This post is a follow-up to our previous conversation on small intestinal bacterial overgrowth and will look at the aspects involved in treatment for SIBO, which typically involves a very low-carb diet, herbal or pharmaceutical antibiotics, nutrients to heal the gut, addressing confounding factors like Candida overgrowth, stress management, and ongoing maintenance.
Pharmaceutical Based Antibiotics
If you take the pharmaceutical route, the most common treatment for SIBO is the antibiotic Rifaximin. However, it is not very effective for the archaea methane-producing organisms by itself. If you recall, SIBO may involve hydrogen-producing bacteria and another organism call archaea that produce methane.
According to Chris Kresser, research indicates that SIBO individuals producing methane only have a clinical improvement about half the time and only clear methane from a breath test about 28 percent of the time with Rifaximin. Another antibiotic called Neomycin produces a clinical response about 63 percent of the time and cleared methane from a breath test about 33 percent of the time. However, if Rifaximin and Neomycin are combined, then improvement rates go up to about 85 percent, and methane is cleared from the breath test about 87 percent of the time.
Therefore, if one tests positive for hydrogen only, then Rifaximin is used alone. But, if one tests positive for methane and hydrogen it is critical to use both the Rifaximin and Neomycin, otherwise, you will not target the archaea. It’s also important to be aware that archaea are resistant to most other antibiotics that are typically used on gram-positive or gram-negative bacteria.
Fortunately, Rifaximin and Neomycin are both broad-spectrum drugs, but they are poorly absorbed antibiotics (remain mostly in the gut). Therefore they do not wipe out all the healthy bacteria like a broad-spectrum antibiotic that is systemically absorbed would, which means it will be less likely to contribute to yeast overgrowth and serious side effects.
Not only that, according to Dr. Siebecker, Rifaximin actually decreases antibiotic resistance rather than increasing it, therefore resistance is not going to develop against it. Since treatment commonly has to be repeated, this means Rifaximin will continue to be effective in re-treatment. However, in Dr. Pimentel’s book, he states that resistance to Rifaximin and Neomycin does sometimes occur. Rifaximin can have a success rate of up to 91 percent. Rifaximin also has an anti-inflammatory effect by decreasing intestinal inflammatory cytokines and inhibiting NF-kb via the PXR gene. So Rifaximin is less harmful than most antibiotics.
However, in my practice, it is not uncommon for me to work with people who have no response at all to rifaximin or neomycin. And some people report that rifaximin is very effective the first time they take it, but less so on the second time around, indicating that resistance is developing. Additionally, rifaximin caused a significant flare in yeast overgrowth (more than most) when I took it myself. It also caused a lot more side-effects than I experience with most other antibiotics that are systemically absorbed, like severe acid reflux and muscle spasms. Not only that, it made my SIBO worse than ever and caused horrific abdominal pain throughout the whole GI tract and all my internal organs. It was one of the worst things I’ve ever taken. I had to discontinue usage before the treatment course was over and the symptoms did not abate. Two weeks after discontinuing rifaximin, I developed a severe respiratory infection and had to take some systemically absorbed antibiotics, and they cleared up the symptoms that were caused by the rifaximin. Other people have reported the development of yeast overgrowth and a worsening of health after treatment with rifaximin as well. So, I don’t agree with the stance that rifaximin doesn’t promote yeast overgrowth or prevent resistance. And, I question whether it is a good choice for treatment. I’ve had good results with doxycycline, full dose erythromycin, cefdinir, and amoxicillin. Minocycline and vancomycin may be options as well. Prior to the emergence of rifaximin, the tetracyclines were the drug of choice for SIBO, so anything in the tetracycline family may be a good choice.
Neomycin is a bit more absorbable than Rifaximin and can be associated with some rather serious side effects. Therefore, some practitioners use allicin in conjunction with Rifaximin, to target the methane-producing organisms instead of Neomycin. Another antibiotic called Tindamax may be used if a resistant clostridia sp. is involved.
Now, although I am not typically in favor of antibiotic use unless absolutely necessary, considering the serious deterioration in health that can result from SIBO, this may indeed be one of those times that meets the criteria of necessity.
However, it is important to be aware that research indicates that one out of every two people treated successfully with antibiotics relapse within a year, and re-treatment is required, perhaps numerous times or even ongoing. In the real world, I think this number may be even higher. If you visit any Internet forum on SIBO, you will discover that almost everyone has relapsed and must treat repeatedly. On the other hand, the people in the forums would be skewed towards those who haven’t been successful, since those that were successful are not likely to be hanging around the forums anymore. Even still, it is clear that the success rate is very low. I haven’t worked with anyone who didn’t have SIBO return after treatment and most people coming to me have already been to a handful of practitioners including some of the most well-known SIBO experts in the nation. The manufacturers of rifaximin state on their website that people using it for IBS-D (typically caused by SIBO) get relief from symptoms for an average of 10 weeks.
On the other hand, there is a study that found herbal antibiotics can be just as effective as pharmaceutical-based antibiotics against SIBO. This study used one of the following two protocols, Dysbiocide and FC Cidal (by Biotics Research Laboratories) or Candibactin-AR with Candibactin-BR (by Metagenics).
Although at this time no other true studies have been done on herbals for this condition, other herbs that are commonly reported to be effective by practitioners for SIBO include cat’s claw, uva ursi, tannins, allicin from garlic, olive leaf, grapefruit seed extract, berberine, Oregon grape root, goldenseal, lactoferrin, colostrum, monolaurin, pau d arco, Artemesia, yerba mansa, Coptis, thyme, neem, oregano oil, cinnamon and peppermint.
However, like antibiotics, not all herbs that are effective against hydrogen producers are effective against the archaea methane producers. Most practitioners use high potency allicin, which is obtained from garlic to address the methane producers. However, garlic is not effective against lactobacillus. There is one case study that found peppermint oil to be effective against both hydrogen and methane, however, there was only one person involved in this study. Nonetheless, many practitioners recommend the use of peppermint oil in the treatment plan. Peppermint has also been found to be effective for reducing methane in rumen microbiome (cows) production. Clove, eucalyptus, and oregano oil have also been effective at reducing methane production in the rumen as well. An herbal product called Atrantil is supposedly effective against methane producers.
The herbs that work for one individual may not necessarily work for another, as it may depend on what species of bacteria you are carrying, whether they are resistant, the potency of herb, level of overgrowth, where they are located, or other unique biochemical factors, so some trial and error will be required. Herbs may have to be exchanged for other herbs if resistance develops. In contrast to pharmaceutical-based antibiotics, since herbs contain many different compounds rather than just one, the upside is that they can have a wider spectrum of activity that may enhance their efficacy not only against SIBO but other microbes as well.
Many of the herbs that have antibacterial qualities are also powerful antifungals (like cinnamon, berberine, cat’s claw, oregano oil, tannins, pau d’arco, grapefruit seed extract) that will be effective against Candida and some may contain anti-parasitical qualities as well. Since Candida frequently accompanies bacterial overgrowth, you may kill two or three birds with one stone, when the right herbs are used. Additionally, several different kinds of herbs can be combined to create a synergistic effect, which may also help prevent resistance and target more microbes at once.
The downside to some herbals is that die off or side-effects can be so severe that they inhibit the individual’s ability to work or fulfill daily obligations and responsibilities. Since they have to be taken for a minimum of four weeks, this disruption is going to go on for an extended period of time. This means herbs may not be an option for some people who have a family and a job that demands one must be able to function. In some cases, the pharmaceutical route can address the problem quicker and with less disruption to one’s life. One should also be sure to give the body a break from herbs and not take them non-stop for months because some of them do have the potential to kill friendly bacteria as well or affect neurotransmitters in the brain.
People are often under the impression that herbs come with no potential side effects, but that isn’t true. Although herbs can be safer than pharmaceuticals in many cases, they are still powerful substances that are foreign to the body. Herbs are not the same as nutritional supplements. Nutritional supplements are nutrients that the body needs. Herbs are not needed by the body; they are basically a natural drug and sometimes can have profound side effects and negative consequences. One should approach the use of herbs in the same manner as a pharmaceutical — with caution and be informed. Be sure to do your homework and communicate with your healthcare professional before and during the use of herbs.
For example, I recommend an extra word of caution in regard to Neem. Neem can dramatically lower your blood sugar levels. It is so effective at lowering blood sugar that it may be used for managing diabetes. When I took Neem, it made my stomach feel absolutely wonderful, which indicates it is very effective against microbes. However, it lowered my blood sugar so low that I nearly passed out on several occasions and therefore had to discontinue use. People with low blood sugar issues, which are very common in Candida overgrowth, SIBO, and adrenal fatigue, may have to avoid Neem.
According to the Organic Consumers Association, grapefruit seed extract has been found to be contaminated with benzalkonium chloride, parabens, and triclosan, with benzalkonium chloride being the most common. Benzalkonium, a synthetic chemical used for disinfection, is known to be toxic to the immune system and may be carcinogenic. Some studies have demonstrated that grapefruit seed extract does not contain any antibacterial qualities inherently without the presence of these contaminants. Grapefruit seed extract is derived through a very long process that uses ammonia chloride and hydrochloric acid. The end product contains 60 percent diphenol hydroxybenzene, “a chemical classified as a quaternary ammonium chloride – the same as benzethonium chloride. In fact, it is nearly chemically identical to benzethonium chloride.” Triclosan is a toxic pesticide, with neurotoxin capabilities and has been linked to the immune system and endocrine system damage and is believed to contribute to resistant strains of bacteria. Parabens are a preservative that is endocrine disruptors and have been linked to cancer. So, it is debatable whether grapefruit seed extract is natural and whether it should be used. However, it may still be less toxic than some pharmaceutical-based antibiotics.
Considering the fact that at least 50 percent of the people treated successfully for SIBO will have a relapse within one year and a large percentage of people are not achieving complete eradication and treatment may need to be repeated numerous times, it may make more sense to try the herbal route before pharmaceuticals. Depending on how quickly overgrowth repopulates, one may be looking at needing treatment several times a year or more. Most of us in the natural health field would not be comfortable using an antibiotic that frequently. Another option would be to alternate pharmaceuticals and herbals with each treatment round. However, I think one of the best options is to hit the microbes hard with a pharmaceutical first and then maintain those improvements with the herbal route. At this point, die-off will not be as severe, so herbs may be tolerated a little better.
However, the decision on whether to use herbals or pharmaceuticals should be determined by weighing the positives against the negatives, how severe the level of overgrowth is and to what extent health has been compromised, the urgency for relief, other health conditions that may be present and what allows the individual to function most optimally during treatment. Someone who has mild overgrowth and impairment to their health may be better off with the herbal route, while someone who is experiencing severe malnutrition and a failure to thrive may need to address the problem immediately with pharmaceuticals.
I’d also like to share something I’ve observed in my own body that can affect treatment. When a severe flare in my SIBO levels occurred, I was experiencing most of my pain, inflammation, and gas in the duodenum area (center of my stomach), pancreas and gallbladder. After I began using herbal antibiotics, most of the pain in that area went away, but it moved down to the cecum and ileocecal valve area (lower right quadrant). It appears that my bacteria moved down to that area to try and escape the herbs and it seems that the herbs I was using were not as effective as killing them when they get that far down in the gastrointestinal tract. Also, I had a lot of brain symptoms when they were located in the duodenum and felt very ill, but not nearly as many when they moved to the cecum, so location also seems to affect the type of symptoms one may experience.
Bacteria also form biofilms within the body. A biofilm is a sticky matrix that allows them to hide from the immune system or antimicrobials. Therefore, agents that can help break down the biofilm should accompany the antimicrobials. Common substances used for this process include lactoferrin, NAC, lumbrokinase, bromelain, lemongrass, clove, nattokinase, serrapeptase, and the antibiotic Tindamax. You can learn more about biofilms on the following page. A product called InterFase by Klaire Labs has been clinically proven for its effectiveness against biofilms. Biofilm Defense by Kirkman Labs is used by many as well. NAC was found to reduce biofilm formation of Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Proteus Vulgaris by 62 percent in one study.
The length of time that the antimicrobial is taken is very important. One of the leading experts on this topic, Dr. Siebecker, recommends 14 days with an antibiotic and 4 to 6 weeks with herbals and she states that treatment will be much less effective if the proper diet is not in place, which we will discuss now. However, the length of treatment will vary with practitioners. According to Dr. Pimentel’s book, he only uses a 10-day course of treatment.
The diet for SIBO is just about the same as it is for Candida, except that it will be even lower in carbs and fiber.
Most bacteria prefer carbohydrates and soluble fiber as their primary source of fuel to survive and produce gas when they ferment them. If there are a lot of carbs and fiber in the diet, the bacteria will multiply quickly in numbers, and inflammation, gas, and all the associated symptoms will be abundant. The higher the level of carbohydrates and fiber, the more bacteria will proliferate. The higher the number of bacteria, the more toxins and gases created and the more symptoms one will experience.
If protein and fat are the predominant macronutrients in the diet, then fewer bacteria will grow and those that do exist don’t produce as much as gas. Therefore a low-carbohydrate diet can be used to reduce their food source. Reducing their food source (polysaccharides, oligosaccharides, and disaccharides) will lower the level of organisms present and consequently the level of gases and toxins that are produced, which leads to a reduction in symptoms. Many people can achieve dramatic improvements in symptoms in a short amount of time with the right SIBO diet.
This is true regardless of whether you have hydrogen or methane-producing microbes. When you limit the foods for the hydrogen-producing bacteria, then you starve them out, which reduces the hydrogen levels that the archaea would then convert into methane, and consequently, this would reduce archaea and methane levels as well, since they wouldn’t have as much hydrogen for fuel to survive and convert into methane.
The primary foods that these bacteria use as a food source are called fermentable carbs and they include the following:
- starch (grains, beans – legumes, starchy vegetables)
- resistant starch (whole grains, seeds, legumes, potatoes, potato flour, plantains other starchy veggies)
- soluble fiber (grains, legumes -beans, nuts, seeds, vegetables, fruit, pectin, psyllium)
- sugar (in all forms, including fruit, lactose, fructose, sucrose)
- prebiotics (inulin, FOS, MOS, GOS, arabinogalactan) beans, agave, vegetables, roots/herbs, supplements, bone broth
- alcohol (feeds bacteria, damages the gut, and inhibits DAO enzyme)
- sugar alcohols are also known as polyols (found in some fruits and vegetables, as well as malitol, sorbitol, isomalt, mannitol, erythritol, xylitol and inositol.
Many of the foods above are not only eliminated because they feed bacteria or Candida but because they also promote inflammation, which will encourage the proliferation of pathogens. Grains and legumes contain a high level of antinutrients that are damaging to the gut. Nuts and seeds also contain some degree of anti-nutrients that can cause inflammation and inhibit the absorption of minerals. In people with healthy guts, nuts are not much of a problem as long as they are consumed in moderation. However, in the individual who already has inflammation from SIBO or Candida, then they may contribute to the problem. Nuts and seeds are also exceptionally high in omega-6, which also promotes inflammation, when not in balance with omega-3.
There are other foods not in this list above that can be inflammatory if the gut is damaged like nightshades, casein, and egg whites.
Raw food (vegetables and fruit) should be avoided or limited because they are higher in fiber and resistant starch than cooked food, which will provide more fuel for the microbes. Cooking your vegetables and fruit until soft will lower the fiber and resistant starch content. Additionally, fruit that isn’t ripe is higher in resistant starch than ripe fruit, so be sure fruit that is eaten is ripe.
Caffeine (including chocolate, raw cacao, and green tea) should also be avoided, as caffeine stimulates the liver to release sugar into the bloodstream, which can then become a food source for bacteria and Candida. Additionally, caffeine depletes vital neurotransmitters in the brain like acetylcholine, GABA, and serotonin that are critical for regulating appetite, brain function, and the migrating motor complex. Caffeine also triggers the stress response system, which as we already established, will weaken immunity, inhibit motility and the migrating motor complex, kill friendly gut bacteria, etc.
Artificial sweeteners should also be eliminated because they are chemicals, not a real food substance, that disrupt your endocrine system and vital neurotransmitters in the brain that would be needed to regulate appetite, mood, and the migrating motor complex. The use of artificial sweeteners is often associated with an increase in cravings for sugar and carbohydrates, a larger appetite, binging, weight gain, and a wide variety of other side effects like panic attacks, hyperactivity, depression, nervousness, attention deficit, headaches, irritability, seizures, dizziness, joint pain, and much more. They also cause numerous digestive disturbances like abdominal pain and cramping, diarrhea, and nausea.
Sucralose, the sweetener known as Splenda, which is often promoted in many of low-carb diets, is derived from a pesticide formula and has been shown to cause a decrease in friendly bacteria in animals and also increases fecal pH, both of which encourage overgrowth of bacteria and Candida. Of course, everyone knows that saccharin causes cancer. Acesulfame potassium known as Sunett or Sweet One and found in many sodas is believed to cause neurological damage, influence prenatal development, and be carcinogenic. At one time, aspartame, the artificial sweetener known as Equal, Nutrasweet, Canderel, or AminoSweet, was registered by the Pentagon as an agent of biochemical warfare. Both sucralose and acesulfame potassium prompt an insulin response, which means it will lead to cravings for sugar and carbs in that way as well and can contribute to insulin resistance, type 2 diabetes, etc. So these substances do not belong anywhere on the menu for numerous reasons.
Many practitioners recommend the Specific Carbohydrate Diet, a low FODMAPs diet, or the GAPs diet for the treatment of SIBO. Each of these diets has a significant amount of success and they are certainly steps in the right direction. However, in my personal experience, I don’t feel that any of these diets are complete enough individually on a variety of different points as they permit an array of foods that are harmful to the gut and produce symptoms in myself and many of my clients. I feel that the best diet for SIBO, or Candida and any other gut disorder, is a combination of a low-carb Paleo diet that eliminates or reduces the FODMAPs group of foods, the high histamine foods the high glutamate foods, and nuts and seeds, and then tailor it specifically for each individual according to their unique biochemical needs in what I call the Individualized Paleo Plan.
In most cases, the carbohydrate level will need to be under 50 grams of carbs per day. If overgrowth is severe, then it may need to be at 25 or 30 grams per day, until some improvements have been made. This includes complex and Paleo-friendly carbs like sweet potatoes, yams, winter squash, taro, fruit, and nuts. As a matter of fact, as demonstrated in Dr. Norm Robillard’s work, complex carbohydrates can be even more problematic for the individual with SIBO than simple carbs. Simple carbs are metabolized quickly, while complex carbs sit around the GI tract a long time, which means bacteria have access to them for a longer period of time to be fermented. Of course, I’m not saying one should eat simple carbs because they are bad for us for other reasons (spike in glucose and insulin, type 2 diabetes, obesity, heart disease, etc.) I’m just wanting to call your attention to the fact that complex carbs are problematic in other ways.
However, one’s intolerance to the foods that feed bacteria can vary widely. Each person may have a different threshold depending on the severity of overgrowth or what types of bacteria are involved, stress levels, other health conditions that may exist, damage to the gut, and whether Candida is present as well. One person may be completely intolerant of all the foods in the list that feed bacteria while someone else may only have to limit a few of them. It may not always be necessary to eliminate a food completely; in some cases, it may only need to be reduced to a smaller serving size or eaten less frequently. Your threshold can change from time to time in response to changes in your body and life or even go and down. Carbohydrate tolerance may increase after overgrowth is reduced or it may go down if overgrowth increases.
For example, in my own life, when my SIBO level was low I could eat a small serving of fruit and nuts (1/2 cup fruit and 2 TBSPS nut butter) three times a week with minimal discomfort. However, when my SIBO was at its highest, I couldn’t touch fruit and nuts. After an experiment with resistant starch, my SIBO level went through the roof and I completely lost my ability to consume fruit or nuts at all and had to stay under 30 grams of carbs per day. Additionally, if I experience some kind of high-stress event in my life, my abdominal pain level will increase significantly and I can barely eat anything. When that stressful event passes, then I return to baseline.
So experimentation will be required to find how your body responds and then adjust accordingly to your threshold. Since many of the foods that feed bacteria can be beneficial to our health when eaten in moderation, (like fruit and nuts) then we don’t want to remove foods unnecessarily. Additionally, be sure to challenge yourself periodically to see if your threshold has changed. However, do be careful when reintroducing carbs. It may take a while for the bacteria to recolonize, so you may get away with increasing your carb intake for a while until the bacteria levels reach a certain point, and then symptoms return. Dr. Siebecker and other SIBO experts state that a low-carb diet must generally be continued even after successful treatment to prevent overgrowth from returning. Additionally, in regard to food sensitivities, memory B cells can make inflammation and leaky gut persist when the particular food comes back into the diet.
Types of Bacteria Involved
Although we have thousands of different species of bacteria inhabiting our gastrointestinal tract, we have two primary classes known as – Bacteroidetes and Firmicutes. Some may be friendly and beneficial and others may cause disease. In a healthy gut, there will be a vast array of different bacterial species that compete for space and nutrients, but microbes in an unhealthy gut will be less diverse and one individual type may become dominant. Bacteroidetes eat a more diversified diet of protein, fat, and carbs, while firmicutes eat primarily carbs, starches, and fiber. Therefore, if Firmicutes are present in abnormally high numbers, and the diet is heavy in carbs, starches, and fiber, it will encourage overgrowth of the Firmicutes. If these bacteria have wandered into the small intestine, as is the case in SIBO, then it will make SIBO proliferate.
Research has found that people with IBS, (which can be caused by SIBO) tend to have a higher number of Firmicutes and less microbial diversity overall. So it is believed that most bacteria involved in SIBO are the ones who love and thrive on carbs. On the other hand, a diet that is high in the foods that firmicutes feed on can be what causes the overgrowth in the first place. In Fast Track Digestion: IBS, Dr. Norm Robillard cites a variety of studies that indicate a diet high in complex polysaccharides encourages an increase in Firmicutes, Actinobacteria, and some strains of clostridia, but a decrease in Bacteroidetes and other strains of clostridia, which can then lead to excess gas and toxin production, and all the associated symptoms and conditions as well as an increase in “microbe-mediated formation of carcinogenic compounds.” Robillard goes on to explain, by eating a diet that is lean in carbs, starches, and fiber and richer in animal protein and fat then we create an environment that encourages healthy competition between our gut microbes “that will favor survival of the well-adapted organisms best suited to be our partners in digestion and health.”
However, if overgrowth involves Bacteroidetes, which feed on protein and fat as well, then restricting the cabs may not provide complete relief of symptoms. Furthermore, just like Candida, bacteria are exceptionally adaptable, and although they would rather have carbs as their food source, they will make do with whatever is present. They may also feed on blood glucose, which is always around to some degree even when carbs are low, due to gluconeogenesis. Keep in mind that bacteria in soil and groundwater will even break down industrial solvents for energy. They are so effective at this, that our government often uses them to clean up toxic waste sites. This demonstrates how bacteria can adapt to and thrive in just about any environment or situation. Some will even survive in radioactive waste sites. So, how much relief is experienced with the diet will be influenced by how severe the overgrowth is and what species of bacteria are involved, and the adaptability of the particular microbes.
I have experienced this in my own life as well. When my SIBO level was mild, I could pretty much control my symptoms with a low-carb, low FODMAPs, Paleo diet. However, when my SIBO level was at its highest, and I was down to nothing but 25 to 30 grams of carbs per day, this did not provide complete relief. I felt significantly better and it was simply impossible to eat more carbs or the suffering was unbearable. However, my bacteria then began eating my protein and fat. If my carb consumption went over 30 grams per day, I had horrific abdominal pain and excess gas that smelled like sulfur. When I ate nothing but protein and fat, I had a milder level of pain and production of gas, but it wasn’t gone completely and the gas smelled like ammonia, which is an indication that bacteria are eating protein. For a while, it was extremely painful to eat anything at all, until I began using herbal antibiotics, which brings me to the next point. In most cases, diet alone is not going to be sufficient. It should be combined with the herbal or pharmaceutical antimicrobials which we discussed previously. According to Dr. Siebecker, diet alone has been successful in infants and children, but not adults.
It is also recommended that one should not eat in between meals. Allowing four to five hours between meals enables the migrating motor complex to occur and move bacteria from the small intestine to the colon. If snacking is taking place in between meals, it will interrupt this process. Water is permitted.
Bone Broth and Fermented Foods
You may have noticed throughout the natural health field that the use of bone broth is often recommended to remineralize and heal the gut from a variety of gastrointestinal disorders. Although bone broth can be highly beneficial in some conditions, that is not the case with SIBO. According to Dr. Siebecker, the joint and cartilage tissue that is still attached to the bones contain mucopolysaccharides (MOS), a substance that feeds bacteria, and therefore will exacerbate SIBO. She recommends that people with SIBO should make broth from meat, not the bone.
Bone broth is also exceptionally high in glutamate, which can contribute to an imbalance in GABA and glutamate in people who lean towards glutamate excess. Excess glutamate is toxic to the brain, causing overstimulation, neurological inflammation, and killing brain cells, which results in a wide array of mental health symptoms like OCD, autism, anxiety, migraines, restless legs, and even seizures.
Furthermore, when glutamate is high, that means GABA is low. In the gut, GABA plays a critical role in bowel contractions and too little can result in abdominal pain, constipation, and slow transit time. It may also contribute to GERD, as it is needed to regulate the lower part of the esophagus. GABA also assists with maintaining sufficient levels of IgA, the antibodies that protect our gut and other mucous linings from pathogenic invaders. High levels of glutamate increase eosinophils, a type of white blood cell, which contributes to inflammation. Furthermore, many types of microbes thrive in an environment that is high in glutamate. It also depletes glutathione levels which is important for controlling inflammation and gut health, as well as detoxification.
In the brain, GABA helps regulate mood, sleep, appetite, sexual arousal, and the autonomic nervous system. GABA is what enables us to relax, calm down, unwind, and deal with stress. Low levels of GABA often result in cravings for sugar and carbs or other addictive substances like drugs and alcohol, as these substances will temporarily increase GABA levels, but then GABA drops even lower after consumption, so these substances actually deplete GABA even further. Other drugs that target GABA receptors like Xanax, Klonopin, Ativan, Valium, and Neurontin also deplete GABA levels. Additionally, GABA can be depleted or transmission may be disrupted by a wide variety of foods and substances like sugar, caffeine, chocolate, whole grains, high starch foods, food additive and dyes, and artificial sweeteners and flavorings. Additionally, GABA needs serotonin to work adequately. Some people are genetically predisposed to have a greater amount of glutamate receptors than others. The more glutamate receptors one has, the higher the level will be. These people will always tend to lean toward excess glutamate, so they will have a lifelong need to monitor their glutamate intake. High levels of glutamate increase the toxicity of mercury when it is present in the body. It also makes cancer cells proliferate and increases tumor growth and survival.
Glutamate and insulin have a finely balanced reciprocal relationship. High levels of glutamate incite an insulin response, which means insulin will promptly bring blood glucose levels down. However, glucose is required to manage glutamate levels at the synapses, so if glucose is too low, this is going to increase glutamate. Therefore, low blood sugar or hypoglycemia is not only going to lead to higher levels of glutamate, but it will also impede your ability to reduce the build-up. This means that it is critical to avoid foods that cause a spike in blood sugar and insulin in order to maintain a balance between GABA and glutamate. While at the same time, keeping glutamate levels from being elevated will be equally as important for keeping your insulin levels from spiking and managing your blood sugar levels.
Bone broth is also high in histamine which can be problematic for people who have high brain histamine (Histadelia) or histamine intolerance. High brain histamine is associated with obsessive-compulsive disorders, sex and gambling addiction, brain racing, abnormal fears, attention deficit, hyperactivity, aggressiveness, disrupted sleep or insomnia, and even schizophrenia. While histamine intolerance may be exhibited as hives, itching, flushing, wheezing, watery eyes and runny nose, nasal congestion, gastrointestinal distress, and motion sickness to name just a few. Ironically, some of the symptoms associated with histamine intolerance include constipation, diarrhea, abdominal swelling and pain, fatigue, which pretty much mimic the symptoms of SIBO.
Fermented foods (including cultured vegetables and kefir) are also high in histamine and glutamate, which will increase symptoms for people who have an abnormal level of histamine in the brain (Histadelia) or a histamine intolerance or an imbalance in GABA and glutamate. They also contain a significant amount of alcohol, which can make people feel drunk and lead to relapse in the alcohol addicted. Alcohol feeds bacteria and Candida. Fermented foods also contain high levels of bacteria that can exacerbate SIBO in some people, depending on which types of bacteria are involved in the overgrowth. We will discuss this topic in more detail further below under the probiotics section.
Therefore, in people with high histamine and/or high glutamate the consumption of bone broth and fermented foods can result in symptoms like anxiety, depression, insomnia, headaches or migraines, OCD, disrupted cognitive abilities, impaired GI function, and much more. Many people with gut disorders like Candida and SIBO may also have high histamine and glutamate levels, so this is something to watch out for. The GAPS diet is very high in histamines and glutamate with all its fermented foods and bone broth.
High levels of histamine and glutamate both activate the stress response system and may keep one stuck in sympathetic dominance, which as we discussed previously can then inhibit motility and the migrating motor complex, kill friendly bacteria, weaken the immune system, and much more.
While it is true that histamine intolerance can be caused by small bacterial overgrowth and that intolerance may improve if overgrowth is reduced, that is not always the case. Some species of bacteria have the ability to convert histidine in the diet into histamine. If these bacteria are present in high numbers, then histamine levels may be elevated, which makes one more vulnerable to high histamine foods. Additionally, the enzymes DAO and HMT (N-methyltransferase) that are used to break down histamine are created by enterocytes (cells) in the gut. Therefore, damage done to the gut from bacterial overgrowth or Candida can impair adequate production of these enzymes, which leads to a buildup of histamine. In these situations, then histamine intolerance may improve when overgrowth is addressed. However, until one is successful in eliminating SIBO, then a reduction in high histamine foods will be necessary.
However, there are genetic polymorphisms that can impair one’s ability to produce both DAO and HMT. Additionally, DAO production can be inhibited by a deficiency in vitamin C or copper as both of these are needed for the synthesis of the enzyme, and B6, which is required as a cofactor to DAO to break down histamine. HMT requires the methylation process to inactivate histamine, so deficiencies in nutrients that are required for methylation like folate, B12, B6, magnesium, or SAMe, as well genetic polymorphisms that affect methylation like the MTHFR gene may lead to under-methylation which will consequently impair one’s ability to break down histamine. Deactivation of histamine in the central nervous system is always achieved through HMT because DAO does not exist in the central nervous system. Therefore, in some of these situations, it would be necessary to avoid high histamine foods permanently even if bacterial overgrowth doesn’t exist. Additionally, even when everything is working right, if one is eating a diet high in histamines, the enzymes may not be able to keep up.
Histamine may also be released when an antibody attacks a protein that escapes from the gut into the bloodstream, so histamine levels will be elevated when you have a leaky gut. Toxins from Candida can also trigger histamine release, so if one has Candida and SIBO, then the histamine load might be even higher.
Another diet called the Elemental Diet may be used for small intestinal bacterial overgrowth and has been quite successful without any type of antibiotic. The Elemental Diet removes all solid food for two to three weeks and consists of nothing but powdered predigested nutrients that are mixed with water. It is commonly used in hospitals to treat a variety of gastrointestinal disorders to give the digestive tract a break. This completely starves out the bacteria as the nutrients in this form are absorbed so quickly that the bacteria do not have a chance to access them. It has a success rate of 80 to 85 percent. Although Elemental Diets are available over the counter, I would not recommend this diet without being under the care of a physician who has expertise with SIBO. Additionally, I personally feel that this option would be best utilized only in extreme cases where the individual is severely malnourished, experiencing a failure to thrive or a lot of weight loss, symptoms are disabling, or their diet is too restricted.
The Elemental Diet formulas on the general market are loaded with ingredients we don’t really want to put in our bodies. To avoid these ingredients a homemade formula can be designed with amino acid formulas and a good source of fat like medium-chain triglycerides. I think it’s best to leave out any sweetener, especially if you have Candida in addition to SIBO.
However, like treatment with antimicrobials, overgrowth typically returns when one returns to eating normally. So, treatment with other methods must be ongoing.
Probiotics and SIBO
One has to be very careful in their choice of probiotics when SIBO or any other gut problems are present. As we mentioned previously, small intestinal bacterial overgrowth can be caused by an overgrowth of D-lactate-producing bacteria, like L. acidophilus.
The two most commonly used probiotics consist of bifidobacteria or lactic acid-producing bacteria known as Lactobacillus. Within the Lactobacillus species, there are some strains that produce mostly L-Lactic acid (L-Lactate) or mostly D-Lactic acid or (D-Lactate) during the fermentation process. L-Lactate is most predominant in the body and easily metabolized. D-Lactate is not an issue for most people, but in high amounts, it can be difficult for some people to break down, particularly people who already have some impairment with carbohydrate malabsorption, which is the case in SIBO, as well as a variety of other conditions like IBS, autism, immune disorders, fibromyalgia, and chronic fatigue.
When in excess, D-Lactate is a neurotoxin that can produce a wide variety of neurological problems like confusion, brain fog, depression, slurred speech, disorientation, headaches, impaired coordination, anxiety, nausea, nervous shuddering, tics, OCD, and in extreme cases encephalopathy. It can also cause weak, aching, or painful muscles, extremely painful muscle spasms, difficulty concentrating, and impair mitochondria function and the production of ATP (our primary source of fuel) leading to fatigue. ATP is also needed in gluconeogenesis (converting protein and fat into glucose), so this may consequently contribute to hypoglycemia or low blood sugar issues. D-Lactate excess is implicated as a possible contributor to a wide variety of conditions like chronic fatigue syndrome, attention deficit, fibromyalgia, autism, and autoimmune disorders. Excess L. acidophilus has even been found in people with Crohn’s.
Additionally, some other species of bacteria like commensal streptococcus and enterococcus, which may be involved in SIBO are D-lactate producing as well. So, if the overgrowth in the small intestine involves one of these D-Lactate-producing bacteria, then D-lactate may be in excess, and supplementing with a D-Lactate-producing probiotic will increase D-Lactate levels even further.
Therefore, if the bacteria involved in one’s bacterial overgrowth include the D-lactate-producing bacteria, then supplementation with some forms of acidophilus will not only encourage overgrowth of the bacteria but will also increase D-lactate levels. The same would be true for probiotic foods that may contain L. acidophilus, like yogurt, fermented vegetables, or kefir. These foods may or may not be helpful depending on what types of bacteria are involved in each person’s overgrowth. In some cases, they could do more harm than good.
The two bacteria commonly found in probiotic supplements that produce primarily D-Lactate include the very popular L. acidophilus and L. Plantarum.
When the overgrowth involved is a D-Lactate producing bacteria, then the D-lactate producing probiotics like L. acidophilus or L.plantarum should be avoided and a special kind of probiotic that is listed as D-lactate free may be helpful. Some studies have found Bacillus calusii, Bifidobacter brevis, Lactobacillus casei to be beneficial. The bacteria that produce primarily L-Lactate include L. Salivarius, L. Rhamnosus, Lactobacillus bulgaricus, L. helveticus, and L. delbrueckii and Streptococcus thermophilus (used to make yogurt.) If there is a worsening of symptoms when one supplements with L. acidophilus, this is a strong indication that overgrowth is caused by the D-lactate-producing bacteria.
An Organic Acids Test can tell you if you have an excess of D-Lactate in your body, which would be an indication that small bacterial overgrowth with a D-Lactate producing bacteria is involved. However, you should note that a diet high in carbohydrates can also cause a build-up of D-Lactate. There are a variety of other factors that can lead to high lactate, which we will not discuss at this time, but they would be mentioned in the commentary of the OAT test.
It’s also important to note that some D-lactic acid-producing bacteria are resistant to antibiotics, so when an antibiotic is used, everybody else may be killed off except them, which allows them to become dominant.
On the other hand, Bifidobacteria can be a bully, take over and grow out of control as well, if L. acidophilus is not around in sufficient numbers. If this is the case, then supplementing with bifidobacteria would be counterproductive and L. acidophilus would be beneficial. So, depending on the gut biome of each individual, there may be times when Bifidus or lactobacillus may be the right or wrong choice. The type of probiotic that is going to be beneficial depends on what microbes each individual has present in their gastrointestinal tract.
Prebiotics, the substances that accompany the probiotic to keep the bacteria alive, like FOS, inulin, and maltodextrin, will be used as a food source by small intestinal bacterial overgrowth. These substances can also feed Candida. So probiotics with a substantial amount of prebiotics should be avoided. A small amount of prebiotic may be tolerated in some people, while none may be tolerated in others.
Additionally, some strains of bacteria that can generate histamine are commonly used in probiotic supplementation as well, so for the person with histadelia or histamine intolerance, these species are best avoided. They include Lactobacillus casei, Lactobacillus reuteri , Lactobacillus delbrueckii, and Lactobacillus bulgaricus.
The dosage of probiotic that is needed can vary widely from person to person as well depending on age, kind of bacteria involved in overgrowth, the extent of imbalances, how well the detoxification system is working, or other unknown factors. Generally speaking, most practitioners feel that the more severe the dysbiosis, the higher the dose needs to be to achieve positive and measurable results. However, in some cases, less is more. Many people may not need the recommended dose, at least in the beginning. When severe dysbiosis is present, then starting at a low dose and slowly titrating up to higher doses may work best. If symptoms get worse, then one should cut back on the dosage and increase slowly. Anytime symptoms increase throughout the process, then go back to the dose that did not produce symptoms for a few days and then try again. However, some people may do best staying with a low dose indefinitely.
Symptoms that are often attributed to die-off may actually be due to the wrong type of bacteria or a dosage that is too high. The symptoms one experiences from the wrong probiotic or too high a dose can be the same as the condition that one is trying to treat, so it can be difficult to differentiate between the two of them. If one is still having die-off after a week or so with a probiotic, then chances are good that it is not die-off causing the symptoms. Additionally, if symptoms are significantly worse, then even if it is die off, this is counterproductive.
Each person needs to experiment to find the right species, strains, and dosages that work best for their body.
Some practitioners recommend Saccharomyces boulardii, which is a yeast that will eat bacteria, and Candida and/or soil-based organisms which secrete antimicrobial peptides for the people who must avoid the D-Lactate producing bacteria. Again, these can be helpful for some people, but these bacteria can become pathogenic as well for others. For example, when I took B. subtilis, one of the most popular soil-based organisms on the market, I experienced disturbed sleep, colorectal inflammation, significant psychological disturbances, and brain dysfunction. After taking B. subtilis, I developed a whole new array of gut problems that I didn’t have previously. I’ve also experienced high levels of anxiety, insomnia, and biofilms in my mouth in response to probiotics that are high in acidophilus and Bifidus. I’ve heard reports of similar experiences with probiotics, Saccharomyces and B. subtilis from clients and there is evidence in the literature of both B. subtilis and Saccharomyces boulardii becoming pathogenic. Since the 1990s there has been an increasing number of reports in regard to Saccharomyces infection. When dysbiosis is present, then the potential for any microbe to gain the upper hand exists.
However, according to Dr. Leonard Smith who is quoting Dr. Timothy Buie, MD (pediatric gastroenterologist), “about 15% of people with autism (and maybe the general population) can’t tolerate any type of probiotic supplements.”
As Dr. Pimentel points out in his book, A New IBS Solution, if the migrating motor complex is not working properly, as is the case with SIBO; then when you take a probiotic, they may accumulate in the small intestine where we don’t want them and make the problem worse.
Considering all this, it is unclear whether probiotic use is beneficial or advisable for the person with SIBO.
HCL Enzymes and Nutrients
Hydrochloric acid is frequently used to help modulate incoming bacteria levels. However, this is only called for if you have low stomach acid levels. Not everyone with SIBO does. You could possibly have high levels of HCL, in which case, supplementation would be counterproductive. HCL levels can be determined with an HCL challenge test. However, if you want to get more scientific, there is a test called the Heidelberg test, which is quite expensive. Other digestive enzymes may also be beneficial like pancreatin.
Dr. Pimentel also states in A New IBS Solution that pancreatic enzymes taken with meals can help digest food before bacteria have a chance to get them. This will not eradicate bacterial overgrowth, but an improvement of 30 to 50 percent could be obtained.
It is critical that one avoids anything that will inhibit stomach acid production like antacids, H2 inhibitors, and proton pump inhibitors (omeprazole -Prilosec, lansoprazole – Prevacid, esomeprazole – Nexium, etc).
Once overgrowth is eradicated, then a variety of nutritional supplements may be used to help heal the gut lining (enterocytes and the brush border) which may include colostrum, glutamine, zinc carnosine, vitamin A, C, D, and E, fish oil, curcumin, resveratrol, glutathione, and NAC. Brush border enzymes may be used as well. However, some of these nutrients can be problematic for other conditions. Although glutamine is the preferred source of fuel and nitrogen needed for epithelial cells that line the gut and therefore promote regeneration and repair, it is also the precursor to glutamate and therefore in people who tend to lean towards excess glutamate, it can contribute significantly to an increase in glutamate levels, which will be counterproductive since it will result in sympathetic dominance, brain cell death, etc. Additionally, some gut bacteria eat glutamine, so in people who have SIBO, glutamine can cause the proliferation of SIBO. And some bacteria convert glutamine into glutamate, which can contribute to excess glutamate.
Zinc is vital for a healthy gut and immune system, however, according to Dr. Amy Yasko, zinc in excess of 60 mg a day can also produce glutamate excess. If heavy metal toxicity is present, then supplementation with NAC too early in the process can move mercury to the brain.
High doses of buffered (with calcium, magnesium, and potassium) vitamin C powder can be used to promote gut motility until it begins to work better on its own.
Many practitioners may recommend a variety of mucilaginous herbs like licorice, slippery elm, marshmallow, and aloe vera that have proven to be beneficial for soothing the gut. However, if one has SIBO that has not been treated successfully, then these herbs may encourage overgrowth of bacteria, because of their high level of mucopolysaccharides which feed bacteria.
If one has developed nutritional deficiencies due to Candida or SIBO, then nutritional support for the deficiencies would be implemented. However, do be aware that some nutrients like iron, calcium, and magnesium can be a food source for bacteria and Candida and their biofilms, so sometimes it is suggested that supplementing with some of them should be held off until bacteria and Candida levels are decreased. Part of treatment requires that these nutrients be restricted from the microbes with lactoferrin or an oral chelator.
Candida often occurs in conjunction with SIBO and they perpetuate one another. The damage that each one does creates an environment in the gut that encourages the overgrowth of the other. If SIBO is not addressed, then reducing the overgrowth of Candida will be difficult to achieve and vice versa. Many of the steps that one will take to deal with Candida will also be beneficial for bacterial overgrowth and vice versa, but each one requires additional attention unique to that condition. We will talk more about the Candida, SIBO, and H. pylori connection next week. You can find hundreds of pages on my site that address Candida or you may take a look at my eBook, Candida Secrets.
Other Factors that Cause Inflammation
There are many other factors that can contribute to inflammation and leaky gut which need to be addressed as well, including intestinal parasites, H. pylori, sugar, grains, legumes, caffeine, chocolate, food additives and preservatives, pesticides, herbicides, artificial sweeteners, heavy metals, birth control pills, too much omega-6, zinc deficiency, lack of sleep, casein, stress, chlorinated water, alcohol, food sensitivities, steroids, proton pump inhibitors, and NSAIDs. Although each of these factors may cause damage in a different way, the bottom line is that they all cause inflammation in the gut, and inflammation regardless of where it comes from, may encourage overgrowth of not only bacteria but Candida or parasites as well.
As discussed earlier, stress can play a major role in SIBO, Candida, and other functional gut disorders because it weakens the immune system, impairs digestion, gut motility, and secretion of stomach acid and digestive enzymes, kills friendly flora, inhibits nutrient absorption, floods the bloodstream with glucose, drains neurotransmitter levels, deactivates the vagus nerve which is needed to modulate the migrating motor complex and for the gut to communicate with the brain and vice versa; all of which can encourage overgrowth of bacteria or other microbes like H. pylori and Candida. Chronic stress can cause dysfunction in the autonomic nervous system, whereby it gets stuck in overdrive and is referred to as sympathetic dominance. Sympathetic dominance keeps the body in a perpetual state of stress. Therefore, it is critical that one manages their stress on a daily basis.
One of the most effective methods for activating the vagus nerve and consequently the parasympathetic nervous system and the relaxation response, which will turn off the sympathetic nervous system, is deep breathing exercises. They should be practiced every morning when you get up and each night when you go to bed and anytime throughout the day when one feels challenged. Mindfulness meditation and spending time in nature are also excellent for this goal. Other good options include walking, Yoga, Tai Chi, Quigong, soothing music, art, and smiling on a frequent basis. In some cases, when permanent damage has been done to the stress response system, then more aggressive methods may be helpful like brain retraining.
Since the vagus nerve is vital for stimulating the migrating motor complex, then other factors that damage or inhibit the functioning of the nerve like heavy metals and pesticides would be critical to address as well.
Pesticides like Roundup (glyphosate) also impair the life cycle and function of healthy bacteria in the gut but don’t affect clostridia or E. coli, so these guys may become dominant. Glyphosate also impairs cytochrome P 450 enzymes that are critical for detoxification, contribute to nutritional deficiencies, and deplete serotonin and dopamine levels. It also fosters overgrowth of an organism called Pseudomonas aeruginosa that will release high levels of formaldehyde (which is a neurotoxin and carcinogenic) and other toxins within the body. All of which may create an environment that encourages the overgrowth of bacteria and/or Candida.
Other Environmental Toxins
Environmental toxins of all kinds, including those found in your common everyday products like dish soap, personal care products, perfumes and colognes, air fresheners, laundry soap, household cleaning products, air pollution, industrial solvents, etc. can all trigger the stress response system and deplete or inhibit neurotransmitters like serotonin, dopamine, GABA, and keep on stuck in sympathetic dominance if they are exposed on a daily basis. Toxins can also get lodged in the small intestine and cause more damage to the already vulnerable gut and pathogens thrive in a toxic environment. Therefore, living an environmentally friendly lifestyle is a critical component of healing as well.
One of the primary symptoms of an under-active thyroid is slow motility, supporting the thyroid may be necessary when low. The thyroid is often under-active because of weak adrenals, so support for the adrenal glands may be needed as well.
Electrosmog (electromagnetic radiation fields discharged from wireless technology and electronic equipment) has been found to make pathogens like bacteria, mold, Candida, and viruses to multiply in numbers and release higher levels of toxins. It may also alter cells within our brain, nervous system, and immune system and disrupt cell-to-cell communication within the body. Furthermore, electrosmog triggers the stress response system.
Getting adequate sleep is absolutely essential for the proper functioning of neurotransmitters that will help regulate the stress response system, as well as immune function and hormones that regulate our appetite and blood sugar levels. It also plays a role in modulating motility and the migrating motor complex. Sleep is also important for neurotransmitter function because lack of sleep causes neurons to become less sensitive to neurotransmitters, which impairs communication.
Problems with the ileocecal valve often respond positively to direct massage of that area. So ileocecal valve massage may be beneficial for the person with SIBO. However, the gas itself created by SIBO can put pressure on the ileocecal valve and cause it to open. Any other issues that may be impairing the function of the ileocecal valve should be addressed.
The pH level of the gut is important because if it is too alkaline, it will encourage the overgrowth of bacteria and Candida. pH can become too alkaline due to antibiotic use, a diet that is too alkaline, not producing enough stomach acid due to age or impaired production, chlorinated drinking water, a lack of acid-producing bacteria, and a variety of drugs like antacids, proton pump inhibitors, and ulcer medication.
Enemas or Colonics
Studies have found that colonics or enemas can lower or even eliminate methane levels, which would reduce symptoms. Both can be highly beneficial for eliminating toxins from Candida or other microbes as well, and they can physically remove the bacteria and Candida itself. However, do use them sensibly. Doing them every day could potentially do more harm than good. Additionally, an enema or colonic only removes toxins and organisms from the colon, not the small intestine. So this means they will not fix the problem of overgrowth, but they can be used to assist with symptom relief.
Getting regular physical activity is vital for gut motility. Mild to moderate exercise has been shown to stimulate gastric motility and enhance the stomach’s processing of food. However, it is critical that exercise is mild to moderate, not too excessive, or for extended periods of time. Too much exercise will deplete neurotransmitter levels, release histamine, weaken immune function, increase blood sugar levels, and trigger the stress response system.
To review the MMC (migrating motor complex) can be impaired by surgery, nerve damage, opiate use, stress, intestinal scarring, gastrointestinal infections, proton pump inhibitors, antacids, anatomical abnormalities, and some disease processes. Anything affecting the migrating motor complex should be addressed.
Maintenance for Small Intestinal Bacterial Overgrowth
As we mentioned previously, at least fifty percent of the people treated successfully for SIBO will relapse within a year. Not only that, anywhere between 15 and 50 percent are not achieving successful eradication of SIBO. One study found that treatment with antibiotics eliminates symptoms for an average of only 22 days. Bacteria can repopulate in as fast as two weeks, but it may happen gradually or be set off by something like a major life stressor or change in the diet or supplementation.
For example, I had significant improvements with an antibiotic I had taken for a respiratory infection and these improvements remained steady as long as I stayed low-carb and low FODMAPS in addition to my standard Paleo. Then I experimented with resistant starch and things got worse than they had ever been.
The reasons for this are many, but are most likely due to the fact that the underlying cause is not corrected; which may lie in the ileocecal valve, the migrating motor complex, chronic stress, or inflammation and perpetuation from some other microbe like Candida. It could also be due to the fact that some bacteria are spore formers and spores are resistant to antimicrobials – when treatment subsides they repopulate. Additionally, some bacteria have the ability to make us excrete zinc in our urine, which weakens our immune system. Gram-negative bacteria are more resistant to antibodies and antibiotics, so perhaps this could influence success rates as well if they are present in overgrowth. Furthermore, many of the bacteria may be taking refuge in the biofilm, which can be very difficult to penetrate. The substances we have at this time for breaking the biofilm are not always effective. Some of the bacteria may be resistant to whatever is being used.
According to Siebecker, other factors that have been found to contribute to unsuccessful eradication include, chronic narcotic use, anatomical abnormalities, Addison’s disease, scleroderma, inflammatory bowel disease, NSAID-induced ulceration, and colonic inertia (inability to properly move the waste from the cecum into the rectosigmoid area.)
Also, I didn’t see the experts mention this, but I think it is entirely possible that the bacteria send out some kind of signal via the vagus nerve that inhibits the migrating motor complex, so they can remain where they want to be. Since we know they have the ability to send out signals that alter thoughts, mood, and behavior and change our internal environment to suit their needs, and disarm the immune system, this seems a logical conclusion as well.
Dr. Pimentel believes that SIBO and IBS are caused by an autoimmune response to a toxin (Cytolethal Distending Toxin (CDT) released by bacteria that cause food poisoning. In the small intestine, we have a particular type of nerve cell called ICC cells that are in charge of regulating the migrating motor complex. These cells look very similar to Cytolethal Distending Toxin (CDT), so the immune system confuses them for the toxin and not only develops antibodies against the toxin but against the ICC cells as well. This causes damage to the cells, which consequently results in the impairment of the functioning of the migrating motor complex, which leads to the overgrowth of bacteria.
Regardless of the reasons why, ongoing maintenance with all the methods presented in the previous treatment section (low-carb diet, managing stress and sympathetic dominance, supporting gut health, maintaining pH, avoiding acid blockers, etc.) will be required to prevent overgrowth from returning, or in the case of people who do not achieve complete eradication, in order to keep symptoms at a minimum. If the treatment did not achieve complete eradication or overgrowth returns, then treatment may need to be repeated periodically as needed.
Both Dr. Pimentel and Siebecker (the two leading experts on the topic) state that following the low-carb SIBO diet must be continued after treatment to prevent relapse even if one is 100 percent successful at eradication. However, restriction of fermentable carbs may or may not be as strict as it was pre-treatment as the threshold may change and can vary from person to person. So one should experiment to find what works for them and they should continue to keep meals spaced four to five hours apart,(with water allowed) to encourage the migrating motor complex to take place.
Since it is believed that dysfunction of the migrating motor complex is a primary underlying cause of SIBO, Dr. Siebecker and Pimentel encourage the use of substances that stimulate the MMC, called prokinetics. Prokinetics are taken for a minimum of three months and may be very long-term. They include low-dose naltrexone, low-dose erythromycin, and low-dose tegaserod. However, each of these comes with a substantial risk of creating new problems. I cannot say I support the use of any of these methods. Naltrexone targets endorphin receptors, anytime an artificial substance is used to manipulate neurotransmitters it results in depletion of the neurotransmitter which then results in addiction and a wide array of physiological and psychological symptoms. Erythromycin is a broad-spectrum antibiotic, so naturally, it would be counterproductive to take this on an ongoing basis. Tegaserod was removed from the market by the FDA because of an increased risk of heart attack and stroke, but it may still be obtained for emergency situations with permission from the FDA. It is my opinion that each of these methods is too risky and research in the field needs to be searching for more natural forms of Prokinetics.
Be sure to check out the third post in this series, where we will discuss how to differentiate between SIBO, Candida, and H. pylori.
Need Help with SIBO?
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Karen Kurtak, LAc. Adventures in Glutamine: How Side Effcts to Glutamine can Help You Identify the Root of Gut Issues https://karenkurtak.com/adventures-in-glutamine-how-side-effects-to-glutamine-can-help-you-identify-the-root-of-the-problem/
60 thoughts on “SIBO Treatment, Diet and Maintenance”
Wow. What a wonderful, informative article. Thank you for taking the time to share your knowledge.
Loving this series on SIBO and your including Candida as well as I suffer from both. I have a few questions, does staying low carb for too long become taxing on the adrenals and thyroid? Also, did you find a probiotic to take that is helpful for both SIBO and Candida? It’s all so complex really knowing whats causing what and how to approach the whole body when you have so much going on – anxiety, major gut issues even on stricter diet, adrenal fatigue, headaches, brain fog, etc. Thanks in advance! Love your blog and all you do to help folks like me!
I am not in agreement with that line of thinking. The adrenal glands do good on a low carb diet because they don’t have to deal with all that glucose. Every time glucose spikes then that is perceived by the body as stress and the adrenals are called upon to deal with it. Then when insulin is released and brings the blood sugar crashing down, then that is also perceived by the body as stress and the adrenals are called upon again to deal with it. Therefore, glucose keeps the the adrenal glands on a roller coaster ride. A diet that consists primarily of animal protein and fat keeps blood sugar and adrenals stable. In my own life, I have found low-carb to be critical for adrenal fatigue.
We are genetically wired to function primarily on animal protein and fat and very little carb. Carbs are non-essential in the diet. It’s the way we are designed, so it isn’t like we are asking the body to do something it can’t do. Asking it to function on carbohydrates is what is foreign and unhealthy. However, the low-carb diet has to be formulated properly. When carbs go down, then fat needs to increase and so does salt intake and water intake. Adequate protein and calories need to be consumed. Problems with a low-carb diet are usually due to the fact that these issues are not being addressed. You should read the book called, The Art & Science of Low Carbohydrate Living by Drs. Volek & Phinney. It will put any fears you have about low carb to rest. They feel the problems with the adrenals and the thyroid stem from insufficient calorie intake, not the low-carb intake.
However, we are all different and one person may need or handle more carbs than another better than another. We should gauge our carb intake by how many symptoms it creates. You can read more about that on the following page.
Glad you are enjoying the SIBO series. A company called Custom Probiotics has a D-Lactate free probiotic, which will meet the needs of Candida and SIBO, if there isn’t a bifidus overgrowth. It is also free of histamine producing bacteria as well. On the other hand, it is possible when SIBO exists that any probiotic can be problematic.
Yes, indeed it is a very complex situation.
I also wanted to thank you for this very informative series.
You’re welcome Frank.
Wonderful article!!! Very helpful. May I ask… What types of food would you recommend for the average sibo sufferer. I am on rifaxamin and vsl now and feel I cannot eat anything wo reflux migraine or vomiting. I react to every food esp and sadly veggies fruit and meat. I have ileitis as well and feel like there are no safe foods and all I’m recommended are potatoes and grains.
You can find details on the diet on the following page. Potatoes and grains are some of the worse things you can eat.
thank you as well, this is very useful! how long would one expect to have to be very strict with diet following treatment with antibiotics + then strict diet? and (to manage expectations) is this then likely to be needing to be managed for life, or do many people who deal with this carefully find healing & balance eventually?
Sorry for the delay in response, I’ve gotten very behind in responding to blog comments, as I have been involved in working on some new books.
This is discussed above in the maintenance section. Carbs must typically be restricted ongoing forever to maintain improvements, but each person may have a different threshold for what is acceptable.
Thank you for the articles on SIBO/yeast/pylori, they were very comprehensive and informative!
I am trying to understand how to d-lactate plays a role as I had a high level on my organic acid test, which was attributed to acidolphilus, although not sure why that particular strain. Does d-lactate show up on a hydrogen breath test? Is the treatment still rifaximin and herbal antimicrobials? There is not much out there that I can find on d lactate and SIBO, yours was one of the only ones to mention it at all. Thanks!
I am absolutely so grateful for your site! I was diagnosed with SIBO about 2 months ago, on a low FODMAP diet since, made an attempt at an herbal approach (drinking a special blend of Chinese herbs as a tea twice a day), but stopped that because I felt heartburn worsened. This morning finding and reading your article gave me more courage and determination to start Xifaxan this afternoon. Having Type 1 diabetes is quite a challenge along with the SIBO, and I have lost weight. Two questions in particular: On the low fodmap diet I was given I cannot have garlic; but it’s still ok to supplement with allicin, the active ingredient in garlic? Also I want to stop the weight loss and begin gaining again. I hope taking the Xifaxan will enable this!
Great article! I’ve been doing a lot of reading on SIBO. I was tested and had both hydrogen and methane SIBO. After going on the GAPS diet for a month and taking a month of herbal antibiotics, I was retested and now have only hydrogen dominant SIBO. I’m about to go on a second round of herbals. I’m still confused about what diet to be on WHILE on the antibiotics. I’ve read in order for bacteria to be eradicated I should have fermentable carbs in my diet. Would it be better to do a GAPS/ paleo diet with FODMAPS included while on them, or be on a fairly regular diet with some carbs? Basically I guess I’m asking if I need a lot of carbs in my diet to feed the bacteria?
You’re welcome. I do not support the GAPS diet because it is very high in glutamate and histamine, which cause a wide array of neurological and GI symptoms in people who already have elevated levels. People with SIBO tend to already be elevated in glutamate and histamine.
I’ve written extensively above what should and should not be eaten. But in a nutshell, it should be low-carb Paleo, that moderates the high histamine, high glutamate and high fodmaps groups. There are links to all of this above.
No, there should not be a lot of carbs in the diet. Carbs feed the SIBO.
1. Given that a + breadth test is not definitive and the herbal ‘antibiotic’ course is 4-6 weeks along with a SIBO diet for 3-4 months, why not initially do an Rx antibiotic as a determinator and if symptoms dissipate then enter into the longer more rigorous naturopathic therapy?
2. I’ve ‘heard’ that the side effects of a multi-herbal treatment are (can be) significant–yet I’m not finding that information on your site?
what can i say, this is the last word on SIBO! just an extraordinary synthesis of everything ive read on the subject. What was new to me was your caution regarding the GAPS diet. Dr Macbride is a pretty sharp tool, but I don’t remember her warning on glutamate in her book, so thanks a lot for that.
I am following Dr. Pimentel closely and I there are noises that something may be in the works. He has a twitter a/c that people should follow.
Thanks again Cynthia, and well done on your work.
Thank you Brian and you’re welcome. Yes, some great work done by Campbell-McBride. However, pretty much everyone I work with finds it impossible to follow the GAPS diet due its high level of histamine and glutamate (including myself). In many cases, the GAPS diet can cause significant deterioration in mental and physical health due to these aspects.
Well, there is not a one size fits all approach. Some people do fine with the herbal approach and other people do better with pharmaceutical. However, my preferred method is to hit hard with a pharmaceutical and then maintain improvements with herbals. All of this, as well the side-effects related to herbals you mention are discussed in great detail in the article above, under the sub-heading of “Herbal Antibiotics”. You must have overlooked it. Be sure to read the entire section.
I have found that the only diet that works for me is a “zero carb” diet, eating only animal based foods like the Inuits and Masai.
I’ve been struggling with sibo for years and have read hundreds of articles and web pages on the subject. This post is by far the best and most complete piece of information I have ever read. All of your suggestions are spot on and your resources are perfect. Thank you for taking your time and for not just throwing an article together. I’m sure you’ve helped many people with this, including me. Great job.
I stumbled upon your site today, it explains all of my symptoms for the last 30 years! I took several courses of antibiotics every year for 40 years from age 5 and proton inhibitors for 15 years! No wonder my digestive system is a mess. I have not taken either for the last 15 years except for Clostridium 2 years ago which made me very ill. My food will not digest and I vomit back up every few days after 6-9 hours! I am too scared to use antibiotics again, should I go the herbal route?
I suffer from SIBO (constipation-dominant) and have been gluten-free, soy-free, and dairy-free for over 10 years. I realized after reading this excellent article that gluten-free grains (rice, etc.) can be aggravating and that bone broth and glutamate mixes (to heal gut permeability) can contribute to gut inflammation. Cynthia, what do you think of Ancient Traditions Bone Broth powder? It supposedly is not high in histamines. Is it still high in glutamates and should be avoided?
I don’t know what the glutamate level is of that bone broth. But the other problem with bone broth, is that it contains substances that feed SIBO, as mentioned above.
Thank you so much for compiling all this information and sharing your knowledge. I concur with Danielle, this is amazing information and I’m grateful you’ve posted it. I’ve just been diagnosed with SIBO and am trying to figure out which antibiotic to take. Can you clarify that if you are going to take both the Rifaximin and the Neomycin, are they taken at the same time or do you do a round of one and then a round of another? The Dr. who diagnosed me is three hours away from where I live and I think I will end up getting these meds from someone here where I live. Also, I have heard that Rifaximin is very expensive, so I wondered if you have any advice on how it should be coded so that insurance might be more likely to pay? Sorry is these questions have already been posed and I missed it! Thank you so much for insights. They are invaluable!
Another question I forgot to ask is if you have heard anything about Atrantil?
Fabulous article! I’m treating myself with herbals due to the expense of the antibiotics (completely out of price range for me) and I’m self-diagnosed. (Adrenals, thyroid have been checked by specialist and are good).
I’ve seen discrepancies on whether or not to go low FODMAP vs. “normal” while treating SIBO. It makes sense that, if you go too low, the bacteria will hide / create biofilms and the herbals/meds can’t get to them. The suggestion is to keep them “fat and happy” so they are where the meds can get to them (although if / when they move as you stated, not sure it remains applicable). What is your take on that – keeping a “normal” diet of FOMDAPS while treating? (I am following an AIP diet, low histamine and FODMAPs).
(I’m currently taking Biotics FC-Cidal and Disbiocide (tried Candibactin and didn’t have good results) and berberine. Once the Biotics are done, I’ll add Allicin to the berberine. I’m hopeful!!)
Thank you for the great information and future response!
Rifaxamin can be bought at a pharmacy in Canada and shipped to you for only about $109, if you can find a doctor to write you the prescription.
Yes, there is not agreement on whether you should be low carb “while treating” for SIBO. However, bacteria is going to make biofilms and be difficult to get regardless of whether you are low carb or whether you are on pharmaceuticals or herbals.
The problem with keeping them “fat and happy” is that this will result in a wide range of overgrowth symptoms that can make life unbearable. I’ve experimented both ways, feeding the microbes during treatment and starving them during treatment. In my experience starving them works best. Especially with herbals. The herbals just aren’t strong enough to kill them quick enough. If I’m taking a pharmaceutical I will increase the carb intake a little, but it simply isn’t possible for me to increase very much if I want to be able to function.
I believe the diet should be low-carb Paleo and moderate the high histamine and high glutamate and high FODMAPS according to each person’s need. If autoimmune is involved, then also eliminating the additional foods that contribute to this (eggs, nightshades, dairy, nuts and seeds, coconut). This should be followed at all times. However, one can experiment during treatment with the carb intake to see what kind of response they have.
Remember that treatment isn’t something you do just once. Treatment must be repeated periodically. Diet must be used to maintain improvements made. And treatment remedies need to be alternated to prevent mutation and resistance.
I’m suffering with many digestion problems that seems to match up with having sibo (methane)
The only thing I’m lacking is the excess gas.. Is it possible to have sibo without having the major gas and bloating symptoms?
Although excess gas is most common, it is not always.
Yes, it is. Some people present with only mental health symptoms, brain fog or other brain symptoms.
Great article. Wish I’d read it before embarking on my SIBO repair programme. 9 weeks in now and have made many mistakes which could have been avoided.
Tried acidophilus and bifido probiotic last week and set me back significantly. Really bad psychological effects (brain fog, tension etc) apart from anything. And feelings of fatigue and inflammation in the body.
When would people recommend getting a follow up breath test done, to check results of my 9 week efforts? I’m on herbals rather than pharma antibiotics, so would 9 weeks be long enough to do the trick?
Thanks again for great information
Mike there’s no black and white answer to any of this. As discussed above, treatment needs repeated periodically. Diet, sympathetic stress, etc. need managed consistently. Herbals should be rotated to prevent mutation and resistance.
One other question, if I may:
How long should I be taking herbals for? You mention in the relevant section not to ‘take them non-stop for months’. – I’ve been taking Biocidin liquid for 2 months now, so should I be giving myself a break for a while?
Thanks so much again for your wonderfully informative article – far more useful than I’ve found my trips to visit the gastroenterologist 🙂
I would like to try Rifaximin for my recently discovered SIBO, but I have two important questions:
* Can Rifaximin cause disruption of the gut flora and create dysbiosis?
I did a comprehensive stool test and it showed that I already have gut dysbiosis (very low levels of hydrogen peroxide-producing lactobacillus) and I’m afraid that Rifaximin could cause even more problems on the gut flora.
* And lastly, can dysbiosis be a cause of SIBO? Like in my case, which I have very low levels of lactobacillus?
I’ve been reading related articles over web as I’ve been a sufferer since last 5 years. I can tell you this is most comprehensive article I’ve seen. I really thank you for providing this information. You are helping others. GBU. I hope it may help me in my condition.
Final question from me, as I’ve been offered new advice in the past weeks –
The suggestion made to me was that the most efficient way to eradicate the offending bacteria in SIBO is to keep them well fed during the eradication phase. This is apparently to stop them ‘hiding’ and making them easier to kill. Therefore it was suggested that I consume carbohydrates during this period and scale back after I finish a course of pharmaceuticals or herbals.
What are your thoughts on this line of thinking?
Does a high d lactate level on an OAT test signify SIBO?
If not, what does that indicate? I have received a lot of conflicting responses from practitioners.
High d-lactate on the OAT is highly indicative of SIBO. But, elevation in d-lactate levels can be caused by other things like eating a lot of carbs. At the end of the OAT test there is commentary that explains all the issues that may contribute to the elevation.
Thank you, thank you and thank you. I can not express how much this information is valuable for me. I have been reading and searching about SIBO and have gained a lot of infromation and knowledge but you have put them all in a well-explained, connected and coherent place. For sure, now I have better insight how to manage and heal my SIBO and other issues.
I came across this page and it’s very informative, thank you. My problem is that after having an abces skin infection I was treated with antibiotics, and I started having gastrointestinal problems such as alternating bowel movements constipation and obstipation. The bigger problem was I started belching excessively even in the morning when i have not eaten yet. These symptoms have been persistent for years and my physian can’t figure it out. I’ve done the hydrogin test and it came out negative. How should i know if I have candida or sibo?
The following pages should help you determine whether it is SIBO or Candida.
I have had very bad reflux and constipation for two years which I treat with fiber, most food eliminated due to intolerance, and a highly reduced fat diet. I lost 25 pounds because of eating minimal fat, which is upsetting due to the loss of important nutrients. All my upper GI tests were negative; gall bladder was contracting, as well as negative parasite, comprehensive stool test and gallbladder ultra sound. Here is my problem: I cannot take the SIBO breath test because it would require going off the fiber which would result in too much pain. I could go off the supplemental fiber one day prior to the test (according to my doctor) but that would require fasting that day and I fear more loss of weight. I must have supplemental fiber with food or I can get into an extremely painful situation. I have a very limited diet avoiding gastric pain by eating most of my calories with rice, yams and spinach and fish for protein. I feel certain that I have SIBO but fear that If I go on the herbal antibiotics I could make my situation worse if it is not SIBO. I tried taking probiotics which seemed to exacerbate my symptoms. . My quality of life has already been reduced and I spend so much of my time scheming ways to gain weight and experimenting with adding foods that never pan out. My last food experiment was a quarter teaspoon of MCT oil which gave me overnight reflux. I never hear of people with SIBO whose main problem is fat. Not sure what to do but beliee I have SIBO.
Thank you much. I have sulfur gas too and feel it’s never mentioned. Really appreciate the review that was needed 🙂
Can you please tell me after how long using Saccharomyces Boulardii in treatment of SIBO, does the Saccharomyces Boulardii become pathogenic? Do you have references to support this? Thanks
I first learned about this issue when I was working with a client who told me she had a friend who had just become infected with saccharomyces through supplementation. So, this led me to do some research. If you look in the Reference section directly above in the blog post, you will see I have a couple references to studies documenting that this can indeed happen.
Here is one of the references
And here is the other
That does not mean it will happen to you. It doesn’t happen often, but it can happen. There is no way I can say how long it would take to become pathogenic, it would vary from person to person depending on what’s going on in their gut.
Thank you for the links. I looked at 3 of your references relating to SB probiotic and noticed in the scholarly journals that problems occurred mainly through cathedra or tube feeding. So would problems arise by mouth administration, by either swallowing a capsule of SB probiotic or mixing the contents of the probiotic in water and drinking it?
The people in the studies were not taking the probiotic through the catheter. They just had a catheter. The probiotic was taken by mouth.
Yes, the problem could occur by taking the probiotic by mouth.
Great article. Really covers so much. Bone broth detail was an eye opener. Also explains why I can handle certain foods at some times and not others. I have been on Prucalopride as a prokinetic and it works great with no side effects (for me). Heathers Peppermint tabs between meals also helps reduce symptoms.
I have lactobacillus overgrowth syndrome which is a gynecological disorder. I have been following a keto diet while omitting all probiotics and prebiotics. I mainly eat salmon, chicken, and cheese as my main sources for energy…I wanted to start eating macadamia nuts or Brazil nuts for something different. However, I saw that nuts and seeds provide fuel for bacteria. Would they be okay in moderation, as long as I am omitting virtually every other sources of sugar, besides small servings of vegetables?
Well, as stated in the article above, nuts and seeds feed SIBO. They can make it proliferate significantly. So they should not be eaten on a regular basis. The can be used as a treat for now and then, but certainly not daily. Besides that, nuts and seeds contain a variety of anti-nutrients that are destructive to the gut and cause inflammation and can contribute to auto-immune disorders, so they should be minimized for that reason as well.
Thank you for all of this information on sibo! It’s been the best source of information for me regarding what it is, it’s symptoms and treatment. I have a question for you regarding two of my son’s that recently went to a pediatric gi doctor. After labs, my older sons (he’s 7) results came back showing high monocytes and eosinophils. He is very gassy (was even being teased at school for it), and emotionally he’s very dramatic (can cry easily and use to tantrum unusually often when he was younger). The gi doctor recommended metronidazole (250 mg 2xs/day) and did not test for hydrogen or methane types (although I suspect it’s methane because he’s constipated without magnesium supplements) and he said this medication would treat both types. Is that true? My younger son (he’s 5) had labs that came back normal surprisingly, despite that he tantrums often, is aggressive and extremely sensitive to most fruit and high carbohydrate foods. The gi doctor also prescribed metronidazole 250mg (2x s/day) and said insurance would not cover rixamifin unless this didn’t work first. I’m concerned because this doesn’t seem like the usual treatment and because many of the reviewers of this medication said people experienced terrible anxiety and some panic attacks when taking it. The gi doctor saw my 5 year old and his behavior and thought he should be on anti-anxiety meds (he was hitting and kicking his brother because he wouldn’t move over where he wanted him to be although he had had fruit earlier in the day (we had been off of most fruit except berries for months and thought we could go back to other fruit but apparently not and I suspect it was in large part, the cause). Any advice regarding the gi doctors approach? I’m worried the sibo meds he prescribed are going to make the anxiety and behaviors worse for my boys and the leaflet that came with it says it caused cancer in rats who were on it long term. I’m concerned about giving them something that’s a possible carcinogen especially considering my older sons labs. Thanks in advance for any help you can give!
Metronidazole is not typically used to treat methane producers. Not only that, it is highly toxic. Additionally, treatment is not something that is done once. Treatment usually needs to be repeated over and over and diet must be followed on an ongoing basis. As stated in the article above there is a high rate of false negatives on the test, so a negative test result does not mean it is not present. However, numerous other factors could be involved as well. Rifaximin can be bought from Canada for cheap. However, in my opinion Rifaximin is not every effective and has numerous problems. Anti-anxiety medications will create a drug addict. Coming off anti-anxiety medications is excruciating.
You should read the treatment page for SIBO found here:
If you would like to discuss this issue in more detail, then you should consider a phone consultation found on the following page:
I have been so grateful for your book on Candida, and learned so much. In fact, your chapter on SIBO led me to get a diagnosis and, subsequently, the beginning of treatment. It’s ongoing, of course.
I’ve been going back through your book looking for references on whether or not you avoid psyllium fiber supplements, such as Metamucil, if you are trying to eradicate SIBO. I tend to have the IBS-D version, with malabsorption of fat issues. Is fiber good or bad for this?
I’m glad to hear the book has been so helpful. Psyllium is in the list of things that should be avoided and it is found on page 141 of the book. It is also on the list in the article above. Fiber feeds SIBO.
This article is phenomenal. You are amazing, Cynthia.