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AFH Restoring the Gut Microbiome : Dysbiosis

The human microbiome is composed of all the microorganisms that have colonized the body, its composition differs according to how the surface is populated, such as the skin, mouth, nose, vagina, and gut. The microbiome is now considered a distinct and essential organ.  The complex and diverse gut microbiome is made up of more than 10 trillion bacteria.

The gut microbiome contains an estimated 500-1000 species and 100 trillion organisms, including bacteria, fungi, and viruses that encode 100-fold more unique genes than our own genome.

There are 5 main areas of discussion regarding the microbiome. To help you remember we’ll call them the 5 D’s.






Today, we’ll be introducing the gut microbiome, discuss dysbiosis, and give you an overview of what a gut restoration program looks like.

The microbiome, in its balanced state, involves a symbiotic relationship between luminal bacteria and our human cells.

These cells communicate and form long-lasting, interactive associations that play a vital role in preserving mucosal immune function, epithelial barrier integrity, motility, and nutrient absorption.

If there is a disruption in the resident organisms in the gut compared with a healthy individual, the condition is called dysbiosis. Dysbiosis is classified as a reduction in the diversity of microbes and or the loss of beneficial microbes which thereby allows for the expansion of potentially pathogenic or harmful microorganisms. The causes of dysbiosis can be attributed to stress, diet, hygiene, and the use of antibiotics. Dysbiosis has been associated with a range of different gastrointestinal (GI) and non-GI diseases including neurologic, metabolic, liver, inflammatory, and infectious diseases.


Restoration of the gut microbiome homeostasis is essential to rectifying dysbiosis. A program to remove certain foods that may cause sensitivity, unhealthy fermentation or change the gut pH is a first step.  Providing adequate digestive enzymes for digestion, repairing the mucosal lining with supplements and nutrients, re-inoculating the microbiome with the right probiotics, and rebalancing lifestyle stressors complete the process.

To get an evaluation of your microbiome, start the AFH gut microbiome restoration program, or benefit from other AFH health programs please email, visit, or call (925)736-9828.  


Take Care and Stay Healthy,


Jeffrey Mark, M.D.

Jeffrey Mark, M.D. Helping clients with compassionate and comprehensive medical care for over 25 years with 4 board certifications in functional medicine, gastroenterology, internal medicine, and anti-aging/ regenerative medicine . IFMCP, ABIM Gastroenterology, NPAS Internal Medicine, ABAARM.

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