The Insider’s Guide to Probiotics for SIBO: Best Probiotics for Methane SIBO, Constipation, Hydrogen SIBO and Soil-Based Options in the UK

Small Intestinal Bacterial Overgrowth (SIBO) is a complex gut disorder where too many bacteria build up in the small intestine  a place where they shouldn’t thrive in large numbers. Depending on the type of gas these bacteria produce, you might experience very different symptoms: constipation, diarrhoea, bloating, or even brain fog.

If you are unsure as to whether your gut symptoms are being caused by SIBO, we offer  SIBO testing in the UK.

Managing SIBO isn’t just about killing off the bacteria it’s also about restoring balance to your gut environment. That’s where probiotics come in. But if you’ve been told that “probiotics are always good” or that “they’ll make your SIBO worse,” you might be confused  and rightfully cautious.

The truth is: not all probiotics are helpful for SIBO, and some might even make your symptoms worse if you choose the wrong types.

In this insider’s guide, we’ll break down:

• When probiotics can help — and when they can backfire
• The best probiotics for methane-dominant (constipation-type) SIBO
• The best probiotics for hydrogen-dominant (diarrhoea-type) SIBO
• Why soil-based probiotics might be the missing link
• UK-specific product recommendations
• How to safely introduce probiotics without worsening symptoms
• Common mistakes to avoid when using probiotics for SIBO

By the end of this guide, you’ll know exactly how to choose the right probiotics for your type of SIBO — backed by real science, not guesswork.

Understanding SIBO and Its Variants

SIBO occurs when bacteria that normally reside in the large intestine proliferate in the small intestine. This overgrowth can disrupt digestion and nutrient absorption. SIBO is classified based on the predominant gas produced during fermentation:

• Hydrogen-dominant SIBO: Often associated with diarrhoea.
• Methane-dominant SIBO (Intestinal Methanogen Overgrowth – IMO): Typically linked to constipation.
• Hydrogen sulphide-dominant SIBO: Characterized by gas with a “rotten egg” smell and gut inflammation.

Accurate diagnosis through SIBO breath testing is essential to determine the appropriate treatment approach.

The Role of Probiotics in SIBO Management

When used thoughtfully, probiotics can be a valuable tool in managing SIBO — but they’re not a one-size-fits-all solution. Because SIBO involves bacterial overgrowth in the wrong place (the small intestine), adding more bacteria through probiotics requires a strategic approach.

Are Probiotics Good for SIBO?

The short answer is: probiotics can be helpful for SIBO  but only when used carefully and strategically.

Because probiotics are live microorganisms, it’s understandable that many patients  and even practitioners worry that adding more bacteria could make SIBO worse.

And sometimes, if the wrong strains or dosages are used, it can.

But when the right types of probiotics are chosen, and they are introduced at the right time, they can actually:

• Help suppress harmful bacterial overgrowth (through competitive inhibition)
• Reduce gut inflammation and calm the immune response
• Support gut barrier healing, lowering the risk of leaky gut
• Restore balance to the disrupted microbiome after antimicrobial or antibiotic treatment
• Improve motility (especially important in methane-dominant SIBO)

When Probiotics Are Helpful in SIBO:

• After or during antimicrobial therapy to prevent re-infection and rebalance the gut
• To reduce diarrhoea, improve gut lining strength, or ease constipation depending on the strains chosen
• When symptoms are stable enough to tolerate a gentle microbiome reset
• When low-fermentation strains (like spore-based probiotics, Saccharomyces boulardii, or specific Bifidobacterium strains) are selected

When Probiotics Can Make SIBO Worse:

• If started too early, before the bacterial or archaeal burden has been reduced
• If using high-fermentation strains that produce lots of gas (e.g., certain Lactobacillus acidophilus blends)
• If doses are too high, causing “die-off” or immune overstimulation
• In people with histamine intolerance, who might react to specific strains that produce histamine

My Clinical Perspective:

In practice, I rarely use probiotics in phase 1 of treating SIBO.
Instead, they are typically introduced after antimicrobials or antibiotics, when symptoms are better controlled and the gut is ready for microbiome repair.

Using carefully selected probiotics  like soil-based spores, Saccharomyces boulardii, or targeted Bifidobacterium strains  can help reduce relapse risk and strengthen gut health long term.

Potential Benefits of Probiotics for SIBO

• Competitive Inhibition: Certain probiotic strains can help “crowd out” the harmful bacteria by competing for space and resources. This can limit the overgrowth and support a healthier balance of microbes in your gut.
  
• Immune Modulation: Probiotics don’t just work locally in the gut — they also interact with your immune system. The right strains can help calm gut inflammation and enhance the body’s natural defences against problematic bacteria.
  
• Gut Barrier Support: A strong intestinal lining acts as a barrier against toxins and bacteria leaking into the bloodstream. Some probiotic strains can strengthen this gut barrier, which is often compromised in people with SIBO.
  
  

Potential Drawbacks of Probiotics for SIBO

• Symptom Exacerbation: Introducing additional bacteria — even beneficial ones — can sometimes worsen symptoms like bloating, gas, and abdominal discomfort, particularly if the probiotic strains produce gases or histamines.
  
  
• D-Lactic Acidosis: Certain probiotics, especially some Lactobacillus strains, produce D-lactic acid. In sensitive individuals, a build-up of D-lactate can cause neurological symptoms like brain fog, confusion, and fatigue.
  
• Risk of Further Overgrowth: In rare cases, probiotics can colonize the small intestine and add to the existing bacterial load, potentially making SIBO worse rather than better — especially if the wrong types or doses are used.

In SIBO, probiotics can act as both friend and foe. Choosing the right strains — and using them at the right time — is critical to getting the benefits without triggering setbacks. Working closely with a practitioner who understands the nuances of SIBO is key to success.

Best Probiotics for Methane-Dominant SIBO (Intestinal Methanogen Overgrowth)

If you’re dealing with methane-dominant SIBO — now often called Intestinal Methanogen Overgrowth (IMO) — you’re facing a situation where archaea like Methanobrevibacter smithii produce excessive methane gas. These organisms feed on hydrogen produced by other bacteria, slow down your gut motility, and often lead to stubborn constipation.

Choosing the right probiotics is critical when managing IMO. Selecting the wrong strains can easily worsen your symptoms, so it’s important to approach this with care and strategy.

Best Probiotics for Methane-Dominant SIBO

1. Spore-Based Probiotics
(e.g., Bacillus subtilis, Bacillus coagulans)

Spore-based probiotics are particularly effective for IMO. They don’t increase fermentation in the small intestine and are highly resilient, surviving stomach acid to reach the intestines intact.
They also help regulate the immune system and support overall gut balance.

Examples: MegaSporeBiotic, Just Thrive

2. Saccharomyces boulardii

Although S. boulardii is best known for its benefits in treating diarrhoea, it also plays a crucial supportive role in methane-dominant SIBO:

• Reduces gut inflammation
• Strengthens the intestinal barrier
• Protects against pathogen overgrowth during and after antimicrobial treatment
  
  

Important to note:
S. boulardii doesn’t directly improve constipation or gut motility. Instead, it creates a healthier gut environment, making it a valuable addition alongside motility-support strategies.

 Examples: Optibac Saccharomyces Boulardii

3. Lactobacillus plantarum (with caution)

L. plantarum is anti-inflammatory and generally well-tolerated. However, in IMO cases, it should be introduced slowly and monitored carefully, as some individuals with sensitive guts or histamine issues may react poorly.

 Clinical Tip: Start with very low doses and monitor for any increases in gas, bloating, or discomfort.

4. Bifidobacterium Strains (carefully selected)

Certain Bifidobacterium strains can support gut healing and motility in methane-dominant SIBO — especially after antimicrobial treatment has reduced the microbial burden.

Key benefits include:

• Reducing gut inflammation
• Supporting the intestinal barrier
• Improving stool frequency and easing constipation (notably Bifidobacterium lactis HN019)

Important considerations:
While generally safe, bifidobacteria still add bacterial mass, so they should be introduced slowly and carefully monitored for tolerance.

 Examples:

• Alflorex PrecisionBiotics (Bifidobacterium infantis 35624)
• Optibac Bifidobacteria & Fibre (for B. lactis and other bifido strains)
  
  

Tip: While spore-based probiotics and Saccharomyces boulardii are typically first-line, carefully adding Bifidobacterium strains like B. lactis HN019 may help support motility and ease constipation in methane-dominant SIBO. Always proceed slowly and monitor symptoms close

Another probiotic that can be used for methane-dominant SIBO is BioGaia Gastrus, which contains two strains of Limosilactobacillus reuteri (DSM 17938 and ATCC PTA 6475).

Why BioGaia Gastrus May Help IMO:

• Stimulates Gut Motility:
  L. reuteri DSM 17938 has shown pro-kinetic effects, meaning it can help stimulate gut contractions and ease constipation.
• Reduces Inflammation:
  ATCC PTA 6475 has strong anti-inflammatory effects, helping to calm gut irritation that often accompanies slow motility.
• Backed by Research:
  A 2020 randomized controlled trial found that supplementation with L. reuteri improved stool frequency and consistency in adults with functional constipation.

In methane-dominant SIBO cases, BioGaia Gastrus can be helpful — but it must be used strategically:

• It is best introduced after antimicrobials, when the microbial burden is lower.
• Always start with small doses and monitor closely, because L. reuteri may produce histamine, which could aggravate symptoms in histamine-sensitive individuals.

Who Should Be Cautious:

• Individuals with histamine intolerance or mast cell activation
• Those sensitive to lactic acid-producing strains
• Anyone with a history of strong reactions to probiotics

While BioGaia Gastrus offers exciting potential for improving constipation and motility, results in my clinical practice have been mixed. Some patients experience significant relief; others notice little change. It’s also relatively expensive compared to spore-based or yeast probiotics.

.

Best Probiotics for Hydrogen-Dominant SIBO (Diarrhoea-Predominant)

If you have hydrogen-dominant SIBO, your main symptoms are usually diarrhoea, bloating, abdominal pain, cramping, and sometimes urgency after eating.

The right probiotics can help calm inflammation, strengthen the gut lining, and rebalance the gut microbiota without feeding the overgrowth.

Here’s what’s typically best:

1. Saccharomyces boulardii (Top Recommendation)

• Why it helps:
  S. boulardii is a yeast, not a bacteria, so it doesn’t feed bacterial overgrowth.
  It’s proven to:
  • Reduce diarrhoea
  • Calm inflammation
  • Support gut healing
• Bonus: It’s also great for helping recover from post-antibiotic dysbiosis.

 Best products: Optibac Saccharomyces Boulardii, Klaire Labs Saccharomyces Boulardii

2. Lactobacillus rhamnosus GG

• Why it helps:
  This strain strengthens the gut barrier, reduces gut permeability (“leaky gut”), and has strong anti-inflammatory actions. It’s particularly well-researched for:
  • Infectious diarrhoea
  • Antibiotic-associated diarrhoea
  • IBS-D (diarrhoea-dominant IBS)

Best products: Culturelle Probiotic (contains Lactobacillus rhamnosus GG)

3. Lactobacillus plantarum 299v

• Why it helps:
  • Reduces bloating, abdominal pain, and stool frequency
  • Improves gut motility without causing gas
  • Supports serotonin regulation in the gut, which impacts gut movement

 Best products: Garden of Life Raw Probiotics, BioGaia products

4. Bifidobacterium infantis 35624

• Why it helps:
  • Potent anti-inflammatory effects in the gut
  • Particularly effective for diarrhoea, bloating, and IBS-like symptoms
  • Supports immune regulation, which can reduce hypersensitive gut reactions

Best products: Alflorex (PrecisionBiotics) — one of the only brands with pure B. infantis 35624

Important Notes for Hydrogen-Dominant SIBO:

• Avoid multi-strain “mega” probiotics early on, especially ones heavy in Lactobacillus acidophilus or fermenting strains — these can cause more bloating.
• Start with single-strain or very simple formulas first.
• Start slowly — even the right probiotics can cause some initial bloating as your microbiome adjusts.

Clinical tip: Some practitioners start only with Saccharomyces boulardii for 2–3 weeks, then gently layer in bacteria-based probiotics once diarrhoea improves.

Soil-Based Probiotics for SIBO: Why They May Be a Game-Changer

When it comes to treating SIBO, not all probiotics are created equal. Traditional probiotics, like many Lactobacillus and Bifidobacterium species, can sometimes worsen symptoms by contributing to fermentation in the small intestine. Soil-based probiotics, however, offer a different — and often safer — approach.

What Are Soil-Based Probiotics?

Soil-based probiotics (also called spore-based probiotics) are beneficial bacteria that naturally originate from the soil. Unlike traditional probiotics, these strains form a tough outer shell (a spore), allowing them to survive stomach acid, digestive enzymes, and bile — reaching the intestines alive and active.

Key soil-based strains include:

• Bacillus subtilis
• Bacillus coagulans
• Bacillus clausii

These spores “wake up” only once they reach the small or large intestine, where they can help restore balance without adding to bacterial overgrowth.

Why Soil-Based Probiotics Are Helpful for SIBO

• Survive the journey:
  Their spore coating protects them from being destroyed by stomach acid, making them highly reliable compared to fragile traditional strains.
• Don’t promote fermentation:
  Unlike Lactobacillus or Bifidobacterium species, soil-based probiotics do not ferment carbohydrates in the small intestine. This dramatically lowers the risk of worsening gas, bloating, and abdominal pain.
• Modulate, not overwhelm:
  Rather than aggressively colonizing, spores help “train” the immune system, reduce gut inflammation, and promote the growth of native beneficial bacteria.
• Support gut barrier integrity:
  Studies show that strains like Bacillus subtilis can strengthen the gut lining and protect against “leaky gut” — common issues in people with SIBO.

Best Soil-Based Probiotic Products for SIBO

If you’re considering soil-based probiotics for SIBO, trusted, high-quality options include:

MegaSporeBiotic (Microbiome Labs)
Just Thrive Probiotic

 Seed Daily Synbiotic (includes both spore-based and non-spore strains carefully selected)

These products use third-party testing to ensure the spores are active, uncontaminated, and clinically viable.

Clinical Tip

Start with a very small dose — even 1/4 of a capsule — especially if you have severe symptoms or are highly sensitive.

Soil-based probiotics can trigger temporary die-off reactions as the gut microbiome rebalances, so a “low and slow” approach is best.

Summary: Choosing the Right Probiotic for SIBO Recovery

Managing SIBO is complex, and probiotics can be an important tool — but only if used wisely.
By understanding your type of SIBO, choosing strains carefully, and introducing probiotics strategically, you can support your gut’s healing and reduce the risk of relapse.

If you’re unsure where to start, working with a qualified practitioner and considering SIBO breath testing can help create a personalised and effective plan.

Ready to take the next step? We offer comprehensive SIBO testing and tailored gut health programmes in the UK — contact us to find out more.

References

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Working with a healthcare provider can help tailor a  tests, dietary advice and a tailored supplement regimen to your specific needs for optimal results.

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Author – Victoria Tyler BSc Hons MBANT

Victoria Tyler owns and runs two busy clinics : Nutrition and Vitality and the IBS and Gut Disorder Clinic.

Nutrition and Vitality, along with the IBS and Gut Disorder Clinic, were founded with the goal of helping patients alleviate IBS symptoms by uncovering and addressing the root causes of their digestive issues.

As a Registered Nutritional Therapist, Victoria holds a BSc (Hons) in Nutritional Therapy and has trained with the Institute of Functional Medicine. She is also accredited by BANT and CNHC.

Before transitioning into health, Victoria earned a degree in Economics and an MBA, working with corporations including Canon and Vodafone. However, her own health challenges led her to pursue a career in Nutritional Therapy.

With a passion for learning, Victoria is committed to staying at the forefront of Functional Medicine. She helps patients manage IBS and other digestive disorders, including SIBO, Candida, and IBD, by identifying and addressing their root causes.

Victoria strongly believes that every symptom has an underlying cause, and there is always a solution to every health condition. To learn more, or to see patient reviews, visit Victoria’s profile on Google.

DISCLAIMER: The information provided in this article is intended for general informational purposes only and should not be construed as medical advice, diagnosis, or treatment. The products and methods mentioned are not a substitute for professional medical advice from a trained healthcare specialist. Always seek the guidance of your doctor or other qualified health professional with any questions you may have regarding your health or a medical condition. Never disregard professional medical advice or delay in seeking it because of something you have read on this website. Use of the information and products discussed is at your own risk.