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Adapted from episode 39 of my podcast, The Perfect Stool: Understanding and Healing the Gut Microbiome.

There are tons of special diets meant to help reveal food sensitivities, address physiological imbalances or reverse autoimmune disease or other chronic conditions. I’ll cover 11 of them in this article. This may give you a starting point for trying a more targeted elimination or other special diet. Or if you’ve already done the elimination diet thing with no luck, even one as strict as the paleo autoimmune protocol or AIP and it didn’t help you, this may give you some completely new ideas, because there are many diets for different health issues that are not a subset of the AIP.

Gluten-free Diet

So let’s start with the most basic: gluten-free. Gluten is commonly known as the protein found in wheat of all kinds, including einkorn, durum, khamut and semolina, as well as barley, spelt, triticale and rye and frequently oats because of cross-contamination. However, gliadin is actually the subfraction of gluten that’s found in the grains I just mentioned and that has received the most attention. And it’s hidden in tons of foods, like soy sauce, soups, salad dressings and spices, so you’ll need to find a thorough list of potential sources and stay away from processed foods with questionable ingredients while you try it. This is step 0 for anyone with gut or autoimmune issues of any type. I did a whole podcast episode on this (episode 21) if you want more detail. However, before you give up gluten, please go to your doctor’s and get tested for celiac disease, which is an inflammatory condition of the small intestine. If you do a lot better on a gluten-free diet and you haven’t been tested, the only way to get tested is to start eating gluten again, and if you’re feeling much better, you won’t want to do that. But having that celiac diagnosis will make you take the diet a lot more seriously and requires a much higher level of vigilance, like separate cutting boards and removing personal care products with gluten in them. Of course, you may not have celiac but could have non celiac gluten sensitivity (NCGS), which you’ll find out by giving up gluten and seeing how you do. If you are gluten sensitive and you just ignore it and eat gluten, you can end up with autoimmune disease, osteoporosis, asthma, mental health issues, fibromyalgia or chronic fatigue.

Another big subset of people that the evidence shows should try a gluten-free diet are those who have already been diagnosed with an autoimmune disease, especially Hashimoto’s thyroiditis (the most common cause of hypothyroidism) and Grave’s disease. This is because the protein in gluten looks a lot like your thyroid cells. This type of autoimmune disease is believed to start when you have a leaky gut (which may be because of the gluten or for some other reason like a gut infection) and the undigested gluten proteins escape into your body, creating an immune attack to remove these proteins. Then because of molecular mimicry, or the resemblance of gluten and thyroid cells, your body attacks your thyroid. But really experts recommend cutting out gluten for any type of autoimmunity.

So I’m not going to lie: cutting out gluten is tough and may seem impossible, but I’ve gone mostly gluten-free for about 7 years now because I was diagnosed with Hashimoto’s thyroidits, and honestly it’s a relief, mainly because it keeps me from eating things that make me feel bloated and terrible like bread and pasta, and encourages me to eat more nutrient-rich foods. And it keeps me from indulging in so many unhealthy, sugary things that have gluten in them. Although I have to admit that I do cheat about 6 times a year, eat pizza and take enzymes to digest it now that my Hashimoto’s antibodies are down to normal levels.

But when first faced with the prospect of going gluten-free, you might be thinking: what about a chewy delicious pizza crust, or a sandwich on beautiful toasted ciabatta bread, or your favorite bowl of pasta? Fortunately, there are lots of great alternatives to those foods now and gluten-free bakeries in most cities. Although, I’ve always been of a mind that you’re better off looking for recipes that are naturally gluten-free, like with a lot of Asian recipes that are naturally gluten-free (provided you use tamari or gluten-free soy sauce instead of soy sauce).

But if you’re looking for good alternative flour options, two of my favorite low-cost and neutral-tasting, grain-based ones for baking are sweet sorghum and millet (which I combine, and then you need to add a starch like cornstarch or tapioca starch as 1/3 of the mix). I don’t add binders like xantham gum to my gluten-free flours. Rather, I look at any individual recipe to see if that addition is necessary and try to use more natural binders like flax or chia seeds, ground up and mixed with water.

My favorite grain-free flours are almond and cassava flours, and then I use tapioca starch (or arrowroot starch) as my starch, which is just the starch from cassava flour, but it’s much less expensive than whole cassava flour. And there are tons more grain and grain-free options including: amaranth, arrowroot, buckwheat, millet, cornmeal, flax, chia, coconut, oat, quinoa, rice, mesquite, bean flours (garbanzo, fava, etc.), tigernut and many more. And if you’re looking for amazing angel hair pasta that’s gluten-free (and very hard to find), I love the BGreen Millet Angel Hair*.

One caution about going gluten-free is not to just switch to gluten-free junk foods with additives and fillers (and often a lot of sugar), or based mostly on rice flour. They have found elevated levels of arsenic in people eating gluten-free because of high rice consumption so think more about following a whole foods diet minus gluten that includes other sources of starch, like root vegetables, nuts and other grains besides rice.  

A final note that while it’s well-known that gluten causes celiac, it’s less-known that gluten can cause inflammation in other parts of the body including the mouth, esophagus, stomach and small and large intestines. I had one client who came to me for weight loss who was also hypothyroid. I had her do an elimination diet including gluten. Wouldn’t you know, after she had been working with me for about 4 months, she saw her dentist, and all of 4’s and 5’s with the depth probe were now healthy 3’s. So she had all this inflammation going on in her body that wasn’t super obvious but cleared up after eliminating gluten. So given gluten is connected to inflammation, and inflammation to most chronic diseases, eliminating gluten is a viable option to address many different conditions, not just celiac.

Grain-free Diet

So if you start with gluten and that doesn’t seem to be enough, you may want to go the whole way to grain-free. More restrictive than the gluten-free diet, the grain-free diet(as the name suggests) involves cutting out all grains, which technically are the seeds of grasses. The reason to try this is because you may not just be sensitive to gliadin but to other prolamines found in other grains traditionally considered gluten-free, like corn, rice, millet, oats, wild rice, fonio, job’s tears, sorghum, millet and teff. So if you find that you’re 75% better off without gluten but not all the way, you may be sensitive to all prolamines in grains and should give a grain-free diet a try.

Anti-inflammatory diet

So the next diet I wanted to cover is an anti-inflammatory diet. Reducing inflammation, as I’ve mentioned, can be a powerful way to reduce your risk of illness and reverse a chronic illness you already have. Chronic inflammation is linked in research to heart disease, arthritis, cancer, diabetes, depression and Alzheimer’s. Since I’ve heard the term anti-inflammatory diet floating around on the internet quite a bit, I wanted to include what that was, but quickly realized that there is no set definition of an anti-inflammatory diet. Pretty much everyone agrees that it eliminates added sugars, deep fried foods, partially hydrogenated oils (which are mostly out of the food supply thanks to the Obama administration, as long as a serving has less than ½ a gram, which will be labeled as 0 grams), ultra-processed foods, and refined carbohydrates like white bread, pasta and desserts. Then depending on who you’re talking to, it may reduce or exclude red meat, saturated fat, processed meats, gluten, dairy, soy and/or processed seed oils. And then also important is what you do focus on, which is getting lots of servings (think 5-9) of fruits and vegetables/day, with a particular focus on green leafy vegetables, cruciferous vegetables like broccoli, cauliflower, cabbage and Brussels Sprouts; alliums like garlic, onions, scallions and leeks, fats like olive oil and avocado oil, nuts, fatty fish and seafood with lots of omega 3 fatty acids (like sardines, anchovies, salmon or tuna, but be sure to choose only brands of canned tuna that boast low mercury like Vital Choice* or Safe Catch*) and anti-inflammatory spices like turmeric, ginger, cloves, rosemary and thyme. And of course you should choose organic and/or pasture-raised foods and for meats, dairy and eggs. And then it’s also important on an anti-inflammatory diet to get lots of fiber, so that can come from fruits and veggies, or whole grains if you’re eating grains, or nuts, for example. Or dark chocolate – that’s one of my favorite sources of fiber.

Basic Elimination Diet

Next item up, the basic elimination diet. So for my clients, if they are having digestive issues and haven’t already done it, I often suggest a basic elimination diet. Because if you’re showing signs of leaky gut, like migraines, brain fog, joint pain, or skin issues, not to mention GI issues, it is often a combination of foods, not just one food like gluten, that’s causing you to react. Eliminating only gluten or only dairy or just those two and not feeling better could leave you with the false conclusion that those foods are fine for you, when in fact the issue is that you are sensitive to several foods.

So generally, I suggest a whole-foods elimination diet for at least a month that excludes gluten, added sugar, dairy, soy, caffeine, alcohol, processed foods and seed oils. Then each item (except crappy processed foods and seed oils, which you shouldn’t reintroduce at all, and the sugar, which should remain limited) should be reintroduced alone for a couple of days Eating the reintroduced item at least 2 servings a day until you feel a bad reaction, or if not, wait a couple days after that for any delayed reaction. Now of course if this isn’t enough for your symptoms to improve, you can start excluding additional foods, like nightshades, nuts or legumes, or go for a full autoimmune protocol, which I’ll get to later. I think this kind of elimination diet is a good start for people who aren’t prepared to try something as extreme as the autoimmune protocol or AIP. I know that when I found out I had Hashimoto’s thyroiditis and saw the AIP, I was like, “No way!” It was just a nonstarter for me because it felt like there would be nothing left for me to eat. But when I tried this pared-down elimination diet, my symptoms improved and I was able to isolate gluten, dairy and soy as the most problematic foods for me. So if you have an autoimmune disease that isn’t profoundly impacting your health yet, this may be a good start.

Paleo

If you haven’t been living under a rock, you’ve likely heard of the paleo diet, which was developed by Robb Wolf. Formerly a research biochemist, Wolf is the bestselling author of The Paleo Solution: The Original Human Diet* and Wired to Eat*. And along with the paleo diet is a whole school of thought known as ancestral health, approaching lifestyle and nutrition from the perspective of our hunting and gathering ancestors, who if you pull out high rates of infant mortality, lived long and healthy lives. And spent a heck of a lot less time working that we do to maintain it. So generally, you can pretty much figure out the foods that would have been accessible to hunter gatherers: meats, animal fats, coconut oil, seafood, root vegetables, other fruits and vegetables in season, nuts and seeds and natural sweeteners like maple syrup and honey in limited quantities.

Processed foods of any kind are out, unless of course they’re made to be paleo, as is alcohol, all dairy except clarified butter or ghee, all grains, starchy vegetables like potatoes, corn and peas, factory farmed meats, beans and legumes, including peanuts and soy, refined or processed sweeteners and processed seed oils. One of the biggest brands of paleo products is Primal Kitchen, which makes very nice dressings* made from avocado oil and now has frozen entrée options for people who don’t cook. I aspire to the paleo diet, except I’m too weak to eliminate all grains when my family eats them in front of me, and fakish foods like sugar alcohols because at the end of the day I have found that added sugar in any form, even if it’s ancestrally okay, causes me to gain weight. Not to mention alcohol, and legumes, which I believe are healthy, high-fiber foods for most people.

On the Paleo diet, ideally you should be eating a wide variety of proteins from as many animal sources as possible. This means not relying on standard cuts of meat and lean meats, but including the fatty meats and organ meats, not shying away from saturated fat in meat or coconut oil, and including bone broth and other good collagen sources. If you’re a baker, paleo baked goods typically use cassava flour or coconut flour, as well as arrowroot or tapioca starch or other non-grain flours. In addition to meat, vegetables, nuts and seeds, avocados, olive oil and fish oil are staples in a Paleo diet. And root vegetables, including sweet potatoes and winter squash, are the primary sources of starches. The paleo diet has been shown to be anti-inflammatory, promote weight loss, reduce digestive issues, and reverse or decrease the likelihood of developing chronic diseases.

Paleo Autoimmune Protocol (AIP)

Next up, AIP or the Paleo Autoimmune Protocol. So if you’re tried the paleo diet and feel better but not all the way better, you may want to implement the AIP, which includes an elimination diet designed to reverse autoimmune disease by addressing the nutritional resources required for immune regulation and tissue repair as well as removing inflammatory factors from your diet. The protocol also focuses on your lifestyle. So what’s involved in AIP? The AIP addresses four areas known to contribute to autoimmune diseases, which are: nutrient density, gut health, hormone regulation and immune system regulation. Meat, seafood, copious amounts of vegetables, fruit and healthy fats are AIP-approved. You might be thinking: isn’t that the same as the Paleo diet? It’s sort of like the paleo diet on steroids and further eliminates eggs, nightshades (which include potatoes, tomatoes, peppers, chilies, eggplant, tomatillo, goji berries and ashwagandha), seeds, nuts, ghee, chocolate, caffeine and seed-derived and nightshade-based spices.

The AIP diet has been attributed to Dr. Loren Cordain, PhD, a scientist responsible for discovering that certain foods trigger inflammation in people with autoimmune disease. Other leading experts in the AIP field are Robb Wolf, for his contributions in The Paleo Solution, and Dr. Sarah Ballantyne, PhD, who researches and writes extensively on autoimmunity and diet. Her research-heavy tome on autoimmune disease is called The Paleo Approach*. The main thing to remember about AIP is that it’s an elimination diet, which involves the removal and systematic reintroduction of potential problem foods, but that it is meant to last a lot longer than a typical elimination diet – pretty much as long as it takes for gut inflammation to settle down. I would generally consider recommending it for someone with an autoimmune disease that involves bad joint pain or other significant pain or disability or potential for future problems, along with gut testing and healing of gut infections that could be at the root of food sensitivities.

Low-Oxalate Diet

The next diet I’m going to talk about is the Low-Oxalate Diet. So if you’ve been rattling around the world of functional medicine for any length of time, you may have heard about oxalates. You probably even know they’re in spinach. What I’ve discovered since I’ve started using the Organic Acids Tests to uncover gut and other health issues, is that pretty much any client who has a high level of yeast metabolites also has a high level of one of three markers of high oxalates, because oxalates are produced by yeast. Oxalates are crystals that can cause kidney stones, most of which are made of calcium oxalate, but are also less known for their role in fibromyalgia, vulvodynia or vulvar pain, autism, anemia, urinary tract infections, interstitial cystitis and crystal formation in other places like bones, joints, blood vessels, lungs, thyroid and even the brain. Wherever they’re found, oxalate crystals can cause pain and damage and increase inflammation.

The first thing to know about starting a Low-Oxalate Diet is that you should reduce your oxalate intake slowly. So for example if you’re eating over 500 mg of oxalate each day, you should be reducing at a rate of no more than 5 percent per week. Basically that means reducing about 25 mg each week. If you’re eating 500 mg or less of oxalates, you can come down 10 percent each week. This is to avoid a phenomenon called oxalate dumping, which is a horrifying thing where oxalate crystals start coming out of your body wherever they are present. So you might be asking at this point, what foods are high in oxalate and how would I even know if I have an oxalate toxicity issue?

Foods that are high in oxalates include:

• beer
• beets
• beans
• berries
• coffee
• dark green vegetables
• nuts
• oranges
• spinach
• soy milk
• soda
• tofu
• wheat bran
• sweet potatoes
• black tea
• rhubarb

This might seem like a random list, but if you’ve noticed difficulty with some of these foods in the past (or perhaps all of them), or you have any of the conditions I mentioned before, it’s possible you have an oxalate toxicity issue. If you suspect oxalate toxicity might be your issue, or you just want to learn more about the Low-Oxalate diet and what’s involved, there’s a great website with recipes and a chart of oxalates in various foods from actual studies measuring oxalates in these foods. They also have a Facebook group called TryingLow Oxalates. Also, one way you can help remove oxalates from your body or diet is by eating a full serving of dairy or a calcium citrate supplement* with meals, which will absorb and usher oxalates out in your urine.

Low-Histamine Diet

Next up is the Low-Histamine Diet. If you have allergies, I’m sure you’ve heard of “anti-histamines,” which are drugs like Claritin, Benadryl and Zyrtec that treat allergic rhinitis and other allergies. But what is histamine? A histamine is a compound released by your MAST cells that plays a part in your body’s immune and inflammatory responses. So when your immune system is triggered by a potential threat, histamine is released through your bloodstream. Then your blood vessels dilate and this creates an inflammatory response with common allergy symptoms like sniffling, sneezing, coughing, tearing up or itching. Histamine intolerance occurs when high levels of histamine are chronically built up in your body. Common symptoms of histamine intolerance include irritability, depression, brain fog, dizziness, rash, flushing, hives, headache, tissue swelling, altered bowel function, nausea, vomiting, abdominal cramps, non-celiac gluten sensitivity, runny nose, difficulty breathing and insomnia.

There are two reasons why histamine can become chronically elevated: either there’s something producing high histamine levels in your body or an inability to clear histamine from your body. So what causes high histamine levels? It could be allergies (as I mentioned), but it could be other things too, for instance gut dysbiosis, environmental mold exposure, a leaky gut, GI bleeding, alcohol, genetics and histamine-rich foods. Foods high in histamine or that cause a release of histamine include:

• avocados
• eggplant
• tomatoes
• sauerkraut
• papaya
• pineapple
• dried fruit
• strawberries
• citrus
• all nuts and peanuts
• fermented dairy products like yogurt and kefir
• coconut yogurt
• aged cheese
• cured or old meats
• shellfish
• smoked fish
• soy sauce
• miso
• mayo
• pickles and olives
• sauerkraut
• kimchi
• relish
• soy sauce/tamari
• chickpeas
• soybeans
• aged cheeses
• chocolate
• alcohol
• energy drinks
• black and green tea

Leftovers are also high in histamines, which build up the longer food ages.

Low-histamine foods include:

• herbal teas
• leafy herbs
• coconut oil
• olive oil
• freshly cooked meat
• poultry (frozen or fresh)
• eggs
• coconut milk
• rice milk
• hemp milk
• almond milk
• gluten-free grains
• fresh fruit
• most vegetables

If a Low-Histamine Diet works for you, then you will probably want to figure out whether there’s a root cause you haven’t addressed, or if you have something called Mast Cell Activation Syndrome, which includes not just a release of histamine but also other inflammatory mediators, of which histamine is one.

Low-Sulfite Diet

The next diet is a Low-Sulfite Diet. One more potential allergen that could be causing your problems are sulfites. Symptoms of a sulfite allergy are typical allergy symptoms, including hives, itching, trouble breathing or swallowing, GI symptoms like an upset stomach, diarrhea and vomiting, flushing, dizziness and a drop in blood pressure. Sulfites are preservatives widely used in the food industry to prevent discoloration and browning of processed foods. Depending on the manufacturer, foods that may (or may not) contain large quantities of sulfites are:

• molasses
• jams and jellies
• tomato paste
• corn starch
• potato starch
• guacamole
• gelatin
• fruit and vegetable juices
• fish
• crustaceans and shellfish
• dried fruits and vegetables
• lunch and processed meats
• condiments
• canned and frozen fruits and vegetables
• bottled lemon and lime juices and concentrates,
• alcoholic and nonalcoholic cider
• wine and sparkling wine
• vinegar

Look for a sulfite-free label to be sure. Sulfites can also be found in medications and personal care products. So if that group of foods speaks to you, you may want to look into a Low-Sulfite Diet.

Low-Salicylate Diet

Next up is a Low-Salicylate Diet. Another potential source of dietary sensitivities may be coming from salicylates. A big tip off to this would be a sensitivity to aspirin or other non-steroidal anti-inflammatory drugs. Reactions can range from the urinary/gastrointestinal, like diarrhea, urgency or stomach pain, to fatigue, to the mental, including depression, memory loss, hyperactivity or trouble concentrating, to typical allergy symptoms like burning or itchy eyes, trouble breathing, tinnitus, headaches, rashes, rhinitis and swelling of hands, feet, eyelids, lips or face.

If you’re sensitive to salicylates, foods you’ll want to try reducing or eliminating include:

• tangerines
• pineapples
• oranges
• most berries
• herbs and spices (including cinnamon, rosemary, thyme, oregano, turmeric and mint)
• nectarines
• green apples
• black tea
• asparagus
• all dried fruits
• fruit juices

You also will want to avoid topical and inhaled exposure, because salicylic acid is easily absorbed through the skin and lungs. Many household items and toiletries typically contain substantial amounts of salicylates or salicylic acid, including: wart and callus removers, topical creams, toothpaste, soaps and cleansers, shaving cream, shampoos and conditioners, muscle-pain creams, mouthwash, lozenges, hair products, fragrances, detergents, cosmetics, cleaning products, chewing gum, bubble baths, breath mints, Alka-Seltzer, air fresheners, acne products, drugs for IBD and supplements containing willow tree bark extract.

Low-Sulfur Diet (for CBS Mutation/Sulfation Issues or Hydrogren Sulfide SIBO)

The last diet I wanted to cover was a Low-Sulfur Diet, which is indicated for someone with what’s called a CBS mutation, which causes issues with sulfation (one of the essential processes for detoxification,  also involved in hormone regulation, cell signaling and molecular recognition). When you eat sulfur compounds, your body produces ammonia as a byproduct, which is toxic, but is usually eliminated through the urine. If you have a CBS mutation that’s high firing, you may end up with excess ammonia, which can cause symptoms like lethargy, fatigue, shortness of breath, tremors, seizures, poor coordination, lack of muscle control, visual disturbances, headaches and nausea. In addition, you could have an overgrowth of microbes that produce ammonia as a byproduct that’s exacerbating your condition. I had a client who had these kind of symptoms every time he ate sugar or carbs and had to go to the urgent care for a three-drug cocktail just to handle it. When we did his Organic Acids Test and I saw his orotate level was elevated, in conjunction with these symptoms, I suspected a CBS mutation. Sure enough, he did a 23andme and confirmed that he did have the mutation. Educating him about supplements to reduce ammonia-producing microbes (including candida) in his gut has greatly improved his condition, as has strategically using certain amino acids. For people with this mutation, Dr. Jockers recommends a diet consisting of 70% fat, 10-20% carbohydrate and 10-15% protein or under 50 grams/day and limiting sulfur intake by removing garlic, onions, cruciferous veggies, eggs, legumes and all protein-rich dairy. And it’s also recommended that you add in one root vegetable, particularly known for removing ammonia, which is yucca, also known as cassava. It’s actually used in aquaculture to control ammonia levels and fed as a supplement to fish and shrimp. Also, in my client’s experience, removing sugar and carbs was a really essential component to feeling better because candida feed on sugar and carbs and were adding to his ammonia load as a byproduct of their metabolism. Lucy Mailing, PhD also recommends a similar diet for people diagnosed with an overgrowth of hydrogen sulfide producing bacteria. Your tip-off that this may be an issue is when your gas smells like rotten eggs. Her recommendations include a diet void of animal foods and dairy for 3-4 weeks, low fat, only olive, avocado and coconut oils, and avoiding sulfur-containing vegetables if they cause symptoms.

So that’s a lot of information, I know, but hopefully it may have given you a place to start on understanding the variety of potential diets that can be used to address gut and health issues.

When I’m working with clients, I help them understand what dietary protocol might be best to try, along with simultaneously testing the gut through the GI Map or Organic Acids Test to see if there is another root cause of their symptoms.

If you want more help with your gut, autoimmune or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

Listen to episode 39 of The Perfect Stool: Understanding and Healing the Gut Microbiome.

*Product links in this article are affiliate links on Amazon. Thanks for your support of the podcast and blog by using my links!

Adapted from my interview with Esther Blum, RD, on episode 37 of the Perfect Stool: Understanding and Healing the Gut Microbiome.

1. Eat plenty of fiber. One common cause of constipation is not getting enough fiber. Esther Blum, RD, recommends getting at least 20 to 40 grams of fiber per day — 20 grams at first because it’s important to start slow. If you’re not eating any fiber and you suddenly start eating a lot, you could experience gas, bloating and discomfort, so you have to build up your fiber intake over time. It’s also very important to increase your hydration as you increase your fiber.
2. Hydration. Wondering how much water you should drink? Here’s a trick: take your body weight, divide it in half, and convert that number to ounces. So, for example, if you’re 160 pounds, you need 80 ounces of water. In addition, for every 20 minutes of intense workouts, you need another eight ounces, and for every cup of caffeine, you need another eight ounces.
3. Magnesium. Try taking 400-800 milligrams of magnesium at night before bed to keep your bowels moving. Magnesium citrate is known for its help in moving bowels (decrease your dosage if your stools end up too soft).
4. Wake up and walk first thing in the morning. This is a wonderful way to gently massage your intestinal tract and keep things moving.
5. Water with lemon. Drinking warm water with lemon upon arising gives your gallbladder and liver a good flush.
6. Celery juice. There isn’t a lot of clinical research to support celery juice as a remedy for constipation. But anecdotally, in her practice, Esther Blum has seen it work really well, because, like with lemon water, it gives the liver a good flush. First thing in the morning, cut the base and tips off of an entire bunch of celery, wash the stocks, then run them through a juicer. Drink the juice on an empty stomach. Wait 20 minutes, and then carry on with your morning routine.
7. Toilet hygiene. Practice sitting on the toilet in the morning for 20 minutes and reading. This will train your body to have a bowel movement first thing in the morning.
8. Exercise. The human body is not designed to sit all day. It’s supposed to be moving and active. If you’re lying in bed or sitting all day, your intestines are not moving around or getting stimulation.
9. Chew your food well. Most people don’t realize that digestion begins in the mouth. You really have to chew your food until it’s a slurry. It should be the consistency of baby food before you swallow it. The better you chew your food, the better chance you have for smooth digestion.
10. Stress-management. Stress is a leading cause of constipation. If you’re holding things in and holding on to your stress – you can become very constipated. Developing regular stress-management activities for yourself during the day can be a great tool for alleviating constipation – and for improving overall wellness, too!

If none of the above solve your problem, a good polyphenol-based product called Atrantil has been successful for some of my clients in improving constipation. You can find it in my Fullscript Dispensary.

And if none of this helps your constipation, you may have a more serious gut health issue that requires testing and more advanced interventions. I can educate you about both. To tell me more about what you’ve been struggling with and hear about my 5-appointment gut health coaching program and decide if it is a good fit for you, you can set up a free, 30-minute Breakthrough Session with me (Lindsey). Individual 1-hour consultations may be scheduled directly here.

Listen to episode 37 of the Perfect Stool: Understanding and Healing the Gut Microbiome.

IBS, or Irritable Bowel Syndrome, is a digestive disorder which affects more than 10 percent of the world’s population. This article explores traditional and functional medicine approaches to treatment of IBS; testing; and the relationship between IBS, SIBO and IBD. And if those initials don’t mean anything to you, don’t sweat it, they’re all covered in this article.

So… what is IBS?
IBS is a cluster of symptoms that include abdominal pain, cramping or bloating that may be alleviated by a bowel movement; excess gas; diarrhea, soft stool, constipation or alternating diarrhea and constipation; and mucus in the stool. Other symptoms of IBS might include changes in texture and color of stools, nausea, acid reflux, easily feeling full or loss of appetite.

There are also non-digestive symptoms of IBS, which people might be less aware of. These can include anxiety or depression, difficultly sleeping, fatigue, headaches, an unpleasant taste in the mouth, muscle aches, sexual problems, body image issues or heart palpitations.

For most people who suffer from IBS, symptoms are worse at certain times, improve at other times, and even disappear altogether for periods of time. For some people, IBS symptoms are not severe, and can be managed with diet, lifestyle and stress management; but for many others, they can significantly impact their quality of life, make it hard to leave the house because of urgent runs to the bathroom with diarrhea, may involve accidents necessitating a change of clothes, and may impact people’s ability to work or be seen as reliable at work or in their social life. And unfortunately, many suffer in silence and don’t get the help they need because of the stigma or embarrassment.

IBS presents itself differently in different people. Clinicians organize the syndrome into three basic types: constipation-predominant (called IBS-C), diarrhea-predominant (IBS-D), or alternating constipation and diarrhea or mixed (IBS-M). According to Dr.Jockers.com, as much as 12 percent of the U.S. population suffers from IBS, or nearly 40 million people, and women and people under the age of 45 are more prone to IBS.

What’s the difference between IBS and SIBO?
SIBO, or Small Intestinal Bacterial Overgrowth, is believed to be the most common cause of IBS, with some experts citing the figure of approximately 60-70% of IBS being caused by SIBO. And the symptoms of SIBO (bloating, constipation, diarrhea, flatulence and abdominal pain) overlap with IBS, so in some sense, one could reasonably say that they’re basically the same thing, but IBS is more of a traditional or allopathic diagnosis, while SIBO is used more in the functional medicine world, although more and more gastroenterologists are using the term SIBO, the American College of Gastroenterology has put out clinical guidelines for treating SIBO, and some gastroenterologists are now using some of the same testing methods as functional medicine practitioners. And like with IBS, SIBO has traditionally been divided up into SIBO-D, SIBO-C and SIBO-M.

However, the nomenclature of SIBO and the issue of whether symptoms are coming from general bacterial overgrowth has been called into question because the testing that has been used to diagnose it, that is hydrogen and methane breath testing, has neither been shown to be terribly reliable, in particular with the hydrogen part (meaning that if you test at one time, do no treatment, and test two weeks later, you get different results), nor has it been shown to be valid in at least two recent studies (Cangemi et al., 2020), (Saffouri et al., 2019), meaning that if you compare aspirates (or suctioning of) bacteria in the small intestine, it doesn’t correlate with what’s showing up on breath testing or with patients’ symptoms. And an article published out of Dr. Mark Pimintel’s lab out of Cedars-Sinai Hospital (a leading SIBO researcher), seems to validate the lack of validity of the hydrogen breath tests in the abstract, where it says that at the 90-minute time point on the lactulose breath test (which is considered the cutoff time for measuring gases coming from the small intestine), 4/7 SIBO subjects had a rise in hydrogen (H2) ≥ 20 ppm above baseline, which would mean they had SIBO, as compared to 2/13 non-SIBO subjects. So first, those are small sample sizes so it’s difficult to call these results definitive, but at least in this study, the hydrogen breath test only correctly identified SIBO 57% of the time, and 15% of the time gave a false positive for SIBO in someone without it as compared to the results of the duodenal aspirates (or sampling of cells in the first part of the small intestine, or duodenum). This is one of the main reasons I never recommend breath testing to my clients.

There is some interesting information coming from that study, however, including that subjects with bloating had a relatively higher abundance of bacteria from the family Enterobacteriaceae, while people experiencing urgency with bowel movements had a relatively higher abundance of bacteria from the family Aeromonadaceae. Also, the subjects with what they were calling SIBO (based on the quantity of the bacteria in their small intestine) had a 4.31-fold higher relative abundance of the phylum Proteobacteria (averaging around 37%) and a 1.64-fold lower relative abundance of the phylum Firmicutes. They also reported that subjects with SIBO also exhibited greater urgency with bowel movement than non-SIBO subjects (P = 0.022), which was the only symptom they seemed to be able to correlate to overgrowth, which again in my opinion calls into question the definition of SIBO as a state of general bacterial overgrowth. And, a brief aside for people who have studied statistics, the p value on that last item was only. 0.022, versus 0.0001 for the relative abundances by family and phylum. So clearly the more statistically significant issue shown in that study is the predominance of proteobacteria, and in particular, Enterobacteriaceae and Aeromonadaceae. And further, they also found that SIBO subjects had relatively more bacteria from the genera (which is the plural of genus by the way) Klebsiella, Escherichia/Shigella, Acinetobacter and a couple more unknown genera.

As a result, “SIBO” may not be the right word. Rather, the term “dysbiosis,” which typically implies that there is an overgrowth of a particular kind of bacteria (but maybe not bacteria in general) may be more accurate. Dysbiosis may be bacterial overgrowth in both the small and large intestines, or an overgrowth of yeast in your intestines (also known as SIFO, or Small Intestine Fungal Overgrowth), an infection with a parasite, a general lack of diversity, or underrepresentation of certain important species. However, in my experience looking at lab results of tests like the GI Map and Organic Acids Test, typically all three things are happening at once when you have symptoms of IBS. But that being said, I have a client now who has an IBS diagnosis and symptoms, and when we did her labs, there were no overgrowths of pathogenic bacteria, no yeast overgrowth, and it seems like the amino acids I educated her about to help bring up her dopamine and serotonin levels have already positively impacted her IBS, which points to anxiety and stress as a likely root cause in her case. So you never know what you’re going to find out until you test. That, by the way, is one of the benefits of doing an Organic Acids Test – it helps identify when things are going wrong with your neurotransmitters, which impact your mental health, which is often impacted when you have gut issues.

As I mentioned above, IBS is divided up by whether it involves diarrhea, constipation or both. For people with constipation, it’s usually caused by an overgrowth of methanogens, or methane-producing microbes. Rather than grouping that under SIBO-C or IBS-C, the newest term being used is IMO or Intestinal Methanogen Overgrowth, because the methanogens may be located in both the small and large intestines, plus the term SIBO has the word bacteria in it, and archaea are not bacteria. [All organisms on earth are separated into three domains: eukarya (which is where you find animals, including humans), bacteria and archaea]. Anyway, IMO can be another cause of IBS, especially if it involves ongoing constipation. 

Now some good news for people who have been suffering and can’t figure out exactly why: breath testing that includes a third type of gas in your small intestine, hydrogen sulfide, has just come online for commercial use. Prior breath testing was for hydrogen and methane, with hydrogen typically being associated with diarrhea and methane with constipation. But up until now, you couldn’t test for hydrogen sulfide in a commercial setting; it was only used in a research setting. This new test was developed by Dr. Pimintel. It’s called trio-smart™ and it’s is available from Gemelli Biotech. It looks like an overgrowth of hydrogen sulfide-producing bacteria is also typically associated with diarrhea. Breath tests can be done in a lab or using a home kit, which is what the trio-smart is. If you drink glucose and do any type of SIBO breath test, which involves breathing into a tube and saving the results, it covers the first part of your small intestine. If you drink lactulose and do the test, it covers the lower part of your small intestine. Dr. Pimentel also developed a blood test for IBS called Ibs-smart, which tests for autoimmune markers which impact your intestinal motility, which can be a root cause of IBS, originally brought on by food poisoning, which likely is the primary root cause of IBS.

But the long and short of it is, what you’ll find out by doing an ibssmart test is whether you have an autoimmune issue, which you’ll need to address after killing any dysbiotic micro-organisms, by using something called a prokinetic. That’s a drug or natural substance, like ginger, that helps the intestines to move. Some of the prescription medicines used as prokinetics are low dose erythromycin, low dose prucalopride and lose dose naltrexone and one neutraceutical one is called Iberogast*. So if you seem to have recurring problems even after SIBO or IBS treatment, try taking a ginger pill before bed, or have a cup of ginger tea in the evening after dinner to stimulate the migrating motor complex as you sleep. Or if those don’t work, you may need something by prescription to deal with your motility issues. Or you can skip the test, cure your IBS, wait and see if it comes back quickly, and if it does, you’ll probably need to take a prokinetic. And at minimum, once you’ve cleared up your IBS or dysbiosis, you should make sure you don’t eat more frequently than every 4-6 hours, you don’t eat at least 2 hours before bed, and you go at least 12 hours at night without eating, to allow your intestines to clear out and let the migrating motor complex do its job.

So if dysbiosis is a root cause of IBS, maybe even covering 60-70% of it, what about the rest? IBS can be related to other things, like adhesions or bands of scar tissue from a surgery, inflammation or an injury that’s keeping your intestines from moving properly. Or it could be from Ehlers-Danlos syndrome, which is a hyperflexibility condition that can impact your intestines. Or it could be from hypothyroidism, blood sugar issues, type 2 diabetes, drugs you’re taking or took, Lyme disease or various autoimmune diseases like scleroderma or rheumatoid arthritis. Or it can be from a traumatic brain injury, which can also impact your migrating motor complex.

What’s the difference between IBS and IBD?
Now just a brief interlude to address the difference between IBS and IBD, or Irritable Bowel Disease. IBD is an umbrella term which describes digestive disorders caused by inflammation of the bowel, and autoimmune issues that affect the gut and intestines, including Crohn’s disease, ulcerative colitis and microscopic colitis. IBD symptoms are typically more serious and less common than IBS symptoms. These might include: loss of appetite, blood in the stool and nutrient deficiencies brought on by malabsorption.

How is IBS diagnosed and treated?
Typically doctors will give a diagnosis of IBS once they’ve excluded everything else, including IBD, which usually involves an endoscopy (or where they put a camera down your throat to look at your esophagus, stomach, and the upper part of the small intestine), and a sigmoidoscopy or colonoscopy (where they put a camera through your rectum to look at your colon, or for a sigmoidoscopy further into your small intestine). That’s one of the reasons Dr. Pimintel has developed the tests mentioned above, to spare you having to have the entire length of your intestines scoped. But typically, if the endoscopy and colonoscopy are negative and gut symptoms continue, including abdominal pain for at least 12 non-consecutive weeks out of the precious year, characterized by a change in how often you have a bowel movement, and your bowel movements are not normal, then a diagnosis of IBS may be indicated.

If you see a functional medicine practitioner with an IBS diagnosis or symptoms, depending on your symptoms, you will likely either be asked to do a PCR-based stool test like Diagnostic Solutions’ GI Map or Doctor’s Data’s Comprehensive Stool Analysis with Parasitology, a SIBO breath test and/or an Organic Acids Test. The results of those tests will give your practitioner a lot more data about what’s actually at the root of your issues.

In terms of treatments, if you see a traditional gastroenterologist and have a positive breath test or just based on symptoms alone, you may be prescribed antibiotics, in particular one called Rifaximin or xifaxin, an antibiotic that only impacts bacteria in the intestinal tract. It’s super expensive though – last I checked it was about $1750 for a two-week course – so if your insurance won’t cover it or your doctor isn’t in the know, you may want to go the herbal antimicrobial route. There are also some other antibiotics that may be helpful, including neomycin, metronidazole, augmentin, bactrim and nitazoxanide. However, although antibiotics may reduce your symptoms in the short-term, many times they may further stress the gut lining and microbiome or cause an incidence or increase in fungal overgrowth, which will cause a relapse or even a worsening of symptoms in the long-term. Rather than an antibiotic approach, many naturopaths, functional medicine practitioners and experts in the field prefer antimicrobial nutraceuticals because they simultaneous address both bacterial and fungal overgrowths. Typical antimicrobial herbs used for dysbiosis include Berberine, Allicin from garlic, Oregano Oil, Thyme Oil and Uva Ursi. And hydrosol silver and bismuth are also used. One of my favorite protocols that kills both bacteria and yeast is using the Candibactin BR* and AR* products. But you’ll want to get help using them because the die-off or Herxiemer reaction can be unpleasant or even dangerous if you have severe overgrowths of bacteria or yeast. That’s when you have flu-like symptoms as you begin to kill stuff in your intestines. And then once you have dislodged the bacteria and yeast, you want to use prebiotics and probiotics strategically to help reset your microbiome in an effective manner.

Some additional supplements that may be effective in addressing IBS symptoms or root causes include Betaine HCl* and digestive enzymes*, especially if there is evidence of a lack of stomach acid or pancreatic enzymes, respectively, on the GI Map test. And if there’s evidence of leaky gut, like food intolerances, or low gut immunity (indicated by low secretory IgA on the GI Map) l-glutamine powder* and an IgG product like MegaIgG* or Megamucosa* can be helpful. And then there are some supplements that help soothe and lubricate or reinforce the mucus lining of the digestive tract, like aloe vera*, which also helps with constipation, as well as marshmallow root, DGL and slippery elm (which can be found in combination products like this one*). And Atrantil (find in my Fullscript Dispensary) is a great over the counter medication that’s very helpful with constipation and actually consists of various plant polyphenols. And another really good one for help with bloating is peppermint oil*, which is good to take prior to meals.

One of my mentors, Lucy Mailing, PhD, believes that treatment shouldn’t focus on quelling bacterial overgrowth by antibiotic means. Rather, she focuses on the depletion of the short chain fatty acid butyrate, which is the food for the cells lining the colon (while glutamine, by the way, is the food for the cells lining the small intestine). Antibiotics, gut infections, low-fiber intake, and stress are all factors that can deplete gut butyrate, causing oxygen leakage into the gut. This encourages gut dysbiosis characterized by an overgrowth of faculatative anaerobes like proteobacteria, which can survive in the presence of oxygen. Therefore, she recommends avoiding antibiotics, treating fungal gut infections, eating plenty of fiber, managing stress and getting plenty of regular exercise. Speaking of which, a study published in the American Journal of Gastroenterology in 2011 found that increased physical activity improves GI symptoms associated with IBS, and improves quality of life to such a great extent, that exercise should be utilized as a primary treatment for symptoms associated with an irritable bowel. If you’re thinking of supplementing with butyrate and some more advanced interventions that Lucy recommends, I’d suggest you do it under the care of an expert gut health practitioner, such as myself. I’ve personally found supplemental butyrate to be one of the most helpful things for me in keeping my bloating in check and my stool at a nice Bristol #3. In case you’re not familiar with it, the Bristol stool chart rates stool from 1 to 7. A 3 or 4 is considered normal, but I’d much rather a 3 than a 4, personally.  

In terms of diet, one of the most commonly recommended for IBS is a low FODMAPs diet (which stands for fermentable oligosaccharides, disaccharides, monosaccharides and polyols), which, along with eliminating gluten, dairy, and a wide selection of fruits and vegetables, eliminates the omnipresent ingredients garlic and onion and their powders. The low FODMAPs diet should not be used long-term or it may result in the extinction of vital gut microbes. Rather, it’s best used to precede treatment to reduce symptoms, as a self-diagnostic tool (if you do better on it, you know your issue is at least partially bacterial) and to temporarily deplete the microbes that cause problems, so your killing regime will be more successful. Or it can be used as an elimination and reintroduction diet to see which of those foodstuffs most affect you. There are also other diets out there that are even more restrictive like the specific carbohydrate diet or the biphasic diet, but honestly, I think low FODMAPs is already a lot to ask of people, so I generally go the route of treating the underlying cause of IBS symptoms quickly rather than playing out a difficult diet like FODMAPs. But honestly, by the time most of my clients find me, they’re usually reduced to a diet consisting mostly of vegetables, meat and fat in their desperation to find a solution to their problems, so I’m not inclined to ask them to restrict their diet even further. 

Could my gut issues cause or be the cause of my autoimmunity?
So if you have a mild case of what seems like IBS, you may just be toughing it out thinking the symptoms are tolerable, but be careful. My gut issues preceded my autoimmune issues, and I know they’re related. Dr. Alessio Fasano, a pediatric gastroenterologist, research scientist, and founder of the University of Maryland Center for Celiac Research, believes three factors are at the center of all autoimmunity issues. They are genetic susceptibility, antigen exposure and increased intestinal permeability. Given that you find increased intestinal permeability in IBS and dysbiosis, it is not surprising to find that they are common underlying causes and precede many autoimmune conditions. Although that association isn’t entirely clear, what it clear is that with its high likelihood of generating leaky gut, it is important to address IBS for the prevention and treatment of autoimmunity.

If you want more help with IBS or other gut, autoimmune or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

Listen to episode 36 of The Perfect Stool: Understanding and Healing the Gut Microbiome podcast.

*Product links in this article are affiliate links on Amazon. Thanks for your support of the podcast and blog by using my links!

Excerpts from my podcast “The Perfect Stool: Understanding and Healing the Gut Microbiome“. Edited for readability. L=Lindsey; I=Inna.

L: How did you get into this work on Crohn’s and colitis?
I: That was my long journey to healing. I got sick with Crohn’s in early 2000. I was originally diagnosed with colitis, and then properly diagnosed with Crohn’s. I tried all kinds of medications, and it didn’t bring me much relief. Being a pharmacist myself, I was also skeptical and worried about the side effects, which doesn’t help at all when you know them all. And I tried different methods. I went for different modalities of healing, and my nutrition was not at the point where it is now. But I tried changes and I did succeed to a degree, until I finally found functional medicine, which really brought me to a whole different level. That’s how I started the practice, because [functional medicine] helped me.

L: Were you already a PharmD at the time when all this started?
I: I was an RP, a registered pharmacist, at the time. The reason I [got a PharmD degree in 2017] is because I wanted to dig deeper into the studies and learn way more about evidence-based stuff. I was a pharmacist, then I took a lot of education and learned about functional medicine, integrative solutions. And then I decided, here’s the time to do my doctorate to be able to really extrapolate all the details and learn about the evidence-based studies.

L: What year were you diagnosed with?
I: –colitis, originally colitis, in 2000. And then, in 2003, I was diagnosed with Crohn’s disease, the final diagnosis.

L: When you see a Crohn’s or colitis patient in your practice, what is your first step in working with them?
I: I take them on a really long consultation, we discuss their history, we go all the way back, I listen to them, I need to hear their goals, I need to understand their gut story. And by the end of the session, I am more or less on top of what functional diagnostics they should run and what route they should take in order to heal.

L: Do you typically have to do some more testing with them or is a diagnosis of Crohn’s or colitis sufficient to start working with them?
I: For most of my clients, I recommend functional diagnostics. They really can open up and show us a whole different picture, especially the stool test with PCR technology right now—even other toxicity-related testing that doctors at this point don’t have an option or don’t have the education to dig for. That could be the root cause. And it’s great. It’s great to find out.

L: So what do you use for diagnosing toxicity?
I: Well, it’s really not diagnosing – I try to steer away from that term. But to recognize and to see and to get a lab check, I really love. First I would do an Organic Acids Test for a client. And sometimes just from that lab alone, we could see we have to dig in and see if there is metal toxicity. Then we’re going to do more extensive testing, for example, for metals, or for mold toxicity or other toxins.

L: Whose testing do you use for metals?
I: I love the Great Plains Laboratory. They’re great. I’ve just had really great success with that lab.

L: What kind of test do you use for mold?
I: Also, I love to use GPL for their mold testing.

L: And what’s that one called?
I: Multi-tox screen. I believe a full tox screen and then the Organic Acids Test.

L: Do you also do that through Great Plains?
I: Yes. For around 10 years. I’ve seen hundreds of these tests.

L: So what made you choose the Great Plains over the other labs?
I: I met the rep at an integrative healthcare symposium. They were very compatible to Genova. Genova at that point changed from Methometrix and a pharmacist’s license was no longer okay to order. And that was a perfect choice for me. GPL.

L: What kind of information will you see on an Organic Acids Test that will lead you to believe that it’s perhaps a metal toxicity issue?
I: It could be a combination of things. It could be the fact that we see that there’s a lot of issues with liver detoxification, a symptomatic presentation, along with a combination of things, plus the liver, plus the look of a client. It’s really at least a few different ways you could see and then go for metal testing. [A client with metal toxicity might have a “look”] that’s often a grayish skin, black under their eyes. They’re often feeling cold, cold sensations in the hands. Sometimes they have a metallic taste in their mouth – that’s the liver, unable to process. Again, if the bile ducts are congested, they usually have that color.

L: And would these be people who have had some knowledge that they were exposed to heavy metals, or people who were just sort of, “Oh, I have no idea how that happened?”
I: I often have someone that says, “Oh my goodness, I had no idea. I have so much lead. I have so much aluminum.” But I did have a client that was completely positive they had mercury poisoning. He goes “I went through so much sushi in the past couple months. Maybe I have mercury toxicity.” And here we go. There it was. That can happen.

L: And that I assume is primarily from fish like tuna?
I: Yeah, yeah, large fish. Again, some companies are very, very responsible and they can grab the fish before it reaches a certain weight. So there’s much less mercury in the tuna like Vital Choice. Yeah, it is BPA free and very, very sustainable and organic, very clean company.

L: Good to know. So we were talking a little bit about the mold. What kind of signs and symptoms might lead you to that or things on the Organic Acids Testing that might lead to you to suspect mold?
I: With my clients, it gets a little harder, because my clients usually are Crohn’s and colitis, and they’re very sick to begin with. So the symptoms can kind of mix in all together. So mold I will mostly recognize from the Organic Acids Test. And that’s like, right in the beginning of the test, we will get Aspergillus being high, the different Furan markers, or Tartaric or 5-Hydroxymethyl-2-furoic. If they’re really high numbers, we will really go straight for mold testing.

L: Okay. And then how often do you find that people with Crohn’s and colitis, the root cause is some gut stuff like Candida or bacterial overgrowth?
I: Super often. Very often. Many, many of my clients have candida overgrowth, many.

L: Have you begun to form theories about what the most common root causes are for Crohn’s and colitis?
I: That’s a question I’ve been asked recently a lot. A common root cause would you believe that it’s the personality? My common thing in my Crohn’s clients is type A personality. They push themselves. It’s a combination of course; it’s a multifactorial situation. There’s so much involved. Type A personalities; very common in Crohn’s patients. And they really push themselves – they’re one of those go getters that go without slowing down, and that can really get them in trouble. It’s a root cause for Crohn’s. It’s a multifactorial base, except that being in overdrive and not letting yourself relax enough and not remembering yourself and not prioritizing your health often is an issue.

L: Tell me how that relates to gut issues. What’s the physiological process there? I assume we’re talking about stress.
I: Sure, it’s adrenal imbalance. It’s the fact that, you know, the gut microbiome, this is something interesting, many people probably don’t know, if you haven’t got a perfectly balanced gut microbiome or as close as perfect as you could get. Probably no one is perfect, but as diverse because we want it to be very diverse, to be to be healthy, as diverse as possible. And overnight, there’s some kind of severe stress, a fire, major fights, something really horrible happening. The next day, if you tested that microbiome, it would show someone super sick; a really, really different microbiome. So the gut microbiome, of course, plays a major role. And so presumably, the stress releases cortisol, and then how do you think that impacts the gut microbiome? Stress, releasing cortisol, we don’t have the exact connection to how it affects the microbiome. When your cortisol is constantly high, you will have some kind of other hormone imbalance, sex hormone imbalance, that leads to possibly blood sugar instability. Now [you get] the release of insulin, now you’ll have the cravings that you’re not going to eat properly. It’s a chain reaction, and then you get indirectly to the gut microbiome imbalance.

L: When you work with clients, do you also test their adrenals?
I: I do. It’s part of fixing the entire body. I really appreciate that from the Kalish course from way over 10 years ago. I know there’s a lot of controversy with the adrenal fatigue diagnosis. Of course, I do not diagnose. But fixing, correcting things, is really helpful for those that have chronic conditions.

L: Tell me what kinds of things you’ll find when you test the adrenals.
I: All kinds of things. High cortisol for someone, super low cortisol for another one. If they’ve really been in severe chronic situations, DHEA falls down. For women sometimes, it affects their sex hormone health, like they’re symptomatic for low progesterone because of pregnenolone steal.

L: Pregnenalone steal?
I: Steal, yes, it’s a term with adrenal health. It’s what happens when you have that low cortisol for too long, when it reaches that point, when it really can’t go back high enough, because it’s exhausted, the adrenals, you cause a situation called pregnenolone steal. And from there you’re going to have trouble making a sufficient amount of sex hormones. And that creates other symptoms. A lot of my Crohn’s patients, for example, have low progesterone, young and old, at any age point, and therefore with low progesterone, it is harder to maintain pregnancy. So no wonder now they’re confused why they’re having miscarriages – low progesterone often leads to miscarriages.

L: I know all about that. That’s exactly what happened to me. So what do you recommend for that? And are you an herbalist type with the drops? Or do you get people to use the pills or?
I: I often mix but my favorite one right now is Adaptocrine from Apex Energetics. I’ve seen great results with it.

L: So is that a mix of different adaptogens?
I: Yes, mix of great adaptogens. But again, it’s a blanket adaptogenic herb combo, but if there is a need for more of plant-derived bioidentical hormone for just a short term, DHEA, pregnenolone, they work well.

L: I know that the adaptogens help both with low and with high cortisol, do you use the same thing in that case or something different?
I: Very often I do yes, more often with low cortisol activity. And if I see them overreact to them and if I see this is just a very recent case, and they’ll be able to fix it with a quick fix. But most likely it would be for both cases.

Q. Is there something different between Crohn’s and colitis in your treatment approach or in typical protocols?
I: It’s a very good question. I understand what you’re asking me. Not one of my protocols has been the same for the past good three or four years. Everything is so individualized for every single person. Like no Crohn’s patient is the same; more probably Crohn’s patients than colitis patients but not one wellness plan that I create looks the same as the other.

L: Do you typically use herbal products in helping people?
I: Herbal and neutraceutical supplements.

L: What kind of diet changes do you recommend for people?
I: Anti-inflammatory. That’s where I really focus on. As long as the diet is very anti-inflammatory and favorable for macro and micronutrients balance. I don’t restrict completely. The SCD (specific carbohydrate diet) diet. SCD can work for a short period of time for sure. Except completely without carbohydrates – usually, weak patients, Crohn’s patients in flares, they really need some carbs to flourish. I create for my clients usually a mix of a Paleo, with a little bit of carbs. I focus on properly-balanced plates, from macros to microbes. All thought out and colorful plates to get the most out of your nutrition, like not having them repeat meals all the time. Very important to rotate.

L: What grains do you recommend to people?
I: I concentrate on gluten-free grains like buckwheat. Many of my clients love buckwheat; actually, they haven’t used it before we speak. So that works.

L: That’s funny because I remember as a child being offered buckwheat pancakes and the first time I tasted them I’m like “this is the most vile thing I’ve ever had, what is this stuff?” And I eat gluten free but when I bake, I make a mix. I usually use sorghum and millet and cassava and tapioca starch as my starch or arrowroot. Sometimes tiger nut or coconut flour.
I: Those are all perfect; all in my pantry. I even managed to be able to make crepes; really, really thin pancakes. Yeah, it takes time. But yeah, you learn.

L: Almond flour of course, that’s my go to flour.
I: And the key is to rotate obviously, you don’t want to be stuck on one. Because then you might create another problem. You might create another food intolerance for yourself.

L: I think I probably live like 50% on almonds. What about elemental diets? Do you use those at all or semi elemental?
I: I try to steer away. Unless there’s a specific rare case. I would recommend that for really short term just to kind of calm everything down, but not for too long. Maybe a week or two.

L: And why is that?
I: Again, I won’t find an evidence-based study on this. Strictly from my experience with so many clients – when the stomach is empty for the first few days it feels great, though there’s no pain. When your gut is inflamed, what happens? Food passes, it creates pain. So food is associated now with pain; people are afraid to eat. This is common with Crohn’s and colitis patients. When you restrict them on chunky food, you will now decrease the pain so they feel better. For a couple of days to a week, things are great. What happens afterwards is that the microbiome cannot be really sustained and be really well-balanced without the chunky meal, or at least the smoothie. You need to feed the intestinal lining. You need to feed the gut microbiome. And, unfortunately, elemental diets won’t provide that in my opinion. With a decade of experience, people start to feel gassy. They will start losing natural probiotics in the gut flora. And they start to feel worse later, in pain. So yes, it’s very short term in my practice only. I’m not putting anybody’s practice down if they have success.

L: What about fiber?
I: Fiber again, very carefully, but it’s a must to reseed that flora. You can’t avoid fiber, but you’re going to have to be very careful and do a proper job putting down the fiber. I’ve learned that if there’s overgrowth of bad bacteria, no good probiotics and you give them fiber, they hurt. That’s gas, that’s pain. And in the beginning, it took me a while to understand how to gently, gradually put it back in.

L: When they’re flaring do you use fiber? Or do you wait until the flare stops?
I: Depends on the flare. If it’s a real flare, then yes, I would wait a little bit until they’re better.

L: And how do you gently introduce fiber?
I: Small amounts, little by little, pinches in the beginning only, and then we grow.

L: And then probiotics. Which probiotics do you use?
I: I really use a lot. I use probiotics depending on the results that I see on the GI map and other labs. I love Garden of Life original professional formulas and Multiprobiotic their soil-based I love. S. boulardii, depending only if there is a need. I love Probiomed from Designs for Health. I am very choosy. And I pick and choose for every case.

L: Will you typically have people do multiple kinds of probiotics, like the spore-based and the lacto-bifido and the S. boulardii?
I: It depends. Most of the cases I do not combine. Most of the cases I don’t. I’ve had a few where I had to, there was a need.

L: And so this is basically based on what you see on the GI map, you’ll decide what they’re most lacking in?
I: Yes, exactly. What they’re lacking in, what they would benefit from, for example, Megasporebiotic by Microbiome Labs for certain cases. But if there’s Bacilli overgrowing, of course, I won’t give that to our clients. So it has to be review and then recommend.

If you want more help with your gut, autoimmune or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

Listen to the entire podcast episode with Dr. Lukyanovsky.

Gastritis
The problems I address in this article happen north of the intestines in the stomach or in the first part of the small intestine, called the duodenum. While some of these are dealt with effectively using traditional medical care, others will be missed by your traditional doctor, or will become advanced and require a functional medicine approach because they’ve been left so long unattended that they’ve provoked problems in your gut microbial balance or because their origins are bacterial gut infections that traditional doctors don’t know how to look for or treat.

Let’s start with gastritis. This is a first line problem where your stomach is bothering you. It can be asymptomatic or can have symptoms such as

• Indigestion
• Nausea or recurrent upset stomach
• bloating, pain, vomiting, including vomiting of blood or material that looks like coffee grounds
• Burning or gnawing feeling in the stomach between meals or at night
• Hiccups
• A low appetite, or
• Black, tarry stools, indicative of blood in your stool

All this means that you have inflammation, irritation and/or erosion of the lining of the stomach. And you can have an acute or sudden case of gastritis or it can come on gradually and last a while, which would be considered chronic. But either way is, if you catch it early, gastritis can be dealt with pretty easily. However, left untreated, it can lead to a severe loss of blood and may increase your risk of stomach cancer.

A lot of people will just figure out they have gastritis from the pain and do something about it without seeing a doctor. But if you have a chronic case and taking antacids isn’t doing the trick, you may see a doctor, who may do an upper endoscopy, and likely blood tests, such as checking your red blood cell count for anemia, or possibly check your B12 levels to see if you have pernicious anemia or a B12 deficiency, which can result from low stomach acid, which can give you some of the same symptoms as gastritis. And if you have evidence of blood in your stools like the black, tarry stools I mentioned, your doctor may do a fecal occult blood stool test. And if your doctor is on the ball, he or she will also check for H. Pylori or helicobacter pylori, which is a bacteria that can cause these symptoms. I’ll touch more on that later. However, your doctor’s test could miss H. Pylori, so often people will end up needing better testing to verify that their problem was H. Pylori all along.

Some of the causes of gastritis are within your control, so if you are using alcohol excessively, stopping or reducing your use is one treatment. If you have an eating disorder, chronic vomiting will also cause gastritis, so you may need to get professional help with that. And of course our old friend stress can also cause gastritis, so either eliminating your sources of stress or mitigating them may help. And taking NSAIDs or non-steroidal anti-inflammatory drugs, including acetylsalicylic acid, which is the drug in medicines like Aspirin, ibuprofen (which is in Advil and Motrin), diclofenac (which is a topical pain cream and is found in a product called Voltaren) and naproxen sodium, found in Aleve, is another way to end up with gastritis, so if you can stop those or reduce your use, that may help. You can take Acetominaphin without these negative side effects, although I’m well aware that it doesn’t take care of the same problems.
The last possible causes of gastritis that will require professional help are H. Pylori or other bacterial or viral infections, and bile reflux, which is a backflow of bile into the stomach from the bile tract (which connects to the liver and gallbladder).

If you are diagnosed with gastritis, one treatment you’ll likely be offered by your doctor is to take either antacids and other drugs (such as proton pump inhibitors, also known as PPIs or H-2 blockers) to reduce stomach acid. Some examples of these are Nexium, Protonix, Aciphex, Omeprazole, Prilosec and Prevacid, and these are offered over the counter, which makes them look innocent, but let me warn you, as someone who took them continuously for like 15 years, they are not innocent. These drugs will reduce your stomach acid by up to 99% and the end result of that can be the development of even worse gut bugs, maldigestion of protein, B12 anemia, leaky gut, and ultimately, autoimmune disease, all of which I believe I developed after long-term PPI use. The only one that wasn’t definitely diagnosed for me was the maldigestion of protein, but I had all the rest. If you have to take a PPI, my recommendation is to follow the instructions on the package that says not to take for more than 14 days. If your problem doesn’t resolve in those 14 days, you may need to look harder for your root cause. In my case, my root cause of bloating and an incessant cough that was coming from stomach acid in my esophagus, was an intolerance to dairy. I thought I was only lactose intolerant and dutifully took my lactose digestant tablets when I ate dairy, but it turns out I was also intolerant to casein. When I completely cut out dairy, my 15 years of acid reflux disappeared. It was a sad day, but as my French friend said to me about a year earlier, “if you have to take a pill to eat something, do you think you should be eating it?” Those words rolled around in my head for about a year before I was willing to face the loss of my beloved dairy, but I haven’t looked back and have learned to replace the creamy, salty, umami of dairy with avocado or just make different dishes that don’t require dairy. And I occasionally cheat and take many pills to digest gluten and dairy for Neopolitan pizza or burrata cheese, but that’s about it.

Back to treatments your doctor may recommend for gastritis, this could include recommending you avoid hot and spicy foods, eliminate gluten and/or dairy, which are two of the most likely dietary culprits for these kinds of issues, or if your issue if pernicious anemia, vitamin B12 shots or like I take, sublingual tablets. And finally, if your root cause is H. Pylori, and a traditional doctor finds, it, you’ll likely end up on a cocktail of several antibiotics plus PPIs, which may mess up your gut microbiome even more and cause you long-term problems, so I wouldn’t recommend that approach. And I’ll address the best way to deal with H. Pylori under the topic of ulcers.

Some more functional medicine type treatments for gastritis include taking DGL* or Deglycyrrhizinated Licorice before meals, which helps with the mucus production in your stomach and intestines and helps coat and protect them. And the probiotic Lactobacillus rhamnosus GG, which is found in Culturelle* and other probiotics, has also been found to help with gastritis.

But the good news is that most people with gastritis improve quickly once treatment has begun, so the moral of the story is, don’t ignore your body’s early signals that something is amiss in your gut because it can get worse.

Ulcers
Left unchecked, some gastritis, depending on its root cause, can turn into an ulcer, which is an open sore on the inside of your stomach (aka a gastric ulcer), or an open sore on the inside of the upper portion of your small intestine, or your duodenum, (aka a duodenal ulcer). Together, both of these are referred to as peptic ulcers. The main causes of these, like with gastritis, are H. pylori and long-term use of NSAIDs and/or taking other medications along with NSAIDs, such as steroids, anticoagulants, SSRIs (or selective serotonin reuptake inhibitors, which are prescribed for anxiety or depression), or the drugs Fosamax or Actonel.

Symptoms of ulcers include:

• Burning stomach pain
• Feeling of fullness, bloating or burping
• Intolerance to fatty foods
• Heartburn
• Nausea

And some more severe but less common symptoms are:

• Vomiting or vomiting blood — which may appear red or black
• Dark blood in stools, or stools that are black or tarry
• Trouble breathing
• Feeling faint
• Unexplained weight loss
• Appetite changes

You may not be old enough to remember this, but I do. They actually used to believe that spicy foods and stress caused ulcers, which we have since learned isn’t exactly true. Drs. Barry J. Marshall and J. Robin Warren, Australian researchers, discovered in 1982 that H. Pylori was in fact the root cause of more than 90% of duodenal ulcers and up to 80% of gastric ulcers, for which they were awarded a Nobel Price for Physiology or Medicine in 2005, after being ridiculed and ignored by the mainstream medical establishment.

But as I mentioned, one other primary cause of ulcers is prolonged use of NSAIDs, like Ibuprophen. I recently had the misfortune of experiencing this during my ongoing bout of sciatica because I can’t survive without some type of pain relief. I was taking 2 Ibuprofen every 4 hours (which was what my doctor described as the maximum safe dose, without any warning about ulcers, although of course I knew better). First it felt like an acidy feeling in my chest, then it felt like a burning or slight discomfort in a particular place in my stomach after taking Ibuprofen. I was so desperate for pain relief I kept taking Ibuprofen for at least 7-10 days after this sensation started, but eventually knew I had to stop or I’d end up with a bleeding ulcer. I have since had to switch to Acetominaphin, even though it’s not as good for my type of pain, but I really had no choice. Now I reserve the Ibuprofen for only my worst days. And the good news is that I was able to reverse this problem relatively quickly by taking a PPI, Omeprazole, for about 10 days along with the probiotic Culturelle, which is also recommended for ulcer prevention, and my symptoms resolved quickly. The bad news is, I’m on another drug to help relax my muscles called Tizanadine, which is starting to cause an acidy stomach, so I may have to dip back into the PPIs, or stop the Tizanadine, so I’ve got a bit of a dilemma, as I imagine many of you have when faced when you’re faced with the choice of taking your needed drug or having digestive issues, which was something I was a bit more flippant about when it wasn’t my body, and which I can now totally appreciate, as I try to control my pain while trying to resolve the root cause of my sciatica.

Getting back to our old friend, H. Pylori, which is the primary cause of ulcers, the dilemma is that it doesn’t always cause ulcers, and many healthy people have it in their systems with no problem. In fact, in developing countries, H. Pylori is found in over 80% of people, and about 20-50% have it in developed countries, but only 10-15% of people who have H. Pylori will develop peptic ulcers. Some strains of H. Pylori cause gastric cancer, but not all, so if you have it, it’s important to find out which strain you have and if it’s a problematic one, which you can find out through the GI Map Test, which costs about $400, and is used by functional medicine practitioners. Unfortunately, it’s not covered by insurance, but the information you get on it is worth its weight in gold. You can order it yourself online too, and I usually recommend it for my clients with upper GI issues, because it will tell you not only if you have H. Pylori, but if you have what’s called virulence factors, or the really bad strains of H. Pylori, and whether your amount of H. Pylori is abnormal, and will also test for all other known gut pathogens as well as signs of gut dysfunction originating in your digestive organs.

The way that H. pylori causes peptic ulcers is by attaching itself to the protective mucous coating of the stomach and duodenum, and weakening it, allowing acid to reach the sensitive lining beneath it, causing an ulcer to form. Left untreated, it can lead to stomach perforation and bleeding. Ironically, some studies show H. Pylori can be protective as well against gastro-oesophageal reflux (aka GERD) and oesophageal carcincoma, and the former is documented in fascinating detail in Martin Blaser’s book “Missing Microbes” that made me want to go out and get H. Pylori, because of the GERD that plagued me for years. Dr. Blaser, who had H. Pylori but was asymptomatic, cleared it out with antibiotics, then found himself with GERD, then reinoculated himself with it. It turns out that certain strains of H Pylori (cagA+ ones) can reduce the acidity of the stomach (thereby raising its pH) which can prevent GERD, Barrett’s oesophagus and adenocarcinoma (a kind of cancer) of the oesophagus.

However, what I have seen in clients with H. Pylori is a sequence of events that leads to problems. First you see a decrease in stomach acid. This is caused by the release of an enzyme from H. Pylori called urease, which breaks down in the stomach into carbon dioxide and ammonia, causing burping and bad breath that are commonly associated with H. Pylori, and which neutralizes stomach acid or hydrochloric acid, or HCl. HCL prompts the release of bile, which helps metabolize fat in the small intestine, so you can get fat maldigestion, which can lead to nutrient deficiencies. If your stool is pale or floating, that may be because you don’t have enough bile production.

As a result of low stomach acid, you get a rise in pathogenic bacteria or overgrowths of commensal or beneficial bacteria that are not killed off in an acidic stomach, such as Escherichia, including certain pathogenic strains of E Coli, Clostridia, including Clostridia Difficile, which you often see people getting after hospital stays and which causes explosive and frequent diarrhea, Enterococcus, including Enterococcus faecalis and faecium, streptococcus, and overgrowths of yeast such as candida albicans, candida glabrata or other fungi and a high ratio of the phylum firmicutes to bacteroidetes or other more pathogenic strains of H. Pylori. Eventually this can turn into an increase in stomach acid, which will also cause symptoms of acid reflux, bloating, gas, etc.

Low Stomach Acid
Now I want to stop for a minute to make sure you understand that low stomach acid can cause the same symptoms as too much stomach acid, but traditional doctors will almost always assume that your symptoms are coming from too much stomach acid, diagnose you will GERD and prescribe PPIs. The normal pH of a stomach for healthy protein digestion is 1.5-2.2. And that proper pH is a trigger for contraction of the lower esophageal sphincter, which is just above the stomach. This protects the soft, delicate tissue of the esophagus from the harsh acids in the stomach. If your stomach acid is too low, the sphincter may remain open, letting acid up into your esophagus, causing GERD symptoms like burning or an incessant cough, which often prompts people to take antacids or PPIs. These medications can exacerbate the problem by preventing proper digestion of foods, especially protein, which you need HCl to digest, and stressing the enzymatic system of the pancreas and other digestive organs, which are prompted to secrete enzymes in response to stomach acid levels. This can lead to calcium deficiencies, iron deficiencies, B12 deficiency, Vitamin A deficiency (which leads to increased inflammation and gut damage), and protein deficiency, all of which lead to other problems in the body.

When you have a low stomach acid situation brought on by H. Pylori or other reasons, like aging, you will often then see low pancreatic elastase 1 on the GI Map test, which is a digestive enzyme secreted by the pancreas. You can also see this decrease in pancreatic elastase 1 for other reasons, such as gallstones and a vegetarian or vegan diet.

Now back to the question of whether stress is a potential cause of ulcers. The reality is that it probably is, but indirectly. While H. Pylori may be ultimate culprit, given that so many people have H. Pylori and no ulcers, the question is, “why do some people get them?”. So here is the route that this commonly follows. First, our bodies’ first line of defense in the mucous membranes, segretory Immunoglobulin A or SIgA decreases in response to chronic stress. As a result, our gut defense systems are down, allowing the overgrowth of pathogenic or opportunistic bacteria like H. Pylori, which can lead to an ulcer. Or it can lead to decreased stomach acid and other overgrowths as I mentioned before.

So the better way to deal with H. Pylori, rather than taking antibiotics, is to take mastic gum* which is quite effective in treating H. Pylori, along with probiotics of various types, DGL*, and slippery elm*, to help coat your stomach. And if you can tolerate it and it appears you have low stomach acid, it helps to supplement with Betaine HCl*, or stomach acid, using a Betaine HCl challenge test approach, which I’ll describe in just a minute.
GERD

Okay, finally let’s finish up the topic of GERD or gastro-oesophageal reflux, which again is when the lower esophageal sphincter lets acid up into the esophagus. We’ve already touched on some possible causes, including low stomach acid and H. Pylori, so other possible causes are a hiatal hernia, pregnancy, scleroderma, which is an autoimmune disease, obesity, smoking, alcohol usage and certain prescription drugs. So it may be that you have excess stomach acid and not low stomach acid, in which case a short-term (meaning no more than 14 day) course of PPIs may be called for, but you should really only use them when necessary and symptomatic, and then start to try to figure out the root cause of your excess stomach acid and address it. So if you have no other possible root cause as I just mentioned and are negative for H. Pylori, you can start by trying the Betaine HCl challenge to see if you have low stomach acid. The way you do that is to start with one capsule per meal with animal protein (they typically are sold in the 500-750 mg range) then increase your dosage by 1 capsule/meal every 2 days until you feel heartburn or a warmth in your stomach (going up to as many as 5 capsules), then back down to previous dose. If you immediately feel a burning, then it may be you have excess stomach acid or perhaps a hiatal hernia or some other issue. You can take an antacid or some baking soda to neutralize the acid if it’s bothering you. But there are some contraindications for using Betaine HCl, which include Barrett’s esophagus, diagnosed malformation of the lower esophageal sphincter, a history of stomach ulcers, any diagnosed disease or pathology of the pancreas, or if you’re taking NSAIDs or have a diagnosed blood-clotting disorder. One alternative to taking Betaine HCl is to have 1-2 tbsp. of apple cider vinegar or lemon juice mixed in water 10-15 minutes before meals. But again, if you have a diagnosis of Barrett’s esophagus, esophageal strictures, or reflux esophagitis, you shouldn’t use these either. In that case, your best bet is just to try digestive enzymes* that don’t include Betaine HCl, but if you do want to try the Betaine HCl* approach, it’s best to find one with pepsin, which is an enzyme normally secreted by the cells in your stomach.

If you want more help with your gut, autoimmune or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

This information isn’t intended to diagnose or treat disease but is for educational purposes only. Please consult with your health care professional before acting on any of this information.

*As an Amazon Associate I earn from qualifying purchases. Thanks for your support in using my links!

Mushrooms have been eaten by humans for thousands of years. There are tens of thousands of different mushrooms species, of which six are cultivated for food in North America. There are about ten “choice edibles,” wild mushrooms for which people forage because they’re especially tasty. In Asia, they cultivate approximately twenty different mushrooms. At any time, you might see at least a dozen of those in an Asian market.

Jeff Chilton, co-author of The Mushroom Cultivator*, founder of NAMMEX (North American Medical Mushrooms Extracts), and my most recent guest on The Perfect Stool podcast, introduced medicinal mushrooms to the supplement market in the United States in 1990. He started NAMMEX in 1989, at a time when no U.S. company offered mushroom-based supplements, even though mushrooms have been used in traditional Chinese medicine for thousands of years. This is partly due to the high cost of cultivating mushrooms in the United States. Developing mushroom supplements is even more expensive. For example, while fresh mushrooms may sell for $5 a pound, once they’re dried, it’s $50 per pound because the process of drying is more involved. Mushrooms, like a lot of vegetables, are 90% water. So the economics of mushrooms as supplements do not work in the United States. For this reason, no mushrooms are grown the United States for supplement use; NAMMEX grows all of its mushrooms in China.

The most important attribute for medicinal mushrooms is their ability to modulate the immune system. Mushrooms contain compounds called beta-glucans. In fact, their cell walls are made up of approximately 50 percent of these beta-glucans. A large body of scientific research has demonstrated that beta-glucans express immunological activity. Mushrooms are often working in the background – so when your immunity is low and you get frequent colds, that’s when mushrooms can stimulate the production of immune cells, including macrophages, NK cells, or T killer cells. The key takeaway is that mushrooms modulate our immunity, which means they help potentiate and strengthen our immunity when we need it; but if our immunity is fine, they don’t do anything.

This is why many people would call mushrooms adaptogens. Adaptogens are non-specific: they sit in the background, available to help when needed. That’s why it’s so important to either include mushrooms in your diet or supplement regularly to enjoy their benefits. It’s not recommended that you supplement with mushrooms for a week or two, stop for a week or two and then start again. Rather, Jeff Chilton recommends that before considering supplementation, everyone include mushrooms in their regular diet as a very healthy food.

There has not been a lot of specific research about gut health issues with medicinal mushrooms. However, chaga mushrooms have been used traditionally for gut issues. Chaga is interesting because it doesn’t even look like a mushroom. It is not cultivated, but wild-crafted. It comes about very irregularly from what is called a canker that grows off of trees when a fungus has attacked a tree. Jeff Chilton suggests chaga as potentially helpful for Irritable Bowel Syndrome or Crohn’s disease, for example. Mushrooms also have a very high level of fiber, which directly feeds the microbiome. Some species are so high in fiber that scientists have suggested they should be processed and sold as a fiber supplement. So that’s a key way in which they help the gut microbiome.

If you want more help with your gut, autoimmune or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

Information in this article was adapted from my interview with Jeff Chilton on episode 33 of my podcast: The Perfect Stool: Understanding and Healing the Gut Microbiome.

*As an Amazon Associate I earn from qualifying purchases. Thanks for your support in using my links!

Excerpted from episode 32 of The Perfect Stool podcast, “What My Sciatica Has Taught Me about Gut Health.”

So by way of history, I’ve been going through a pretty awful bout of sciatica over the last 5 months, which had been, up until about a week ago, what felt like a slow and inexorable slide into disability. With each passing day, despite all my best efforts, I could see a little bit of loss of function over the previous day. And by the end of August, 2020, I was even finding it challenging to sit up straight, I couldn’t walk more than three steps without having to stop to stretch, so that my muscle spasms would let up, and my nights were spent writhing in pain until I could feed myself enough Ibuprofen, pharmaceuticals and melatonin to finally knock me out, only to wake up two hours later when my hip got sore from only sleeping on my right side. Then I’d have to spend an hour on the floor doing stretches to stop the muscle spasms and kill time, because there was no other comfortable position I could lie in. You’ll be glad to hear that things have finally started turning a corner, and I can now sit up easily and walk a bit but I’m still taking it easy as I heal. But during this time, I did a lot of thinking about gut health and how my journey with sciatica related to it. So here are some lessons I learned that I think may be useful to those of you who are struggling with a gut health, autoimmune or other mystery health issue.

1. Don’t wait too long to see a professional.

When I first started having back pain, I assumed that if I just kept doing the right stretches and used good posture, that my back pain would eventually go away as it had before. But the reality was, I was two years into pretty consistent back pain. If I could say something to the Lindsey of December 2019, or even July 2019, I would have said: “Go see your doctor! Get a referral for physical therapy! Take care of this before it gets worse!” I had no idea how bad it could get.

Similarly, if you’re having gut health problems and you’ve been trying to take care of it on your own, or only seeing traditional MDs, while you’ve been doing that your problem may be going from what Dr. Daniel Kalish calls a stage 1 gut problem involving some loss of gut diversity, to a stage 2 gut problem with compromised organ function that could impact your hydrochloric acid, enzyme or bile production and consequent damage to your gut lining and gut immunity, to a stage 3 problem in which you’ve acquired or your system has allowed the overgrowth of a pathogen because of the weakness of compromised organ function and lowered gut immunity. Left even longer, this can lead to autoimmune disease, increasing food intolerances, and Mast Cell Activation Syndrome, in which you quickly have what appears to be an allergic reaction to a whole slew of inputs, including many foods. The longer you wait, the harder, more expensive and the longer it will take for you to solve your problem, and honestly, the more you’ll suffer. Whatever concern I had in July or December of 2019 regarding spending the time or money to solve my problem, it pales in comparison to the amount of lost time, suffering that I could never have imagined, and money I have now spent on many modalities to try to solve my problem. Not to mention the opportunity cost of not spending time on my business while I’ve been trying to get well.

2. Don’t reject traditional modalities if they can bring you relief while you search for the root cause.

With my sciatica, I held out hope that the right kind of physical therapy with consistent follow-through, eating a super low inflammatory diet, taking the right supplements, and staying active would help me recover. However, my decline just continued. I waited way too long to see a doctor, and when I heard that the next likely step would be a hydrocortisone injection, I purposely delayed following up in hopes that things would get better and I could avoid the shot. As a result, I probably spent an additional 5 weeks of sleepless nights writhing in pain and got much worse before I finally had my first injection, which I don’t regret at all, no matter the potential side effects. I also tried for so long to avoid taking NSAIDS (Non-steroidal anti-inflammatory drugs) for pain, but finally realized that I was suffering a lot unnecessarily, and am now up to the maximum dose of ibuprofen each day, while protecting my stomach with DGL and shilijat. I sometimes hear from clients that they have refused certain treatments from their doctors (especially around autoimmune disease and biologic drugs) that might bring them relief. While I’m a strong advocate of finding and addressing the root cause of any problem, if you’re really suffering or your health is in serious danger, it’s okay to try traditional treatments for a time while looking for the root cause.

3. Don’t let the medical-industrial complex put you off from finding solutions.

One of the biggest roadblocks in getting to the root of my problem was my insurance wanting me to do at least a month of physical therapy before I got an MRI. But it was clear from almost the beginning of physical therapy that I was in too much pain to do most of the exercises I was being given, nothing was helping and I was going downhill. I finally resolved to just pay for the MRI myself because I felt it was important to have some insight into what was going on inside of me and they were clearly trying to make me jump through 1000 hoops to approve it. I didn’t want to have to pay for the test, but in the end, testing can give you real insight into root causes.

So if you’re hesitating to spend the money on gut testing that isn’t covered by your insurance and that your doctor doesn’t know about or won’t order, I’d urge you to reconsider. For gut health, there are two tests that I recommend to clients. They are the Organic Acids Test, which is $325, you can order it online yourself and it can enlighten you as to yeast and fungal overgrowths, bacterial overgrowth and dysbiosis, problems with carbohydrate, fatty acid and amino acid metabolism, detoxification issues, energy production issues and neurotransmitter problems. The other test I recommend, if problems are mostly confined to the gut, is a thorough gut health test like the Diagnostic Solutions GI Map or Doctor’s Data GI 360, which each run around $399, and you can order them yourself online. These tests will alert you to problems in your digestive system like a lack of hydrochloric acid, pancreatic enzymes or bile, indicating problems with fat metabolism, as well as test for specific pathogens, including pathogenic bacteria and parasites. It will also tell you how certain medications will work against those pathogens. It’s a rare insurance that would pay for these, although HSAs or FSAs might, but they’re worth their weight in gold for the information they will give you so that you’re not shooting in the dark. If that’s not financially possible, a less expensive option is doing a metagenomic sequencing of your gut through Sun Genomics. That’s only $147 if you go through my affiliate link, and if you look at the raw data, it will tell you everything that’s in your gut, if you know how to interpret that. So if you’re hesitating on testing, just think about how over time, you can waste a lot of money buying every supplement you hear someone recommending on a podcast or in a health summit, while building up a lovely supplement graveyard and getting no closer to a solution. Better to go around the medical-industrial complexes rules, order your own tests and get a functional medicine provider to help you understand the results.

4. Listen to anyone’s and everyone’s advice – you never know where your solution may come from.

As things got worse and even the checkout clerks at the grocery store knew about my sciatica, I started getting advice from them and everyone else who heard my story. I also joined a Facebook group on sciatica and frequently popped in there to commiserate and find advice. Some of the advice didn’t work out, but some was useful. And some of the most useful stuff was about the mental game. I had been working myself into a giant pity party in which I was focusing so many hours a day on my pain and helplessness that my mind was feeding into my problem rather than helping solve it. Someone in my sciatica Facebook group said she would meditate and picture her nerves flowing freely through her spine. This image has helped me go to sleep so many nights, as I used my mind to help calm my muscle spasms. And it was a health summit on toxic mold where I heard about a special modality of physical therapy and a machine that helps reduce inflammation that may be one of the key elements of my healing, in addition to the injections. Even my plumber showed me a stretch no one else had shown me that helped him with his sciatica. So don’t reject advice because of the source – give everything a good listen and if you’re not ready to try it, put it in your back pocket for later.

5. Don’t be afraid to ask for help.

As I was falling into disability, I realized that the more I was up and around, trying to cook, clean and do the things of everyday life, the more it was hurting me. The moment I had to tell my family that I really needed them to step up and help make my food and do my dishes, I couldn’t hold back the tears. I never considered myself one of those self-sacrificial people who always did for others and never asked for anything herself, but this was one of the hardest things I’ve ever done. But of course my husband stepped up and started filling in and got our boys to do more, and his kindness in this has really brought us closer. If you’re really suffering, let people help you. Don’t do things that will make you worse. It truly brings others joy to help, even if it forces us to humble ourselves, but there is growth in that humility. And also, don’t be afraid to reschedule or cancel things. People will understand. People have been very understanding with me when I’ve been honest with them. When you’re well again, you can pay it backward to those who helped you or forward to someone else who’s suffering.

6. Don’t keep it all inside. 

Chronic pain and illness is not just physically debilitating, it’s mentally debilitating. And sometimes you can feel very alone in your pain and suffering. I had moments in the middle of the night where I had spent over an hour trying to get the agonizing muscle spasm in my glutes to let up through stretches, exercises and using a massage wand. One night, after an hour, I was still in agony, lying on the floor and sobbing because I felt so sorry for myself. That night, I finally woke my husband up and asked for help. He told me that from then on, he didn’t want me suffering alone, but that I should wake him up. After I stopped worrying about waking him and started relying on his help, my nighttime suffering quickly decreased and he was able to help me settle back down to sleep sooner, and also started asking if I needed anything when he woke up at his usual 5 a.m. That helped me go back to sleep for several more hours. Even if you’re single, there is probably someone in your life you can lean on more if you’re suffering. Someone who would be happy to help you research treatments or doctors, someone who you can share your fear or tears with, someone who will make you a meal if you’re not up to it. Or friends who’d be willing to contribute to help fund your care. There’s actually a charity called efundyourhealth that matches up to $250 for functional medicine care if you can raise the rest. New campaigns are currently on hold while they’re updating their web site, but they’re still soliciting donors, so hopefully they’ll be up and running again soon. But back to the original message, don’t suffer alone. 

7. Find the gift in your pain and suffering.

When you’re deep in the midst of pain or suffering, it may be hard to find the positive, but doing so will leave you with a gift of wisdom that may help carry you through. For me, one of the biggest gifts will be the empathy I now have for people in chronic pain. I confess that before going through this, I assumed that anyone who had chronic back pain must have a terrible diet, or they didn’t exercise, use good posture, or try the right kind of physical therapy (speaking of which, if you’re dealing with chronic back pain, I’d highly recommend seeing a Mackenzie method practitioner). I looked down on people who got addicted to opiates because of their pain. After spending a desperate night in pain and like a crazy person rummaging through our medicine cabinet to find the two oxycodone’s left over from my husband’s dental surgery and washing one down without hesitation, I finally understood firsthand what drives people to desperation and addiction. I also know now how much a kind word helps. It may drive someone to tears, but it means so much to hear someone say “I’m so sorry about how much you’re suffering.” So if you’re the loved one of someone dealing with chronic pain or illness, you can’t ask how they’re doing or express your empathy enough. It’s like a balm on our wounds. So look for the good in your experience, the learning, the opportunity to grow as a person and then help others. It will make your situation just that much more bearable.

If you want more help with your gut, autoimmune or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

Over the course of my podcast (The Perfect Stool: Understanding and Healing the Gut Microbiome), I have done seven interviews with people who have had fecal microbiota transplants (FMT), some in clinics overseas, some self-administered, and I’ve also shared about my own ill-conceived  experience with DIY FMT. I also covered the research being done on a purified form of FMT for children with autism. As a result, I often hear from potential clients who are interested in trying FMT to heal their gut issues. Consequently, I decided to summarize the kinds of results that have been discussed in my interviews, and share my perspective on whether FMT is a good fit for various conditions and the practicalities of doing it, both in clinics and on your own.

One of my most striking FMT stories was episode 23: “PANDAs, Autism, Anxiety and Depression: One Family’s Miraculous FMT Healing Story”, in which Mary talked about using FMT from a clinic in Australia to treat her daughter’s auditory and tactile hallucinations, her son’s autism symptoms, and her own anxiety and depression. About FMT in general, Mary shared, “This is like the golden elixir of life. If you have a very sick child, you are going to get over the ick factor very quickly because it’s just a miracle that we have such a beautiful, natural solution all along.” About changes to her daughter’s affect, Mary said, “[Before FMT], she just had a darkness pulling in, she had a fearfulness on her face, and a lack of affect, [and after FMT]… she’s off and running, she’s just doing beautifully.” About changes to her son’s affect, Mary said, “Whatever the interferences that autism causes, [after FMT] he’s just present, he’s looking you right in the eye, he’s listening to what you’re saying, he’s calm in his body, he wants to be part of the group instead of hiding from the group… He’s more friendly. He goes up to people and introduces himself… His desire for independence has just exploded.”

In episode 10 ““Designer Sh*t” – Coming Soon to a Theater Near You:
One Filmmaker’s Story of Overcoming Colitis”, I interviewed Saffron Cassady, a filmmaker in the process of making a film about FMT, including her own personal story of healing from colitis thanks to repeated FMTs from her boyfriend.

In episode 5, “DIY Fecal Transplants for Irritable Bowel Syndrome (IBS): One Patient’s 9 Experiences and the Urgent Need for High Quality Stool Donors” Michael described his nine experiences with DIY FMT to address IBS, irregular heartbeats and severe fatigue, the benefits and drawbacks of each experience, and the urgent need for healthy donors, which led him to collaborate on the formation of a donor/recipient connection tool, Microbioma.org. He also shared numerous resources including a sample donor questionnaire.

My very first episode “SIBO Recovery and Fecal Microbiota Transplantation (FMT)” was with Amy Hollencamp, a now-dietitian whose microbiome was decimated by antibiotics and an extended restricted diet used to treat SIBO, resulting in unwanted weight loss and continuing bowel issues. She chose the Taymount Clinic in the Bahamas for her FMT. After the procedure, she reported “better gut function mainly . . . less bloating . . . I felt like my bowel movements were a lot better.”

On my most recent episode (31), “How FMT Helped One Woman Read Emotions and Normalized Sound and Touch Sensitivities,” I interviewed Amanda, who sought out FMT at a clinic in Argentina for gut issues and psoriasis and benefitted from other unexpected benefits:  “[My constipation and diarrhea] got a lot better. My skin didn’t change at all. It completely did not change, which was weird. But everything else got way better: the social awkwardness got better, the sound sensitivity got way better, my energy level got better, my ability to connect words in my head got better… I could remember things from pop culture, I could remember the plot of a TV show and I could not do that before… Yeah, I mean everything except my skin, ironically, got better.”

In episode 12, “Healing Autism via Microbiota Transfer Therapy with Dr. James Adams” (whose title I realized subsequently was not the best choice and was offensive to many in the adult autism community), we learned about the amazing research using purified FMTs on children that Dr. Adams and his collaborators had conducted, resulting in a 47% decrease in symptoms of Autism Specturm Disorder three years post-FMT. The results were published in the prestigious journal Nature.

And finally, in episode 19, “How I Reversed My Autoimmune Diseases and Got Interested in Gut Health”, I shared my own health journey, my ill-conceived DIY FMT and some of my continuing personal opinions about FMT: “I definitely think there are a lot of mental health issues and things like autism, where fecal transplants can clearly help… To be perfectly honest, if I were a parent of a child with autism, I would not hesitate to try and give my child a fecal transplant because it’s going to jump start their development.” I also shared about FMT’s success in treating C. Difficile, “I think there are some conditions that we’re seeing, obviously C. Difficile, there’s a 92 percent success rate in some studies with the fecal transplant and it’s a shame, frankly, that [FMT] is still only essentially approved for C. Difficile that is recurrent and resistant to antibiotics, given that the antibiotic success rate is only in the 30 percent [range]. That’s the only use that you can get [FMT] for officially from a doctor in the U.S.”

So if you are you considering a fecal transplant, all these success stories might make you anxious to try it, but there are a lot of drawbacks. First of all, if you’re in the U.S. and can’t afford the ~$10,000 fee of doing it at a clinic overseas, you’ll need to find a donor and have the donor thoroughly tested. Of course you’ll have to have complete faith that the donor is honest in their questionnaire or well-known to you, as testing won’t reveal inactive viruses, such as Human Papillomavirus or Herpes Simplex Virus. If you don’t have your donor tested, you also risk catching a nasty bug from your donor that may not have caused them problems but will cause you problems if your microbiome is unstable and dysbiotic (like C. Difficile or H. Pylori). And if you’re lucky enough to find a potential donor who’s willing to give you 5- 10 samples (typical sequences of FMTs in a clinic run over the course of 5 days for C Diff and 10 days for conditions like IBS or colitis), thorough testing could be very expensive and most tests won’t be covered by anyone’s insurance. But at minimum to cover the microbiome end, you should run either a metagenomic sequencing of their gut microbiome and examine the raw data or do a test like the GI Map or Doctor’s Data GI 360. And clinics typically put patients on strong antibiotics like vancomycin for two weeks prior to FMT, so you’d need to get access to the same or use longer herbal protocols to properly prepare the terrain to receive new residents. The Power of Poop website is a great resource for all your FMT questions and lists other tests that should be done for a donor.  It includes instructions about How to Safely do a Fecal Transplant at Home and comprehensive information about Donor Registry Requirements.

But before you get your heart set on FMT, you should realize that FMT is not likely the quickest, easiest or least expensive way to solve your gut or other health issues. Most gut issues have at their root dysbiosis of some sort, be it an overgrowth of the wrong type of bacteria or an overgrowth of candida or other fungi, many of which take place in the small intestine, making it unlikely that FMT would reach the problem, unless you take it in crapsule format. However, herbal interventions following testing to determine the root cause of your problems, coinciding with dietary interventions and probiotics, followed by prebiotics, are likely to bring about substantial relief for most gut issues. And of course there are more complex interventions for more complex issues, like mold exposure, histamine intolerance or Mast Cell Activation Syndrome, that a good practitioner can guide you through.

So I’d encourage my listeners who are thinking of FMT as a first-line treatment to investigate other possibilities before taking the risk of using a donor who is not properly screened and a DIY fecal transplant. But if you are determined to move forward, please take as many precautions as you can afford in terms of donor selection and testing.

If you want more help with your gut, autoimmune or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

Excerpts from episode 30 (“Food for Thought: Mental Health and the Gut”) of my podcast, The Perfect Stool: Understanding and Healing the Gut Microbiome, edited for readability.

Relationship between Brain Activity and Gut Inflammation

One example of gut-brain dysfunction can begin with decreased brain activity. This could come from a brain injury, concussion or stress. Decreased activity can lead to a decrease in the activation of the vagus nerve, which is the main component of the parasympathetic nervous system (which is one arm of the enteric nervous system, or the two thin layers of more than 100 million nerve cells lining the gastrointestinal tract from the esophagus to the rectum, the other branch being the sympathetic nervous system, which controls the fight or flight response to a stressor). The parasympathetic nervous system oversees many crucial bodily functions, like digestion, control of mood, immune response and heart rate, specifically undoing the work of the sympathetic nervous system after a stressful situation and bringing your body into the rest and digest mode by decreasing respiration and heart rate and increasing digestion when you’re resting, relaxing or eating.

Returning to the vagus nerve – the vagus nerve connects the brain and the gastrointestinal tract and sends information about the state of the inner organs to the brain via fibers. Decreased activation of the vagus nerve then suppresses the intestinal immune system and decreases intestinal blood flow. This slows digestion and can cause increased growth in pathogenic yeast and bacteria, which then cause intestinal permeability or leaky gut. Leaky gut causes a state of chronic low grade inflammation. And then the inflammatory cytokines or chemical messengers produced in the gut travel through the blood and cross the blood-brain barrier, which activates the microglial cells, which are the immune cells of the brain, and the brain gets inflamed. That inflammation creates a leaky blood-brain barrier, also known as leaky brain. The blood-brain barrier is a single-layered lattice of cells joined by tight junctions that regulates which substances are allowed into the brain, not dissimilar to the way that the intestinal epithelial cells regulate what’s let in and out of the intestines. Generally, it keeps out toxins like heavy metals, pesticides and damaging proteins, while allowing in oxygen, hormones and nutrients. So this brain inflammation decreases nerve conductance, which in turn can cause depression and reduced activity of the vagus nerve, which controls mood, and we’re back where we began: caught in a vicious cycle, in which reduced activity in the brain causes gut inflammation, which inflames the brain, which leads to reduced brain activity.

It’s important to recognize that when gut symptoms persist even in the context of a healthy diet and lifestyle, this could be an indication of a gut-brain axis problem.

And likewise, the problem can also originate in the gut, with a poor diet lacking in fiber and high in sugar, simple carbohydrates, gluten, dairy or other common food allergens creating intestinal permeability, which then sets off the same series of events terminating in mental health issues.

Depression and the Microbiota

In a study published in the journal Nature Microbiology in 2019, researchers in Belgium sequenced the gut microbiome in 1,054 individuals, correlating their findings with measurements of both quality of life indicators and depression status of the participants. They found that those with lower levels of Bacteriodes enterotype 2 displayed lower measurements of quality of life and a higher prevalence of depression while those with higher quality of life indicators were consistently correlated with higher levels of Faecalibacterium and Coprococcus, which produce the short-chain fatty acid butyrate, which feeds gut epithelial cells and helps maintain a healthy gut barrier. They also found that a lack of Dialister and Coprococcus species also correlated with higher levels of depression. The researchers also looked at the genetics of these particular organisms and their role in manufacturing the neurotransmitters dopamine and GABA, which led to the suspicion that this may be another role that the microbiome is playing in mental illness. So overall, while we can’t say that precisely those organisms cause depression, what we do know for sure is that a healthy gut microbiome decreases inflammation, and the inverse, an unhealthy one increases it, and this has an impact on depression, which is at its core an inflammatory disorder.

Another study, which was a systematic review of studies on major depressive disorder and the gut microbiome, found that nine genera were higher in major depressive disorder (Anaerostipes, Blautia, Clostridium, Klebsiella, Lachnospiraceae incertae sedis, Parabacteroides, Parasutterella, Phascolarctobacterium and Streptococcus), six were lower (Bifidobacterium, Dialister, Escherichia/Shigella, Faecalibacterium and Ruminococcus), and six were divergent, meaning different results in different studies. What they suggested is that studying microbial functioning, or the function that any genera of microbes may play, may be more productive than a purely taxonomic approach, or singling out specific families, genera, phyla, etc. of bacteria to understanding the gut microbiome in depression.

Going into a bit more detail on the role of specific gut bacteria in creating neurotransmitters, studies have shown that Lactobacillus and Bifidobacterium, typically genera in multistrain probiotics, synthesize GABA from monosodium glutamate which is notable because it’s hypothesized that depression may be caused by a deficit in GABA. Escherichia coli (aka E. coli), Bacillus and Saccharomyces produce norepinephrine (which you may know also as noradrenaline), whose general function is to mobilize the brain and body for action. Candida (a yeast, not a bacteria), Streptococcus, Escherichia and Enterococcus produce serotonin, which is the key hormone that stabilizes our mood, feelings of well-being and happiness and helps with sleeping, eating and digestion. And Bacillus and Serratia produce dopamine, which plays a role in how we feel pleasure. This is leading to research on a new class of drugs called “psychomicrobiotics” for the treatment of psychiatric disorders.

Another study that sheds some light on the mechanism by which the gut microbiome can cause depression was a controlled clinical trial on patients with major depressive disorders that helped validated the existence of an immune response to LPS or lipopolysaccharide, which is a component of the cell walls of gram negative bacteria. LPS is believed to also play a role in depression, along with inflammatory cytokines. The study looked at concentrations of the immune cells IgM and IgA against the LPS of 6 gram negative bacteria from the family Enterobacteria, which would indicate an immune response in the blood to bacteria. They found that the prevalence and median values for serum IgM and IgA against LPS of enterobacteria are significantly greater in patients with major depressive disorder than in normal volunteers, which led them to conclude that “. . . the results show that intestinal mucosal dysfunction characterized by an increased translocation of gram-negative bacteria (leaky gut) plays a role in the inflammatory pathophysiology of depression.” That means that the blood-based immune response indicates that this LPS is escaping the intestines and creating this immune response. They go on to suggest that patients with major depressive disorder should be checked for leaky gut by means of the IgM and IgA panel used in the study and be treated for it if found.

The Gut-Brain Axis and Anxiety

If you’ve ever had an experience that made you “feel nauseous” or had “butterflies” in your stomach before a public speaking event, you are probably clued into how your gut responds to anxiety-producing situations. Conversely, conditions in your gut can trigger various emotional responses in your brain, like anxiety, which studies have shown may affect up to a third of people at some point in their life. The enteric nervous system doesn’t just send messages to regulate the digestive system, it also receives information from the digestive system, creating thoughts in your brain. For a long time, researchers and clinicians thought that anxiety and depression contributed to conditions like IBS and other problems like constipation, diarrhea, bloating, pain and upset stomach. However, new research suggests the reverse is true too: that people suffering from IBS and other functional bowl problems are at much higher risk of developing depression and anxiety. As a result, you may find your gastroenterologist suggesting antidepressants to treat your IBS, not because they think the problem is in your head, but because these medications can calm symptoms by acting on nerve cells in the gut, as can cognitive brain training or other psychotherapies.

Looking at the research evidence on gut-based interventions for anxiety, a systematic review of 21 studies with 1503 people from 2019, examined the evidence from observational studies to support improvement of anxiety symptoms by regulating the intestinal microbiota. Of the 21 studies, 14 had probiotics as interventions to regulate the microbiota and 7 had non-probiotic interventions, like diet adjustments. Overall, 11 of the 21 studies showed a positive effect on anxiety symptoms by regulating gut microbes. Of the 14 studies that used probiotics, more than a third found them to be helpful in reducing anxiety symptoms, while 6 out of the 7 remaining studies that used others means found those to be effective. The researchers concluded that more studies are needed to clarify the conclusion that non-probiotic interventions are more effective that probiotic interventions in reducing anxiety, but overall, they did affirm that regulating intestinal flora is effective in alleviating anxiety symptoms.  

If you want more help with your gut, autoimmune or mental health or other health issues, you can set up a free, 30-minute Breakthrough Session with me (Lindsey) to share what you’ve been going through and decide whether my 5-appointment gut health coaching program or a longer program for autoimmunity or weight loss is a good fit for you. Individual 1-hour consultations may be scheduled directly here.

Episode 30 show notes