Probiotics for SIBO – Helpful or Harmful?

Are probiotics helpful or harmful when treating SIBO?
For years, the advice was to avoid probiotics if you have small intestinal bacterial overgrowth (SIBO). But new research is challenging that belief. Certain probiotic strains can actually help reduce bacterial overgrowth, support gut healing, and even improve symptoms like bloating and constipation, sometimes with results comparable to antibiotics.

In this article, we’ll break down the evidence, the best probiotic strains for SIBO, and when to proceed with caution.

What is SIBO?

Small intestinal bacterial overgrowth (SIBO) is a common gut imbalance where bacteria build up in the small intestine, leading to bloating, gas, burping, and changes in bowel habits, from constipation to diarrhoea.

In this article, we’ll explore how probiotics can help (or harm) during SIBO treatment. For a deep dive into causes, testing, and treatment strategies, see The Complete Guide to SIBO below.

Really, this article is intended for people that have read, heard on podcasts or have been told by their practitioner that probiotics can’t be used in SIBO treatment. I feel that the story is slowly changing, but I still frequently hear this from new patients at the Byron Herbalist clinic. 

Probiotics For Gut Health 

While we won’t be covering the nuanced details of how probiotics beneficially influence gut health, we will cover some of the basics. 

First off a definition. Probiotics are defined as ‘live microorganisms that, when administered in adequate amounts, confer a health benefit on the host’ (1).

Now that we have a working definition let’s jump into some basics of how probiotics can beneficially impact our gut health. 

Antimicrobial Actions of Probiotics 

Probiotics are antimicrobial in their own weird and wonderful way.

A term called competitive exclusion outlines a number of methods that probiotics use to deter bacterial infections and overgrowths. These methods include the production of bacteriocins, competition for nutrients and reducing the luminal pH (2).

Let’s focus on bacteriocin production for a moment. 

Certain probiotics can manufacture what are known as bacteriocins. These antimicrobial peptides consist of 30 to 60 amino acids and target specific bacterial overgrowths and infections (2).

There are a number of great examples of targeted bacteriocin production from different Lactobacillus species including studies showing action against the following species of bacteria (3). 

Benefits of Probiotics on Leaky Gut

Speaking broadly, the jury is still out as to which probiotics can improve leaky gut and how good they are at doing it. Some studies show benefit while others don’t. There is a good foundation of preclinical data but more human trials are needed.

With that said we do have good human research showing benefit from some probiotic species in healing leaky gut.

While all of the above consists of clinical studies in humans (the best research we have to draw from) there is ample pre-clinical evidence supporting the use of Saccharomyces boulardii in leaky gut. 

This beneficial yeast is helpful in a range of gut conditions. The table below outlines some beneficial impacts Saccharomyces boulardii has shown in pre-clinical studies. 

Saccharomyces boulardii has been shown to help with the following (8).

Different Types of Probiotics 

Probiotics come in a range of different shapes and forms.

Popular and well studied probiotic bacteria include species of Lactobacillus and Bifidobacteria. Escherichia coli Nissle 1917 is a third, well studied bacterial probiotic. We also have the widely used beneficial yeast Saccharomyces boulardii. Finally spore based probiotics, often referred to as soil based probiotics are becoming more widely studied (9).

Which of these probiotics are helpful in SIBO? Let’s get to that now!

Probiotics For SIBO 

So what does the research tell us about probiotics for small intestinal bacterial overgrowth? This is the big question. Are probiotics helpful in SIBO treatments? 

A resounding yes! 

A systematic review with meta-analysis of human trials – the best science we have – was published in the Journal of Clinical Gastroenterology in 2017. It showed that probiotics alone led to successful SIBO decontamination in 53.2% of patients (10).

From the study 

‘In the case of patients suffering from SIBO, the treatment efficacy of probiotics was remarkable. The SIBO decontamination rate achieved with probiotics alone was 53.2%, which was comparable to that observed in a meta analysis on antibiotics (51.1%).’

Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth A Meta-Analysis and Systematic Review of Current Evidence

I would hate to be accused of cherry picking the data so let’s get something out of the way up front. 

Not every study included in the systemic review found probiotics to be helpful in SIBO.

Let’s dive into some of the studies.

Lactobacillus and Bifidobacteria Probiotics for SIBO  

One study evaluated the effects of a 6 species probiotic with Lactobacillus and Bifidobacteria species and an added Streptococcus thermophilus probiotic on patients with liver disease and SIBO (11).

The blend contained the following species of probiotics.

They found that SIBO was improved in 24% of patients and in none of the placebo group. 

I often recommend different probiotics for methane SIBO as well as customised herbs and prebiotics too. For more info on methane SIBO see our started guide here.

Image taken from – Short-term probiotic therapy alleviates small intestinal bacterial overgrowth, but does not improve intestinal permeability in chronic liver disease

Yakult Probiotic and SIBO

In a small study the strain Lactobacillus casei strain Shirota known as Yakult was found to clear SIBO in 64% of patients. Taking 1 bottle of Yakult daily for 6 weeks pushed the median time of the hydrogen spike (proximal fermentation time) back from 45 minutes to 75 minutes (12).

Mixing in Saccharomyces boulardii for SIBO treatment 

In another study a blend of bifidobacteria and lactobacilli species along with the beneficial yeast Saccharomyces boulardii were assessed for SIBO and IBS treatment (13).

The blend consisted of a number of well researched strains including

The study was a bit unusual as it was looking at the overlap between SIBO and IBS. They found a significant improvement in IBS symptoms in the patients that had SIBO after taking the probiotic blend above compared to the IBS patients without SIBO who also took the probiotics. Again it was a small study so we need to keep this in mind. Each patient in the study that did have SIBO had at least a 50% improvement in their symptoms after 30 days on the probiotics. 

The study also found a significant improvement in bristol stool types in the constipated IBS patients after the probiotic intervention. 

Spore Based Probiotics For SIBO 

Spore based probiotics are the new kids on the block. I have seen some pretty remarkable results using probiotics like Megaspore in certain SIBO patients. 

One thing that I will mention before we dig into the spore based studies is that some people will need to take it low and slow with this particular class of probiotics. Some feedback from the more sensitive patients include abdominal pain, trapped gas and even loose stools. If you do trial spore based probiotics take it slow and gradually build up to the therapeutic dose over time, particularly if you are sensitive and tend to react to new therapeutics. 

Bacillus Species 

One study took patients with SIBO (defined as an increase in 12ppm on a glucose breath test). Each patient received 1 capsule, three times daily containing 2 billion CFUs of Bacillus clausii for one month. Using the glucose breath test on follow up they found a normalisation of 47% from just the single strain intervention. 

Bacillus clausii has been shown to impact the gut in the following ways (14).

• Adhere to the intestinal wall
• Secrete antimicrobial peptides against gram positive bacteria 
• Resist common antibiotics 

Another study assessing probiotics for SIBO used a spore based species called Bacillus coagulan. Instead of trialling probiotics alone they used this particular spore based probiotic as a maintenance treatment after aggressive antibiotic interventions. When the results were tallied 93.3% of the probiotics post antibiotic group had negative SIBO breath tests whereas only 66.7% of the antibiotics alone group had negative breath testing (15).

Case Study: How Saccharomyces boulardii Helped Stop Diarrhoea from SIBO

One of my patients, a 35-year-old woman, came to me exhausted from months of bloating, urgency, and racing to the bathroom 3–4 times a day. Her breath test showed hydrogen-dominant SIBO.

Instead of starting with a standard bacterial probiotic, I used Saccharomyces boulardii, a beneficial yeast that can calm loose bowels and protect the gut lining. We paired this with a low-FODMAP approach, gentle antimicrobials in a herbal tincture and strong digestive enzymes.

Within 30 days, she went from constant diarrhoea to just one or two formed bowel movements a day. Her bloating improved, and she could finally leave the house without fear of sudden urgency.

Why it worked: SB doesn’t feed SIBO bacteria and has solid research for repairing the gut barrier and reducing inflammation.

Final Thoughts: Should You Use Probiotics for SIBO?

In the Byron Herbalist clinic, SIBO is by far the most common digestive disorder I see, and probiotic therapy is part of nearly every treatment plan. I select strains based on each patient’s symptoms, lab results, and history, but I rarely find a case where probiotics aren’t helpful. I’ll use them for slow motility (a common root cause for SIBO), as antimicrobials and to heal the gut lining too. Often I’ll pair them with herbal medicine for SIBO, either antimicrobials or motility herbs if indicated.

Occasionally, a patient may react to a specific probiotic blend (e.g., more bloating, loose stools, or mild discomfort). This is why working with a gut health professional matters, it allows for fine-tuning, adjusting strains, and achieving the best results with minimal side effects.

Work With Me

Struggling with digestive issues like bloating, abdominal pain, constipation, diarrhoea, or histamine reactions? I work with patients one-on-one to uncover the root causes of chronic gut issues — whether that’s SIBO, Candida, dysbiosis, or inflammation.
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References and Resources

1. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic
2. Mechanisms of Action of Probiotics
3. Antimicrobial effects of lactobacillus plantarum and lactobacillus acidophilus against multidrug-resistant enteroaggregative escherichia coli
4. The effects of perioperative probiotic treatment on serum zonulin concentration and subsequent postoperative infectious complications after colorectal cancer surgery: a double-center and double-blind randomized clinical trial
5. Effect of probiotics on gastrointestinal symptoms and small intestinal permeability in children with atopic dermatitis
6. Immune Response and Intestinal Permeability in Children With Acute Gastroenteritis Treated With Lactobacillus rhamnosus GG: A Randomized, Double-Blind, Placebo-Controlled Trial
7. Influence of Saccharomyces boulardii on the intestinal permeability of patients with Crohn’s disease in remission
8. Beneficial effects of Saccharomyces boulardii CNCM I-745 on clinical disorders associated with intestinal barrier disruption 
9. Probiotics, Immune Function, Infection and Inflammation: A Review of the Evidence from Studies Conducted in Humans
10. Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth A Meta-Analysis and Systematic Review of Current Evidence
11. Short-term probiotic therapy alleviates small intestinal bacterial overgrowth, but does not improve intestinal permeability in chronic liver disease
12. Probiotic effects on intestinal fermentation patterns in patients with irritable bowel syndrome
13. Effect of a Preparation of Four Probiotics on Symptoms of Patients with Irritable Bowel Syndrome: Association with Intestinal Bacterial Overgrowth 
14. Bacillus clausii as a Treatment of Small Intestinal Bacterial Overgrowth
15. Evaluating the efficacy of probiotic on treatment in patients with small intestinal bacterial overgrowth (SIBO) – A pilot study