Medical Compass: How do we build a healthier gut?

Medical Compass: How do we build a healthier gut?

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              The microbiome may have an impact on susceptibility to autoimmune diseases

By David Dunaief, M.D.

Dr. David Dunaief

Every human carries in its body a microbiome, consisting of bacteria, viruses and single-cell eukaryotes. Our relationship to these organisms is complex, and much of it is still only loosely understood. What we do know, however, is that these trillions of microorganisms have key roles in our healthy functioning.

The microbiome is found throughout our bodies, including the skin, the eyes and the gut. Here, we’re going to focus on the gut, where the majority of our microbiome resides. The microbiome has been getting a lot of attention of late, because of its possible role in preventing and promoting diseases. Among these are obesity, diabetes, irritable bowel syndrome, autoimmune diseases, such as rheumatoid arthritis and Crohn’s, and infectious diseases, such as colitis.

The Human Microbiome Project

Like the Human Genome Project, which mapped our genes, the Human Microbiome Project, funded by the National Institutes of Health from 2007 to 2016, sought to map and sequence the composition and diversity of these gut organisms and to prompt future research. Already, there have been some enlightening preliminary studies.

What affects the microbiome?

Drugs, such as antibiotics, can wipe out microbial diversity, at least in the short term. Also, lifestyle modifications, such as diet, can have a positive or negative impact. Microbiome diversity also may be significantly different in distinct geographic locations throughout the world.

The microbiome and obesity

Many obese patients continually struggle to lose weight. Obese and overweight patients now outnumber malnourished individuals worldwide (1).

For a long time, the paradigm for weight loss had been to cut calories. However, extreme low-calorie diets were not having a long-term impact. It turns out that our guts, dominated by bacteria, may play important roles in obesity and weight loss, determining whether we gain or lose weight.

The results from a study involving human twins and mice are fascinating (2). In each pair of human twins, one was obese and the other was lean. Gut bacteria from obese twins was transplanted into thin mice. The result: the thin mice became obese. However, when the lean human twins’ gut bacteria were transplanted to thin mice, the mice remained thin.

By pairing sets of human twins, one obese and one thin in each set, with mice that were identical to each other and raised in a sterile setting, researchers limited the confounding effects of environment and genetics on weight.

The most intriguing part of the study compared the effects of diet and gut bacteria. When the mice who had received gut transplants from obese twins were provided gut bacteria from thin twins and given fruit- and vegetable-rich, low-fat diet tablets, they lost significant weight. Interestingly, they only lost weight when on a good diet. The authors believe this suggests that an effective diet may alter the microbiome of obese patients, helping them lose weight. These are exciting, but preliminary, results. It is not clear yet which bacteria may be contributing these effects.

This suggests that gut bacteria diversity may be a crucial piece of the weight-loss puzzle.

Rheumatoid arthritis

Rheumatoid arthritis (RA) is an autoimmune disease that can be disabling, with patients typically suffering from significant morning stiffness, joint soreness and joint breakdown. What if gut bacteria influenced RA risk? In a study, the gut bacteria in mice that were made susceptible to RA by deletion of certain genes (HLA-DR genes) were compared to those who were more resistant to developing RA (3). Researchers found that the RA-susceptible mice had a predominance of Clostridium bacteria and that those resistant to RA were dominated by bacteria such as bifidobacteria and Porphyromonadaceae species. The significance is that the bacteria in the RA-resistant mice are known for their anti-inflammatory effects.

Can you counteract antibiotics’ negative effects?

Many have gastrointestinal upset while taking antibiotics, because antibiotics don’t differentiate between good and bad bacteria when they go to work. 

One way to counteract these negative effects is to take a probiotic during and after your course of antibiotics. I recommend Renew Life’s 30-50 billion units once a day, two hours after an antibiotic dose and continuing once a day for 14 days after you have finished your prescription. If you really want to ratchet up the protection, you can take one dose of probiotics two hours after every antibiotic dose.

Although nobody can say what the ideal gut bacteria should consist of, we do know a few things that can help you. Diet and other lifestyle considerations, such as eating and sleeping patterns or their disruptions, seem to be important to the composition and diversity of gut bacteria (4). Studies have already demonstrated prebiotic effects of fiber and significant short-term changes to the microbiome when eating fruits, vegetables, and plant fiber. The research is continuing, but we’ve learned a lot already that may help us tackle obesity and autoimmune disorders.


(1) “The Evolution of Obesity”; Johns Hopkins University Press; 2009. (2) Science. 2013;341:1241214. (3) PLoS One. 2012;7:e36095. (4) Nutrients. 2019 Dec;11(12):2862.

Dr. David Dunaief is a speaker, author and local lifestyle medicine physician focusing on the integration of medicine, nutrition, fitness and stress management. For further information, visit or consult your personal physician.