The Effect of Physical Exercise on Our Gut Microbiome

The Effect of Physical Exercise on Our Gut Microbiome

A large body of scientific evidence supports the fact that physical exercise is good for cardiovascular and brain health. In particular, a previous study from Ireland comparing professional rugby players and sedentary healthy control subjects suggested that exercise increases short chain fatty acid production by gut microbes and thereby improves your gut health.1 However, as the Irish study did not control for the dietary differences between the two groups (professional athletes consuming more calories and a different diet), it was not clear if the observed microbiota effects were not simply diet-related.

Three recent studies, one performed in mice and two in healthy human subjects, demonstrate that endurance exercise does indeed have an effect on the community structure and function of the gut microbiome, which is independent of exercise-related dietary changes.

In one study,2 the investigators wanted to find out if high intensity endurance exercise altered the gut microbiota composition and metabolic activity, and if this effects was related to a change in intestinal permeability, or the leakiness of the gut. 73 soldiers were provided three rations of food per day with or without protein- or carbohydrate-based supplements during a 4-day cross-country ski-march. Intestinal permeability, blood, and stool samples were measured before and after the 4-day strenuous exercise. The leakiness of the gut increased by 60% and was associated with the activation of the immune system, measurable in the circulation. The observed exercised induced changes in gut microbial composition (increase in the less common taxa and decrease in the more abundant ones) and microbial function (metabolites) were associated with the increased leakiness.

In the other human study,3 investigators explored the impact of six weeks of endurance exercise on the composition and function of the gut microbiota in lean and obese adults with multiple-day dietary controls. 18 lean and 14 obese subjects, previously sedentary, participated in six weeks of supervised, endurance-based exercise training (3 days per week) that progressed from 30 to 60 minutes per day and from moderate to vigorous intensity. Subsequently, participants returned to a sedentary lifestyle activity for a period of six weeks. Fecal samples were collected before and after the six weeks of exercise, as well as after the sedentary washout period. The investigators found that the exercise-induced alterations of the gut microbiota diversity were dependent on the participant’s obesity status. Exercise increased fecal concentrations of short chain fatty acids in lean, but not obese, participants. Exercise-induced shifts in metabolic output of the microbiota paralleled changes in bacterial genes and microbial taxa capable of short chain fatty acid production. Interestingly, exercise-induced changes in the microbiota were largely reversed once exercise training ceased. The authors concluded that exercise training induces compositional and functional changes in the human gut microbiota which are dependent on obesity status, independent of diet, and contingent on the sustenance of exercise.

But how do the microbes know that their host (e.g. us) is exercising? Physical exercise activates the autonomic nervous system which sends signals to the gut, which can change peristalsis, regional transit, and secretion of fluid and mucus. All these changes alter the environment the microbes live in, and the microbes likely adjust to these changes. During a high intensity endurance exercise, these autonomic nervous system signals can increase the leakiness, reduce blood flow to the gut, and even directly affect gut microbial behavior.

What is the take home message from this growing evidence that physical exercise is associated with changes in the gut microbiome?

  • Regular moderate exercise has a beneficial effect on gut health (via increased production of short chain fatty acids), but unfortunately, this benefit is only seen in lean subjects, and the effect only lasted as long as people continued to exercise.
  • In contrast, too much strenuous exercise may not be good for your gut health, resulting in increased leakiness and immune system activation.


  1. Barton, W. et al. The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level. Gut, doi:10.1136/gutjnl-2016-313627 (2017).
  2. Karl, J. P. et al. Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiological stress. Am J Physiol Gastrointest Liver Physiol 312, G559-G571, doi:10.1152/ajpgi.00066.2017 (2017).
  3. Allen, J. M. et al. Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans. Med Sci Sports Exerc, doi:10.1249/MSS.0000000000001495 (2017).
Putting Your Mind Back into Food

Putting Your Mind Back into Food

As health-conscious consumers, we are constantly concerned about finding the healthiest foods in the market. We perform calorie counts of our meals and worry that we may not get enough protein, vitamins, calcium or other minerals. Millions of people with a syndrome called non-celiac gluten sensitivity spend a lot of their attention and money on gluten-free foods. A similar number of individuals suffering from symptoms of irritable bowel syndrome struggle to adhere to a diet called the Low FODMAP diet, which relieves their symptoms temporarily, yet is unhealthy and cannot be adhered to for long.

What many (not all!) of these individuals have in common is the fact that they are part of what has been called a National Eating Disorder. Just like the eating disorders anorexia nervosa and bulimia, anxiety is one of the major risk factors for this phenomenon. People are probably more worried about what they eat and shouldn’t eat today than at any other time in modern history. This anxiety often leads to the ritual of restricted diets and avoidance of certain food items, which come in ever new variations. Reflecting this situation are the labels on many processed foods, which seem to list more items that are NOT contained in a particular food (sugar free, gluten free, fat free, GMO free, etc.) than the healthy ingredients that should be in it (antioxidants, polyphenols, fiber). Furthermore, there are hundreds of dietary supplements, including different mixtures of probiotics, that promise wellness and miraculous improvement of all kinds of common symptoms.

Speaking with many of my patients, I have learned that sticking to some of these popular recommendations actually does make people feel better: less bloating, more energy, less brain fog, better concentration, better sleep, less worry about their food (at least temporarily). Interestingly, the same individuals still come to see me in my clinic for their persistent symptoms!

So here is the big question: do these symptom improvements have anything to with the postulated and heavily advertised beneficial effects on our digestive system, gut health, gut permeability, or gut microbes? Or, could there be some powerful underlying mechanism that most people either ignore or vehemently reject, like the powerful mechanisms of the mind called nocebo and placebo effects?

If you believe something will harm you, your brain will make predictions about a high likelihood of this harm to occur in the future. For example, if you are convinced that eating grains will make your headache and stomach symptoms worse, your mind will translate this belief into a prediction that these bad things will happen to you. On the other hand, if you believe something will be good for you, your brain will make a prediction about a high likelihood of you feeling better. In the first case, your worry and anxiety will go up, while in the second case, it will decrease or disappear, at least temporarily. These changes in your anxiety level are associated with corresponding changes in the activity of your gut and likely the behavior of your gut microbes. When you eat something while stressed out about its likely bad effects, it will be processed by your digestive system in a different way than when you are relaxed. The stress may even make your gut more permeable or “leaky.” This chronic anxiety will, in many people, cause symptoms of indigestion, fullness, bloating, and brain fog. On the other hand, if someone puts you on a strict diet or makes you avoid certain food items with the assurance of you feeling better, your anxiety will go down. Adhering to any ritual has this beneficial effect on one’s anxiety level. Then, the signals that your reassured mind sends to the gut will indeed be good for your gut functioning, the wellbeing of your gut microbes, and yourself.

While these powerful mechanisms of the mind almost certainly contribute to our current eating disorder epidemic, the increasing prevalence of true food allergies and sensitivities are likely to play a role as well. The problem is that with our current diagnostic tools, we have not been able to find an objective and biological measure that underlies these non-allergic food sensitivities. One such mechanism could be through the systems within our brain that regulate our sensitivity to multiple sensory stimuli. Individuals with a generalized hypersensitivity are sometimes even overly sensitive to the tiniest dose of medication entering their system. And there is no reason to believe why such individuals may not be sensitive to a variety of food items that interact with nerve endings in the gut which then signal to the brain.

So if you do feel better, does it matter if it is due to some advertised effect on your gut health, or if it is due to the power of your mind, the placebo effect? As a physician who takes advantage of the powerful placebo effect all the time, my answer is no, it doesn’t make a difference. However, regarding the nocebo effect, my recommendation is: spend less time worrying about the food and harmful components, read less about the hidden dangers of our food and indulge in the evidence-based dietary recommendations of a balanced, largely plant based (e.g. high fiber), low fat, low sugar diet for optimal health and prevention of disease. By working closely together, your mind and gut will figure out the rest!

Why the Mediterranean Diet Is Good for You

Why the Mediterranean Diet Is Good for You

If you want to stay healthy, slim, maintain your cognitive function, and live longer, there is no question that sticking to a traditional Mediterranean-type diet is the best investment you ever make. As diet fads come and go (including high fat, paleo, vegan, and ketogenic diets) there is a consistent flow of studies that confirm the health benefits of the Mediterranean diet in children, elderly, and patients with depression and early Alzheimer’s disease. High amounts of fruits (in particular berries), vegetables, grains, and nuts, low intake of poultry, meat, and dairy products, and regular consumption of olive oil and moderate amount of red wine transformed into Italian, Greek or Spanish recipes seem to be better for all aspects of your health than any other diet.

Even though we don’t know which of the individual dietary components are responsible for this remarkable salutogenic effect, it appears that consuming a combination of all its components is more beneficial than the individual items. Moreover, enjoying the meal with friends or family adds further health benefits. Seasonal variations in food items, small scale local productions of many foods, and a minimal amount of processed foods may play additional roles. Based on the emerging microbiome science, it seems highly plausible that the higher intake of dietary fiber and polyphenols (in olives, red wine, berries and nuts) lead to a healthier and more diverse gut microbiome which in turn reduces low grade immune activation in the gut and in distant organs.

So if you are healthy yet have risk factors for certain diseases, from metabolic syndrome to cardiovascular disease, Alzheimer’s disease or cancer, adhering to such a diet from early on in life, enjoying your meals in social settings, and exercising regularly are probably the best life insurance you can buy. If you are already affected by one of these disorders, adhering to such a diet has the potential of slowing disease progression or reducing disease severity.

Do All Diseases Start in the Soil?

Do All Diseases Start in the Soil?

According to recent science summarized in a blog post by Anne Bikle and David Montgomery published in Nautilus and discussed more extensively in their book “The Hidden Half of Nature,“ the answer is a definitive yes.

The authors describe not only the astonishing interconnectedness between what we feed our plants and how these plants feed us. But they also draw attention to the intriguing parallels between how the roots and microbes living in the soil (the root microbiome) communicate with each other, and the interaction between the gut microbiome and our intestinal tract. Just like their cousins in the gut, soil microbiota, including fungi produce thousands of bioactive molecules from the organic matter in the surrounding soil which they use to communicate with each other and with the plants. “Soils rich in organic matter are like human diets rich in fiber. Each is an important food source for the root and the gut microbiome respectively” say Bikle and Montgomery. For example, while the gut microbes metabolize the amino acid tryptophan into serotonin and other neuroactive substances, which regulate our sleep, appetite and overall wellbeing, the soil microbes metabolize the same amino acid into another compound called indole-3-acetic acid, which is a major growth hormone for the plant.

In order to provide a friendly environment for the surrounding microbes, the roots excrete a cocktail of molecules which attract and nourish the microbes. As a matter of fact, it has been estimated that up to 1/3 of the plant’s energy goes into the production of this microbe meal! The symbiotic relationship between plants and soil microbes results not only in abundance and diversity of the root microbiome, but also in the optimal supply of minerals and other metabolites back to the plant. These microbe derived substances are essential for the production of thousands of so called phytochemicals, which help the plant to defend against pests and diseases. For example, when a pathogenic microorganism infests the leaves of a plant, the plant sends a chemical message down to its roots, instructing them to send out signals to nearby microbes which colonize the roots and provide them with phytochemicals which are transported back up into the plant to repel the pathogen!

And here the story really gets interconnected!

Phytochemicals include antioxidants, anti inflammatory compounds and the so called polyphenols. The latter are a family of several thousand large molecules that give some fruits and vegetables their natural colors, but also exhibit health promoting properties: Polyphenols are contained in many food items, in particular in red grapes, many berries, almonds, flax seeds, coffee, tea, pomegranate juice and olives. Presumably these fruits, seeds and leaves contain high concentration of these molecules to protect them against diseases. The older and healthier the olive tree, the higher the concentration of these polyphenols are contained in the fruits as well as in the leaves of the tree! So what happens to the polyphenols we consume with a glass of red wine made from organically grown grapes or a teaspoon of olive oil from ancient trees? As these molecules are too large to be absorbed intact by our small intestine, they end up as food for our own gut microbes which are eager to gobble them up and metabolize them into smaller molecules which can then enter our own circulation and continue their health promoting functions: Protecting us against cancer, low grade inflammation, cardiovascular and neurodegenerative disease. These disease fighting molecules can be seen as the words of a universal biological language which are used by microbes in the soil and in our gut, by plants, and by our body.

Besides the fascinating story about interconnectedness of what goes on in the soil and how we grow our plants, there are important practical lessons for our health. Just as antibiotics and hygiene have played a major role in eliminating many infectious diseases and have contributed to the longevity of people living in developed countries, modern agriculture has been extremely successful in increasing the yield of macronutrients through intense use of fertilizers and pesticides. However, both achievements have come at a major and often ignored cost: While antibiotics, excessive hygiene (and the Western diet) have greatly reduced the diversity and abundance of our gut microbiota, increasing the risk for chronic disease, modern agriculture has resulted in beautifully looking plant based foods which are depleted in the thousands of health promoting and disease fighting molecules which are essential for our health.

So if you follow the prudent recommendation of eating a largely plant based diet, make sure you base it on fruits and vegetables that not only look good, but have been produced with considerations of a healthy soil microbiome. In addition, taking supplements of individual molecules provided by a multibillion dollar industry is no substitute for the healing power of thousands of different health promoting molecules generated by the invisible microorganisms living in the soil, that come with an organically grown plant based diet.


  1. Davis, D.R. Declining fruit and vegetable nutrient composition: What is the evidence? Horticultural Science 44, 15-19 (2009).
  2. van Dam, N.M. & Bouwmeester, H.J. Metabolomics in the rhizosphere: Tapping into belowground chemical communication. Trends in Plant Science 21, 256-265 (2016).
  3. McNear Jr., D.H. The rhizosphere—roots, soil and everything in between. Nature Education Knowledge 4(3):1 (2013).
  4. Idris, E.E., Iglesias, D.J., Talon, M., & Borriss, R. Tryptophan-dependent production of indole-3-acetic acid (IAA) affects level of plant growth promotion by Bacillus amyloliquefaciens FZB42. Molecular Plant-Microbe Interactions 20, 619–626 (2007).
  5. Rudrappa, T., Czymmek, K.J., Pare, P.W., & Bais, H.P. Root-secreted malic acid recruits beneficial soil bacteria. Plant Physiology 148, 1547-1556 (2008).
  6. Pandey, K.B. & Rizvi, S.I. Plant polyphenols as dietary antioxidants in human health and disease. Oxidative Medicine and Cellular Longevity 2, 270-278 (2009).
Caveats to the Ketogenic Diet

Caveats to the Ketogenic Diet

If you listen to the proponents of the ketogenic diet, everybody should be increasing their consumption of animal products, particularly red meat and animal fat, while restricting the intake of processed carbohydrates such as sugar. There is no question that the scientific literature supports the effectiveness of ketogenic diet in rapid weight loss and in the improvement of indicators of the metabolic syndrome. Similarly, it makes total sense to greatly reduce the excessive intake of processed carbohydrates that are part of the typical North American diet. Given the worldwide epidemic of obesity, metabolic syndrome, and the failure of most therapies to reverse this epidemic, the ketogenic diet seems like the perfect solution to this problem.

However, there are a few things you should consider before jumping on the bandwagon of this trend:

  1. There is an overwhelming evidence for the health benefits of largely plant-based diets (including the Mediterranean and traditional Asian diets). The latest microbiome research provides the explanation on why diets high in fiber are optimal for the health of your gut, your gut microbes, and for the prevention of cardiovascular disease, cancer, and even neurodegenerative diseases such as Alzheimer’s disease. These diets contain a small amount of lean meat, in particular coming from poultry and fish.
  2. There is overwhelming evidence from preclinical studies (1-4) that high-fat intake causes changes in the gut microbial composition and function, resulting in an increased leakiness of the gut and low grade inflammation of the gut and other organs, including the brain.
  3. Would every obese person in the world switch to a ketogenic diet, it would dramatically increase the population of cows. Why should we worry about such a development? The production of meat compared to plant-based food to generate the same amount of calories requires 15 times more water, and the global contribution of green house gases from animal agriculture already exceeds that from transportation. An increase in animal agriculture would not only lead to even greater production of greenhouse gases, but also to a further increase of water consumption at a time of growing global water shortages.

Take-Home Messages:

  1. The full ketogenic diet is probably the best and fastest way to loose weight, and to bring your metabolism under control if you suffer from metabolic syndrome and type II diabetes.
  2. However, the ketogenic diet is not our human default diet, and an increase in animal agriculture has detrimental longterm effect for the health of the planet.
  3. Staying away from refined carbohydrates and sugar, eating lots of fiber containing plants (not in the form of juices), moderate amounts of plant oils and fats (as contained in olive oil, avocados and nuts), and eating a lot of berries (in particular blue ones) is the best thing you can do for your own health, and for the health of the planet!


  1. Moreira AP et al. Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia. Br J Nutr. 2012 Sep;108(5):801-9. doi:10.1017/S0007114512001213. Epub 2012 Apr 16. Review. PubMed PMID: 22717075.
  2. Cani PD, Everard A. Talking microbes: When gut bacteria interact with diet and host organs. Mol Nutr Food Res. 2016 Jan;60(1):58-66. doi:10.1002/mnfr.201500406. Epub 2015 Aug 26. Review. PubMed PMID: 26178924; PubMed Central PMCID: PMC5014210.
  3. Guillemot-Legris O et al. High-fat diet feeding differentially affects the development of inflammation in the central nervous system. J Neuroinflammation. 2016 Aug 26;13(1):206. doi:10.1186/s12974-016-0666-8. PubMed PMID: 27566530; PubMed Central PMCID: PMC5002131.
  4. Cani PD. Gut microbiota – at the intersection of everything? Nat Rev Gastroenterol Hepatol. 2017 Jun;14(6):321-322. doi:10.1038/nrgastro.2017.54. Epub 2017 Apr 26. PubMed PMID: 28442782.