2.Methane Dominant SIBO- Prescription Drugs. Why Prescription Antibiotics Aren’t Working That Well ? Pros and Cons Of the Antibiotics
3.Why Natural Antimicrobials Offer a Better Solution for Archaea Overgrowth. Methane Dominant Neem for SIBO, Other SIBO Herbal Treatments. SIBO Herbal Treatment Side Effects
4. My Approach to Methane Dominant SIBO (SIBO-C) Treatment
SIBO (small intestinal bacterial overgrowth) can be methane producing, hydrogen producing or both. Bacteria produce hydrogen where archaea produce methane. Excess hydrogen is usually associated with diarrhea (SIBO-D) where methane dominant SIBO is typically linked with constipation (SIBO-C).
There are a few breath tests for SIBO that your doctor can order, and also some home kit tests available in some countries. These tests measure the levels of methane and hydrogen. However, they are not always accurate, yelding false negative results. For this reason, it makes a lot of sense to interpret the results of the methane dominant SIBO test in combination with symptoms.
I mentioned in my other articles about the fact that chronic constipation, IBS-C and SIBO -C being as one disease, not three different conditions: an archaea overgrowth. More and more studies support the significant overlap between SIBO and IBS. Many individuals report a history of chronic constipation before developing SIBO and IBS. This means that I find useful for chronic constipation and IBS-C some supplements described here for managing methane dominant SIBO (SIBO-C).
Back to the topic of this article. Let’s look at how SIBO-C treatment.
I do emphasize the need for treating this condition. It is more common that was previously thought. Research suggest that up to 15% of people with no symptoms may have SIBO and over 80% of those with IBS have associated SIBO.
SIBO is a sign of dysbiosis (altered gut flora), which can complicate with other-and more serious conditions -including autoimmunity. SIBO is also more commonly diagnosed in MS [1].
The small intestine and its flora plays an important role in overall health. The beneficial flora helps protect against bad (pathogenic) microbes, help absorb essential nutrients and produce vitamins like vitamin K and folate, as well as short fatty chain acids. The overgrowth of methanogens or other microbes will impair the metabolism of proteins and fats, nutrients such as vitamin B 12, A, D, E, iron, calcium and the overall digestion. The small intestinal microbiome also supports normal intestinal motility and transit, which is slowed down by excess methane.
To no surprise, someone with SIBO will experience abdominal discomfort, signs and symptoms of nutrient deficiency (ie anemia) poor absorption of the food and food intolerances, bloating, heartburn and constipation (SIBO-C), weight changes (weight gain with SIBO-C is common), malnutrition, rashes (ie eczema, rosacea), joint pain. Other symptoms include brain fog, poor concentration and fatigue (because of the brain-gut connection), anxiety and depression.
Methane Dominant SIBO- Standard Treatment (Prescription Drugs)
Standard treatment includes dietary changes and antibiotics. You may receive a low FODMAP diet handout like this along with the prescription for antibiotics. Laxatives are also recommended for sibo constipation relief. .
Rifaximin is the preferred antibiotic for SIBO- although the success rate is about 40% for SIBO-D and even less of SIBO-C. For this reason, SIBO-C treatment involves a combination of two antibiotics- for example rifaximin and metronidazole (or neomycin). Guar Gum appears to increase the efficacy of rifaximin. Unlike all other antibiotics, rifaximin is absorbed locally, does not appear to significantly alter the gut microbiome and there are low chances for microbes to develop resistance to it. However, rifaximin is never given alone, but with another antibiotic, therefore there will have a significant impact on the gut flora.
Laxatives are given often, perhaps too often and for too long- for example osmotic laxatives like polyethylene glycol (brand Miralax).
Why Prescription Antibiotics Aren’t Working That Well ? Pros and Cons Of the Antibiotics
Since we are dealing with Archaea overgrowth, it makes a lot of sense to use antimicrobial agents, right? Currently, the antibiotics are used for treating SIBO, but they have limited success rate and relapse rate are common. If you wonder why, here is my explanation:
Archaea microbes are not bacteria ! Archaea are biochemically and genetically different from bacteria. No wonder studies show consistently that Archaea are resistant to most antibiotics- that’s because Archaea are not bacteria, but a different form of microbes, which are actually closer to fungi/parasites than to bacteria in the way they behave. An example: the antibiotic metronidazole is working against methanogens not because is antibacterial- but because of its strong anti-fungal/ anti-parasitic effects.
Technical: Archaea form a distinct kingdom of life, in addition to eukaryotes (fungi/parasites), bacteria, and large viruses. Archaea possess genes and several metabolic pathways that are more closely-related to those of eukaryotes, notably the enzymes involved in transcription and translation (although they are prokaryotes) [2]. Archaea display a broad-spectrum resistance to antimicrobial agents. Their cell wall lacks peptidoglycan, making them resistant to antimicrobial agents. Archaea is however susceptible to fusidic acid, imidazole derivatives, and squalamine [3]. Fusidic acid is derived from the fungus Fusidium coccineum and has antibacterial, antifungal, and antimalarial activities. Squalamine has a broad spectrum coverage- antifungal, antibacterial, antiparasitic and even antiviral actions. Imidazole derivatives have mostly antifungal/antiparasitic effects [4],[5],[6].
The Side Effects of Antibiotics: While prescription antimicrobials can help treat some cases of SIBO-C, the recurrence rate is frequent (up to 44% of people treated with antibiotics will experience recurrence after 9 months; increased relapses correlate with older age, appendix removed and used of acid blockers PPIs) [7]. Here is a review of some side effects of the antibiotics.
Antimicrobial drugs have a negative impact on gut flora. They kill both bad and good bugs. Microbes compete one with another, so they have their “spots” within the GI tract. What happens when you kill some of them ? They will be replaced by the overgrowth of other species. The typical example is Candida overgrowth after taking antibiotics. Also consider how important is the gut flora for the overall health. More details here. Just one round of antibiotics can negatively impact your gut microbiome for several years. It may be hard to treat SIBO, but even harder to reverse the side effects of antibiotics.
I do see a lot of value in antibiotics for treating acute, life threatening infections. However, I prefer natural treatments for treating chronic infections like SIBO, IBS, H pylori or Candida.
3. Why Natural Antimicrobials Offer a Better Solution for Archaea Overgrowth. Natural Treatments for SIBO-C.
Unlike prescription antibiotics, natural herbs and supplements contain multiple active ingredients (antimicrobial chemicals). This means they typically have broader coverage -for bacteria, fungi, parasites and even viruses. Since they are so versatile, it is less likely for those microbes to develop resistance to herbal supplements vs antibiotics (resistance to antibiotics is a very big problem nowadays). Many herbs with antibacterial qualities also have antifungal effects, thus there is a lower risk to develop Candida, while increasing the success rate of killing Archaea species.
SIBO Herbal Treatment Side Effects: Natural antimicrobials are more gentle for the gut microbiome and won’t kill as many friendly bacteria compared with prescription drugs (if they are used right). However, natural treatments should also be used properly to avoid problems. For example, oregano oil is very effective but also very strong it can cause damage to gut flora if overused. Yes, herbal antimicrobials can kill some probiotics too, but overall are safer than prescription drugs. For this reason, I always keep the herbal treatment as short as possible (no more than 10 days for oregano oil, up to 3 weeks in total) and recommend them along with probiotics. Herbs can cause allergic reaction in susceptible individuals and can also interfere with prescription drugs and other herbs (drug-herb and herb-herb interactions). I think herbs should be chosen wisely based on other health concerns (ie some can lower blood pressure or low sugar levels- thus should be used cautiously in those who already those issues). Not a side effect, but rather disadvantage — we don’t have enough research studies to see which herb inhibits methanogens thus herbs with broad antimicrobial coverage are the best choice. This is a problem for standard treatment (drugs) as well.
Herbs are wise. They had to learn to protect themselves to survive in a harsh environment with plenty of archaea, bacteria, fungi, parasites and viruses around. Certain herbal compounds had been found specifically to inhibit methane production -for example saponins, tannins, essential oils, organosulfur compounds, flavonoids and many other metabolites [8].
Neem for SIBO or Other Herbal Combinations — How Do They Work ?
The best study in humans evaluated a combination of supplements Candibactin-AR with Candibactin-BR (Metagenics brand) which was found as effective (actually a bit more effective) than rifaximin for treating SIBO [9]. There are many herbs included in these two supplements- the key ones being Red Thyme Oil, Oregano Oil and Berberine.
Other natural protocols include combination herbs — for example Oregano Oil with Garlic, Berberine, Neem and Cinnamon for 4 weeks or longer.
A quick note about neem for SIBO-C : seems to be popular supplement for treating SIBO-C naturallly. There is very little research about its benefits specifically on methanogens [10]. However, this herb has a broad antimicrobial activity (including antifungal/antiparasitic action) and great for gut detox, and there are over 100 research papers about this herb. Thus, I do consider neem for SIBO-C as a good option [11]. You can read here more details about the health benefits of neem.
Atrantil is a smart combination of peppermint, quebracho and conker tree and these ingredients work synergistically. Peppermint decreases local inflammation, quebracho targets gas and reduce hydrogen (thus starving the methanogens). Conker tree (a saponin) is the one that inhibits methanogens.
Diet. There are a few diets recommended along these natural supplements, for example low FODMAP, SCD (Specific Carbohydrate Diet) or GAPS (Gut and Psychology Syndrome Diet), low fermentation diet and a few more. There is a lot of information available online for all these diets. Basically they all reduce the foods that feed the bacteria that overgrow (mostly carbohydrates). The goals of these diets are to relieve symptoms of IBS, SIBO, constipation, diarrhea and bloating, lower the gut inflammation, while increasing nutrient absorption and promote gut health.
4. My Approach to Methane Dominant SIBO Treatment
Diet and supplements are very important, of course. Based on my experience, diet and supplements or drugs can work short term. There are another lifestyle changes you need to make if you want to be symptom free long term.
I looked at the following question: What methanogens love (and will make them overgrow)?
Dietary Factors:
Methanogens love when you eat sugars. To be more specific-FODMAP foods (highly fermentable but poorly absorbed short chain carbohydrates and polyols), especially if you eat them in moderate and large quantities. Technical: The anaerobic fermentation of the undigested polysaccharide fraction of carbohydrates produces hydrogen in the intestine (hydrogen is an important substrate for methane production by methanogens) [12]. Quick note here: most online resources will give you a long list of high FODMAP foods that you suppose to feed the bad bacteria like this, but I prefer the option from Monash University (details below).
Unhealthy foods and dehydration. Methanogens will love foods that negatively impact your gut microbiome (either the count of friendly bacteria or its diversity) as these foods will allow them to overgrow. Examples: highly processed foods with lack nutrients, but have added sugar, salt and artificial additives, wheat and other lectins (as they promote inflammation/leaky gut).
Not enough healthy fibers in the diet and not drinking enough water- that’s because lack of fibers and water are the two big triggers for constipation and unbalanced gut microbiome, which make a favorite environment for methanogens to overgrowth). Chlorine and fluoride in water kill friendly bacteria [13].
When you eat late at night (both digestion and sleep are affected), when you eat at irregular hours and snack between meals (this affects MMC, thus increasing the risk of poor digestion and methanogen overgrowth). MMC (migrating motor complex) are waves of electrical activity that sweep through the intestines in a regular cycle (1.5- 2 hours) during fasting.
Other Lifestyle Factors That Methanogens Love
Stress. Methanogens love when you are stressed, especially when you express negative emotions such as anger, anxiety and depression [14],[15].Stress also creates sympathetic dominance (being constantly in the fight or flight mode) which among others- will shut down digestion (decrease gut peristalsis, the production of hydrochloric acid, nutrient absorptions), thus promoting the overgrowth of methanogens.
Sleep. Whether is interrupted sleep, not enough sleep (less than 7 hours per night), not sleeping at the ideal time (beneficial sleep is between 10 pm-2 am), changing time zones and jet lags. All changes in the circadian rhythm (sleep-awake cycle) will have a negative impact on the gut microbiome and digestion, as well as the immune function and stress levels [16],[17], [18]. The gut microbiome has its own circadian rhythm [19], which should work synchronizes with your circadian rhythm. (this is another problem with antibiotics-they affect the sleep as well) [19]
Lack of physical exercise promotes altered gut microbiome and obesity, affects MMC and digestion, weakens the immune system, promotes stress and more [20].
What Methanogens Really Hate (So Do This More Often)
Obviously, methanogens will hate the opposite -a healthy diet, improving your sleep and stress levels as well as getting more active. If you want to treat SIBO and avoid relapses, you should address all these factors.
I. Diets:
A low lectin diet such as this one during the treatment with antimicrobial herbs (the main benefit is not to inhibit methanogens, but rather decrease gut inflammation and allow the herbs to work)
A modified low FODMAP diet (during the second phase- of preventing relapses)
Regarding the diet, here is the thing: methanogens love high FODMAP foods if you eat them in moderate or large quantities. But they won’t overgrow if you eat these foods in moderation or low quantities.
I don’t like super restrictive diets simply because they can make you more stressed – and stress impairs digestion. I recommend the FODMAP diet recommended by Monash University. It encourages variety of foods (thus a healthy flora), so is less restrictive You can eat certain foods that are banned on other low FODMAP diets, but in small quantities. I used a modified version (ie removed most grains and other lectin rich foods, margarine, etc but overall is a good diet to use a guideline. Bacteria that overgrow in SIBO-C do not feed on insoluble fibers (which are beneficial for managing constipation)- thus I recommend these fibers are found in flax seeds, vegetables, legumes and berries.
Food intolerances and allergies should also be addressed
Fermented foods (if tolerated) can be consumed in small quantities as they are a good source of probiotics and are easier to digest. (red fermented cabbage has lower FODMAP than the white cabbage).
I recommend a lot- I mean a lot of herbs (as much and as many as you can tolerate). Think indian dishes. They can help improve digestion and absorption of the nutrients, plus they have antimicrobial and anti inflammatory effects on their own. If you can’t eat certain foods, try to cook them with fennel, cumin, coriander, parsley, dill, etc and you may have a nice surprise and notice you aren’t intolerant anymore to them.
Meals should be small, at regular times (3-4 hours apart) to allow digestion and optimal function of MMC (migratory motor complex).
Never eat when you are stressed. Try to eat more with company, people you enjoy being around
Elemental diet seems to be the most effective, and is reserved for severe, stubborn cases of SIBO associated with many food intolerances or allergies. It works well alone, without antibiotics. However, it is not for everyone. Fasting can also be very helpful.
Low FODMAP should be kept short term, as the main long term goal is to enjoy a variety of foods.
II. Supplements
Supplements for both phases: 1. SIBO-C treatment and 2. to prevent relapses
I. SIBO-C treatment
antimicrobial herbs plus probiotics (along with a low lectin diet)
I choose few (not all !) antimicrobials from the following: oregano oil (no more than 10 days), peppermint oil, red thyme, mastic gum, black seeds (ground seeds or oil), garlic (aged garlic, Kyolic brand), Tryphala (an ayurvedic combination), yucca, cinnamon extract, neem (berberine is great but can aggravate constipation).
Here is why: Methanogens are sensitive to many plant compounds, but are particularly inhibited by plant chemicals called saponins and polyphenols.
Essential Oils: Clove Oil, Eucalyptus Oil, Garlic Oil, Oregano Oil, and Peppermint oil. This study evaluated 5 essential oils: Clove Oil, Eucalyptus Oil, Garlic Oil, Oregano Oil, and Peppermint Oil, in 3 different doses for their effect on methane production, fermentation, and antimicrobial effects. All the essential significantly reduced methane production when the highest dose was use, with methane reductions between 17-87%, Oregano Oil yielding the highest reduction [21].
Other natural supplements: Mastic Gum and Black Seed have also strong broad spectrum antimicrobial effects and can help promote healthy microbiome [22],[23].
Natural Factors has a good combination of Peppermint plus Oregano and Caraway Oils (Oregano Oil should not be used for more than 10 days as it can have a negative impact on gut flora).
Yucca ? No one talks about Yucca for SIBO, but I do. Here is why:
Yucca (Yucca Schidigera) : Based on a review of 23 studies that evaluated numerous plants and how they can reduce methanogens and methane emission in ruminants, yucca showed the best results, followed by green tea [24]. Yucca contains steroid-like saponins, thus anti-inflammatory, antimicrobial, antioxidant, antispasmodic effects [25]. Yucca is also a rich source of polyphenols, including resveratrol and yuccaols. Technical: These phenolics have anti-inflammatory activity. They are inhibitors NFkappaB. NFkB stimulates synthesis of iNOS [26]. Other benefits of Yucca: antimicrobial [27] ,decreases the risk of cardiovascular diseases [28], anti-cancer qualities [29] , improves cholesterol levels [30] and has detox effects [31]. Note: Most studies for Yucca had been conducted in animal studies. In humans, I did not find this supplement working alone, but rather in combination with others (perhaps because animals have a different way to digest foods and different gut microbiome (more parasites, when compared with us ?)
Probiotics: used during the treatment with antimicrobial herbs and after (taken a few hours away from herbs)
Probiotics benefits: 1.they help restore the gut flora and digestion 2. They have antimicrobial effects on their own (for example- a combination of probiotics was found as effective as the antibiotic metronidazole) [32]. Some probiotics help improve gut motility. Plus they modulate the immune system. Not everyone will respond to the same probiotic strains, some will experience side effects. Until we will prescribe probiotics based on microbiome tests like Viome, here are some beneficial strains : Lactobacillus plantarum, Lactobacillus casei, Streptococcus faecalis, Bifidobacterium brevis, Lactobacillus sporogenes, Saccharomyces boulardii [33], [34], [35], [36].
VSL #3 probiotic can be very helpful, too.
I add S salivarus K12 to improve the GI microbiome from its starting point (mouth and throat). For women, I also consider a probiotic that supports healthy vaginal microbiome.
If regular probiotics are not tolerated, Saccharomyces boulardii (which is yeast) and soil based microorganisms (SBO) could be helpful.
Laxatives- I see a lot of value of them. Research shows that chronic constipation increases methanogens and the intestinal permeability (leaky gut) and treating constipation can quickly reverse these issues. I prefer Senna (antimicrobial herb, promotes gut motility) along with fibers (ground flax seeds, hemp protein) for sibo constipation relief- short term. Flax seeds and hemp can be used long term, daily.
II. Preventing SIBO relapses (diet, prokinetics and supplements that promote healthy gut flora)
Low FODMAP diet plus prokinetics (5-HTP, Ginger or Iberogast are my favorites). They help improve gut motility and prevent the overgrowth of methanogens.
Probiotics should be taken a few hours away from prokinetics
Ayurvedic herbs and teas : Triphala can be continued from phase 1 (or replaced with amla, one of the ingredients of Triphala). Herbals teas based on various seeds and root powders (cumin, coriander, fennel, clove, cardamon, curcumin plus black pepper, etc) can be used daily, ongoing. There are no particular studies on these herbs for treating methanogens, but they have broad antimicrobial activity and improve digestion. I started to look into indian herbs when I realized that indian population has lower rate of IBS compared with Western word (4% vs up to 20%) [37]. So I wondered if the diet, and other lifestyle practices (ie meditation, yoga) could be the reason why Indians have fewer problems.
Other lifestyle changes to eliminate methanogens:
Stress control provides tremendous benefits. It can make a big difference. You need to see what works for you- meditation (10 minutes 2x/day), yoga stretches, etc. Emotional stress has similar impact on your digestion compared with physical stress of the gut (ie from food intolerances or processed foods), in my opinion.
Sleep well, at least 7-8 hours a night, in dark rooms without electronic devices around, and set the room temperature around 17-18 C.
Exercise : 4-5 times a week. Combine yoga with strength training and high intensity training (HIIT). There are variations of all these exercises if mobility is an issue.
In the future
Could we use a unique methane eating bacteria found in the under the antarctic shelf to treat archaea overgrowth in humans? Hope someone will look into this option.
Did you know?
A sheep can produce about 30 litres of methane each day and a dairy cow up to about 200 ? We, humans produce a lot less methane- but we still do, especially when we experience an overgrowth of Archea. Treating SIBO-C would actually make us more environmental friendly, not just healthier.
What do you think about my approach to treating SIBO-C naturally? I can tell you there is a lot more than what I wrote here. Do you have questions or do you need personalized consultations via skype? If so, feel free to email me (via “contact” page of this blog).
