Many people with Hashimoto’s feel significantly better when they remove reactive foods, replenish nutrient depletions with restorative foods and supplements, and support the gut with probiotics. But what if those steps alone don’t work? You’ll have to dig a bit deeper.
It took more than the implementation of the strategies above for me to resolve all my symptoms related to Hashimoto’s. In fact, in some cases, my attempts to produce healing led to the development of additional, different symptoms altogether. Searching for the solution that will work for you can sometimes feel like trying to find a needle in a haystack, but the right combination of protocols for you is out there.
When symptoms don’t subside in response to what might be considered the standard approach in functional medicine — removing, replenishing, and repairing — there is a good chance that you have an unaddressed infection.
Many people with hypothyroidism may have SIBO, or small intestinal bacterial overgrowth. While this is not technically an infection, SIBO does have a bacterial component and can be a trigger or exacerbating factor for Hashimoto’s!
In fact, a 2007 study found that about 50 percent of people with hypothyroidism have SIBO, while a 2017 study found that levothyroxine use can contribute to the development of SIBO! (1,2)
In this article, we’ll explore:
- What SIBO is and what causes it
- How to test for SIBO
- Determining which SIBO treatment option is right for you
- How to prevent a SIBO recurrence
What Is SIBO?
“SIBO” is an acronym for small intestinal bacterial overgrowth. Our small intestine is meant to be relatively clear of bacteria, while the large intestine houses most of our bacterial friends and foes. In some cases, bacteria from the large intestine may make their way up and overgrow into the small intestine. (3) Too much of any bacteria, good or bad, can lead to SIBO. The key is to keep the bacteria in the large intestine, where it belongs, and out of the small intestine.
Once you have SIBO, it can lead to intestinal permeability and contribute to a long list of digestive symptoms, including acid reflux, belching, bloating, and irritable bowel syndrome (diarrhea, constipation, or mixed type). (4) SIBO often presents with bloating after eating, and is associated with the annoying “I woke up with a flat stomach and now I look pregnant syndrome.” (This is caused by bacteria in the small intestine creating too much gas.)
Conditions like irritable bowel syndrome (IBS), hypothyroidism, fibromyalgia, and restless leg syndrome have all been tied to SIBO. (5-8)
SIBO can also cause a depletion of vitamin B12 and iron, as well as lessen levels of digestive enzymes like lactase (digests lactose in dairy) and amylase (digests starch), making it more difficult to digest many foods. (9)
If you’ve noticed that fibrous foods, fermented foods, histamine-containing foods, prebiotics, cruciferous veggies, and/or the use of probiotics seem to cause a flare-up in your digestive symptoms, there’s a good chance you have an overgrowth of bacteria in your small intestines. That is because these foods feed the bacteria in your intestines and cause them to multiply, contributing to the overgrowth. (For this reason, most probiotics, with the exception of one, are not recommended for those with SIBO. I’ll discuss this in further detail in a minute.)
Also, if you’ve found that using antibiotics or antimicrobial herbs, even when used for unrelated reasons, makes you feel better, this could also indicate the presence of SIBO. Substances with antimicrobial properties can suppress the bacteria, leading to temporary relief of symptoms. (3)
Additionally, I’ve found that people who feel better when fasting and skipping meals and have the flattest stomachs when they first wake up (but tend to look “pregnant” in the evenings), are more likely to have SIBO, as fasting, skipping meals and of course our lack of eating at night will prevent the bacteria from gorging on our food, producing gas, and replicating.
What Causes SIBO?
A SIBO overgrowth can be caused by issues such as low stomach acid (sometimes due to H. pylori), antibiotic use, the use of acid-suppressing medications (Pepcid, Protonix, Nexium, Prilosec, and Omeprazole are some potential names), slowed gut transit (where food moves along the gastrointestinal tract too slowly), and food poisoning, among others. (3,10) All of these things can suppress digestion and slow the passage of food through the intestinal tract, giving bacteria time to “set up shop” and colonize the small intestines.
Hypothyroidism in itself may contribute to SIBO because of its propensity to slow down gut motility. A 2017 study also tied the use of levothyroxine to SIBO — however, I’m not sure if this is a chicken or egg thing… (2)
SIBO can be a root cause, consequence, or exacerbating factor of Hashimoto’s. I have seen people with Hashimoto’s resolve symptoms like IBS, restless leg syndrome, low ferritin, and low B12 levels by treating SIBO. In some cases, I’ve also seen thyroid antibodies reduced — and even go away — with SIBO treatment.
How to Test for SIBO
While yeast overgrowth and most causes of gut infections can be detected in a stool test, SIBO is best revealed via a breath test. This is because the breath allows us to determine the presence of gas-producing bacteria. The gas is emitted because of fermenting bacteria, which will usually produce measurable levels of hydrogen and methane.
Because SIBO is a hot new topic in the gut world, more and more progressive conventional medicine doctors may be willing to test you for it — although you may have to be proactive and ask for the test yourself. Functional medicine practitioners, gastroenterologists, and major Academic Treatment Centers will have access to advanced diagnostic tests, possibly administered using a breath-testing machine.
Otherwise, you can order a SIBO breath test kit that uses lactulose (to stimulate the bacteria) to release their gasses. SIBO breath tests are offered by Direct Labs. Choose the Small Intestinal Bacterial Overgrowth 2-Hr Lactulose (SIBO, BOSI)-Genova Kit.
It’s important to find out if you have SIBO, as treating a bacterial overgrowth may not only greatly improve digestion, it may also result in remission from Hashimoto’s in some cases.
SIBO Treatment Options
There are several protocols that can be used in the eradication of SIBO, including a pharmacologic approach, which relies on antibiotics, and an herbal approach that focuses on the use of antimicrobial herbs. (11,12)
It’s important to realize that there is no “one-size-fits-all” cure for SIBO, and what works well for one person may not work for the next. Some people may need to undergo several rounds of treatment in order to eliminate the bacterial overgrowth and find relief from symptoms, while others may need to tackle the problem by using more than one intervention — for instance, by incorporating some dietary changes and using antimicrobials.
According to Dr. Allison Siebecker, creator of the informative website SIBOinfo.com, the antibiotics metronidazole, rifaximin (Xifaxan™), and neomycin have been used to treat small intestinal bacterial overgrowth because of their ability to stay in the intestines, which prevents them from causing systemic adverse events. Most of my clients who have used this approach have reported positive results, though it’s important to note that not all insurance companies cover Rifaximin — and the out-of-pocket cost may be high.
I typically recommend the following dosages. However, I encourage you to consult with a practitioner in your area, as they will be familiar with your health history:
- For hydrogen-producing bacteria: 1200 mg of Rifaximin daily, for 14 days
- For methane-producing bacteria (which are more likely to cause constipation): 1600 mg of Rifaximin per day, for 10 days; combined with neomycin (1000 mg per day, for 10 days) or metronidazole (750 mg per day, for 10 days)
Herbal and Alternative Approach
Many people have found herbal antimicrobials to be as effective — or more effective — than their pharmacological counterparts. In fact, one recent study showed that herbal treatments (consisting of oil of oregano and berberine-based herbal blends) had a 46 percent success rate, while 34 percent of the participants using Rifaximin experienced a resolution of their SIBO. (12) Furthermore, those on Rifaximin experienced symptoms such as anaphylaxis, hives, diarrhea, and Clostridium difficile bacterial overgrowth, while only one participant using the herbal remedy experienced diarrhea.
In general, the anti-bacterial compounds derived from plant sources tend to spare the healthy gut bacteria more so than pharmacological antibiotics, which may decrease the risk of diarrhea and other digestive complications. Additionally, combining herbs can produce a synergistic effect on microbes and reduce the likelihood of resistant bacteria, which is a common problem with prescribed antibiotics. (13)
Other benefits of using herbal treatments include reduced cost, no prescription needed, and fewer side effects. On the other hand, an herbal treatment course usually lasts at least four to eight weeks, whereas prescription antibiotics usually show improvement within one to two weeks.
There are several different herbal antibiotics that have proven effective in the treatment of SIBO. Keep in mind that different herbal combinations are usually chosen based on the gasses produced in your gut, and the symptoms you are experiencing. For example, herbs that work on methane-producing organisms, such as Allimed and Atrantil, are usually chosen for methane-producing SIBO bacteria.
Herbs for SIBO treatment include:
- Garlic extract (allicin) (14)
- Oregano oil (12)
- Berberine (12)
- Neem (15)
- Pomegranate husk (16)
- Clove (14)
- Thyme (12)
- Atrantil (17)
Some of the protocols that I have seen the most success with for SIBO are focused on using berberine with oil of oregano for 60 days, with an addition of garlic extract in the case of methane-producing bacteria. I’ve provided a few of my favorite options for berberine, oil of oregano, and garlic extract, so that you can select the one that works best for you. 🙂
Berberine-containing brand options and dosing:
- Rootcology Berberine: one capsule, three times per day for 60 days
- Candibactin-BR (an herbal formulation containing berberine): two capsules, three times per day for 60 days
- Integrative Therapeutics Berberine: one capsule, three times per day for 60 days
Oil of oregano-containing brand options and dosing:
- Rootcology Oil of Oregano: two capsules, three times per day for 60 days
- Designs for Health Oil of Oregano: two capsules, three times per day for 60 days
- Candibactin AR: one capsule, three times per day for 60 days
Garlic extract-containing brand options and dosing (add on for methane-producing bacteria):
- Rootcology’s Garlic Oil: two capsules, 3 times per day for 60 days
- Allicillin (garlic extract): two capsules, 3 times per day for 60 days
These are my recommended dosages, but please consult with your functional medicine practitioner to determine the dosage that is appropriate for you.
In addition to taking antibiotics (herbal or pharmacological), I usually recommend taking the beneficial yeast S. boulardii. While most people will need to avoid probiotics while working to eradicate SIBO, S. boulardii doesn’t colonize the intestines as most other probiotics do. Thus, it doesn’t contribute to the overgrowth of bacteria in the gut. Instead, S. boulardii helps to clear out the existing bacteria in the small intestine, and speeds up the process of clearing the gut infection. (18) I recommend starting out slowly and building up to a therapeutic dosage of as much as 4000 mg of a supplement such as Rootcology S. Boulardii per day.
I have seen many people clear their SIBO through a simple course of oil of oregano, berberine, and S. boulardii, and often recommend this line of treatment to my clients.
Dietary Treatments for SIBO
Some people have had success using specific dietary approaches, such as the elemental diet, the Specific Carbohydrate Diet, the low FODMAPS diet, or the GAPS diet, to reduce the bacterial overgrowth. However, many people will find that these dietary approaches work best when combined with one of the antimicrobial treatments mentioned above.
Even if you don’t choose to take a dietary approach, it is recommended during the treatment of SIBO (or suspected SIBO) that you limit starchy foods, fiber, and the use of probiotics that contain prebiotics like fructooligosaccharides (FOS), inulin, and Arabic gum, as well as foods with high amounts of prebiotics (this is similar to the low FODMAPS diet, see below).
Foods with high prebiotic content to avoid include chicory root, Jerusalem artichoke, dandelion, garlic, leek, onion, and asparagus.
Peppermint oil has been found to be helpful for SIBO as well. (19) (Please work with a professional who knows how to safely prescribe essential oils, before ingesting peppermint oil.) However, most brands of peppermint oil contain soy, so drinking peppermint tea may be a better alternative.
The elemental diet is a liquid diet that is free of non-digestible substances such as fiber, complex carbohydrates, and protein structures. It contains our essential macronutrients in a state that requires little to no digestion, and results in complete absorption. (20) In doing so, it does not provide any food for pathogenic bacteria to feed on, thus starving them.
It has been traditionally used for rehabilitation of severely malnourished individuals (like in the case of anorexia), people with bowel inflammation, and those experiencing diarrhea.
The elemental diet is also considered a “low-residue” diet, which means that it is composed of free-form amino acids and fat in liquid form. Amino acids, glucose, fat, and vitamin/mineral supplements (in liquid form) are utilized instead of food. Because it results in a reduced secretion of pancreatic and gastric juices, this diet gives the stomach and pancreas a rest from digestive activity, and allows for healing and reduction of inflammation to take place.
Additionally, free-form amino acids allow for the body’s own protein (muscle tissue) to be spared during the diet, helping the rest of the body heal quicker.
An elemental diet may be incredibly beneficial in kick-starting the thyroid healing process. This diet causes a rapid shift in bacterial flora within one to two weeks. (21)
SIBO is thought to be a primary cause of IBS, and clinical trials have shown that this diet is effective in reducing SIBO within two weeks in people with IBS, resulting in a substantial improvement of symptoms in as many as 80 percent of people. (22)
Of course, there are some drawbacks to the diet. First, the amino acid supplements are expensive and taste pretty disgusting, if not properly prepared. Many people report feeling nauseated after drinking the solution, and aspiration has resulted when people lie down too quickly following ingestion. Furthermore, commercially available formulas (e.g. Vivanox®) contain a lot of artificial ingredients that people with Hashimoto’s may not tolerate. They also include a lot of carbohydrates, which can cause high blood sugar and harm adrenal function.
In recent times, the company Integrative Therapeutics came up with a cleaner version of the elemental diet — the Physician’s Elemental Diet. This formulation has become my go-to recommendation for people with Hashimoto’s who are interested in the elemental diet. Please note, Integrative Therapeutics has removed distribution of this formula from retail channels, as it is an FDA-regulated medical food. As always, I do recommend working with your personal health care provider to ensure this (or any other) intervention is appropriate for you. However, if you and your practitioner are having trouble obtaining this elemental formula, Dr. Siebecker’s homemade Elemental Diet may be a suitable alternative.
A modified homemade elemental diet is also available in the Companion Guide to my book, which you can download at thyroidpharmacist.com/guide. As this diet requires the purchase of expensive amino acids, however, it can be quite pricey.
Some critics of the elemental diet also noticed that symptoms sometimes return after a period of time ranging from months to years. I think this is likely because people go back to their high sugar/carbohydrate diets too soon. However, if an elemental diet was followed by a grain-free FODMAPS diet, Specific Carbohydrate Diet (SCD), or a similar diet, this could result in permanent remission.
I do not recommend attempting the elemental diet for those with compromised adrenal function and/or other types of infections, such as parasitic infections. Elemental diets should be used under the supervision of a health care professional and in the case of confirmed SIBO.
Specific Carbohydrate Diet/GAPS Diet
The Specific Carbohydrate Diet (SCD) and the Gut and Psychology Syndrome (GAPS) Diet are other diets that have been found to be helpful for SIBO. (23,24) It eliminates grains, sugars, and starches — and only allows carbohydrates to be eaten in the form of fruits, honey, and certain kinds of specifically fermented yogurts.
The SCD diet is very similar to the Autoimmune Paleo Diet (AIP) well-known in the Hashimoto’s community, with the exception that it does not allow sweet potatoes due to their starchy content, and unless customized, allows other foods like nuts, seeds, and nightshades that are not AIP-approved.
I love the website SCDlifestyle.com if you’re looking for more information on the SCD approach.
Low FODMAPs Diet
The low FODMAPs diet is considered an effective nutritional therapy for certain digestive disorders, including SIBO. (23) By removing foods high in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (short-chain carbohydrates), this diet essentially cuts off the food supply to the bacteria that may be running amok in your intestines. This can help eliminate SIBO by multiplying the flora we need for absorption and, potentially, starving the pathogenic flora by avoiding the foods that are fermented by pathogens.
Certain foods —specifically onions, garlic, and beans — will always be malabsorbed in all individuals, whether they have IBS or not. (25) These three foods also cause gas production in all individuals. However, when pathogenic bacteria are present, toxic byproducts are produced, causing more severe symptoms.
A 2012 study showed that 75 percent of individuals with IBS who follow a low FODMAP diet have been found to see an improvement in symptoms. (26)
The low FODMAP diet allows some fruits, but advises against eating too many of them. Bananas, blueberries, boysenberries, cranberries, grapes, grapefruit, honeydew melon, kiwi, lemons, limes, oranges, raspberries, and strawberries are allowed. Vegetables included on the low FODMAP diet are carrots, celery, endives, ginger, green beans, lettuce, olives, parsnips, potatoes, pumpkin, red bell peppers, spinach, squash, sweet potatoes, tomatoes, turnips, and zucchini, as well as most herbs.
Gluten-free cereals and grains, such as rice, oats, polenta, quinoa, psyllium, sorghum, tapioca, and arrowroot are allowed.
Most dairy products are not permitted unless they are lactose-free. Sweeteners such as sugar and maple syrup are allowed, but not in large quantities.
You’ll notice that meats and eggs are not restricted on the low FODMAP diet, as they do not contain fermentable carbohydrates.
Here’s a graphic with an overview of high FODMAP foods, that you can save and refer to later:
For those following another type of diet, such as the Paleo or gluten-free diets, modifications can be made to the low FODMAP diet to meet your specifications. Examples of how you may want to modify your diet include:
- Gluten-free: Eliminate all gluten-containing grains (wheat, barley, and rye in all variations).
- Dairy-free: Eliminate all sources of dairy, including lactose-free dairy products.
- Paleo: Eliminate all grain, dairy, legumes, and processed food products. Focus on meats and low FODMAP vegetables/fruits.
- Autoimmune Paleo: Avoid all processed foods, grains, legumes, dairy, eggs, soy, sugar, food additives, alcohol, and most nuts and seeds. Focus on pasture-raised meats, and low FODMAP fruits and vegetables.
For more information on how to implement a low FODMAP diet, please see my full article.
The Importance of Retesting and Tips for Preventing SIBO Relapse
Regardless of the method you choose to combat SIBO, it’s important to retest for SIBO 5-14 days after the completion of your treatment protocol to determine if, in fact, the SIBO has been appropriately treated, or whether it may be growing back.
One way to keep the bacteria from growing back is to ensure that you have sufficient stomach acid to properly digest and absorb the food you consume. (27) This is especially important for those with thyroid conditions to look into, as many people with Hashimoto’s may have low stomach acid. (28)
In my clinical experience, many people with low stomach acid find betaine with pepsin helpful. However, it’s important to note that low stomach acid may often be caused by H. pylori. After studying gut health for almost a decade, I have come to realize that this important pathogen can be behind “treatment-resistant SIBO.”
Another important factor in keeping bacteria overgrowth from returning is making sure that your bowels are able to move food through the intestines properly. We call this process gut motility. When food sits in the intestinal tract for too long, as is the case with constipation (often experienced by those with hypothyroidism), bacterial overgrowth is more likely to occur. (29)
Prokinetics are agents that work to stimulate the intestinal tract so that it can move food along effectively and prevent bacteria from “snacking” on the food as it passes. These can include herbal treatments, medications, and physical devices. Many people will find that these agents are an important part of their strategy to keep SIBO from recurring.
Prokinetics and substances that may help with bowel motility include:
- Low dose naltrexone
- Motilpro by Pure Encapsulations
- Low dose erythromycin
- Thyroid medication
- Vagus Nerve Stimulation (VNS)
- Magnesium citrate
Picking the Right Protocol for You
I advise you to discuss these potential protocols with your practitioner and let them help identify the best starting point for you based on your health history. While it may take some time, eradicating SIBO can allow for your gut to heal and, ultimately, resolve the intestinal permeability that may have been your Hashimoto’s trigger.
The first step is to get tested for SIBO and then make a plan to decide which diet, antimicrobial, and preventative options are right for you.
SIBO can be challenging to conquer, and may take some time and persistence on your part. However, I have seen many people overcome their infections and experience huge relief from their symptoms, and I know the same is possible for you. I’m rooting for you!
Have you already been tested for SIBO? What methods have you tried to treat it?
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Note: Originally published in February 2020, this article has been revised and updated for accuracy and thoroughness.