How Your Microbiome Controls Your Health

How Your Microbiome Controls Your Health

The interconnectedness of your gut, brain, immune, and hormonal systems is impossible to unwind. The past few years has brought a scientific flurry of information about how crucial your microflora is to your genetic expression, immune system, body weight and composition, mental health, memory, and minimizing your risk for numerous diseases, from diabetes to cancer.

Researcher Jeroen Raes, featured in the TED Talk, discovered that you might even belong to one of a few “microflora types”—which are similar to blood types. Research into the human microbiome is in its infancy, and there is much we do not yet understand.

That said, there are some facts of which we are already certain. It is becoming increasingly clear that destroying your gut flora with pharmaceutical drugs, harsh environmental chemicals, and toxic foods is a primary factor in rising disease rates.

Recent research suggests intestinal inflammation may play a critical role in the development of certain cancers. Until we begin to appreciate this complex relationship, we will not be able to prevent or intervene effectively in many of the diseases that are devastating people’s lives today.

In order for true healing and meaningful prevention to occur, you must continuously send your body messages that it is safe, not under attack, and that it is well nourished, supported, and calm. This article will focus on exactly how you can send your body these messages and why caring for your personal microbiome is so critical to every aspect of your health.

How Can You Feel Lonely with 100 Trillion Constant Companions?

The idea that microorganisms are to be “divided and conquered” is now an outdated view of our world. We not only live with them and are surrounded by them, but we depend on them for our very existence. Pamela Weintraub skillfully describes the symbiosis between humans and microorganisms in her June 2013 article in Experience Life magazine.1

Your body is a complex ecosystem made up of more than 100 trillion microbes that must be properly balanced and cared for if you are to be healthy.

This system of bacteria, fungi, viruses, and protozoa living on your skin and in your mouth, nose, throat, lungs, gut, and urogenital tract, is referred to as the “human microbiome.” It varies from person to person based on factors such as diet, health history, geographic location, and even ancestry.

When your microbiome falls out of balance, you can become ill. Those organisms perform a multitude of functions in key biological systems, from supplying critical vitamins to fighting pathogens, modulating weight and metabolism.

This army of organisms also makes up 70 percent of your immune system, “talking” directly to your body’s natural killer T-cells so that they can tell apart your “friendlies” from dangerous invaders. Your microbiome also helps control how your genes express themselves. So by optimizing your native flora, you are actually controlling your genes.

Gut Instincts—Your Second Brain Talking

Your microbiome is closely intertwined with both of your brains—yes, you have TWO! In addition to the brain in your head, embedded in the wall of your gut is your enteric nervous system (ENS), which works both independently of and in conjunction with the brain in your head. According to New Scientist:2, 3

“The ENS is part of the autonomic nervous system, the network of peripheral nerves that control visceral functions. It is also the original nervous system, emerging in the first vertebrates over 500 million years ago and becoming more complex as vertebrates evolved—possibly even giving rise to the brain itself.”

Your ENS is thought to be largely responsible for your “gut instincts,” responding to environmental threats and sending information to your brain that affects your well-being.

I’m sure you’ve experienced various sensations in your gut that accompany strong emotions such as fear, excitement, and stress. Feeling “butterflies” in your stomach is actually the result of blood being diverted away from your gut to your muscles, as part of the fight or flight response.

These gut reactions happen outside of your conscious awareness because they are part of your autonomic nervous system, just like the beating of your heart. Your ENS contains 500 million neurons. Why so many? Because eating is fraught with danger:4

“Like the skin, the gut must stop potentially dangerous invaders, such as bacteria and viruses, from getting inside the body.

If a pathogen should cross the gut lining, immune cells in the gut wall secrete inflammatory substances including histamine, which are detected by neurons in the ENS. The gut brain then either triggers diarrhea or alerts the brain in the head, which may decide to initiate vomiting, or both.”

We now know that this communication between your “two brains” runs both ways and is the pathway for how foods affect your mood. For example, fatty foods make you feel good because fatty acids are detected by cell receptors in the lining of your gut, which then send warm and fuzzy nerve signals to your brain.

Knowing this, you can begin to understand how not only your physical health but also your mental health is deeply influenced by the health of your gut and the microbial zoo that lives there. Your gut microbes affect your overall brain function, from basic mood swings to the development of serious illnesses like autism, Alzheimer’s disease, and schizophrenia.

When It Comes to Inflammation, Your Microbiome Rules

Your gut is the starting point for inflammation—it’s actually the gatekeeper for your inflammatory response. According to Psychoneuroimmunologist Kelly Brogan, your gut’s microorganisms trigger the production of cytokines. Cytokines are involved in regulating your immune system’s response to inflammation and infection. Much like hormones, cytokines are signaling molecules that aid cell-to-cell communication, telling your cells where to go when your inflammatory response is initiated.

Most of the signals between your gut and your brain travel along your vagus nerve—about 90 percent of them.5 Vagus is Latin for “wandering,” aptly named as this long nerve travels from your skull down through your chest and abdomen, branching to multiple organs.6

Cytokine messengers produced in your gut cruise up to your brain along the “vagus nerve highway.” Once in your brain, the cytokines tell your microglia (the immune cells in your brain) to perform certain functions, such as producing neurochemicals. Some of these have negative effects on your mitochondria, which can impact energy production and apoptosis (cell death), as well as adversely impacting the very sensitive feedback system that controls your stress hormones, including cortisol.

So, this inflammatory response that started in your gut travels to your brain, which then builds on it and sends signals to the rest of your body in a complex feedback loop. It isn’t important that you understand all of the physiology here, but the take-away is that your gut flora’s influence is far from local! It significantly affects and controls the health of your entire body.

Your Gut Flora Is Perpetually Under Attack

Your gut bacteria—and therefore your physical and mental health—are continuously affected by your environment, and by your diet and lifestyle choices. If your microbiome is harmed and thrown out of balance (dysbiosis), all sorts of illnesses can result, both acute and chronic. Unfortunately, your fragile internal ecosystem is under nearly constant assault today. Some of the factors posing the gravest dangers to your microbiome are outlined in the following table.

Refined sugar, especially processed high fructose corn syrup (HFCS) Genetically engineered (GE) foods (extremely abundant in processed foods and beverages) Agricultural chemicals, such as herbicides and pesticides. Glyphosateappears to be among the worst
Conventionally-raised meats and other animal products; CAFO animals are routinely fed low-dose antibiotics and GE livestock feed Gluten Antibiotics (use only if absolutely necessary, and make sure to reseed your gut with fermented foods and/or a good probiotic supplement)
NSAIDs (Nonsteroidal anti-inflammatory drugs) damage cell membranes and disrupt energy production by mitochondria) Proton pump inhibitors(drugs that block the production of acid in your stomach, typically prescribed for GERD, such as Prilosec, Prevacid, and Nexium)
Chlorinated and/or fluoridated water Stress Pollution


Obesity, Cancer, Depression, and Others Linked to Dysbiosis

With increasing regularity, modern science is linking more and more illnesses to dysbiosis. I suspect that in time, we will find evidence that dysbiosis contributes to just about EVERY human disease—the implications for your health are that vast. The following is just a handful of examples:

  • Psychiatric Illness: The key to your mental health is in your gut. Probiotics (psychobiotics or “bacteria for your brain”) are being used to successfully treat depression, anxiety, and other psychiatric problems.8, 9
  • Type 2 Diabetes and Obesity: Scientists have found a specific pattern of intestinal microbes can increase your risk for type 2 diabetes. This pattern can serve as a biomarker for diabetes risk. Obese mice have a much higher proportion of Firmicutes bacteria, while thin mice have a much higher proportion of Bacteroidetes bacteria.10 Similarly, researchers have also found differences in bacterial strains between overweight and non-overweight people. A strain of beneficial bacteria called Lactobacillus rhamnosus appears helpful for weight loss in women.
  • Colorectal Cancer: Inflammation resulting from infection, injury, or other bodily insults changes your gut’s ecosystem, which can allow cancer-causing pathogens to invade and increase your risk for colorectal cancer.
  • Infant Immune Deficits: Breast-fed babies receive microbes from their mother’s milk, which allows early microbial colonization of their gut. This enhances the expression of genes involved in immunity. The end result is that breast-fed babies show enhanced resistance to pathogens.
  • Asthma and Sinusitis: Dysbiosis in the respiratory tract may be responsible for chronic rhinosinusitis (CRS) and asthma; with CRS, overgrowth of a single organism, Corynebacterium tuberculostearicum, is frequently the cause.

Out with the Bad…

The best way to optimize your gut flora is through your diet. A gut-healthy diet is one rich in whole, unprocessed, unsweetened foods, along with traditionally fermented or cultured foods. But before these powerful foods can work their magic in your body, you have to eliminate the damaging foods that get in their way.

A good place to start is by drastically reducing grains and sugar, and avoiding genetically engineered ingredients, processed foods, and pasteurized foods. Pasteurized foods can harm your good bacteria, and sugar promotes the growth of pathogenic yeast and other fungi (not to mention fueling cancer cells). Grains containing gluten are particularly damaging to your microflora and overall health.11, 12 This would be a good time for you to review the table above that lists foods, drugs and other agents that harm your beneficial microbes—so that you can avoid as many as possible.

And In with the Good!

Consuming naturally fermented foods is one of the best ways to optimize your microbiome. Not only are your gut bacteria important for preventing disease, but they also play a critical role in your body weight and composition. Fermented foods are also a key component of the GAPS protocol, a diet designed to heal and seal your gut. Scientific studies have revealed a positive-feedback loop between the foods you crave and the composition of your microbiome, which depends on those nutrients for survival. So, if you’re craving sugar and refined carbohydrates, you may actually be feeding a voracious army of Candida!

Once you’ve begun eliminating foods that damage your beneficial flora, start incorporating fermented foods such as sauerkraut, naturally fermented pickles, miso, tempeh, and fermented dairy made from raw, unpasteurized milk (yogurt, kefir, etc.). These probiotic-foods will help heal, repopulate, and “re-educate” your gut. An article in the Journal of Physiological Anthropology makes the case that properly controlled fermentation amplifies the specific nutrient and phytochemical content of foods, thereby improving brain health, both physical and mental. The authors write:13

“The consumption of fermented foods may be particularly relevant to the emerging research linking traditional dietary practices and positive mental health. The extent to which traditional dietary items may mitigate inflammation and oxidative stress may be controlled, at least to some degree, by microbiota.”

They go on to say that the microbes associated with fermented foods (for example, Lactobacillus and Bifidobacteria species) may also influence your brain health via direct and indirect pathways, which paves the way for new scientific investigations in the area of “nutritional psychiatry.”

Developing a healthy gut flora begins at birth. Childbirth and breastfeeding set the stage for what organisms are going to inhabit your baby’s body. Therefore, if you’re a mother-to-be, it’s important that you optimize your own microflora, as you will be passing it along to your child. During your baby’s first few months, he relies on your breast milk to help inform his immune system of what’s dangerous. This is the beginning of natural immunity, which is much more complex than vaccinologists would have you believe.

Fermenting Your Own Veggies Feeds Your Immune System

The good news is, fermented vegetables are easy to make in your own kitchen. They are also the most cost-effective way to get high-quality probiotics in your diet. If you watch my video, you will see just how simple it is to make delicious fermented veggies at home!

Your goal should be to consume one-quarter to one-half cup of fermented veggies with each meal, but you may need to work up to it. Consider starting with just a teaspoon or two a few times a day, and increase as tolerated. If that is too much (perhaps your body is severely compromised), you can even begin by drinking a teaspoon of the brine from the fermented veggies, which is rich in the same beneficial microbes.

You may also want to consider a high-potency probiotic supplement, but realize that there is no substitute for the real food.

Since your gut microbes are the frontline army of your immune system and responsible for keeping all of your systems in check, it is vitally important to take care of them. Everything from your daily moods to your risk for debilitating disease rests largely on the health and strength of your microbiome. If you take good care of your 100 trillion little companions, they will return the favor!


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