What’s the best probiotic for SIBO
and should you take one?

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We asked our team of doctors and naturopaths what they thought about SIBO and probiotics.

Probiotics have become increasingly popular in recent years. However, research is ongoing. Although they can be very beneficial in some cases, many experts agree they are being over and misused.

SIBO (small intestinal bacterial overgrowth) is a condition where probiotics may be particularly harmful if misused and there are a few things to consider before deciding which one to take. There’s a risk they may cause a worsening of symptoms or relapse in some people.

Here are some things to consider if you’re looking for a probiotic for SIBO:

7 things to consider when taking a probiotic for SIBO

1. The state of your migrating motor complex

SIBO can occur for many reasons, but a leading cause (often with an underlying cause itself) is a lagging migrating motor complex.

The MMC is the wave-like motion that sweeps through our small intestine roughly every 90 minutes.

Think about the migrating motor complex like the house cleaner for the small intestine.

The migrating motor complex often doesn’t function properly in people with SIBO. This can contribute to why they developed the condition in the first place and why they couldn’t get their bacterial load in the small intestine back to normal levels.

The migrating motor complex can become damaged or lag for a range of reasons. These include immune conditions, an event of food poisoning, certain drugs, surgeries, PPI use, structural damage to the gut lining, a history of eating disorders, poor diet, lack of physical activity, surgery and a whole list of other reasons.

A lagging MMC can cause issues with probiotics.

If you have a slow or damaged migrating mirror complex, the probiotics you take (which are live bacteria) have a higher chance of staying in the small intestine and not being pushed downstream. That can lead to a risk of repopulating or further populating the small intestine if your MMC isn’t functioning correctly.

Simply put, the bacteria you introduce might not get to where you intend or achieve what you want them to.

What to do instead?

Instead, those with SIBO might want to consider something that either 1) enhances the MMC or 2) can influence the balance of “good” bacteria via a different mechanism (more on this later).

Things that influence the MMC and passage through the gut are known as prokinetics. They can be either drugs or natural ingredients you can find in some supplements like Fix No1, Fix No2 and Gut Fix or the FixBIOME system.

A prokinetic refers to a type of drug or natural ingredient that promotes travel through the gastrointestinal tract and keeps the gut pushing things downstream.

They are mainly used for treating motion problems (like a slow MMC) caused by various conditions and gastroesophageal reflux disorders.

A natural alternative to prokinetic drugs are things like ginger (also known as ginger rhizome), marshmallow (not the fluffy sweet kind but the kind known as Althea officinalis L.) and pepperment oil.

Ginger is a natural prokinetic that helps improve stomach emptying to relieve nausea. Ginger is known to increase the motility of the gastrointestinal tract and has antibacterial, antiviral, analgesic, and antipyretic properties.[1]
Marshmallow (Althea officinalis L.) contains a mucilage quality which helps to coat the esophagus and stomach lining, creating a protective barrier against stomach acid.[2]
Peppermint is also a well established potent prokinetic herb in that it contains special constituents (like menthol) that stimulate receptors in the gut to help promote motility.[3]
FixBIOME system contains all of the above ingredients to help stimulate the gut daily for those looking to go the natural route but many prescription drugs also do an excellent job at this.

2. Probiotics and the risk of retriggering symptoms

Nothing is worse than finally getting your bacteria levels or symptoms under control, only to take a probiotic and be back at square one. Here at FixBIOME, our doctors and naturopaths have seen that happen many times before or after the introduction of a probiotic, so exercise caution.

3. The evidence for the use of probiotics for the treatment of SIBO

Although some evidence suggests probiotics may be helpful in different circumstances, no studies have found that probiotics can be used for the successful treatment of SIBO.

According to the scientific literature, antibiotics and natural antimicrobials are what have been shown to be the most effective methods for treating SIBO.

If you’re looking for the most studied drug treatment method for SIBO, visit your doctor and speak to them about antibiotic treatment options.

If you want to consider the natural antimicrobial route by using the most studied ingredients for SIBO, then you might want to look at the FixBIOME system that includes these ingredients.

The FixBIOME system doesn’t just include the most studied ingredients for SIBO treatment but has many other ingredients that promote the rebalancing and functioning of the gut as a whole.

Antibiotics for SIBO pros and cons

✔️ Pros
Manufactured in a lab and identical every time (no big variables to consider)
No need to control the source of synthetic ingredients
Brand to brand won’t differ much – it’s all the same active
Highly tested
Biggest body of research to support their use
You can be sure you’re not being sold a product that is inactive by the time it reaches the gut
Most studied and researched option
Shown to be effective
✖ Cons
Costly often requiring multiple courses
High relapse rates recorded in studies
Not covered by most insurance companies for SIBO
Doesn’t support the gut’s overall health and function
Aimed only at killing off bacterial overgrowth
Requires a script from a doctor
Multiple rounds are often required for long-term management

Won’t work for everyone

Natural antimicrobials for SIBO pros and cons

✔️ Pros

Shown to be very effective in treating SIBO in studies

Studies have found they can be as effective as the goldstandard drug Rifaxamin

Provide other benefits besides just killing off bacterial overgrowth

Can help to support the balance of ‘good bacteria’

Can help support the gut’s daily movement

Often cheaper than the drug for the amount required

Great option for antibiotic non-responders

Both a great first-line or second-line treatment if you face relapse post antibiotics treatment

✖ Cons

Not all supplements are created equal

Ingredients need to be optimised for dispersion along the gut, not absorption into the blood

The source of the ingredient matters to its effectiveness

The active component of the listed ingredient needs to be considered by the brand in the formulation

Common for products to skip the stabilisation process

Particle size of ingredients matters and effect the dosage and potency required

Need to be tested adequately for active components before being bottled by the company

Won’t work for everyone

4. The structural integrity of the gut

When someone has SIBO, there is constant stretching from the gas build-up in the small intestine. Unlike the large intestine, the small intestine was not designed to be stretched like that.

The small intestine’s walls contain tight junctions that act like a very selective draw bridge, deciding what to let out of the gut and into the bloodstream.

When functioning correctly, your tight junctions let things like nutrients out and keep waste in. When someone has SIBO, that constant stretching can cause the tight junctions to become loose.

Your gut also contains mucus that protects the gut lining from bacteria by promoting their clearance and separating them from the epithelial cells (which can be found in the gut). This mucus helps inhibit inflammation or irritation from bacteria.

With SIBO studies observed this can become thin and compromised.

Ingredients like Glutamine, Marshmallow Root, Glycyrrhizinate Licorice Root and Quercetin Dihydrate have all been shown in the scientific literature to help restore the gut’s structural integrity.[4][5][6][7]
For this reason, they have all been included in Gut Fix which may be a better option than a probiotic if you have compromised structural integrity.

Gut Fix was designed with ingredients to help speed up the 48-hour cell turnover of your gut lining and promote structural integrity. It includes clinically proven ingredients to help repair tight junctions while improving mucus content in your GI tract. These ingredients have also been shown to help with stimulating nerve endings to help further boost mucus secretion. That means when the time comes to introduce a probiotic the risk of bacteria irritating your gut lining further may be reduced.

5. An alternative natural option for SIBO

Antimicrobials remain the most studied natural option proven to treat SIBO if you’re looking for a natural way. Studies have even found them to be as effective in the treatment of SIBO as the most recommended and successful drug and they may have other benefits. FixBIOME system contains the most studied ingredients for the treatment of SIBO.

6. You can support and encourage beneficial bacteria growth without the need for a probiotic

Studies have found there are other ways to promote good bacteria in the gut without the use of probiotics.
Natural ingredients like Chinese Rhubarb root can assist in restoring gut microbiota balance, restore disrupted flora, and prevent microbiota shifts.[8][9][10]
Ingredients like quercetin have also been shown to affect the progress of microbiota-associated diseases in a positive way.[11] Notably, a study found quercetin supplementation increased gut microbial diversity, which may improve gut protection and achieve the same result many people seek with probiotic use.
Coptis root and rhizome extract have been used to promote healthy digestive and microbial environments and have also been found to improve gastrointestinal motility function.[12] That may help regulate bowel movements in those struggling with issues of constipation and diarrhea.
Berberine has also been researched for its beneficial influence on microbes in the gut.[13]
Neem leaf has been shown to influence beneficial bacteria in the gut.
Neem is a scrub for intestinal villi (finger-like projections of the gut), an antagonist to bacterial biofilm accumulation[14][15][16] and is naturally cleansing and detoxing for the blood, skin, and liver.[17][18][19] It supports the growth of good intestinal bacteria without supporting the growth of bad intestinal bacteria.
L-Glutamine can help to promote the growth of beneficial gut bacteria, which are essential for maintaining gut health. While oregano oil is well-known for its capacity to inhibit the “bad” bacteria, it can also increase the growth of beneficial bacteria.
The FixBIOME system contains all of the above ingredients to help promote a healthy and balanced gut microbiome while also including ingredients to help with the MMC, restoring the gut lining, and promoting motility. It includes prokinetic ingredients, restorative ingredients and ingredients that have been shown in the scientific literature to influence and increase the development of microbiome diversity or “good bacteria” without the need for a probiotic.

You can review the research on the ingredients in the FixBIOME system by going here: FixBIOME Shop – Research

7. SIBO and histamine intolerance

Although not everyone with SIBO experiences histamine intolerance, SIBO can lead to histamine issues by impairing the gut’s ability to break down histamine.

Probiotics can be particularly risky when it comes to histamine intolerance. Some probiotics can potentially worsen histamine intolerance symptoms due to their histamine-producing properties.


what our
have to say

“After relapsing post-antibiotic treatment for SIBO, I decided to try the antimicrobial route. I had tried others without luck, but this system was a godsend for me! Highly recommend.”
– Pia
“I had struggled with IBS for years, and for the first time in my life, I can eat what I want without symptoms! Including dairy and gluten! Amazing stuff.”
– Emmy
“This is a great product, I’ve struggled with IBS and SIBO for a few years now. As a doctor myself I was looking for a specific formulation and this was very close to what I wanted without having to take numerous individual supplements.”
– Anonymous

“This has made the biggest difference in my life. I can finally eat freely and without pain”
– Vida

“I had many gut issues. Including SIBO and leaky gut. After week 5 I felt completely different. No bloating or pain.”
– Jennifer C.

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– Kassandra K.

“Was an absolute last ditch effort and glad I found it.”
– Rylee

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1 Ginger rhizomes (Zingiber officinale): A spice with multiple health beneficial potentials
2 Alternative Treatments for Minor GI Ailments
3 Peppermint Oil
4 Role of Glutamine in Protection of Intestinal Epithelial Tight Junctions
5 Aqueous extracts and polysaccharides from Marshmallow roots (Althea officinalis L.): Cellular internalisation and stimulation of cell physiology of human epithelial cells in vitro
6 Glycyrrhiza glabra Root
7 Potential Implications of Citrulline and Quercetin on Gut Functioning of Monogastric Animals and Humans: A Comprehensive Review
8 A Systematic Review of Rhubarb (a Traditional Chinese Medicine) Used for the Treatment of Experimental Sepsis
9 Rheum officinale
10 Gut Microbial Diversity in Rat Model Induced by Rhubarb
11 Dietary Quercetin Increases Colonic Microbial Diversity and Attenuates Colitis Severity in Citrobacter rodentium-Infected Mice
12 Coptidis Rhizoma: a comprehensive review of its traditional uses, botany, phytochemistry, pharmacology and toxicology
13 Effects of Berberine on the Gastrointestinal Microbiota
14 Leaf extract of Azadirachta indica (neem): a potential antibiofilm agent for Pseudomonas aeruginosa
15 Effect of aqueous extract from Neem (Azadirachta indica A. Juss) on hydrophobicity, biofilm formation and adhesion in composite resin by Candida albicans
16 Biofilms
17 Neem (Azadirachta indica): Prehistory to contemporary medicinal uses to humankind
18 Therapeutics Role of Azadirachta indica (Neem) and Their Active Constituents in Diseases Prevention and Treatment
19 Medicinal properties of neem leaves: a review