Foundations of Integrative Health

Foundations of Integrative Healing Manual
Foundations of Integrative Healing Manual

Gut Biome


The term “microbiome” was first used over 30 years ago when we knew almost nothing about it. In the last decade, there has been a renaissance of scientific discovery illuminating the influence of the microbiome on essentially all aspects of health. In the last 5 years alone, there’s been an explosion in microbiome research, with over 12,900 papers published. 

The depth of the microbiome is hard to fathom. Keeping a balanced the gut biome is not a frivolous health optimization. By most estimates, human cells are outnumbered by bacterial cells by a factor of about 10 to 1. We carry 39 trillion microorganisms in the microbiome! Sixty percent of the weight of your stool is actually bacteria. We are actually more bacteria than we are human.

If you’ve heard some interesting things about the gut biome, it’s likely just the tip of the iceberg. The science is evolving very quickly, and as practitioners, we continually make adjustments based on what emerges. It takes an average of 17 years for scientific discoveries to be implemented into clinics, and most doctors (including integrative doctors) are still operating in the old paradigm. 

The gut biome is truly an ecosystem, interconnected to almost every aspect of our health. It’s just as much of an ecosystem as a rainforest. It thrives on diversity, balance, and harmony. In the rainforest, all plants, animals, and microbes serve an important role, even the rodents. It’s easy to villainize the rodents, but the truth is we need them too. 

The biome in your gut works to transform your food, allowing you to transform food into the vital nutrients you need. Everything you eat is processed by your microbiome; they eat what we eat. Every microbe eats different food and each food choice you make strengthens a specific group of microbes. If you stop eating a certain food, the microbes that require that food will starve and eventually become extinct. They procreate so rapidly, that the food you eat in a single day will drastically alter your entire biome ecosystem. Actually, every bite of food you take changes the ecosystem of your biome. The good news is, you control what you eat, therefore you control your biome. 

Even pharmaceuticals and nutritional supplements are processed by your microbiome. This explains why the same drug can have a healing effect in one person and a life-threatening effect in another. For example, the chemotherapy drug cyclophosphamide depends on the gut biome to activate it*. A study published in Science in 2013 showed the healthier the gut, the better the chance of fighting off cancer with this drug*.

The primary indicator of gut biome health is; diversity. Health, harmony, and balance always come back to diversity. In the rainforest, it’s the symbiotic relationships between plants, animals, and microbes that breed a thriving, ecosystem. It’s the same in the gut. The diversity of bacteria, fungi, and viruses within the gut maintains symbiotic relationships amongst themselves and human cells.

The Mysterious Properties of the Microbiome

There’s a vicious strain of bacteria found in the gut called Clostrdium difficile, or C. diff. It was first noticed in the early 2000s in hospitals when doctors notice something strange about it. C. diff only showed up in patients who were hospitalized and taking intense rounds of antibiotics. The antibiotics they were giving would essentially nuke the entire ecosystem, and what was left was C. diff. And the treatment for C. diff? More antibiotics!

Now, 20 years later, we understand that nuking the biome with antibiotics is extremely dangerous. Antibiotics decimate your gut biome, causing all sorts of health problems. It’s scary to think there are 269 million antibiotics prescribed in the United States every year. Just five days of the common antibiotic ciprofloxacin wipes out a third of your gut bacteria, and it’s very difficult for them to fully recover. Most species of biome recover within four weeks, but some are still absent after 6 months. In the antibiotics clarithromycin and metronidazole, the effects are still evident four years after treatment. And just four days of three broad-spectrum antibiotics can permanently destroy nine beneficial species of bacteria in the gut.* 

And it’s not just antibiotics. In one study, 24 percent of drugs tested altered gut bacteria. Proton pump inhibitors increase the risk of SIBO, and C. diff. Nonsteroidal anti-inflammatory drugs (NSAIDs) like ibuprofen and naproxen alter the gut microbiota, destroy the intestinal lining to create ulcers, and predispose IBS and colitis*. Oral contraceptives have been associated with developing both Crohn’s disease and ulcerative colitis. And this is all just the tip of the iceberg.

What is the most interesting part of C. Diff is what has emerged as its leading treatment. Surprisingly, C. diff can be effectively treated with fecal transplant. You read that right, poop transplants! Chinese Medicine practitioners documented the use of fecal transplants over fifteen hundred years ago. When doctors transfer the stool of a healthy person into someone with C. diff, the person is cured in a matter of 2-3 days! It’s an amazing, highly reproducible result. As a result of this, there’s a blossoming explosion of research and practice of fecal transplants for a number of health conditions. 

One study analyzed the diapers of three hundred toddlers at three months of age. They discovered that specific changes in the gut bacteria at three months predicted which children would develop asthma later in life. Next, they transferred the toddler’s poop into mice. What happened? Every single one of the mice developed inflamed lungs. Incredible!

Another interesting case of a fecal transplant patient happens when a woman received a transplant for C. diff. Her doctors couldn’t explain why in the 16 months following her procedure, she suddenly began to gain weight, going from 136 to 170 pounds. Nothing in her life changed, only the fecal transplant. 

All of this points to something incredible, that we are just beginning to understand. The gut biome is one, if not THE most important determinant of our overall health. It has extreme control over the way we process food and almost every one of our biological processes. The microbiome does so much more than just process our food. It is like an operating system, almost like a second, complimentary set of DNA. And we are just beginning to scratch the surface of its power. 

Actually, 99% of your DNA comes from microbes. Our human genomes are surprisingly similar. We share 99.9 percent of our genes with other humans. We share around 99% with chimps and 50% with a banana! However, our microbiomes may be as much as 90% different from one person to the next. This simple discovery has helped spark the reinvigoration of truly individualized medicine.

Another interesting study took two identical twins; but one was thin, and the other was obese. Keep in mind these twins have identical genes. Researchers performed a fecal transplant, again transferring the stool of each twin into mice. What happened? The rat got the obese twin’s stool became obese. The mouse that got the lean child’s stool stayed lean. Both mice were fed the exact same diet, nothing had changed other than their microbiome. 

This is such a crucial finding because it explains why, in many cases, some people do everything right: they eat all the right foods, they exercise, they reduce stress, but they still don’t see any results. Two people can be given the exact same foods, yet have a totally different biological reaction in their body, solely based on the quality of their microbiome. 

Dysbiosis: The Root Cause of Gut Issues.

The term dysbiosis describes the state of microbial imbalance within the guts which is present in vast portions of the population today. Emerging evidence suggests many health problems – not just digestive issues – have their roots in intestinal dysbiosis. Some of these health problems include cardiovascular disease, diabetes, autoimmunity, inflammatory bowel disease, irritable bowel syndrome, cancers, food intolerances, and more. 

While it is common to hear that we need more “good bugs” and fewer “bad bugs” in our guts, the truth is that there are very few true disease-forming bacteria in the world. Yes, they do exist, and yes, they can cause issues, though it’s the overall diversity and health of the ecosystem that matters more. In other words, the bad bugs are going to be there always, and what matters more than whether or not pathogens exist is the and diversity of microbes, and the immune systems function that regulate them. These factors determine the degree to which a pathogen can cause damage or symptoms, not necessarily their mere presence. 

Imagine two neighborhoods in different parts of a city. The first is a utopian society of loving, compassionate, and respectful citizens all looking out for one another. They come from all different backgrounds, religions, and beliefs though they share a common intention of living peaceful and healthy lives. They all share food and cook delicious meals together with food from a community garden. Children play together and have fun outside in nature without worry. Now let’s imagine a criminal gets into this community and steals a child’s bicycle. Bike theft doesn’t happen in such a place, so this really catches the community’s attention. This “outsider” is easily caught, confronted, and then calmly leaves town after returning the bicycle. 

The other neighborhood on the other side of town is a different story altogether. In this part of tow, people are driven to compete with one another to get by. They are possessive, argumentative, and take things from each other. Violence and theft are common in the community, and citizens do their best to harden and adapt to the unrest. When a criminal comes into this neighborhood, he gets away with all sorts of mischief. In fact, there are plenty of other criminals who have moved into town to call this place home.

The peaceful neighborhood is like a healthy and diverse microbiome. There are way more “good guys” than “bad guys,” so when any troublemaker makes their way into the community, very little damage is done before the immune system takes care of things to reestablish balance. The state of unrest in the other neighborhood is like dysbiosis. There are plenty of “good guys” around; in fact, there are more “good guys” than “bad guys.” However, those troublemakers who set up shop in the community create widespread chaos that completely disrupts all peace in the neighborhood. 


The Biome, Hormones, & Insulin

Our biome affects much more than just our weight. It also helps regulate our endocrine system, responsible for the production and regulation of all our body’s hormones. We now understand the gut is the largest endocrine secreting organ in the body. 

As one example, the biome secretes an enzyme B-glucuronidase, which activates estrogen all over the body. When it’s working right, estrogen levels are flowing in a balanced state throughout the body. When dysbiosis happens, it throws this delicate balance off, leading to brittler bones, higher cholesterol, skin flareups, hormonal diseases like PCOS, and decreased sex drive. 

Traditionally, we have thought of insulin response as a factor of genetics and diet. We’ve assumed that high glycemic foods like white bread, sugar, and white rice, will cause a similarly high insulin spike in everyone. Researchers have recently discovered foods have a very different blood sugar responses in different people, depending on their gut biome. We can now use participants’ microbiome profiles to predict which foods would cause sugar spikes.

This dispels the notion that there is “one ideal diet” for anyone. Every person will have a unique metabolic process to foods, which reflects the quality of their gut. It also explains why, mysteriously, it seems different foods feel different to us at different times. The way we metabolize food depends on the present state of our gut microbiome. We might eat a gluten-free muffin today, and have it wreak havoc on our digestion. 2 weeks later, with a healed microbiome, that same gluten-free muffin might have a totally different, less damaging effect. 

It’s these studies, and thousands of others causing doctors to re-write the fundamental rules of what we think we know about metabolism, hormone issues like type 2 diabetes, and weight loss. 


Mental Health & The Biome

Perhaps the most interesting aspect of biome research is in the relationship between the gut biome and our brain and mental health. This has totally revolutionized the way integrative doctors think about the treatment of mental health. 

The brain and the gut are in constant communication. We have over 500 million nerve endings in the gut, constantly sending communication signals up to the brain, creating a significant influence over the way we feel and respond to situations. This second set of neurons has become known as the “enteric nervous system” or second brain. The enteric nervous system has 5 times more nerves than the entire spinal cord!

Because scientists now know the gut creates hormones, the primary communication channel for the body, it’s not much of a surprise that it also is the primary source of the creation of neurotransmitters, like serotonin, dopamine, BAGA, and norepinephrine. Your gut produces more than 30 neurotransmitters in total, including 90% of serotonin and 50% of dopamine. Serotonin and dopamine are essentially your body’s “feel-good” hormones. If our gut biome is off, it can no longer create the vast majority of the hormones we need to simply feel good. 

If you’ve been to therapy, and have felt some relief, but have always felt a nagging sense of anxiety and or depression, this could certainly be the reason. We see it all the time; patients who’ve been going to therapy and taking anti-anxiety or depression meds for years or decades. We see many patients who have accepted this as an inevitability in their life. As they begin to address the real root cause of the condition; the gut biome, they begin to see regular improvements in their mood. It’s a slow process, it doesn’t happen overnight, but the transformation is real! This is why so many patients with IBS, Crohns, leaky gut, or SIBO also experience coexisting conditions of depression and anxiety. 

What Causes Dysbiosis?

So you might be wondering, what causes dysbiosis? Like so many things within the human body, the microbiome is complex. There are somewhere around 100 trillion bacteria in each human gut, and many more coexisting microorganisms, including archaea, fungi, and viruses. There are about 1000 different bacterial species that amount to those 100 trillion bacteria, though about 99% of them come from just 30-40 different species. This means that there are an additional one trillion bacteria made up of 900+ different bacterial strains. Much less is known about the archaea, fungi, and viruses that also add to our gut ecology.

There are a handful of things that can contribute to a dysbiotic state:

1 – Pharmaceutical Medications – Antibiotics are known for their ability to indiscriminately wipe out life, including the bacteria living within the gut. Even a single course of antibiotics can alter the microbiome for up to a year (or more in some cases). Other drugs, both prescription and over the counter, have direct effects on the microbiome, such as antacids, nonsteroidal anti-inflammatory drugs (NSAIDs), hormonal birth control, antihistamines, diabetes medications, antidepressants, anxiolytics, diseases modifying antirheumatic drugs (DMARDs), and likely many more. With more than half of our population taking at least one prescription drug, this alone can account for the epidemic of dysbiosis. 

2 – Toxin Exposure – Many environmental contaminants such as heavy metals, herbicides, pesticides, nanoparticles, and endocrine-disrupting chemicals (like BPA) can wreak havoc on a vulnerable microbiome. Most herbicides and pesticides are, in fact, antimicrobial compounds that kill bacteria in the soil and human gut, in addition to weeds and pests. The most widely used toxic herbicide is glyphosate, the active ingredient of Roundup, studied to have a whole host of systemic effects in the body, all due to its ability to create dysbiosis (glyphosate will be covered in more depth to come). Many herbicides and pesticides, including glyphosate, are water-soluble, meaning that they invariably make their way into the soil, food, air, and water around the globe. We can excrete these toxins when we nourish ourselves and maintain healthy detoxification pathways, though we must mitigate exposure by whatever means possible. The fat-soluble toxins like dioxins, benzenes, PCBs, and heavy metals bioaccumulate in the fat cells of animals, making even grass-fed beef and wild-caught salmon a source of potential exposure. These contaminants make their way into the human digestive tract to effect significant disruption to a normal microbial population. This makes it always safest to eat nutrient-dense foods that are naturally low on the food chain. 

3 – Chronic Stress – The physiologic stress response has direct effects on absolutely every organ system of the body. Within the digestive system, physiologic stress decreases the secretion of hydrochloric acid in the stomach, digestive enzymes from the pancreas, and bile from the gallbladder. This inhibits the degree to which we can properly break apart food and absorb the nutrition a meal has to offer. Meanwhile, peristaltic activity also halts as energy and blood flow are shunted away from the digestive tract. This all leads to undigested foodstuff sitting around in the gut to ferment and feed unwanted opportunistic bacteria and promote a dysbiotic environment.

4 – Inadequate Bacterial Acquisition – The microbiome is seeded during vaginal birth. In the U.S., about ⅓ of births are by cesarean section (C-section), a 500% increase in the last 40 years. C-section delivery, though life-saving when medically necessary, creates a baseline state of dysbiosis, a significant risk to many childhood (and adult) ailments. Breastfeeding is also an important means by which babies develop a healthy microbiome and immune system. Additionally, playing outside being exposed to microbes (“germs”) in nature plays a huge role in microbiome development and immunity programming. Studies also indicate that children who grow up with dogs tend to have a stronger, more diverse microbiome. 

5 – Plant deficiency – The most significant factor in perpetuating gut dysbiosis is the food we eat. While the pharmaceuticals, toxins, stress, and general bacterial deficiency can stack the cards against us, focusing on proper nutrient-dense whole plant foods ensures that we are continually feeding microbes to promote biodiversity within the gut. It is all the varieties of fiber in plant foods that feed unique beneficial bugs that promote a healthy population with the effect of crowding out the “bad guys.” The daily recommended intake of fiber of a measly 25 grams for women and 35 grams for men is only met by 5% of the American population! Since the beneficial bacteria of the microbiota cannot exist without an adequate fiber source, this means the 95% who fail to meet the low bar set by the FDA are very likely deficient in the microbes their guts and health depend upon.


Prebiotics, Probiotics, and Postbiotics

By now, we understand the importance of maintaining a diverse and balanced microbiome, but we haven’t yet discussed how exactly the symbiotic relationship between humans and microbes works. 

Prebiotics: It all starts with prebiotics, a new fancy term for plant fibers. Prebiotics are what the biome in your stomach eats. These plant fibers are like the food and fuel for the healthy gut bacteria which helps them flourish. Different strains of bacteria prefer different types of fiber. For example, there are potato-loving bacteria, broccoli-loving bacteria, banana-loving bacteria, etc. Therefore, it’s best to eat a wide variety of plant foods to accommodate all the various microbes in the gut. While prebiotic supplements (fiber supplements) are available for purchase and can be helpful in some situations, the best way to sustainably receive the widest variety of plant fibers is by eating whole plant foods!

Probiotics: Probiotics refer to the gut bacteria themselves. When we feed the microbiome soluble plant fiber (prebiotics), we promote healthy and flourishing gut bacteria (probiotics). We cultivate our own healthy populations of probiotics by providing them with the right fuel. While the majority of the focus so far has been put on probiotic supplements and fermented foods, it’s actually quite possible to create all the probiotics your gut needs just through a diverse diet of prebiotic plant fibers. When the fuel is in place, the right microbes will quickly follow.

While there is a time and place to receive the benefits of probiotic supplements and fermented foods, these products will never provide the gut with the diversity of microbes that we need for optimal gut health. These products only ever offer a few strains of bacteria to the gut. If we consume those same products day after day, we don’t allow the space for the other 300-500 hundred species to thrive. A 2018 study looked at the rate of microbial reconstitution after antibiotic use. The study showed that probiotic use after antibiotics actually delayed and caused incomplete reconstitution of the microbiome compared to those without probiotic treatment. Remember, when it comes to a healthy gut, diversity is key! The best way to foster the diversity of microbes is to eat a wide variety of whole plant foods!


Our favorite products to support microbial diversity:

Best All-Around Gut Support Product:

  • Ion Gut Support – (Creates a fertile environment in which healthy microbes can flourish and protects the gut lining from environmental toxins)


Probiotic Supplements:


Probiotic Foods:


Postbiotics: Postbiotics refer to the chemicals created by the bacteria in the gut. When the beneficial microbes in the gut digest the fiber we feed them, they create a number of beneficial nutrients, including short-chain fatty acids (SCFAs). These SCFAs have powerful anti-inflammatory and healing effects within the gastrointestinal tract and throughout the body. SCFAs like formate, acetate, propionate, butyrate, and valerate actually serve as a fuel source for the cells lining the colon to promote healthy regenerative potential. This could be one reason why SCFA compounds are protective against gastrointestinal cancers, particularly colon cancer. 

For each unique prebiotic fiber source, the body grows a unique strain of bacteria and in turn, receives a unique combination of postbiotic SCFAs. The SCFAs directly prevent the growth of opportunistic pathogens like e. Coli and salmonella, thereby contributing to the harmony of gut ecology. SCFAs also promote a healthy immune response while inhibiting excessive inflammatory pathways. The wide-spanning benefits that postbiotics offer to humans indicate the essential symbiotic relationship between humans and bacteria. Postbiotics can also be found in supplement form and can be helpful to those who are healing their guts. But what is better than supplementing with SCFAs is having a diverse, plant-centric diet where the microbiome creates all the SFCAs the body needs!

By now, you have likely picked up on the fact that the very best way to heal dysbiosis and support a healthy microbiome is to eat a diverse array of fiber! But can it really be that simple? Simple, yes, in theory anyway! Our work together is to get your biome right, which given all the things that can go wrong, is no small task. It does take time (often a year or longer), and there are other factors at play, which we will cover next.


Food Sensitivities:

Nothing is more frustrating than feeling like you’re doing everything right and seeing no results. If you’ve taken the steps above already– eliminate processed foods, practice proper eating rituals, and regularly consume bitters and other important taste profiles– and yet you’re still suffering from digestive issues, you’re likely dealing with some form of food sensitivity. If you have a history of a sensitive gut and several food intolerances, making the thought of eating more plants intimidating.

Food sensitivities are quite common and can be complex. Dysbiosis is one of the main causes of food sensitivities, and it can be possible to reverse the intolerance by slowly reintroducing that particular plant fiber back into your diet. However, other times food sensitivities are from genetic reasons, like is the case with celiacs. This is a top to discuss in-depth with your doctor, and an area where you can benefit significantly from testing. 

It can help to reduce or eliminate the consumption of that food for some time. However, permanent avoidance is not recommended (unless, of course, you have a true allergic response to that food). In general, sensitivity to a food means that we lack sufficient gut bugs (or enzymes) to properly break down and use the fiber from the food. For example, If we have just a few microbes who like to chow down on the prebiotic fuel from garbanzo beans, then a big garbanzo bean salad could be a little much for those guys to handle. However, slowly eating more garbanzo beans will help to increase the population of those specific beneficial bugs in the gut, thereby eliminating the symptoms one may have previously experienced. So, experiencing mild digestive symptoms from a whole plant food is an invitation to mindfully consume more, not less. That being said, it is always best to listen to one’s body. There is no rule that you must eat and enjoy garbanzo beans in order to be healthy!

Healing the Sensitive Gut: Ironically, those who need fiber the most tend to be the ones who struggle with fiber-rich whole plant foods, like legumes, whole grains, or green leafy vegetables. It’s actually quite common to experience a degree of gas, bloating, or indigestion when increasing fiber content in one’s diet. This is the natural effect of shifting the status of the microbiome. Those who do suffer from eating high-fiber plant foods should follow a few basic guidelines. While a little bit of gas is normal, you should not feel any burning, pain, or acidity in your diet. This is a sign of something going off.

1 – Take it slow – Don’t go from “low fiber” to “high fiber” overnight! The shift of the microbiome takes time. Sometimes it helps to eat just one spoonful of beans a day for a few days, before increasing to two, and then three, and so on. Remember to rotate food varieties to serve your expanding microbiome with different prebiotic fuel sources.

2 – Focus on quality – A lot of digestive issues are due to the dysbiosis caused by toxin exposure from herbicides, pesticides, or food additives/preservatives. Eat organic grains and legumes, and try soaking and pressure cooking legumes if canned beans cause digestive upset. Check out this sprouting guide which is a way to make all legumes, nuts and seeds more digestible.

3 – Practice your mealtime rituals – How you eat is just as important as what you eat. A huge amount of digestive issues come down to chronic physiological stress. Since the body only digests food when it is in a relaxed state, put into practice the following tips before, during, and after a meal:

  1. Remove stimuli, screens, and stressful thoughts or conversation
  2. Sit down, center yourself, take an exhale, and express gratitude
  3. Slow down, chew, and enjoy the food
  4. Put fork or spoon down between bites
  5. Don’t overeat

4 – Be mindful of water during meals– Excess water consumption right before, during, or after meals can potentially dilute hydrochloric acid and enzymes in the gut required for proper digestion. It’s ideal to drink 8 ounces of water about 20 minutes before your meal. If you are going to drink water during a meal, take very small sips of water occasionally in between bites. Avoid drinking too much 15 minutes before or after your meal, particularly if it’s ice water as ice water can tense the stomach and release digestive chemicals.

5 – Start with digestive bitters – Bitter herbs activate bitter receptors on the tongue to stimulate the digestive process. About 10 to 15 minutes before a meal, take a couple of drops of a bitters tincture or spray, or just chew on a bitter green leaf to promote the release of hydrochloric acid in the stomach and digestive enzymes from the pancreas.