The Best Probiotic for IBS and GERD: How to choose?

Choosing the best probiotic that works for both IBS and GERD is challenging. the two golden rules for choosing the best probiotic for IBS & acid reflux is to go Multi-strain and to avoid probiotic with high FODMAP constituents. 

We dug into the research and investigated different probiotic brands to find what works for IBS and Acid reflux.

Here are How to choose the best probiotic for GERD and IBS:

1- Choose the right probiotic strains for IBS and GERD.

Probiotic research is heavily directed towards the diseases of the lower gut tract (the colon and small intestine). Before we dig into the details, Remember that Probiotic research is relatively new and evolving. 

We know more about the role of probiotics for  IBS more than its role in GERD. We previously discussed the role of probiotics in IBS in this in-depth article

Best Probiotic strains for IBS:

The probiotic strains that work for IBS are summarized in this table.

IBS Subtype or prominent symptomPossible probiotic strains that can help
IBS Diarrhea.

Saccharomyces Boulardii (yeast) (ref)

Lactobacillus Plantarum CECT 7484 (ref)

Lactobacillus Plantarum CECT 7485 (ref)

Pediococcus acidilactici CECT 7483 (ref).

IBS-Constipation.Bifidobacterium lactis BB-12 (ref)
Gas and BloatingLactobacillus Plantarum (DSM 9843) (ref)
Best overall, mixed, or unspecified types of IBS

Combination of Lactobacillus acidophilus NCFM® and Bifidobacterium lactis Bi-07 (ref)

Bifidobacterium lactis HN019 (ref)

Tips on Selecting the best probiotics for your IBS
  • Results are not typical, Trial & Errors is The Best strategy.
  • Select multi-strain probiotics containing combinations of the above according to your main complaint.
  • Stick to one type at least 4 weeks Before experimenting with another type.

The best probiotic strains for GERD.

There is no enough data about the efficacy of probiotics for GERD symptoms. This metanalysis investigated 14 clinical trials about the effect of probiotics on GERD.

Here are our  conclusions:

  • Most of the studies are of low quality (a small number of participants or poor study designs). 
  • However, some studies showed promising results. Probiotics can help decrease gastric acidity and regulate its motility.
  • Some probiotic species that are associated with improvement of GERD symptoms include:
    • Lactobacillus gasseri LG21
    • Prevotella species.
    • Bifidobacterium bifidum YIT 10347.

How to Pick the right probiotic:

Too many probiotic brands exist, and too many strains to pick from according to your IBS subtype, and GERD.

To simplify this, use a strategy consisting of:

  • Going multi-strain: choose probiotics with multistrain. This is related to a better response in clinical trials (ref).
  • Trial and error: Pick one probiotic, give it a trial for 4 weeks, and monitor the response.
    • If it improves your symptoms, continue to take it.
    • If it is not effective or resulted in worsening of your IBS or GERD symptoms, switch to another multi-strain probiotic with a different formulation.

2- check the probiotic dose.

The dose of probiotic is expressed in CFU (colony forming unit). It is the number of bacteria in a sample capable of dividing and forming colonies.

Research indicates that doses between 10-20 CFU achieve adequate responses. Recent trends in probiotic products have MEGA numbers of CFS as up to 60 billion CFUs or more.

However, Bigger is not always better, especially in people with IBS. this is because large doses of probiotic bacteria can harm more than good.

Also, Note that CFU is used nowadays as a marketing tool where the manufacturers are not able to deliver such enormous doses (Probiotics are not regulated by the FDA).

What really makes a difference is the dose-per-strain and not the overall dose. But more interestingly, a new form of measurement has emerged, it is called AFU.

AFU stands for “Active Flourescent Units”. a more precise measurement by a laser-assisted technique called “flow cytometry”.

Whether in the dose and the unit of measurement doesn’t really make sense. Choosing a manufacturer with a good reputation seems to be more important.

3- Choose a stable probiotic.

Probiotic activity decrease with time. Poor manufacturing standards can greatly affect the efficacy of your probiotic.

Refrigeration helps prolongation of the probiotic efficacy. However, a decline of 5 per month in the number of active CFU is expected. 

Low-quality probiotic brands lacking the proper technology can lead to a completely useless probiotic. make sure of good storage, good transportation, good packaging, and more importantly, the manufacturing and the expiration date.

Quality probiotics are usually shelf-stable. But once you open them, put them in a refrigerator.

Don’t buy more than one month supply packed in one container. 


4- Enhance the effect of probiotics with a “prebiotic”.

Prebiotics are specialized fibers. They are of plant origin and act like fertilizers or food for the good bacteria (probiotics).

Taking a prebiotic supplementation not only boosts the effectiveness of your probiotic supplement but also enhance the healthy bacteria already existing inside your gut.

A long list of prebiotic foods and supplements exist. Common prebiotic foods include:

  • Asparagus.
  • Bananas.
  • Barley.
  • Oats.
  • Flaxseeds.
  • Yacon root
  • Wheat bran.
  • See weed.

Consult your dietitian to determine the best food for your condition or take a Prebiotic supplement.

Learn more about Prebiotics.

4- Double-check for the manufacturing quality.


As we mentioned before, Probiotics are categorized as a dietary supplement, not a drug. Meaning that the FDA doesn’t regulate this industry.

Thousands of probiotic brands exist in the USA alone.  Typing the word “Probiotic” in the search bar will bring +2,000 results.

Too much to choose from. The quality of probiotic manufacturing is important. Actually, we think it is the most critical factor to look for in a probiotic.

The drawback of choosing low-quality brands for probiotics:

  • Not enough variety and doses of the recommended strains.
  • Dead (ineffective) probiotic bacteria due to bad manufacturing techniques.
  • No proper protection against stomach acid: low-quality brands will not invest in proper protection against stomach acid.
  • misleading about the dose: as individual probiotic supplements are not tested and validated by a third party; n guarantee that the claims are true except for the quality and trustworthiness of the manufacturer.

So, investing in a quality probiotic seems to be a very important factor for a probiotic to work for IBS and GERD.

5- Avoid probiotic constituents that may worsen your IBS or GERD.


Probiotics can do more harm than good for many reasons. Choosing the wrong strains and doses can worsen your IBS or GERD symptoms.

Moreover, Some other “inactive” probiotic constituents can affect your IBS and GERD. Generally, avoid probiotics containing:

  • High FODMAP sugars such as fructose or lactose.
  • GOS or FOS (Galacto- or Fructo-oligosaccharides).
  • Inulin
  • Artificial sweeteners such as Xylitol, sorbitol, or maltitol.


6- Perform your own experiments!


Too many factors play a role in your response to a certain probiotic. Also, having both IBS and acid reflux can make you intolerant to certain probiotics. 

Currently, No single probiotic can fit all people with IBS and GERD. The response is variable even in people with the same IBS subtype, same severity, and similar acid reflux severity.

Why people are different in their response to the same probiotic:

  • Different strains living inside them.
  • Different patterns of disturbances of their microbiome.
  • Differences in age, sex, genes, race, and weight.
  • Differences in their IBS cause, and subtype.
  • Differences in the severity of GERD symptoms.
  • Different stress and anxiety levels.
  • Differences in other medications their take for IBS and GERD.
  • Differences in diet and lifestyle compliance.

Therefore, You shouldn’t give up probiotics too early. Instead, use a “trial and error” strategy. 

  • Pick a quality, multi-strain probiotic for your IBS and GERD.
  • Give it a one month trial and watch for the response and side effects.
  • If you are not satisfied, Move to another Probiotic with different strains, doses, or both. 
  • Always document how your symptoms are going and if any side effects.

Our recommended Probiotiotics for IBS and GERD:


Earlier in this article, we mentioned the strains that are adequately studied for IBS and GERD. However, this doesn’t mean improvement is exclusive to the use of these strains.

Probiotic research is still new, and too many strains are to be tested. So, choosing multi-strain probiotics with trial and error is your best option to discover what works for your IBS and GERD. 

After more than 10 hours of researching different probiotic brands for a product containing the largest variety, here are our recommendations:

1- Seed Daily Symbiotic (both probiotic and prebiotic in the same capsule):


Seed probiotics appear to be the most promising company sticking to real science (as described by Forbes).

Also, FDA authorized seed daily symbiotic as an investigational new drug (IND) in a clinical trial for its use in IBS.

Seed sticks to the highest manufacturing quality. The link to the product in the resources section below.

2- Dr. Matthew #1 Probiotic.


We choose this product Because: 

  • The multi-strain formula is close to the recommended strains for IBS and GERD.
  • It contains L. gasseri which is important for GERD symptoms.
  • Doesn’t contain high FODMAP constituents that can worsen IBS.

The link to the product is in the resources section below.