Allicin for SIBO: A Natural Antimicrobial for Bacterial Overgrowth

Allicin for SIBO? Why Now?

The rise of herbal alternatives for SIBO treatment

When it comes to SIBO (small intestinal bacterial overgrowth) treatment, herbal antimicrobial therapy is an increasingly popular option. Interestingly, this trend is seen across alternative and conventional medicine. 

Though traditional antibiotic therapy does exist for SIBO treatment, many doctors, functional medicine practitioners, and patients find better outcomes when herbal alternatives are used in conjunction or entirely on their own.

The truth is that herbal therapies treat SIBO as effectively as antibiotics and tend to have fewer side effects. This gives people the option to choose their preferred treatment option or have a backup plan if one course of treatment fails (1).

What makes allicin different from conventional antibiotics?

Allicin is an antimicrobial compound extracted from garlic bulbs. It has been the topic of much research due to its potency in treating bacteria that are typically resistant or hard to treat with conventional antibiotics.

Can a compound from garlic really help with bacterial overgrowth?

Data suggests that allicin is a potent antimicrobial agent that can slow the growth and kill many harmful bacteria while promoting the growth of beneficial bacteria and enhancing immune function in humans (2,3).

What is Allicin?

The Science Behind Allicin

How garlic produces allicin

Allicin is a sulfur-compound that is produced when garlic is chopped, crushed, or chewed. The act of crushing the garlic causes enzymes within the garlic cells to produce allicin. This produces the characteristic garlic odor and is meant to deter animals from eating the plant. 

Why it’s so powerful

Besides deterring pests and animals from eating the garlic bulb, allicin also serves an antimicrobial role to protect the plant from infection. It turns out that we can take advantage of these qualities for our own health!

Allicin’s Role in Natural Medicine

It turns out that humans have known about the benefits of allicin for a long time! Though we may have not known exactly how it works, garlic has been a part of medicine since the time of the pyramids.

There are ancient Egyptian medical texts documenting garlic’s use for infections, parasites, and circulatory health. The Greeks prescribed garlic to soldiers for strength and resilience, while Hippocrates recommended it for digestive issues and lung conditions. Meanwhile, ancient Chinese medicine recognized garlic’s ability to aid digestion and fight respiratory illnesses (4). 

All this to say—using garlic to promote health is nothing new, but modern science is now uncovering exactly why it works.

What is SIBO?

Understanding Small Intestinal Bacterial Overgrowth (SIBO)

How bacteria overgrow in the small intestine

At this point, we all know about the microbiome. This is the collection of bacteria, yeast, and sometimes even parasites that live in our intestines at all times. They help us with digestion, vitamin synthesis, and communicate beneficially with our immune system.

However, this is meant to mainly occur within the large intestine. When this bustling microbial community moves north into the small intestine, we start to run into issues. This means there are too many microorganisms where they really shouldn’t be.

There are many reasons why this can happen, but the most common reasons I see in my clinical practice are slow bowel motility, low immunity, post-viral autoimmunity, nutrient deficiencies, low-fiber diets, bowel disease, and antibiotic use.

Common symptoms of SIBO

It can be really hard to pin down SIBO symptoms, but the most common per the Mayo Clinic are as follows:

• Reduced appetite
• Stomach discomfort or cramping
• Feeling nauseous
• Excessive bloating
• Persistent fullness after meals
• Loose stools or diarrhea
• Unexplained weight loss
• Nutrient deficiencies and malabsorption

Conventional treatments

Based on the American Gastroenterological Association (AGA) guidelines for SIBO, the following is the best practice advice for SIBO treatment (5):

• Antibiotics: Rifaximin is the most commonly prescribed antibiotic for hydrogen-dominant SIBO, while methane-dominant cases typically require a combination of rifaximin with neomycin or metronidazole. Though antibiotics can be effective, recurrence is common, and some patients require multiple courses or alternative approaches to see lasting results.
• Diet: Diet plays a key role in managing SIBO, with low FODMAP diets helping to limit bacterial fuel sources and elemental diets essentially starving bacteria out over a few weeks. While diet alone isn’t a cure, it’s a powerful tool for symptom relief and relapse prevention, especially when used alongside antibiotics or herbal antimicrobials.

Why SIBO is Hard to Treat

Despite the above advice from the AGA, SIBO is incredibly difficult to treat. Even “successful” antibiotic therapy has a 43% relapse rate 9 months from the time of treatment (6). This highly relapse rate is due to a variety of reasons.

Biofilms and antibiotic resistance

SIBO often occurs in what is called a “biofilm.” This is where the bacteria causing SIBO create somewhat of a gel to protect themselves. Think about fruit in a jello mold. The SIBO bacteria are able to create a protective gel that prevents antibiotics from being able to reach them.

Even when antibiotics do get to the SIBO-causing bacteria, it might not work. Many SIBO bacteria are antibiotic resistant, which means that they have evolved to become immune to the antibiotics we typically use to kill them.

How gut motility and diet play a role

Beyond killing the bacteria, it is important to consider how they ended up colonizing the upper GI tract in the first place. Our intestines are supposed to constantly be sweeping materials (food and bacteria) downwards towards the colon. We refer to this as gut motility.

When gut motility is slowed for whatever reason, it gives bacteria an opportunity to move from the colon into the small intestines where there is much more food present for the bacteria to ferment. This is why SIBO is typically characterized by bloating.

This is where diet comes into play. Bacteria love to eat a very specific diet of fermentable oligo-, di-, mono-saccharides, and polyols (FODMAPs). These are present in many foods that we regularly eat and they can become a large fuel source for SIBO-causing bacteria.

When we remove high-FODMAP foods from the diet, the SIBO-causing bacteria lose their food source and can start to starve. This will reduce SIBO symptoms and provide relief. That being said, a low-FODMAP diet cannot treat SIBO.

How Allicin Works for SIBO

Current research shows that allicin works well as both a standalone and complementary SIBO treatment.

Direct Antimicrobial Effects

Targets Gram-negative bacteria (like E. coli, Klebsiella)

Allicin has great affinity for targeting gram-negative bacteria. These are a specific type of bacteria that have specialized cell walls that make them very hard to treat with antibiotics. They also release a potent endotoxin called lipopolysaccharide (LPS) that can cause a variety of health issues.

Gram-negative bacteria like E. coli, klebsiella, enterobacter, citrobacter, proteus, and pseudomonas can be present in different kinds of SIBO cases.

The sulfur compounds present in allicin are able to directly damage the cell membrane of gram-negative bacteria which makes them more vulnerable to antibiotic treatment and our own immune system (7).

Allicin also reduces the levels of the LPS toxin. This helps protect the gut lining and lower inflammation (8).

Inhibits DNA gyrase (prevents bacterial replication)

Bacteria need an enzyme called DNA gyrase to unwind and copy their DNA so they can grow and multiply. In SIBO, harmful bacteria like E. coli, Klebsiella, and Proteus use this enzyme to spread and form protective biofilms, making them harder to kill.

Allicin shuts down DNA gyrase by blocking a key part of the enzyme, preventing bacteria from copying their DNA and stopping them from multiplying. Without DNA gyrase, SIBO-related bacteria weaken, struggle to repair themselves, and become easier to eliminate (9). 

Disrupts bacterial thiol-dependent enzymes

Like the above effect on DNA gyrase, allicin is also able to shut down many other enzymes bacteria need to survive and cause SIBO. Apart from stopping bacterial growth, allicin is also able to disrupt bacterial energy production, detoxification, and antibiotic resistance mechanisms (10, 11). 

Reduces Biofilms That Protect Bacteria

As I briefly stated before, SIBO bacteria tend to hide in biofilms, which is a sticky goo that hides them from antibiotics and the immune system. This makes SIBO very difficult to treat. Allicin is able to break down these biofilms in a few ways:

1. Weakens the biofilm structure – Allicin dissolves the sticky layer that holds biofilms together, making it easier to break apart.
2. Prevents new biofilms from forming – It stops bacteria from sticking together and building fresh protective layers.
3. Disrupts bacterial communication – Bacteria send signals to organize their defenses, and allicin blocks these messages.
4. Exposes hidden bacteria – Once the biofilm is weakened, bacteria inside become easier to eliminate with antibiotics or herbal antimicrobials.

Supports Gut Barrier Health (“Leaky Gut”) (12)

Besides directly treating bacterial overgrowth in SIBO cases, allicin also plays a significant role in the resolution of intestinal hyperpermeability (aka leaky gut). This is important because people with SIBO often have significant leaky gut.

When SIBO-causing bacteria build up in the small intestine, they release toxins (LPS) that damage the gut lining and cause increased leakiness in the gut. As toxins and whole food proteins pass from the gut into the bloodstream, it can cause inflammation, immune activation, and systemic symptoms.

It is for this reason that SIBO is often associated with extraintestinal symptoms like brain fog, fatigue, anxiety, and chronic pain.

Reduces inflammation caused by bacterial toxins

Allicin first works to resolve leaky gut by stopping the production of LPS within bacteria. It then chemically modifies existing LPS so that it can not trigger inflammation as robustly in the gut lining and bloodstream.

Strengthens tight junction proteins

Allicin is also capable of healing a broken down intestinal barrier. It is able to do this by protecting tight junction proteins like zonula occludens-1 (ZO-1) and occludin that effectively act like glue between intestinal cells, keeping toxins out of the bloodstream.

Works Synergistically With Other Treatments

For all the reasons stated above, allicin is not only a potent agent for potentially treating SIBO, but it is excellent when combined with other conventional and alternative therapies.

Enhances rifaximin’s effectiveness

Since allicin is able to slow bacterial growth, decrease antibiotic resistance, and break the cell walls of SIBO-causing bacteria, it works wonders to make standard Rifaximin therapy much more effective. In vitro data shows that combining allicin with Rifaximin increases the kill rate of bacteria 5.5 fold! (13)

Combines with other herbal antimicrobials

For similar reasons, allicin is also added to many herbal treatments for SIBO. Commonly allicin is combined with berberine, oregano oil, or neem oil to provide synergistic effects in lowering SIBO-causing bacterial populations in the small intestine.

Which Type of SIBO is Allicin Best For?

As current science understands it, there are three subtypes of SIBO. These are typically referred to as hydrogen, methane, and hydrogen sulfide SIBO. Each subtype is characterized by the predominant gas created by an individual’s unique microbial overgrowth.

Hydrogen-Dominant SIBO (H-SIBO)

H-SIBO is the most common subtype of SIBO and is typically the most responsive to allicin treatment. H-SIBO is caused by an overgrowth of gram-negative bacteria like E. coli, Klebsiella, and Citrobacter which are incredibly susceptible to allicin.

Allicin can be used alone or in combination with herbal/prescription antibiotics to break down biofilms, slow growth, and decrease inflammation from LPS. 

Methane-Dominant SIBO (M-SIBO)

M-SIBO is not caused by bacteria, but other microorganisms called archaea. Allicin cannot directly kill archaea, but it can play a complimentary role in treatment. Archaea need hydrogen gas in order to thrive and allicin can reduce hydrogen levels and make the archaea more susceptible to other treatments.

Though data is still lacking, a recent study showed allicin treatment lower to archaea levels in sheep (14). This research suggests that allicin can also be used to improve M-SIBO in humans when combined with other antimicrobial agents like berberine or neem. 

Hydrogen Sulfide SIBO (H2S-SIBO)

It is unclear if allicin is appropriate to use for H2S-SIBO. As opposed to H-SIBO and M-SIBO, H2S-SIBO bacteria consume sulfur-containing compounds to fuel their growth. Since allicin is broken down into sulfur-containing metabolites in the gut, there is a possibility that it may aggravate symptoms.

However, allicin can still help to lower the amount of bacteria that cause H2S-SIBO. Therefore, its use in treating H2S-SIBO should be cautious and well monitored. Allicin is often paired with bismuth in these cases since bismuth is able to absorb excess hydrogen sulfide gas while allowing allicin to treat the bacteria.

How to Use Allicin for SIBO

Forms of Allicin Supplements

As previously stated, allicin is rapidly degraded once it is produced from crushing garlic. For this reason, many companies have worked hard to create allicin supplements that keep the allicin intact until it is released into the intestines.

Stabilized allicin capsules

To get consistent and isolated results from allicin, you should look for a stabilized allicin product. The most popular brand is Allimax, which has patented Allisure® AC-23 allicin powder to reliably deliver allicin into the intestines.

Garlic extracts vs. pure allicin

Garlic extracts are not the same as pure and stabilized allicin. You may see products like garlic oil, garlic powder, or aged garlic extract marketing for their health promoting qualities. While these products are not inherently bad, they are not well tested for SIBO treatment.

Garlic extracts contain a plethora of active ingredients like sulfur compounds, antioxidants, and some allicin precursors. However, they likely do not have enough allicin to reliably treat SIBO.

Whole food garlic

Similar to garlic extracts, whole food garlic (raw or cooked cloves) does not contain predictable amounts of allicin to reliably treat SIBO. In fact, garlic intake is often poorly tolerated during an active SIBO infection. This is because garlic is high in fermentable fibers that aggravate symptoms.

That being said, garlic is incredibly healthy and can be a great source of health promoting compounds, fibers, and small doses of allicin when there is no active SIBO.

Dosage Guidelines

There are no standardized dosing recommendations for allicin in SIBO treatment, but research and clinical use suggest an effective range of 900–1,200 mg per day, taken in divided doses. Most stabilized allicin products come in 450 mg capsules, meaning a typical dose would be one capsule two to three times daily.

For biofilm disruption, higher doses of up to 1,800 mg per day may be used, while those with hydrogen sulfide (H₂S) SIBO or sulfur sensitivity may need a lower starting dose of 150–300 mg per day to assess tolerance.

Allicin is often combined with other herbal antimicrobials or antibiotics to enhance treatment effectiveness. Since responses vary, dosing should be tailored to the individual, ideally under the guidance of a healthcare provider.

How long should you take it?

Allicin is typically taken for 4–6 weeks, as herbal antimicrobials work more gradually than antibiotics. This timeframe allows for bacterial die-off, biofilm disruption, and relapse prevention. Tougher cases may require up to 8 weeks, especially if biofilms are present.

Best Practices for Using Allicin

With or without food?

For the maximum effectiveness, you should take allicin on an empty stomach. This means at least 30 minutes before a meal or 2 hours afterwards. If you have a sensitive stomach, you can take allicin with a small amount of food.

Should you combine allicin with probiotics?

Taking bifidobacteria, soil-based, or saccharomyces probiotics can be beneficial for SIBO treatment and recovery. Be sure to take these probiotics 2-3 away from allicin to give them the best chance of survival.

Allicin vs. Antibiotics: How Does It Compare?

Many people choose herbal antimicrobials in order to avoid antibiotic treatment. Though allicin is effective and safe, it is important to know the pros and cons of choosing allicin over conventional antibiotic treatment.

Does Allicin Have Side Effects?

Like any other concentrated plant extract, allicin can have side effects to look out for.

Common Side Effects

Digestive discomfort

Most side effects from allicin are going to be localized to the GI tract. These symptoms include bloating, gas, stomach cramps, nausea, and diarrhea. These symptoms are typically caused by the allicin killing off SIBO-causing bacteria which then release toxins into the gut.

These side effects are usually temporary and can be mitigated by starting with a low dose and increasing slowly.

Who Should Be Cautious?

People with sulfur intolerance (CBS mutations)

Allicin contains sulfur, so those with sulfur intolerance, H₂S-SIBO, or CBS gene variations may struggle to metabolize it, leading to worsened symptoms instead of relief.

If this is you, start with a low dose (150–300 mg), support sulfur detox pathways (molybdenum, B12), or consider non-sulfur antimicrobials like berberine or oregano oil.

Pregnant and young individuals

Allicin has not been well studied in pregnant and juvenile populations. For this reason, allicin use is not recommended for these individuals.

Is Allicin Low FOMDAP?

Pure stabilized allicin is Low FODMAP, but fresh garlic is not due to its high fructan content. If you’re following a Low FODMAP diet, stick to allicin supplements, not whole garlic.

Final Thoughts: Is Allicin Right for You?

Allicin is a powerful, research-backed antimicrobial that offers a natural alternative to traditional antibiotics for SIBO. It targets gram-negative bacteria, disrupts biofilms, reduces inflammation, and helps restore gut barrier function—all key factors in effective SIBO treatment. 

While it works well on its own, allicin is even more effective when combined with other herbal antimicrobials or antibiotics like rifaximin.

That being said, SIBO is complex, and treatment should always be tailored to the individual. Factors like SIBO subtype, biofilm formation, gut motility, and sulfur tolerance all play a role in determining the best approach. Allicin is highly effective for hydrogen-dominant SIBO and can support methane-dominant cases, but it should be used cautiously in hydrogen sulfide SIBO.

If you’re struggling with SIBO symptoms, treatment resistance, or relapse, working with a functional medicine dietitian can help you develop a personalized treatment plan that goes beyond just bacterial clearance—addressing the root causes of your SIBO and preventing it from coming back.

Need Help with SIBO? Let’s Talk!

SIBO is complicated, but you don’t have to navigate it alone. If you’re unsure about whether allicin is right for you or need a customized treatment and recovery plan, book a discovery call with me today. Let’s get to the root cause and find a plan that actually works.