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SIBO Treatment, Diet and Maintenance


SIBO Treatment, Diet and Maintenance

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 clears 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 (remains 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, and cefdinir. Minocycline and vancomycin may be options as well. Prior to the emergence of rifaximin, the tetracyclines were the drug of choice for SIBO.

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 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.

Herbal Antibiotics

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, tanilbit, allicin from garlic, olive leaf, grapefruit seed extract, berberine, Oregon grape root, goldenseal, lactoferrin, colostrum, monolaurin, pau d argo, 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, tanilbit, 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 being 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 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 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 on 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, length of treatment will vary with practitioners. According to Dr. Pimentel’s book, he only uses a 10-day course of treatment.

SIBO Diet

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 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 the 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 to 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 up 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 is 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 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 build up 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 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 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 leaky gut. Toxins from Candida can also trigger histamine release, so if one has Candida and SIBO, then the histamine load may be even higher.

Elemental Diet

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 which can produce a wide variety of neurological problems like confusion, brain fog, depression, slurred speech, disorientation, headaches, impaired coordination, anxiety, nausea, nervous shuddering, ticks, 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 which 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 sacchromyces 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, sacchromyces and B. subtilis from clients and there is evidence in the literature of both B. subtilis and sacchromyces boulardii becoming pathogenic. Since the 1990s there has been an increasing number of reports in regard to sacchromyces 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 promotes 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.. 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 feeds 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 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 Overgrowth

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 overgrowth of the other. If SIBO is not addressed, then reducing 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.

Manage Stress

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 functioning of the nerve like heavy metals and pesticides, would be critical to address as well.

Pesticides

Pesticides like Roundup (glyphosate) also impair the life cycle and function of healthy bacteria in the gut but doesn’t affect clostridia or E. coli, so these guys may become dominant. Glyphosate also impairs cytochrome P 450 enzymes that are critical for detoxification, contributes to nutritional deficiencies and depletes 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 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.

Thyroid Function

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

Electrosmog (electromagnetic radiation fields discharged from wireless technology and electronic equipment) has be 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.

Sleep

Getting adequate sleep is absolutely essential for 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.

Ileocecal Valve

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, gas itself created by SIBO can put pressure on the ileocecal valve and cause it to open. Any other issues that may be impairing function of the ileocecal valve should be addressed.

pH

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 it 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.

Physical Activity

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.

MMC

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 waste from 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 impairment of the functioning of the migrating motor complex, which leads to 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 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 maybe very long-term. They include low dose naltrexone, low-dose erythromycin, and low-dose tegaserod. However, each of these come 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 are 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.

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  • Shana December 4, 2017, 12:58 pm

    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?

  • Admin - Cynthia Perkins December 8, 2017, 3:45 pm

    Hi Shana,
    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.

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