Diseases Rooted in Gut Microbiome and what to do about it:

The microorganisms in an environment (including the body or a part of the body) are called microbiome.

Scientists at the Weizmann Institute of Science redid the estimate and found that there are about 39 trillion bacterial cells in the body. They play a profoundly important role in human health and disease, from helping us absorb nutrients, to synthesizing vitamins and breaking down cellulose. We couldn’t survive without this microbial zoo inside us.

Shortly after birth, we are colonized with over 1000 species of gut bacteria. Influences such as vaginal delivery vs Cesarean section, breast-feeding vs bottle feeding, antibiotic use, industrialized processed food, heavy metal toxicity, stress levels, chronic illness and poor dietary choices, glyphosate in non-organic foods all have a profound impact on which bugs are selectively destroyed  leading to further imbalance and disease.

Bacteroidetes and Firmicutes are the main bacteria in our gut which aid metabolization of undigested food remnants.  Healthy bacteria in the gut promote the integrity of our gut lining, preventing “leaky gut” and thus prevent antigens and microbes from crossing over into the bloodstream.  They also contribute to our host defense by regulating innate immune system.

Diseases rooted in dysbiosis:


The human gut mucosa consists of epithelial cells, lamia propria, and the muscularis mucosae (see figure below for cross sectional view of gut lining), which is colonized by microbes. Furthermore, the intestinal microbiota stabilizes to a more adult-like profile around the age of one year, usually after the introduction of solid foods.

Human Gut mucosa (Dartmuth.edu)

There is a clear link between autoimmune diseases, like rheumatoid arthritis and the gut microbiome. In study done by Chana et el.(Development of the Human Infant Intestinal Microbiota”  ) joint inflammation did not develop in animal models who were germ-free.    Rheumatic arthritis patients had significantly lower levels of Bifidobacterial and Bacteroides fragilis. That in turn affects gut lining integrity causing leaky gut. Leaky gut happens when the tight junctions that hold your intestinal wall together become loose. In addition, increased LPS uptake through the gut lining is a one of the risk factor for development of many conditions through inflammation, like:

Autoimmune conditions

Thyroid disease Hashimoto’s


brain fog

Rash and eczema



food sensitivities and much more.

Steps to Repair a Leaky Gut

  • REMOVE:Remove the bad. The goal is to get rid of things that negatively affect the environment of the GI tract such as inflammatory food (including gluten, dairy, sugar, corn, soy, eggs, Peanuts, all processed food, fried foods, any grain in large amount)  and can lead to food sensitivities.
  • RESTORE:Restore the good. Add back in the essential ingredients for proper digestion and absorption that may have been depleted by diet, drugs (such as antacid medications) diseases, or aging.
  • REINOCULATE:Restoring beneficial bacteria to re-establish a healthy balance of good bacteria is critical. This may be accomplished by taking a probiotic supplement that contains beneficial bacteria such as bifidobacterial and lactobacillus species. Only taking probiotic is not enough. Along with finding the root cause we need to provide proper food for beneficial good bacteria to continue grow.
  • REPAIR:Providing the nutrients necessary to help the gut repair itself is essential. One of supplements is collagen which is rich in amino acids that quite literally, “seal the leaks” or perforations in your gut by healing damaged cells and building new tissue. Another one is L-glutamine, an amino acid that helps to rejuvenate the gut wall lining.
  • Rebalance: As stress and emotions affect us, they also affect gut microbiome.  A growing body of preclinical literature has demonstrated bidirectional signaling between the brain and the gut microbiome, involving multiple neurocrane and endocrine signaling mechanisms. While psychological and physical stressors can affect the composition and metabolic activity of the gut microbiota, experimental changes to the gut microbiome can affect emotional behavior and related brain systems. Gut Microbes and the Brain: Paradigm Shift in Neuroscience .
  • Bidirectional signaling between brain & gut microbiome

Journal of Neuroscience 12 November 2014, 34 (46) 15490-15496; DOI:

So rebalancing gut environment and our limbic system, emotions and stress reactions will benefit our health.

Repairing and rebalancing the gut (along with brain) is the first, crucial step to better health for anyone with an autoimmune disease.

Author: Rekha Shah

Dr Shah practices Functional & Integrative medicine. She is Board certified by American Board of Medical Specialists in Internal Medicine and Gastroenterology. She is also a Certified Functional Medicine Practitioner.

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