The Complete Functional Medicine Guide To Thriving Gut Health
Your gut’s influence over your health cannot be overstated. The trillions of microbes and colonies located in your microbiome are the manufacturers and managers of how you look, feel, and think. It makes up 70-80% (1) of your immune system, produces (2) a large amount of your “happy” neurotransmitter serotonin, and contains 10 times more bacterial cells than you have human cells!
You are, in truth, more bacteria than human. And researchers are quickly learning just how much it regulates all aspects of your health.
When your microbiome is healthy your health is likely to be quite good. However, many lifestyle behaviors, toxic exposures, and dietary choices can compromise gut health and lead to many downstream health issues.
For example, when your microbiome is weakened or damaged, it can “switch on” a number of potential disease processes throughout the body that may, on the surface of things, seem to have very little to do with your actual gastrointestinal system.
That is why it’s vital to educate yourself on the microbiome. By doing so you are taking back control of your health. Read on to learn more about what happens when your gut is unhealthy, what causes poor gut health, how to heal your gut, and more. This is your definitive guide to all things gut health.
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Health Problems That are Triggered by Poor Gut Health
Because your gut controls so many areas of your health, you don’t have to have typical gut symptoms to have gut problems. These are a few of the far-reaching health problems your gut has influence over.
1. Autoimmune conditions
As of now, there are around 100 recognized autoimmune conditions and about 40 other diseases that have an autoimmune component. Since your immune system mainly resides in your gut, it is no surprise that a damaged microbiome and leaky gut syndrome are preconditions for autoimmunity.
2. Mental health disorders
The gut-brain axis links your gut and brain, which is why, in the medical literature, your gut is actually referred to as “the second brain.” An unhealthy microbiome has been linked to mental health conditions such as anxiety and depression. (3)
3. Poor immune health
The opposite of autoimmunity (an overactive immune system), suppressed immunity can be gut-related, too. If you find yourself sick often, you’ll want to support and improve your microbiome health. Chronically low immune system health can be largely due to imbalances in the microbiome, especially due to an overgrowth of opportunistic bacteria, yeast, or fungus, or a parasite. (4)
4. Heart disease
Scientists recently discovered a possible link between the microbiome and cardiovascular disease. (5) Certain bacteria in the gut produce TMAO (trimethylamine-N-oxide), which is linked to a higher risk of heart attack and stroke. It is still unclear which microorganism produces these excessive levels of TMAO, but researchers are hoping that, in the future, manipulation of the microbiome species can help in the prevention and treatment of heart disease.
5. Type II diabetes
This chronic degenerative disease has recently been linked to microbiome disturbances. One study found that transplanting the microbiome of diabetic mice into healthy mice made the healthy mice diabetic as well! (6)
6. Skin conditions
Skin problems like acne, (7) psoriasis, (8) and eczema (9) all have microbiome and inflammatory-autoimmune components to them. For many, the missing link to healing their skin issues is healing their microbiome.
7. Weight gain and obesity
Weight loss resistance and obesity have been linked to an imbalance of bacteria in the microbiome. Studies in mice found that overweight mice had a higher number of the bacteria Firmicutes, while thin mice had a higher proportion of the Bacteroidetes bacteria. (10) In human cases, the beneficial bacteria called Lactobacillus rhamnosus was found to support weight loss in women. The microbiome factor may turn out to be a key component for many people seeking to lose weight their body has been holding on to for years.
8. Acid reflux and GERD
Millions of people suffer from acid reflux, or the more serious GERD, and these problems have been correlated with a microbiome dysfunction called SIBO, or small intestinal bacterial overgrowth.
A fascinating study out of the University of North Carolina suggests that damage and inflammation of the gut severely decreased the variety of bacterial species in the microbiome. (11) This loss of microbiome diversity allowed a pathogenic bacterial overgrowth of E. coli. Eighty percent of mice with E. coli infection then developed colorectal cancer. This suggests that there may be a cancer-microbiome connection, and I expect researchers may find more evidence of this connection.
10. Asthma and chronic sinus infections
Dysbiosis (imbalance) of microbiome bacteria and an overgrowth of Corynebacterium tuberculostearicum, were shown to be a frequent underlying culprit for asthma and chronic rhinosinusitis (CRS). (12)
11. Constipation and/or diarrhea
This is obvious, and is digestive so it doesn’t exactly go on this list, but I still feel like it’s important to mention that one study found that there was significantly lower amounts of the bacteria Prevotella and increased levels of Firmicutes in constipated patients. (13) Interestingly, the conventional probiotics that people take, Lactobacillus and Bifidobacteria, were not decreased in the microbiomes of the constipated patients, suggesting that supplementing with these may not be the solution to that issue.
What causes poor gut health?
Everyone’s microbiome configuration is unique, kind of like a fingerprint, but there are certain elements that can cause trouble for most of us. While every person is different, these are the top lifestyle and medical contributors to an unhealthy gut.
1. Poor diet
Like it or not, food can either fuel health or fuel disease. One very common way food fuels disease is by damaging the balance of the microbiome. Processed and sugary foods are the most obvious culprits because they feed the more pathogenic types of bacteria as well as Candida albicans, but underlying food sensitivities to even so-called healthy foods can also lead to gut-damaging inflammation. Grains are one common example – even gluten-free grains and whole grains contain amylose sugars that “bad” bacteria and fungi love to consume, and that contribute to inflammation. The best diet isn’t always obvious, and depends on your personal microbiome makeup, genetics, and lifestyle.
2. Gut-meddling medications
Medications may be necessary (although many people take them unnecessarily), but even the ones that help you can have side effects—have you educated yourself on what they are? One of the most common side effects of both prescription and over-the-counter (OTC) medications is compromised intestinal barrier. In other words, medications can make your gut more permeable, leading to “leaky gut syndrome.” A few of the most notorious culprits:
- Antibiotics can save lives, but frequent use and overuse of these drugs kill gut bacteria without distinguishing between good and bad. With more good guys gone, pathogenic bacteria and fungi can take over, especially if you are not making efforts to restore the balance through probiotic supplements or fermented foods.
- Non-steroidal anti-inflammatory medications like ibuprofen, naproxen, and aspirin, relieve pain by blocking the enzyme cyclo-oxygenase, but this also inhibits it from doing its important job of protecting your stomach from the corrosive effects of its acid. The result can be an increase in intestinal inflammation and consequent permeability. Research estimates that 65 percent of people who consistently use NSAIDs have intestinal inflammation and 30 percent have ulcers. If left unchecked, gut permeability can trigger an autoimmune response.
3. Chronic stress
We are all meant to handle stress now and then, but when stress becomes chronic and you experience consistently high levels of the primary stress hormone cortisol along with decreased oxygen delivery to the gut, damage can be the unfortunate result. Blame the gut-brain axis because the emotional turmoil of chronic stress can directly impact gut inflammation.
4. Alcohol overuse
A glass of wine every once in a while probably won’t do much to your gut in the grand scheme of things (unless you are already experiencing inflammation and severe gut dysfunction). However, consistent alcohol consumption in even the healthiest people can be an intestinal irritant, as well as suppressing the hormones that protect against inflammation and gut permeability.
The negative impact of gluten is well documented now, but in a few years, I believe research will confirm the similar, possibly even worse, negative impact of all grains, including those that are gluten-free. With their abundance of amylose sugars that cause inflammation, anti-nutrients such as lectins and phytates that bind to the intestines (14) and make nutrients inactive (15) in the body, and a low nutrient density trade-off for the calories that contain (especially when refined), grains can cause a wide array of damage to your gut and your general health.
6. Autoimmune conditions
Chronic inflammation can destroy the integrity of the gut lining and cause undigested food particles and the toxic by-products of digestion to leak out of the gut into areas where they are not meant to be. This can cause your body to mount an attack against these perceived “invaders,” increasing levels of pro-inflammatory cytokines that destroy your gut lining to even higher levels, in a vicious cycle of inflammation.
7. Hormone imbalances
Imbalances in the hormones estrogen, progesterone, testosterone, thyroid hormones, and cortisol have all been linked to sluggish healing of intestinal damage. This can lead to leaky gut syndrome, as the chronic inflammation in the gut lining damages it, causing it to become more permeable. This may explain why you may not be able to heal despite your best efforts—it’s those pesky hormones! Many people need to focus on balancing their hormones before they can successfully heal their guts.
8. Imbalanced blood sugar
When blood sugar skyrockets due to excessive carbohydrate intake or insulin resistance, compounds known as advanced glycation end products, or AGEs, go sky-high too, which can increase the permeability of your gut as well as inflict free radical damage on other tissues, accelerating aging.
9. Neurological problems
Your gut and brain are forever linked. They were formed from the same fetal tissue while you were growing in your mother’s womb. They continue this special bond throughout your life through a connection known as the gut-brain axis. Because of this bond, brain problems like depression, anxiety, autism, ADHD, stress, and dementia can lead to leaky gut syndrome and vice versa.
Types of gut problems
Gut problems don’t always look the same. Even if your symptoms look similar to another person, healing can only truly begin when you uncover what is happening underneath the surface.
1. Leaky gut syndrome
An intestinal lining damaged by years of unhealthy eating, food intolerances, stress, and toxins, can allow undigested food particles and bacterial endotoxins called lipopolysaccharides (LPS) to pass out of the digestive tract and into the rest of the body where they don’t belong. Sensing an “invader,” the body can react with systemic inflammation that can become chronic.
In functional medicine, leaky gut syndrome is considered a precondition for autoimmune diseases and many other health problems and requires intervention to heal the gut lining in order to stop the inappropriate immune reaction.
2. Bacterial imbalances
Your microbiome contains a delicate balance of bacterial and fungal species that live in symbiosis with you, but some of those species are pathogenic and can cause health problems if they are allowed to overgrow, crowding out more beneficial species – a condition called gut dysbiosis.
This can lead to health-damaging conditions like small intestinal bacterial overgrowth (SIBO) which in turn have been linked to a wide variety of health problems, from irritable bowel syndrome to autoimmune disease. For example, anxiety and depression have been linked to lower levels of Lactobacillus helveticus and Bifidobacterium longum, and weight gain was linked to higher amounts of Firmicutes.
Ironically, when someone with dysbiosis or SIBO starts to eat healthier, by increasing vegetable intake for example, it can cause an increase in gut symptoms like constipation and bloating. But it is the underlying microbiome issue, not the vegetables that is the root problem.
3. Histamine intolerance
Another issue I often discover in patients with leaky gut syndrome and bacterial overgrowths is histamine intolerance, which is a dysfunction or deficiency of the enzymes that break down histamines – the chemicals produced during an allergic reaction. In people with histamine intolerance, foods that naturally contain histamine or trigger the release of histamine in the body, become problematic. Without the enzymes to effectively get rid of excess histamine, the overflow can cause digestive problems like heartburn, acid reflux and stomach pain after eating, among other issues like anxiety, headaches, hives, and asthma.
4. Yeast overgrowth
We all have some yeast in our gut microbiome, but overgrowths of yeast such as Candida albicans can cause chronic low-grade inflammation and immune stress. People with an already weakened immune system or an autoimmune condition can find candida overgrowth to be a trigger for more health problems.
How do I know if my gut is healthy?
While you may suspect you have gut problems because of your symptoms, without running any labs, you won’t know for sure. These are the labs that I typically recommend to my patients, to determine if any of these gut problems are a factor in a particular health case:
1. Gut permeability labs
I always run tests for Zonulin and occluding antibodies. These two proteins control gut permeability, and the presence of antibodies can indicate damage to the tight junctions that keep your gut lining sealed. I also test for actomyosin antibodies, which can indicate destruction of the gut lining, and lipopolysaccharides (LPS) antibodies, which can also indicate leaky gut syndrome, if these antibodies are not contained within the digestive tract.
2. A comprehensive stool analysis
This test can uncover everything from the presence of parasites to bacterial imbalances to conditions like candida overgrowth or SIBO (small intestinal bacterial overgrowth) or SIFO (small intestinal fungal overgrowth)—any of which can negatively impact gut health.
How long does it take to heal your gut?
Let’s begin by imagining the surface area of your gastrointestinal tract. If you spread it all out, it would cover about the size of a tennis court! This internal “court” is covered in special cells called enterocytes that constantly regenerate so that you get an entirely new gut lining every two to three weeks. (16)
If you are healthy and don’t have any chronic conditions like autoimmunity or inflammation, and if you don’t have any food sensitivities, you could heal a not-so-perfect gut in as little as two weeks or as long as 12 weeks, studies suggest. (17) In fact, a study from Harvard, published in the medical journal Nature, found significant changes in gut bacteria actively happening just three days after a dietary change!
Unfortunately, most people who are trying to heal their guts do have other health issues that make healing happen more slowly. If you have chronic inflammation, Lyme disease, viral infections, blood sugar issues, adrenal fatigue, SIBO, an autoimmune condition, histamine intolerance, candida overgrowth, or leaky gut syndrome, it’s going to take longer to get you back on the right track. You are on what I call the autoimmune-inflammation spectrum, so you are going to have to come at your healing from multiple directions at once to get results.
What is the autoimmune-inflammation spectrum?
Autoimmune disease doesn’t just pop up one day out of nowhere. It begins with the slow burn of inflammation, which can simmer and spread for years before you get a diagnosis. This means if you have some inflammation, you don’t necessarily have a diagnosable autoimmune disease, but you could be headed in that direction. Did you know that to be diagnosed with an autoimmune disease, your immune system has to have already destroyed a significant amount of tissue (such as the brain, gut, or thyroid)? For example, there has to be a 90 percent destruction of the adrenal glands to be diagnosed with Addison’s disease (a disorder in which the adrenal glands don’t produce enough hormones) and massive destruction of small intestine tissue to be diagnosed with celiac disease (CD). (18)
This is why I look at this process as just that, a process, not a state. This process has, three stages:
1. Silent autoimmunity: You have positive antibody labs but you have no noticeable symptoms.
2. Autoimmune reactivity: You have positive antibody labs and symptoms.
3. Autoimmune disease: You have enough body destruction to be diagnosed with a specific condition.
Only around 10 percent of people with CD have obvious digestive symptoms. Instead, they end up struggling with other seemingly unrelated symptoms like skin problems, anxiety, or depression. Therefore only about 5 percent of celiacs ever get diagnosed which leaves close to 3 million Americans with celiac disease who have no idea that they have it and another 15-20 percent with gluten sensitivity. (19) It can take up to six months just to begin reducing inflammation and antibody levels that can result from eating a reactive food like gluten. (20)
For anyone struggling on this severe end of gut dysfunction with chronic inflammation, leaky gut syndrome, or an autoimmune condition, healing can take anywhere between 12 and 24 months before true, sustainable healing is achieved. While many people see improvements each month, long-term healing can only be accomplished after this one- to two-year period of implementing various natural healing tools.
How to heal your gut naturally
1. An elimination diet
An elimination diet is my gold standard for uncovering hidden food intolerances. In order to heal your gut, you need to stop eating foods that continue to damage your gut and increase inflammation, but you can’t know what foods are irritating to your individual gut until you remove all potential irritants for a certain amount of time and slowly reintroduce them one at a time, monitoring your body’s reaction. This will allow you to determine which foods your body loves and which foods your body hates. My mindbodygreen video class gives you step-by-step instructions on how to do an elimination diet the right way.
2. Rotating your food
Variety is the spice of life as well as the salve to an inflamed gut. Eating many types of foods will not only give you a wide variety of much-needed nutrients, and rotating these foods to avoid having any one food too often will help you heal and keep your immune system balanced. A good rule of thumb is to never have any one food more than once a day, or even better, no more often than every three days. For example, if you love leafy greens, have Romaine lettuce one day, kale the next day, and collard greens the day after that, before rotating back to Romaine lettuce.
3. Taking probiotics
Probiotic-rich fermented foods like sauerkraut, kefir, and kimchi will reinoculate your microbiome with good bacteria—especially important if you’ve recently had a round of antibiotics or been under a lot of stress. A probiotic supplement will also give your gut a much-needed boost of essential bacteria.
4. Drinking bone broth regularly
This superfood brims with collagen and minerals that can soothe and repair a damaged gut. Sip it alone as a warm drink or use it as the base for soups and in other recipes. I recommend making bone broth yourself at home in a slow cooker or pressure cooker (it’s easy), using bones from grass-fed cattle or organic chickens. If you don’t want to make it yourself, Bare Bones and Kettle & Fire are both great options.
L-glutamine is considered a conditionally essential amino acid because your body uses so much during times of intense physical stress. Essential amino acids must be obtained from diet whereas nonessential amino acids—an example being D-glutamine—are synthesized by your cells. L-glutamine is essential for maintaining the health and growth of enterocytes in your gut since it is the preferred fuel source of these cells. So if you want to win the battle against leaky gut syndrome, L-glutamine should be a go-to resource in your toolbox.
There are many studies that support L-glutamine’s ability to improve gut permeability. (21) One study, in particular, looked at a group of 107 children and how they responded to L-glutamine. Half of the children took L-glutamine and the other half took a placebo. In just 120 days the children who received the L-glutamine supplement had improved intestinal barrier function. (22)
It’s also evidenced that increased glutamine levels can protect against gut permeability. In a study of 20 patients with intestinal permeability and in need of parenteral nutrition (total intravenous feeding), those whose food was enriched with l-glutamine saw no deterioration in gut permeability or mucosal structure whereas the other group did. (23)
Research has even shown that L-glutamine can reduce inflammatory bowel disease symptoms including in people with ulcerative colitis! (24) After four weeks, patients receiving an L-glutamine supplement saw a reduction in symptoms as well as an increase in Bifidobacterium. Surprisingly enough, once patients stopped the use of glutamine their symptoms returned. That just goes to show the powerful connection between L-glutamine and your gut.
There are many food medicines that contain L-glutamine such as grass-fed beef, bone broth, and grass-fed dairy. For those who want a plant-based option, red cabbage is an abundant source. Eating cabbage in the form of sauerkraut will increase its gut-healing abilities since the fermentation provides your gut with probiotics that also help make L-glutamine more bioavailable.
If you decide to start supplementing, anywhere between 2 and 5 grams per day is typically a good dose for most people. You may also want to look for an l-glutamine powder rather than capsules since it can be easier for your gut to digest.
6. Trying intermittent fasting
By going extended periods of time without eating, you’re able to give your digestion a much-needed break. There are many ways to do this, such as fasting every night for at least 12 hours (many people do 16 hours) or fasting for one day every week.
7. Managing your stress
If you are feeding yourself a giant slice of stress every day, all the healthy food in the world isn’t going to help heal your gut. Chronic stress can suppress the immune system, decrease blood and oxygen flow to the intestines, and contribute to gut lining permeability. Making time to de-stress through pressure-relieving activities like tai chi, yoga, or meditation can make a huge difference in your stress levels and in turn, your gut health.
8. Coconut oil
How did we ever live without coconut oil? This versatile superfood is full of the healthful saturated fats that are integral to gut healing, as well as lauric, capric, and caprylic acids that have important antimicrobial, anti-fungal, and antiviral properties. This real food medicine gently cleanses your GI system but is also great externally to nourish your skin. Choose organic, extra virgin, cold pressed varieties for maximum benefit.
9. Eating more cooked foods
Raw foods are packed full of nutrients but they can also be difficult to digest. Cooked foods decrease the amount of work your digestive system needs to do to break down food because some of that has been done for you through the cooking process. Even easier to digest are pureed foods like smoothies and pureed soup. Going easy on your digestion can help reduce bloat and lead to a healthier gut. As you heal, you will be able to tolerate raw foods better.
10. Taking targeted natural supplements
Nobody wants to take a giant fistful of vitamins every day, but there are a handful of gut-healing supplements I often call upon to help my patients in digestive distress. These can help speed healing and make a big difference in symptoms:
- Colostrum: The lactoferrin in colostrum works as a prebiotic to feed good bacteria and fuel its growth. It also promotes cell growth in the intestines to repair a damaged gut.
- Slippery elm: This natural botanical works as a demulcent to reduce inflammation in the gut. You can find this in tea or supplement form.
- Turkey tail: This adaptogenic mushroom works wonders against gut overgrowths like SIBO and candida overgrowth. Try it in a warm drink.
- Deglycyrrhizinated licorice: Sip on licorice tea to soothe and heal your gut lining and ease digestive trouble.
- Marshmallow root: This root supports the repair of a damaged gut lining by coating the stomach to protect it against increased inflammation. You can find this in tea or supplement form as well.
11. Lemon Water
Lemons contain ample amounts of phytonutrients, vitamin C, and fiber which are all needed for supporting gut health. Vitamin C is a powerful antioxidant that helps to lower inflammation in the gut and boost the immune system. It also works as a natural antimicrobial to bring balance to the bacteria in the microbiome.
Lemons are also high in a type of fiber called pectin. This is good for your gut bugs and helps to promote healthy gut bacteria balance and encourage growth of beneficial bacteria. Multiple studies have shown that these particular fibers, like the ones in lemons, stimulate the growth of important probiotics in the microbiome like bifidobacterium. (25)
The whole-food fusion of vitamin C, prebiotic fiber, and phytonutrients also lends itself to leave the drinker with a cleaning-like effect, especially if drunk first thing in the morning on an empty stomach.
In order to really get the most positive impact on your gut health, I suggest not using lemon juice as a stand-alone tonic. Try to keep as much of the lemon pulp as you can with the lemon juice in your water since the pectin fiber and phytonutrients are mainly found in the lemon pulp. Also, make sure the water is either warm or cold, not hot, as the hotter water denatures the Vitamin C.
12. Apple Cider Vinegar
Research has shown that vinegar can mildly lower the growth of gram-negative bacteria like Pseudomonas aeruginosa and Staphylococcus aureus. (26) These bacterial colonies are higher in bacterial endotoxins called lipopolysaccharides (LPS). Higher LPS levels are implicated with a whole slew of inflammatory health problems as well as leaky gut syndrome.
ACV has also been shown to have anti-yeast, anti-fungal, and antiviral benefits which are all helpful at supporting the microbiome and immune balance. (27)
Another potential benefit of apple cider vinegar is its ability to prove indigestion and heartburn. One of the most common causes of heartburn I find in my patients is low stomach acid or hypochlorhydria. I have found that many patients see improvement with their heartburn, acid reflux, and overall digestion when they take a small amount of apple cider vinegar with their meals.
Overall, I usually always see the best results when using ACV in it’s raw, unfiltered form with the “mother” included. You’ll be able to see the mother as a sediment in the bottle but it usually always also says so on the label. Since ACV is very acidic, you may find that diluting it with water or juice can make it easier to swallow. Drinking straight apple cider vinegar can damage tooth enamel and the throat. Typically, I find people to well with 1 to 2 tablespoons mixed with 1 ounce of water.
13. Digestive enzymes
Digestive enzymes are proteins that break down the food you eat into smaller pieces that are easier for your body to absorb, utilize, and turn into energy. Some people have food intolerances (like lactose) where they lack the enzymes to break down this specific protein or don’t make enough digestive enzymes which can slow digestion and lead to uncomfortable symptoms like bloating, cramping, and gas. This is not uncommon, especially in people who are over 50, have low stomach acid, or you have IBS or IBD.
While digestive enzymes aren’t the go-to solution for those with specific intolerances, they can be helpful to have on hand for when you come in contact with a food you weren’t expecting to eat or if you need a little help with enzyme production.
14. Eat more fiber
Fiber is essential for a healthy gut. Not only does it help you build up good gut bacteria, it keeps you regular and having healthy, solid bowel movements. Fiber can be found in vegetables like artichokes, carrots, and broccoli.
Exercise is great for all areas of your health, but it can also increase beneficial bacteria in your gut and overall bacterial diversity. (28)
16. Digestive bitters
Digestive bitters are herbs that have a bitter taste including burdock root, bitter melon, and dandelion. Digestive bitters are taken with meals and work to stimulate the production of digestive enzymes that help break down food and make the digestion process easier on your gut. You can find digestive bitters in herbal tincture form but I personally love adding bitter greens into soups, salads, and stir-frys.
Ginger has been used for thousands of years to soothe stomach problems due to its anti-inflammatory properties. It also helps to alleviate heartburn and acid reflux as well as stimulate the production of stomach acid. Try adding ginger to more recipes or cut up fresh ginger root to make a gut-soothing tea to sip on.
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FUNCTIONAL MEDICINE CONSULTATIONS FOR PEOPLE AROUND THE WORLD
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BY DR. WILL COLE
Dr. Will Cole, IFMCP, DNM, DC, leading functional medicine expert, consults people around the world via webcam and locally in Pittsburgh. He received his doctorate from Southern California University of Health Sciences and post doctorate education and training in functional medicine and clinical nutrition. He specializes in clinically researching underlying factors of chronic disease and customizing a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. Dr. Cole was named one of the top 50 functional medicine and integrative doctors in the nation and is the best selling author of Ketotarian and The Inflammation Spectrum.
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