One of the most common questions I get from people is if it is OK to take probiotics, or consume fermented foods, while they have SIBO. After all SIBO is a “bacterial overgrowth” and adding fermented foods will add bacteria. Some people have even had their doctor tell them SIBO is often an overgrowth of “good” bacteria, this is simply not true.
So first a little background.
Until recently it was thought the small intestine was suppose to be sterile. Why would they think that? Because when they extracted fluid from the small intestine of healthy people and tried to culture it, nothing grew. Why was that? Because they could only culture aerobic bacteria, those that can grow in an oxygen rich environment, the anaerobic bacteria died when removed from the gut. Now that we have DNA testing they’re finding that the healthy small intestine is actually a very rich bacterial environment. Not as dense in bacteria (CFUs) as the colon, but far more bacteria than any other place in the body, other than the colon.
Most symptoms, and all of the damage, from bacteria overgrowth comes from pathogenic and opportunistic bacteria. These strains of bacteria can produce toxins, probiotic bacteria can not. The confusion comes from the fact that SIBO is usually caused by coliform bacteria, such as Escherichia Coli. E.Coli is a lipopolysaccharide (LPS) producing bacterium often found in the colon of many animals, including humans. However e.Coli also produces a large amount of histamine and can trigger the body to produce histamine. The LPS they produce is an endotoxin and linked to many health issues (there are literally thousands of research studies on the problems caused by lipopolysaccharides. In the colon, some coliform strains do provide some benefits to the host (us), but usually much more beneficial strains (probiotic strains) can provide these benefits in their absence. Many coliform bacteria are “opportunistic” meaning they are just waiting for the right conditions to overgrow and cause problems. These strains do not belong in the small intestine, and even though commonly found in the colon, should not be considered “probiotic”.
Our guts are full of opportunistic bacteria just waiting for the right conditions to take over; we need to avoid giving them those conditions. Some of the things that lead to SIBO are:
- food poisoning – this can temporarily decimate our beneficial bacteria leaving us defenseless to an opportunistic infection
- antibiotics – again, they have a major impact on the microbiome leaving our gut much less able to protect itself from an opportunistic infection
- Non-discriminating botanical kill supplements – these can actually sometimes be worse than antibiotics as they can be broader in spectrum and can kill beneficial yeasts as well. This includes grapefruit seed extract and silver products taken internally, both of these should be avoided. Even the commonly used oregano oil is non-discriminating.
- overconsumption of food – especially carbs between meals. Animal studies show this to be one of the top causes of SIBO in livestock and there is no reason to believe this isn’t true with humans as well.
- carbohydrate malabsorption – this includes lactose intolerance and fructose malabsorption, among other conditions where the body doesn’t absorb sugars and carbohydrates correctly.
- Alkalizing – when you artificially alkalize the pH of the gut you are creating an environment more conducive to certain bad bacteria strains and yeast. The intestine is actually suppose to be slightly acidic. “Alkalizing” vegetables are OK as they contain minerals the body uses to maintain the pH the gut and the rest of the body. But it is the minerals you want, not an immediate increase to the pH of the gut.
Probiotic strains are usually “transient” and can not overgrow in the small intestine. Again they are transient, they do not stay in the small intestine, they get flushed out in a day or two.
If good bacteria caused SIBO, everyone taking probiotics and consuming fermented foods would have SIBO. This simply is not true, in fact it proves my point. I consume fermented foods, they have trillions of probiotic CFUs, I also still take the Phage Complete probiotic, and I never have diarrhea (I no longer have SIBO-D). In fact I can consume these things several times per day with no diarrhea. Why? Because they contain beneficial bacteria, they do not release toxins, and they do not cause SIBO (again, coliform bacteria, and other unwanted strains cause SIBO).
Here is how Dr. Pimentel defines SIBO:
“Small intestinal bacterial overgrowth (SIBO) is defined as the presence of an abnormally high number of coliform bacteria in the small bowel.” — doi: 10.1177/2040622313496126 or see the abstract at PubMed ID#PMC3752184
(Dr. Mark Pimentel is Director of the Gastrointestinal Motility Program at Cedars-Sinai Medical Center and one of the inventors Rifaximin / Xifaxan)
Note that this definition does not include beneficial bacteria.
Probiotics are NOT coliform bacteria. No one with even a semi-functioning immune system gets SIBO from consuming too much kefir or sauerkraut, and they are VERY high in probiotic bacteria. My book, The Gut Health Protocol, summarizes dozens of research studies showing that probiotics are useful in fighting SIBO. They create an environment that is very hostile to bad bacteria. This is how nature takes care of problems and is FAR better for us than the scorched earth approach of antibiotics.
We need to stop thinking of all bacteria as bad.
“Patients on probiotic usage showed an insignificant trend toward low SIBO incidence… The probiotics group showed a significantly higher SIBO decontamination rate than the nonprobiotic group. Also, the H2 concentration was significantly reduced among probiotic users” — PubMed ID#28267052
“The result of hydrogen breath test and the clinical symptoms in patients receiving the maintenance regimen with lactol probiotic showed a better response. The hydrogen breath test turned negative in 93.3 per cent of those receiving lactol compared to 66.7 per cent of the controls.” — PubMed ID#PMC4311312 (Lactol is a single strain lactobacillus probiotic sold in some countries. I don’t recommend this probiotic as it contains FOS, a very high FODMAP fiber)
“Probiotics are live microorganisms, which, when administered in sufficient quantities may alleviate symptoms of IBS than placebo as shown by several clinical trials. Probiotics may work by suppressing proinflammatory cytokines, modulating gut microbiota, sustaining the integrity of intestinal epithelium and altering the visceral hypersensitivity and brain function” — PubMed ID#PMC5347643
“The primary study endpoint was the efficacy of probiotics in improvement of symptoms of IBS in patients with SIBO. Thirty days after the end of treatment, a 71.3% decrease of the total IBS score was detected in patients with IBS and SIBO… This is the first study that prospectively demonstrated superior clinical efficacy of probiotics in patients with IBS with SIBO. Analysis also showed considerable benefit from probiotic intake regarding certain symptoms of patients with diarrhea-predominant and constipation-predominant IBS.” — PubMed ID#PMC6541575
There are some preexisting conditions where a person may have issues with fermented food and probiotics. For example, if a person has histamine intolerance they need to avoid fermented foods, perhaps completely. They should also avoid probiotics that produce histamine; most commercial probiotics contain strains that produce histamine, Phage Complete does not, in fact 3 of the strains in Phage Complete are histamine degrading! Some probiotics also contain strains that produce d-lactic acid, if someone has acidosis they should avoid these probiotics. Phage Complete does not contribute to d-lactic acidosis. Some people also need to avoid megadose probiotics; Phage Complete contains a modest level of bacteria (7.5 billion CFUs) and relies on the phage complex to amplify this in the colon (where high levels of beneficial bacteria are needed).
To summarize, fermented foods, and probiotics, do not cause SIBO. The problem with SIBO isn’t too much bacteria, it is too much of the wrong kind of bacteria and the toxins / issues that come with them.
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John – this clears up a very basic misunderstanding!
Is water kefir beneficial, or does it need to be milk kefir?
Part of the benefit from milk kefir comes from the peptides it contains. These can not be found in water kefir. Milk kefir also has a more diverse number of beneficial strains as it contains far more nutrition than water kefir does. If a person is allergic to dairy, water kefir does provide some benefit.
Hello, thanks for the informative article and your site! What are your thoughts on coconut water kefir in general?
Water kefir has almost none of the peptides found in dairy kefir, and the less bacterial diversity. But for people that can not consume dairy kefir (homemade is best), then it is an OK substitute.
How does one know if they have d-lactate acidosis? Is there a test for this?
Pam, it can be difficult; however, there is a medical blood test for it. Getting the doctor to run isn’t always easy as they want to look at total lactate levels (which can widely fluctuate based on diet, exercise, etc). The following article has more information.
I have a question please. How does one heal their gut, if they have high histamine issues and most high histamine foods are the ones that heal the gut? High histamine caused by bad bugs in the gut and spreading throughout biome due to leaky gut.
It is more difficult, but still possible. For one thing you will need to avoid fermented foods, or consume them in very strict amounts (such as starting with 1 tsp of kefir). You can also consume a histamine free probiotic such as Phage Complete which has a lot of the same benefits (and in many way, greater benefits). Many people in the Facebook group have greatly improved their histamine intolerance and leaky gut (many using the word “cured”).
btw: Histamine seems to get into the systemic environment even without leaky gut. But since it can cause leaky gut (due to inflammation) that is a bit of a mute point.
Interesting explanation. I was of the thought that all the water kefir, milk kefir and kombucha I was drinking caused my SIBO. Even my naturopath was of the same conclusion. So in theory, all these fermented drinks should have actually prevented SIBO. I also have connective tissue disorder which I have stumbled onto a few talks that the valve from small to large intestine can be lazy, allowing bacteria to backup. I have ordered Phage Complete and hope it helps.
Hi, two months ago I consumed a probiotic of Lactobacillus Acidophilus and I started having symptoms like blurred vision, dizziness and nervousness. Then I found that d-lactate strains could cause these bad effects, but I haven’t found a solution. No natural remedy (and I’m afraid none synthetic antibiotic) has been able to stop it, so… is another probiotic, d-lactate-free, the solution for it? And, would the phages in Phage complete act against a Lactobacillus? Thanks
The phages in Phage Complete do not kill any beneficial bacteria. This includes not harming any lactobacillus or bifidobacterium. Phage Complete does not increase d-lactate levels and contains no strains that produce histamine. It is also FODMAP free.
I have another article on l-lactic acid and l.Acidophilus that you can find here.
Hi, In your protocol you indicated that during the kill phase it will be good to use SBO like Prescript assist and to eat fermented foods. I tried fruit kefir one time and it was worst after, horrible…I also read that the new version of Prescript assist contains no recommended flora and, in general, SBO should not be used if the gut is not in a perfect state…what do you think about? What can I use as probiotics to start with the kill phase (I have high sibo and very high methylacetate dysbiosys, can’t support kefir/fermented food in general).
Thanks for your help
Have you looked into Histamine Intolerance (or, more accurately, “Mast Cell Activation Syndrome” (MCAS). That would be the primary reason someone would react to kefir.
The trouble with Prescript Assist has been greatly over stated. This was all brought on by a dispute with one a company they allowed to bottle their product. The formula also hasn’t changed very much in many years. That said, there are enough reason for me to no longer recommend it as a brand.
SBO’s can be used even if the gut is in bad shape. There are a few people propagating misinformation about SBO/HSO probiotics. There is a whole lot of information available showing that those sold commercially are safe and beneficial.
I would recommend Phage Complete. I formulated this probiotic specifically for people with gut issues. Phage Complete contains no histamine producing bacteria (unlike most probiotics), and the testimonials for it have been fantastic!
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thanks for your return. Along should be taken the Phage complete?
also, did you heard about mycotherapy? Here, in France, few physicians and naturopathes are using it: one of them proposed me Mico Mix from Phyto Vie ind. ( composed with Reishi, Shiitake and Maitake) with allimed 180 (but contains malodextrin…)
Mycotheraphy does hold a lot of promise, especially for problems with the immune system and cancer. There is some evidence of benefits to the gut as well, but will probably not help with issues such as SIBO.
I was told it was a waste of money to buy probiotics in plastic bottles as it does not preserve the product. Get Probiotics in Amber glass!
This is absolutely not true, and yet another internet myth. UV light can harm probiotic bacteria, so you do not want to store them in clear glass, or clear plastic. But opaque plastic is 100% fine.
I’m taking and antibiotic Flucloxacillin at the moment. haven’t had antibiotics in a couple of years. I generally try to avoid them. they make me feel yucky with wicked heartburn. I have diverticulosis in the bowel that flares up now and then with bloating, diarrhea, constipation, cramps/pain, bloody stool once. I can’t tolerate onions or garlic at all. Only a CT scan done as Doctors here in NZ are still working out what to do for bowel problems.
so I asked the chemist for a probiotic to help balance out the antibiotic in my gut as I’m worried about a weakened immune system (have had lots of colds and flu lately) and penicillin based antibiotics usually give me thrush. he sold me Go Healthy with howaru restore formulation on probiotics. I have to use a magnifying glass to read the bottle and it doesn’t say much. I can’t figure out if these probiotics will feed the candida and cause me more problems or not. Are you able to answer that for me?
I assume this is the Probiotic your chemist suggested. It isn’t a bad probiotic, it has research showing that it helps the gut after antibiotics. But whether you will have problems or is very individual. For instance, the Lactobacillus acidophillus strains produce d-lactate acid, for someone issues removing d-lactic acid this can cause a number of symptoms (see the following article). If you have histamine intolerance this probiotic may trigger histamine symptoms. It should not feed candida.
Phage Complete, on the other hand, was designed to avoid those problems.
I understand the logic, but in my particular case ingesting either probiotics or probiotic foods like kefir, yogurt, and sauerkraut bring on an intense brain fog. If I take any of these daily, after a week I am nearly neurologically disabled for hours during the day.
I do not understand the process of SIBO or candida infection well enough to put together a hypothesis to explain this. Maybe the good bacteria are fighting the bad ones and the bad ones are releasing endotoxins that end up causing the brain fog. But my case makes clear that it is not as simple as just ingesting good bacteria.
You may want to look into Mast Cell Activation Syndrome (MCAS), commonly referred to as Histamine Intolerance (HIT). This sounds much more like what you are suffering from. Most probiotics produce histamine, and nearly all fermented foods do. But brain fog is certainly one of the symptoms. Symptoms vary from person to person but they can include; hives, nasal stuffiness, flushing, rapid heart rate, nausea, fatigue, low blood pressure, etc. There is a more comprehensive list in the book in Chapter 20.
This can still have a root cause of an overgrowth of bad bacteria. But certain probiotics can still make the situation worse. I specifically formulated Phage Complete to avoid this issue, it contains not histamine producing probiotics.
If you are not already a member of the Facebook group (The Gut Health Protocol) I recommend that you join. There are many people there with the exact same problem and they can be very helpful.
Hi , I am diagnosed with overgrowth bacteria,doc put on antibiotics what cost thousand dollar and now symptoms are back can’t eat starches is a lot pain & constipation is horrible because can’t take psilyium fiber what was the only one help me I am bloat ,I am tired go to doctor and telling me he gave all he knows and nothing help me , what I can do ???
Carlos, Sorry for the slow reply. The first thing I would do is join the Facebook group “The Gut Health Protocol”, you can get a lot of your questions answered there. The second thing I would do is to purchase the book The Gut Health Protocol. It explains a lot of what is going on.
I have dealt with SIBO for about 3 years now. I have been on Xifaxan and different herbal preparations to help. I noticed about 6 months ago my symptoms returning. I started drinking a kefir that I purchased at a local grocery store recently. I noticed my stools are returning to normal, but I have constant belching now and my tongue looks like it is getting thrush. Is this common in the beginning or should I stay clear of kefir and try your phage probiotic?
Leslie, It is possible (even probable) that the thrush is not related to the kefir. Yeast infections (of various kinds) are common after antibiotics. Taking non-selective kill supplements can cause the same thing. Anytime the bacterial microbiome is weakened it is an invitation for yeast to form. If you are not a member of the Facebook
group
I would recommend joining (The Gut Health Protocol). The book also discusses this. As to Phage Complete, because it helps rebalance the microbiome and feeds the microbiome, it might help. However, there is generally more to it, especially with your past gut issues.
How fresh are the probiotics in Phage complete? How long can they be stored?
The current batch has a manufacture date of late 2/19. Phage Complete is guaranteed to have the bottle specified colony-forming units (CFU) for 18 months from manufacturer if stored under normal shelf conditions (this can be further extended through refrigeration, but refrigeration is not otherwise necessary). Phage Complete is bottled in a cGMP facility and independently tested by NSF.ORG (one of the largest independent testing organizations and FDA certified). Each batch of Phage Complete undergoes multiple tests to guarantee potency, lack of common allergens, lack of harmful bacteria, etc. I recommend giving a bottle a try, there is a 30 day money back guarantee if you are not satisfied. You may also want to read the testimonials, I get more almost everyday but I figure this is enough.
I read that the shelf life of the cultures are one week? How can yours survive 18months? How come they don’t have to be refrigerated? Some products have to be shipped fresh in cold packs? I am so bewildered by all the info I’ve read about probiotics!
Also I read they shouldn’t be in plastic bottles because the plastic leaches into product over time. Some say use Amber glass. Others say they must be in sealed pocket packages? From the product to the packaging there is such a mind boggle a person doesn’t know which way is best !!
I was also read that you should be using a probiotic with over 10 strains of cultures was the best? Sorry I keep thinking of more questions. I have yet to feel any differences with probiotics, I’ll have to give Phage one a try?
This is just people theorizing, there is no evidence for this. Phage Complete was formulated to contain the 5 best strains for helping the gut. Manufacturing costs for 10 strains is no more than for 5 strains, what counts are the type of strains and the total CFUs. I chose the best strains, not the cheapest.
The bottle for Phage Complete is made from HDPE. This is the safest plastic and does not leach. If storing shelf-stable probiotics long term you want to store them away from heat and humidity. If you home gets hot and humid you may want to store your probiotics in the refrigerator in a sealed ziplock bag.
Phage Complete is different than other probiotics. The phage complex kills certain unwanted bacteria, this bacteria becomes a PREbiotic food the beneficial bacteria in the capsule. Most probiotics die off long before reaching the end of the large intestine (measuring zero CFUs in stool measurements). With Phage Complete the probiotics multiply 10-100x when measured in the stool.
Freeze dried probiotics can remain viable for years if properly stored. The probiotics in Phage Complete are guaranteed to have the label specified CFUs (colony forming units) for 18 months after the manufacture date (printed on the bottom of the bottle) when stored at normal shelf conditions. This time can be double if refrigerated in a closed bottle.
Some probiotic companies make false claims in order to promote their products. One of these false claims is that refrigerated probiotics are better than freeze dried ones. There is NO evidence of this.
I started taking a probiotic that is supposed to be good for SIBO called Just Thrive, similar to Megaspore but it makes my bloating worse when I take it along with berberine and oregano for Hydrogen SIBO. Is this a good probiotic to take? Just got your book today. I’m excited to read. Thanks for your feedback!
Courtney,
Sorry for the slow reply. Yes, many people take Phage Complete specifically for bloating and have reported great results. There is a possibility of a short adjust period (where there may be some “die-off” of unwanted bacteria), but after that it should not produce any bloating (and may actually help reduce bloating).
John
Re: Phage Complete:
“Delayed Release capsule ensures probiotics travel safely through the harsh conditions of the stomach to where they belong, in the intestines.”
Because I have 2 congenital esophageal strictures, 1/4″ inch diameter each (think of my esophagus as a long thin balloon tied at each end), it is impossible for me to swallow tabs or caps whole. I have always pulled caps apart and dumped the contents into food or water. When the contents are vitamins this works quite well, but probiotic survival may be different.
Would consuming Phage Complete by pulling apart the cap and mixing the powder with water kill too many bacteria and severely lessen the benefits? Would timing my dose by taking it on an empty stomach help more of the probiotics survive?
I agree with Lana — there is a lot of confusing consumer marketing info out there (and I worked in a health food for 2 years!). When I read articles written by microbiologists, bacteriologists and similar scientists, sometimes there is even more confusion. Sigh. How do probiotic bacteria survive in acidic fermented foods? Before probiotic supplements became available, that was the only way to consume probiotics.
Barbara, you are correct, there is a lot of confusing marketing out there. And I’m afraid some of it has been ingrained into people’s mind, mostly for the sake of simplicity. Some probiotic strains are acid sensitive, they can live fine in the small intestine, but may have trouble making it through the stomach. Strains that can not tolerate acidity are not found in fermented foods that are high in lactic acid. Other strains are fine with the acidity, but may have problems with bile.
The phages in Phage Complete are fine with both the acidity and the bile. B.Subtilis is also fine with both. Some of the other strains in Phage Complete show a “high” tolerance to both, while a couple show “moderate” tolerance to bile. When formulating Phage Complete I worked with the scientists at the company that supplies the ingredients and bottles it. I was told that this formula didn’t need the Delayed Release capsule but I decided to include it anyway. This was mostly because people expect to see it. Yes, marketing.
So it is fine to open Phage Complete and take the powder in liquid or food (under 140°F). There are many customers that do this and they report great results.
Hello! I have SIBO and I am going to start an herbal treatment ( allicin, neem and Atrantil with a prokinetic ( iberogast)). I am in a foodmaps diet too.I have the doubt if I can take probiotics at the same time or Kefir because I have the theory that if you kill “bad ” bacteries but you don’t have a great number or “good” flora you will return to the same point after the treatment. Sorry for my english, is not my language. Greetings
Thank you for the article. It was very interesting. Your probiotic looks great.
I just have a couple questions.
How we can find out if a probiotic releases
Histamine or d-lactic acid? I have never heard about this before. They are so many brands in the market.
I keep hearing that there are probiotics designed specifically for women’s health. Is this true?
The microbiome for men and women are substantially the same; what differences there are not available as probiotics. I recommend looking at Phage Complete, it contains no histamine producing strains (in fact 3 are histamine degrading) and do not contribute to d-latic acidosis.
is Kombucha bad for Sibo? Some say yes, some say no.
Rhonda, Some people seem to think that all probiotics are bad if a person has SIBO; this simply is not true. There are dozens of research studies showing that probiotics, even fermented foods, can help with SIBO or a dysbiosis in the colon. However, I’m not a huge fan of kombucha for gut health; it simply does not have the types of bacteria needed for the gut. But in general it isn’t bad for the gut.
This article (that I wrote) explains this better.
I recently began drinking alkaline water (ph 9.5+)n because I read that it may deactivate pepsin in the throat which could be good for acid reflux. Is alkaline water bad for people with SIBO? Or would it not significantly affect the acidity of the intestines?
I would stay away from alkaline water, it is what specifically caused my SIBO. I was fine before, now my stomach is a mess! I would fix the root cause of your acid reflux. The alkaline water is a bandaid.
I completely agree with you! Most unwanted / pathogenic bacteria and yeast prefer an alkaline environment. In fact, once established most of them change their environment to be more alkaline. Strong stomach acid is also what prevents this bacteria from getting established in the gut in the first place.