Probiotics For SIBO

Probiotics for SIBO: A Paradox That Makes Sense

Small Intestinal Bacterial Overgrowth (SIBO) is a condition characterised by an excessive concentration of bacteria in the small intestine. This overgrowth can disrupt digestion, lead to uncomfortable symptoms such as bloating, diarrhoea, or constipation, and interfere with nutrient absorption. On the surface, the idea of supplementing with probiotics—live bacteria—might seem counterintuitive when the problem is already “too many bacteria.” Yet, a growing body of research suggests that targeted probiotics may in fact help rebalance the gut, ease symptoms, and improve underlying mechanisms contributing to SIBO.

The Paradox of Probiotics in SIBO

It is natural to question why one would add bacteria when bacterial overgrowth is the very issue at hand. The key lies in the type of microbes and what they do. Probiotics are not simply “more bacteria”—they are specific strains with unique properties that can help suppress harmful microbes, regulate immune activity, and restore intestinal function.

A 2024 clinical trial in pregnant women with subclinical hypothyroidism and SIBO showed that supplementing with a multi-strain probiotic (including Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus) plus prebiotics for 21 days significantly improved outcomes. Participants experienced reductions in hydrogen and methane breath test positivity, lower inflammation markers (C-reactive protein), and improved gastrointestinal symptoms such as constipation, indigestion, and diarrhoea.

This illustrates a key principle: not all bacteria fuel overgrowth—some actively restore balance.

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Mechanisms by Which Probiotics May Help SIBO

1. Production of Antibacterial Compounds

Probiotic strains can directly combat pathogenic and overgrowing species.

• Lactobacillus species produce lactic acid, which lowers intestinal pH and suppresses harmful bacteria.

• Bifidobacterium and Enterococcus species generate short-chain fatty acids (SCFAs) and other organic acids that strengthen the gut barrier and inhibit pathogens.

• Some probiotics even induce the host to release antimicrobial peptides such as lysozyme, providing an extra line of defence.

This antimicrobial activity means that probiotics don’t just “add bacteria”—they help regulate the ecosystem by selectively suppressing unwanted strains.

For example the probiotic Lactobacillus Reuteri DSM 17938, contained in Biogaia produces the antimicrobial compound reuterin and has been shown to lower methane levels in those with methane-induced constipation.

2. Immune System Modulation

SIBO is often associated with low-grade inflammation and impaired immune responses. Probiotics can help by:

• Increasing regulatory T cells (Tregs), which calm excessive immune activity.

• Reducing C-reactive protein (CRP) and inflammatory cytokines such as IL-6.

• Enhancing gut barrier integrity, preventing bacterial translocation that can fuel systemic inflammation.

This dual role—lowering inflammation while strengthening defenses—supports a healthier balance in the small intestine.

3. Supporting Intestinal Motility

One of the key risk factors for SIBO is impaired motility. Conditions like hypothyroidism, IBS, or connective tissue disorders can slow the migrating motor complex (MMC)—the gut’s natural cleansing wave that sweeps bacteria out of the small intestine.

Some probiotics help restore this rhythm:

• Probiotic metabolites (like SCFAs) stimulate serotonin and acetylcholine pathways, promoting peristalsis.

• Animal studies suggest probiotics may modulate enteric nervous system activity, thereby reducing stagnation and bacterial build-up.

The 2024 study highlighted this effect by showing significant reductions in methane positivity, which is strongly associated with constipation and slowed transit.

4. Repairing the Intestinal Barrier

SIBO often damages the mucosal lining of the small intestine, increasing permeability (“leaky gut”) and impairing nutrient absorption. Probiotics contribute to repair by:

• Strengthening tight junction proteins in intestinal cells.

• Promoting mucous layer thickness.

• Reducing pathogen-induced barrier disruption.

A more intact barrier means better digestion, fewer immune triggers, and improved tolerance to food.

5. Improving Nutrient and Hormone Metabolism

In SIBO, microbial overgrowth can deconjugate bile acids and inactivate hormones, interfering with nutrient and drug absorption. Probiotics help normalise these pathways. For example, Lactobacillus acidophilus has been shown to reduce β-glucuronidase activity, an enzyme that can inactivate thyroid hormones and other compounds. This may explain why probiotics improved thyroid stability in the clinical trial.

What Is The Best Probiotic For SIBO

There is one best probiotic for SIBO and the the right one for you will depend on the type of SIBO you have, and the symptoms you are experiencing. As discussed previously in our blog Bests Probiotics For Gut Health research shows us that probiotics are disease and symptom specific. This means the best probiotic for you is the one that has evidence behind it in achieving what you want to achieve (i.e you want to improve bloating choose the probiotic that has the best evidence behind it for improving bloating). Examples include:

• Probiotics for bloating: Bifidobacterium lactis HN019
• Probiotics for diarrhoea: Saccharomyces boulardii and Lactobacilus Rhamnossus GG
• Probiotics for constipation: Bifidobacterium lactis HN019
• Probiotics for intestinal methanogen overgrowth: Lactobacillus reuteri DSM 17938 (BioGaia)
• Probiotics for stress: Bifidobacterium longum 1714

Multi-Strain Advantage: Why Diversity Matters

Research does discuss that perhaps a multi-strain probiotic may be superior than single strain probiotics – yes I know I am contradicting myself but hear me out! Let’s use the example of constipation. Constipation can be caused by a variety of mechanisms including:

• Excess methane production.
• Low serotonin.
• Low SCFAs (short chain fatty acids).
• Dysbiosis such as candida overgrowth.

Each of these can be manipulated by single strain probiotics. But what if you have more than one mechanism at play? Then, we would need either a single strain that has evidence for improving more than one of the mechanisms, or, several strains. And considering we may not always know what the mechanism is, we might need a probiotic that contains several strains that have been shown to improve constipation via several mechanisms. This has been researched but I am unaware of any constipation specific multistrain formulation. So for now we can continue using singla strains, as well as the other numerous evidence based interventions (changes to diet, hydration, physical exercise, postbiotics, prebiotics, fibre supplements etc).

In other words, different strains offer complementary mechanisms:

• Lactobacillus species acidify the environment.

• Bifidobacterium enhance SCFA production.

• Enterococcus may enhance immune regulation.

• Spore-formers like Bacillus add resilience and help with gut motility.

This synergy allows a more robust rebalancing effect on the small intestine’s ecosystem.

Probiotic Foods vs. Supplements for SIBO: Weighing the Options

When it comes to managing Small Intestinal Bacterial Overgrowth (SIBO), probiotics can be introduced either through foods or supplements. Both approaches come with unique strengths and potential drawbacks, and the “better” choice often depends on the individual’s health priorities, symptoms, and lifestyle.

Probiotic Foods

Naturally fermented foods—such as yogurt, kefir, sauerkraut, kimchi, and other cultured products—are a traditional way of consuming live beneficial bacteria. Alongside probiotics, these foods deliver the nutrients of their base ingredients, making them a nourishing option.

Benefits:

• Nutrient-Rich Whole Foods: Fermented foods provide probiotics in combination with proteins, vitamins, and minerals, integrating gut support into an overall healthy diet.
• Microbial Diversity: These foods often contain a mix of bacterial strains, which can encourage a broader balance within the gut microbiome.
• Enjoyable and Accessible: For many people, eating probiotic-rich foods is both satisfying and culturally familiar, making it easier to maintain long-term.

Things to Keep in Mind:

• Uncertain Strains and Doses: Fermented products don’t always specify which bacterial strains they contain, or in what amounts—making it difficult to tailor them specifically to SIBO management.
• Symptom Sensitivity: Some probiotic foods are naturally high in FODMAPs, which can worsen bloating, gas, or discomfort in those with SIBO.

Probiotic Supplements

Supplements provide concentrated doses of carefully selected bacterial strains. They are available in capsules, powders, or liquid forms, designed to target specific health needs.

Benefits:

• Targeted and Measurable: Supplements allow for precise delivery of strains and dosages shown in research to support gut balance in SIBO.
• Reliable and Convenient: They offer a consistent daily intake, particularly helpful for individuals with dietary restrictions or those who do not tolerate fermented foods.
• Potentially Stronger Impact: Because they are designed with specific therapeutic goals in mind, supplements may offer a more effective way to influence SIBO-related symptoms.

In short, fermented foods contribute to overall gut wellness and dietary variety, while supplements provide precision and consistency that may be better suited to those actively working to rebalance the gut in SIBO. For many, a combination of the two—guided by symptom response and clinical advice—can provide the best of both worlds.

The Role of Prebiotics For SIBO

In the 2024 trial, probiotics were paired with dietary fibers (inulin, oat fiber, microcrystalline cellulose). These prebiotics act as fuel for beneficial bacteria, amplifying their effects. Prebiotics can enhance SCFA production, lower inflammation, and help reshape the gut microbiome toward balance.

Also research has shown that using the prebiotic PHGG alongside antibiotics improved the efficacy of the treatment.

Conclusion: Rethinking the Paradox

While it may seem counterintuitive to give probiotics in SIBO, evidence shows they do not worsen the problem—in fact, they can correct the imbalance. By producing antibacterial compounds, regulating immunity, restoring motility, repairing the intestinal barrier, and improving metabolism, probiotics offer a multi-pronged therapeutic effect.

SIBO treatment is not one-size-fits-all. Antibiotics, diet, and motility support are important, but probiotics and prebiotics represent a promising adjunct. Helping not by “adding bacteria” indiscriminately, but by carefully selecting microbial allies that restore harmony.

As research grows, we may increasingly turn to these strategies not only to treat SIBO but also to prevent relapse and support long-term gut health.

References

Redondo-Cuevas et al., (2024) Do Herbal Supplements and Probiotics Complement Antibiotics and Diet in the Management of SIBO? A Randomized Clinical Trial (click here)

Zhong et al., (2017) Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth: A Meta-Analysis and Systematic Review of Current Evidence (click here)

Wagner et al., (2025) Use of Probiotics and Synbiotics in the Treatment of Small Intestinal Bacterial Overgrowth (SIBO) and Other Gastrointestinal Symptoms After Metabolic Bariatric Surgery: a Systematic Review and Meta-Analysis (click here)

Martyniak et al., (2025) A Comprehensive Review of the Usefulness of Prebiotics, Probiotics, and Postbiotics in the Diagnosis and Treatment of Small Intestine Bacterial Overgrowth (click here)

Hao et al., (2023) Efficacy evaluation of probiotics combined with prebiotics in patients with clinical hypothyroidism complicated with small intestinal bacterial overgrowth during the second trimester of pregnancy (click here)

Ouyang (2024) Probiotics and Prebiotics in Subclinical Hypothyroidism of Pregnancy with Small Intestinal Bacterial Overgrowth (click here)

Zhang et al., (2024) Evaluation of probiotics in the treatment of hypothyroidism in early pregnancy combined with small intestinal bacterial overgrowth (click here)

Zhang et al., (2023) The Different Ways Multi-Strain Probiotics with Different Ratios of Bifidobacterium and Lactobacillus Relieve Constipation Induced by Loperamide in Mice (click here)