The Germs That Love Diet Soda

The Germs That Love Diet Soda

The Germs That Love Diet Soda is an excellent article in the New York Times by science writer Moises Velasquez-Manoff about the potential dangers associated with consuming processed foods.  While it cannot be emphasized enough that eating organic, fresh, fiber rich, low fat and low sugary foods is good for our health, caution is necessary when extrapolating from recent microbiome research performed largely in mice to human health. Some reflections:

  1. Findings obtained in experimental rodent models generally living in artificial living conditions and eating unnatural food are often not translatable to humans.  So unless confirmed in well controlled human studies, avoid premature conclusions from such studies for your own health.
  2. Not all “processed” food are the same.  Cooking, fermenting, baking food all involve the processing of raw materials to increase flavor or digestibility.  There is nothing wrong with eating your fermented milk products, cheese, pickled olives  or a good glass of wine.  On the other hand the term processed food with negative implications should be reserved for adding artificial sweeteners, high amounts of fructose, high amounts of vital gluten, chemical preservatives, food colors and other substances to food. While our gut microbes with their millions of genes are pretty good at breaking down such chemicals which they have never been exposed to in evolution, so called xenobiotics, evolution hasn’t foreseen the potentially harmful effects of these breakdown products, and the food safety testing by the FDA is based on acute toxicology essays, and not on the long-term effects such chemicals may have on our bodies.
  3. The problem with the modern western diet that it not only contains many of these bad purposefully added substances, but a whole range of other “hidden” chemicals associated with modern food production and environmental toxins.  This is particular the case with the constant stream of low dose antibiotics from meat and plant products (in addition to the overprescribed, and unnecessary antibiotics for presumed bacterial infections), and residues of pesticides (microbes are masters in metabolizing the active ingredient of glyphosate, the weed killer better known as round up into a potentially toxic chemical for our bodies.

Despite these caveats, the evolving microbiome science is confirming what people and cultures around the world have either intuitively practiced or consciously pursued for centuries:  the benefits of a largely plant based diet, limited intake of sugary and high fat foods, grown without the addition of chemicals, and consumed in modest amounts.

For a more in-depth exploration of topics related to the microbiome, read The Mind Gut Connection.

The “National Eating Disorder” Epidemic and What You Can Do About It

The “National Eating Disorder” Epidemic and What You Can Do About It

In this excellent summary by Mark Bittman and David L. Katz about what you need to know about healthy nutrition, the authors address some of the most commonly asked questions that I get from patients and audiences around the country. Some people may disagree with some of these recommendations, but overall, I cannot think of a better and more evidence-based way to answer these questions – all in one article.

I would like to emphasize two aspects related to the mind-gut connection and the gut microbiome that are important factors in the “national eating disorder” epidemic, also known as the Standard American Diet. One has to do with the psychology of eating, and the other one with the influence of signals produced by the gut microbiome, which can affect the structure and function of the brain. First, read these quotes from the article:

“Every wild species on the planet knows how to do it (e.g. proper eating); presumably ours did, too, before our oversized brains found new ways to complicate things. Now, we’re the only species that can be baffled about the “right” way to eat.”

“.. we know how we should eat, but that understanding is continually undermined by hyperbolic headlines, internet echo chambers, and predatory profiteers all too happy to peddle purposefully addictive junk food and nutrition-limiting fad diets”.

As I have discussed in detail in The Mind-Gut Connection, our belief systems about food, and what is good and bad for us, have a major influence on how we experience the most natural functions of our digestive system.

Worrying and having strong negative beliefs about food like “gluten is bad for me,” “I have sensitivities to many foods,” “carbs are toxic,” “there is nothing I can eat without ingesting large amounts of pesticides,” etc., ring the alarm bells in our brains every time we sit down for a meal, creating chronic food-related anxiety. The worried brain sends out nerve signals to the gut as if we are in imminent danger. These nerve signals can alter gut function, microbial metabolism and increase the sensitivity of your gut to food components. In other words, more often than not, it is not the food items that many people believe are the cause of their symptoms, but the increased sensitivity of the worried brain to normal signals from the gut. Elimination diets, other strict dietary recommendation or the daily ritual of consuming supplements suppress the food related anxiety, but don’t improve the dysfunctional brain-gut axis.

Internet echo chambers are a highly effective way to amplify the worries of patients only to channel them towards remedies (supplements, and special diets), which will generate large placebo effects (as well as large profits). On the other hand, having a positive attitude towards food, enjoying the hedonic aspects of a meal, and indulging in a piece of chocolate or a small desert on a special occasion with friend or family will stimulate the brain to send positive signals to the gut and optimizes a sense of well being. In the long-term, such a positive attitude towards food will contribute to the health of body and mind.

The second point to mention relates to the gut microbiome’s effect on the brain. The science about the effect of molecules produced by gut microbes on the brain, which are influenced to a large degree of what we eat, (mind-gut connection) is still in its infancies. HoweTver, there is considerable evidence from experimental studies in mice and epidemiological studies in humans that optimally “farming” our gut microbes by eating a largely plant-based diet and avoiding excessive (harmful) fats and refined sugars will have a beneficial effect on our brain, from the time before we are born all the way into old age.

“The Last Conversation You’ll Ever Need to Have About Eating Right” | Grub Street

Chronic Stress Is Bad for Your Gut Microbes

Chronic Stress Is Bad for Your Gut Microbes

Psychosocial stress has long been known to affect the gut as well as its microbial residents. More than 10 years of research in rodents, monkeys, and human subjects have shown that even mild stress can transiently reduce the abundance of certain types of microbes, including the lactobacilli in the stool of the animals.

In chronic stress models, this decrease in lactobacilli has been shown to interfere with the metabolism of tryptophan, an important amino acid and a precursor of serotonin. Serotonin is not only essential for your gut health, but it also plays an important role in mood, pain sensitivity, sleep and other vital functions. Instead of metabolizing tryptophan to the beneficial serotonin, the stress-induced decrease in lactobacilli tryptophan is metabolized into a molecule called kynurenine, which plays a role in the inflammatory and degenerative changes in the nervous system. Even prenatal stress in pregnant mice has been shown not only to influence the mothers gut microbes, but also the gut microbiome of the offspring.

How does stress influence gut microbial abundance and function? For one, stress via its effect on the autonomic nervous system can change gut contractions, transit, and secretion of mucus and fluids. More surprising, stress can also have more direct effects on microbial behavior, via changing the expression of so-called virulence genes leading to some microbes being more hostile toward their host. This direct stress effect is mediated by the stress hormone norepinephrine, which is not only released into the bloodstream during a stressful situation, but also leaks into the gut and binds to the specialized receptors on gut microbes.

The findings by Patrick et. al. that the similar gut microbial changes occur in both “winners and losers” of a conflict is somewhat surprising. However, it is possible that there were differences in the metabolites that these stressed microbes produced, which are the language that microbes use in order to communicate with the host.

And keep in mind that these studies were performed in rodents; extrapolating the results to human behaviors should always be done so with caution.


“Scientists Find Social Stress Changes Your Gut Bacteria” | Neuroscience News & Research

“Social Stress Leads To Changes In Gut Bacteria, Georgia State Study Finds” | Georgia State University News Hub

“Acute and repeated exposure to social stress reduces gut microbiota diversity in Syrian hamsters” | Behavioural Brain Research

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!