Platter of varied foods

How To Feed Your Microbiome





Progressive Medical Center has often written about the microbiome’s importance to human health. In fact, we’ve been describing this fascinating feature of (primarily) the gut for the last two decades. The conventional medical world is finally beginning to catch up and accept the fact of its existence and even that it might impact your health far beyond the gut.


So what is the microbiome? 


The microbiome is a vast collection of commensurate bacteria and other life that lives in the gut and forms a complex ecosystem that works with our processes of digestion, absorption, and elimination to keep our guts in balance and working smoothly. This amazing ecosystem is a finely balanced web of life that has formed in symbiosis over the ages and has become integral to a healthy gut, and therefore healthy body. You inherit much of your microbiome from your Mother as you develop your own gut in the womb and natural birth further seeds you with beneficial bacteria that populate your gut, particularly your intestines. These bacteria are augmented by your environment, and especially by what foods you eat and whatever else goes into your body.


How does the microbiome work?


Your population of gut bacteria is composed of many varieties that all work together to keep your gut functioning smoothly. These bacteria help you break down foods into smaller pieces, help break apart foods into their constituent elements (fats, proteins, sugars, and various minerals and vitamins), help the body absorb these nutrients, and help eliminate waste products by stimulating the body to move them through the intestines to the bowels or by assisting to break down or convert substances that will end up in the liver. When the microbiome is functioning smoothly, your gut likely functions smoothly, with no pain, no constipation, no diarrhea, no cramping, and with optimal extraction of nutrients. You’ll usually feel good and think clearly, barring other extraneous conditions. Your whole body is likely to function better, as we’ll see.


How is the microbiome connected to the rest of the body?


Although the primary function of your microbiome is to help manage your gut, your gut helps regulate the rest of the body and things that go wrong in the gut can affect the rest of the body. Think about how you can feel sleepy after a full meal, or how you may not feel hungry if stressed. This is an indication about how blood flow can be triggered to shift between the brain or the stomach. More insidiously, damage to the lining of the gut can cause inflammation in the gut that can spread to other systems in the body, including the brain. When the lining of the gut is inflamed due to infection, food allergies, autoimmune diseases, accumulation of toxins, or by a diet that irritates the gut, or any other cause, it can cause the tight junctions that line the intestines to loosen and become permeable. We call this “leaky gut”. When this occurs, the lining of the gut becomes inflamed causing pain, cramping, and diarrhea, among other symptoms. It also risks that particles of food, bacteria, and other substances will enter the bloodstream. When this happens it is likely to cause inflammation in places far from the gut- other organs, including the brain, as well as systemic and possibly chronic inflammation throughout the body. Dr. Elisio Faisono from Italy first demonstrated that a mechanism that allows this to occur is the production of Zonulin as a result of the loosening of the tight junctions in the intestines. He demonstrated that Zonulin production triggered inflammation, often chronic, and his research has even posited that almost all autoimmune diseases may ultimately arise from this Zonulin catalyst. 


The connection of the gut to the brain has also been researched, most seminally by tracing synucleins in the gut and brain. These compounds have been posited as a cause of Parkinson’s, Alzheimer’s, and other chronic brain disorders. It’s been suggested that the origin of these synucleins in the brain stems from the presence of these compounds in the gut as well. Several experiments have been done to try and confirm this. It was noted that the spread of these compounds proceeded from the brain stem (at the base of the brain) slowly toward the frontal lobe. The brain stem is connected to the gut (and the lower body in general) by the vagus nerve. In experiments in mice, the vagus nerve was severed versus a control group where it was not. Synucleins were then introduced into the gut of all of the mice in the study. In the group of mice with intact vagus nerves, the synucleins were found in the brainstem, and over time spread throughout the brain. In the mice that had their vagus nerves severed, there was zero presence of synuclein in this group of mice. These experiments have been followed up by tracking human patients who also had the vagus nerve severed (sometimes done to treat severe heartburn/reflux). In the human patients that had their vagus nerve severed, there was zero presence of synucleins in the brain, even though they had been found in the gut, compared with patients with intact vagus nerves who had synucleins in both their guts and brains. These experiments demonstrate the direct gut-brain connection.


How can a microbiome gone wrong affect the gut and the rest of the body?


When your microbiome is healthy, your gut is well-regulated and most likely not inflamed. This is because you have a well-balanced and diverse mix of bacteria and other flora present in your gut. When your microbiome is disrupted, it means that your mix of gut flora changes. Beneficial flora can be killed off and replaced by bad bacteria that can harm your gut. This opportunistic bacteria can overwhelm the good flora and cause what we call “gut dysbiosis”. Think of the microbiome as an ecosystem (which it is)- any major disruptions to that ecosystem by toxins, by an imbalanced influx of nutrients, or by other means. In the gut, eating the wrong things, getting food poisoning, having food allergies, or taking antibiotics can wreak havoc on your microbiome. Study after study has shown that when this happens, the gut itself suffers. If your microbiome  remains disturbed, not only are you likely to have chronic gut problems, but you might very well have systemic inflammation that can cause everything from diabetes, to brain fog, to neuropathy, to heart conditions. In fact, recent research demonstrates the connection between the gut and the heart.  It turns out that independent mechanisms like trimethylamine N‐oxide may increase the risk of atherosclerosis, thereby increasing the risk for heart disease, heart attack, and stroke. “Trimethylamine N‐oxide (TMAO) is an amine oxide mainly derived from the oxidation of trimethylamine (TMA), the intermediate product of the microbial metabolic pathway (15). TMA can be primarily generated from dietary choline and L‐carnitine by intestinal bacteria and absorbed into hepatic portal circulating blood (25)” (sourced above). This means that this important link between TMAO and the heart is modulated by the microbiome. When the microbiome is damaged, the gut is more likely to produce TMAO, which is absorbed into the bloodstream, and increases (perhaps greatly) the risk of cardiac events. Not only that, the increase in TMAO also may trigger diabetes, chronic kidney disease, high cholesterol, and high blood pressure. When your microbiome is damaged, it can spell real trouble for many other systems in your body.


How can you keep your microbiome healthy? 


We’ve known for a long time that the microbiome responds to the foods you eat, to toxins, to food allergies, and to antibiotics. One dose of antibiotics can be like a bomb going off in your gut. A huge swathe is cut into the flora of your microbiome. Good and bad bacteria alike are devastated. The problem is that the bad bacteria outcompetes the good and repopulates the microbiome more completely. Repeated doses of antibiotics just worsen the problem.


Toxins have a similar effect.  A single toxic event can have the same effect as antibiotics. More common is chronic toxicity from environmental toxins (including molds), tobacco use, consistent drinking of alcohol, excessive and habitual caffeine use, and other common pollutants we might ingest. 


Food allergies can have a devastating effect on your microbiome and gut in general. We think of allergies as immediate reactions that cause hives or trouble breathing, but those are IgE reactions. Food allergies can often manifest as IgG reactions that manifest as a slow burn, taking up to three days to cause a reaction. That means you aren’t likely to identify the allergen because of the time that passes. Because of this, food allergies can have a long-term toll on your gut. When you don’t identify the allergen, it can erode your gut for years. This can cause leaky gut, and all that entails, and alter your microbiome for the worse. The only way to really tell if you have IgG food allergies is to take a comprehensive test for them.


How do you feed the microbiome?


Exercise and eating right can have a huge impact on your microbiome. Many studies have demonstrated how exercise can improve the microbiome. Diet is more nuanced. We know a few things for sure- processed foods, sugars, toxins, and excessive protein is bad for the microbiome. We also know some positives- eat lots of fiber, especially those from whole fruits and vegetables. Increasingly we are learning that a varied diet is key to the microbiome. It’s not enough to have that grapefruit and bowl of oatmeal every morning- you have to vary your diet considerably. On average, having more than thirty types of fruits, vegetables, and spices in a week is the key to variety, which leads to the most positive outcomes for your microbiome. Look at it like a new food pyramid- the top best supports the microbiome, and the bottom most harms it. At the top of microbiome success is regular exercise, plenty of fiber from vegetable and fruit sources that are varied from day to day, little to no processed foods, limited to no toxin intake (including alcohol), few simple sugars, moderate amounts of complex carbohydrates, and moderate protein intake. At the bottom of the pyramid is a low exercise, free consumption of sugars and carbs, low fiber intake, above recommended toxic intake, high protein consumption, and a monolithic diet that repeats every day or week. Meatloaf Monday? Taco Tuesday? Wings Wednesday? These ruts turn out to have an oversized impact on your microbiome. Vary your diet, eat lots of fiber, avoid excessive toxins and exercise. These simple diet changes may have a bigger impact on your health than anything else you could possibly do. Your microbiome will thank you, and you should feel remarkably better for it.