A slew of diseases have been associated with disruptions in the microbiome. Here’s a summary of the diseases that might actually be microbiome diseases, including irritable bowel syndrome (IBS), obesity, Parkinson’s disease, Clostridioides difficile (C diff) infections and inflammatory bowel disease (IBD).

Irritable Bowel Syndrome (IBS)

The poster child of microbiome diseases is IBS. We know for a fact that it’s a microbiome disease. The rest of the microbiome-associated diseases are at still in the research stage, while IBS is a true prototypical microbiome disease. Diagnostic tests based on the gut microbiome include breath testing to identify if you have IBS with diarrhea or IBS with constipation and a blood test of antibodies associated with IBS. IBS remains the only GI disease of the lining of the intestines that the FDA has approved a microbiome-modulating drug, the antibiotic rifaximin, for its treatment.


Microbiome experts are focusing on one of the world’s biggest epidemics — obesity. A look at the stool microbiome reveals some patterns in the ratio of bacteroidetes to firmicutes bacteria. An alteration in this ratio of these two bacteria seems to be a signal for obesity. In addition, researchers are examining a link between methane-producing microbes and obesity. Methane produced by microbes slows down gut transit. If your gut works more slowly, it has more time to absorb nutrients, so you have more time to digest and absorb more calories in each meal, leading to obesity.

Parkinson Disease

The microbes that populate the guts of Parkinson’s disease patients appear to differ from those of healthy people. It turns out that people with Parkinson’s disease often have digestive issues, such as constipation, long before the disease appears. This can occur two to 10 years prior to the appearance of Parkinson symptoms. So Parkinson’s disease may be considered a microbiome disease since the GI symptoms precede the neurological symptoms.

One theory holds that Parkinson’s disease is caused by an inflammatory reaction that alters the gut microbiome. A hallmark of Parkinson’s disease is the presence of Lewy bodies, an abnormal aggregation of proteins, in the brain. Researchers have found signs that Lewy bodies start to form in the colon before they show up in the brain. This provides another hint that something in the colon may trigger or initiate the development of Parkinson’s disease. One day doctors may be able to test for microbiome changes that put people at higher risk for Parkinson’s disease and restore a healthy microbiome through diet or some other means to delay or prevent the disease.

C diff

C diff has emerged as the leading cause of hospital-based infections in the United States. This spore-forming microbe is hard to eradicate and it frequently recurs after treatment. The risk factors of C diff infection — advanced age, immunosuppression, IBD and use of proton pump inhibitors — are all associated with changes in the composition of the gut microbiome.

Disturbances in the gut microbiome play a central role in C diff infections. The presence of C diff in the gut reduces microbiome diversity and changes specific microbial populations. If you disturb your microbiome, you are more likely to get a C diff infection.


IBD includes two main diseases, Crohn’s disease, and ulcerative colitis, both chronic relapsing conditions of the GI tract. Scientific evidence now supports the gut microbiome’s involvement in the development or propagation of IBD, and shows IBD leads to dramatic changes in the gut microbiome. It appears that gut inflammation is triggered or facilitated by the gut microbiome.

Some encouraging treatment results have emerged with optimized microbial concoctions that include beneficial strains of bacteria. Fecal transplantation is also one of the more promising microbiome-modulating IBD therapies, leading to improvement in remission rates of ulcerative colitis in small studies. Novel therapies to treat and prevent IBD will undoubtedly have to include modulation of the gut microbiome. This may include probiotics, prebiotics, antibiotics and fecal transplant in a personalized approach to identify those who will benefit the most.


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A must-have resource for anyone who suffers from IBS or SIBO, or who wants to better understand their microbiome, this book will help you live a gut-happy and gut-healthy life.