward such as heart disease, and of course changes our susceptibility to digestive dysfunction and irritable bowel disease. Therefore, who we are and how we function as a being is a result of the bacteria that we carry around.


The gastrointestinal tract holds thousands of bacterial strains. What makes the gut healthy is having a large amount of microbial diversity. One concern with globalization and GMO foods is that they may be implicated in decreasing the microbial diversity in the gut. In GMO foods, the GMO genes may be cross reacting with our own microbial genome, ultimately affecting our microbial diversity. Decreased microbial diversity leads to increased immune dominance and/or increased susceptibility to harmful pathogens. A low variety of bacteria is pathogenic, meaning we need commensal bacteria and a wide array of bacteria in the gut. Over the past 50 years, the incidence of irritable bowel disease, allergies, and autoimmune diseases such as multiple sclerosis has increased, while the incidence of mumps, tuberculosis, and pathogen driven diseases has decreased. Yet this brings up the question of probiotics, are we over treating with probiotics and pushing the microbiome in the wrong direction? Are we overdoing probiotics like we overdid antibiotics? This question remains to be answered. Probiotics remain to be an effective treatment when indicated, but in a healthy gut how are they affecting the tolerance and balance of healthy microbial diversity?



The microbial diversity is first formed during infancy. It has been long known that a vaginal delivery delivers the microbiome of the mother to the infant. Breastfeeding continues to direct the development of the microbial ecology, directing the development of the immune system. Yet an overuse of antibiotics and a cultural push towards sterile environments changes the microbe ecology. 50% of all antibiotics are put into animal feel. Once ingested in food or the water supply, it can alter gut ecology.  All bacteria produce biofilms, a mucus like covering that protects them from the immune system. In a healthy gut, the microbial diversity creates a healthy biofilm that prevents pathogens from taking over the gut. But in dysbiosis (altered bacterial ecology), the biofilm concurrently changes and can lead to chronic inflammation. In what is labeled as leaky gut, the biofilm is thinning. In irritable bowel disease, the biofilm is disrupted. Stress also affects the biofilm composition. IgA, an antibody that is found lining the gut and any internal mucous membranes, is lowered during chronic stress and adrenal depletion. Because IgA stimulates biofilm production in the gut to create a healthy gastrointestinal barrier, treating stress and sympathetic nervous system dominance becomes an important factor to create healthy gut function.


Fortunately, nutrition plays a large role in regulating the microbial ecology in the gut. It has been shown that a diet high in fiber and complex carbohydrates, and low in fat and protein supports bacteroidetes microbial species and production of short chain patty that protect against inflammation in the gut. A diet high in fat, sugar, and protein promotes firmicutes microbial species that is seen to be dominant in allergies and irritable bowel disease. In obesity, the pattern is seen where firmicutes are dominant over bacteroidetes by a ratio of 4:1. Firmicutes are calorie extractors and promote fat storage. Where bacteroidetes are poor calorie extractors. Changing the diet can alter the bacterial ecology within a number of days.


How does the gut ecology change our moods and how we think?

95% of all serotonin in the body is in the gut, 3% is located in platelets (used for clotting), and only 2% is located in the brain. Almost every known neurotransmitter is found in the gut. So the next time that you have a gut reaction and think you should follow your gut, think about what is happening.

The take home message, a healthy gut mucosa is the best protection against autoimmune disease, cancer, and chronic inflammation. Diet, lifestyle, stress, and medical practices will alter the microbiome in favor or against a healthy microbial diversity. • 310-926-4415