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Evidence based

Evidence Based

This article is based on scientific evidence, written by experts and fact checked by experts.

Our team of licensed nutritionists and dietitians strive to be objective, unbiased, honest and to present both sides of the argument.

This article contains scientific references. The numbers in the parentheses (1, 2, 3) are clickable links to peer-reviewed scientific papers.

How to Use Probiotics for Stomach Problems

Written by on March 3, 2023

Probiotic Bacteria Can Be a Game Changer for Digestive Issues

Key Takeaways:

  • Probiotics can help stomach issues by rebalancing gut flora, and easing symptoms such as bloating, constipation, and stomach pain.
  • Choosing a reputable probiotic is more important than worrying about exactly which strains it contains.
  • However, a combination of probiotics for stomach problems is likely to be more effective than just one.
  • Having a gut-healthy diet (e.g. a Paleo diet) alongside probiotics gives them the best chance of working.
  • You may want to take probiotics on an empty stomach (e.g. before breakfast) when stomach acidity is likely to lower.

Probiotics (good bacteria) are very popular and can help get things back on track if you’ve been having digestive symptoms. 

But though you will find probiotic bacteria in many supplements, as well as some fermented foods, they are not always used to their full potential. 

Over the years at the Ruscio Clinic for Functional Health we’ve refined how to use probiotics for stomach issues, based on research findings, clinical experience, and patient feedback. Recent success stories include Anna, who used probiotics together with a Paleo diet to turn around bloating, daily diarrhea, and fatigue symptoms, and Mona who combined probiotics with the low FODMAP diet and antimicrobials, to ease chronic reflux, bloating, stomach growling, and constipation. 

In this article, I want to share some of the things we’ve learned about using probiotics successfully for problems such as stomach pain and bloating, IBS, and other stomach/gut issues.

Let’s dig into using probiotics for stomach problems in more detail.

The Basics: How Do Probiotics Help Your Gut?

Understanding how probiotics can help correct gut problems means understanding what can go wrong in the first place — more specifically dysbiosis.

Gut dysbiosis is when the healthy balance of gut microbes throughout the digestive tract, collectively known as the microbiota or microbiome, is disrupted. Many different things can contribute to dysbiosis,  including poor diet, a bout of food poisoning, or a stomach virus. Stress, smoking, too much alcohol, and being inactive can also contribute. These can all lead to  bad bacteria getting the upper hand.

Stomach conditions that have been linked with gut bacteria imbalances or harmful bacteria include [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]:

  • Helicobacter pylori infection
  • Gastroenteritis 
  • Gastric cancer 
  • Reflux 
  • Functional dyspepsia 
  • Peptic ulcer

Wider digestive system issues (involving other parts of the gastrointestinal tract, such as the small intestine and bowel) may also be caused by, or indirectly related to, gut dysbiosis [11, 12, 13, 14]: 

Probiotics introduce good bacteria back into your gut, tackling the underlying gut microbiome imbalance. I go into more detail in the table below, but studies show that probiotics help in many different conditions including:

  • IBS (bloating, diarrhea and/or constipation) [15, 16, 17, 18, 19]
  • Inflammatory bowel diseases (IBD) such as ulcerative colitis [20, 21]
  • SIBO (Small Intestinal Bacterial Overgrowth) [22, 23]

Probiotics probably won’t work alone though — you need to make other more fundamental changes, like eating a healthful diet, to successfully restore balance to your gut flora and ease symptoms.

Stomach Ailments that Respond to Probiotics

Improving stomach problems by manipulating the microbiome is more than just theoretical. While the amount and quality of research varies, there are several studies that show a benefit to stomach and gut symptoms from taking probiotics. For easy reference, we’ve compiled some of this research in the table below.

Stomach/Gut ProblemResearch Showing a Benefit from Taking Probiotics 
H.pylori infectionSeveral meta-analyses have shown that probiotics taken with antibiotics can improve H.pylori eradication rates and reduce the side effects of treating H.pylori (such as antibiotic-associated diarrhea, nausea, and vomiting) [24, 25, 26, 27, 28, 29, 30]. 
GastroenteritisFour meta-analyses found some evidence that probiotics may reduce the duration of diarrhea and hospitalizations related to gastroenteritis in both children and adults [31, 32, 33, 34]. 
RefluxA systematic review of several trials found that probiotics were beneficial for treating GERD (gastroesophageal reflux disease) [35].
Irritable bowel syndrome (IBS)Five separate meta-analyses have shown the efficacy of probiotics as a likely effective treatment of IBS, with very few side effects [15, 16, 17, 18, 19]
SIBO (small intestinal bacteria overgrowth)A meta-analysis summarizing 18 clinical trials concluded that probiotics reduced bacterial overgrowth and improved symptoms, including abdominal pain in people with SIBO [22]. One SIBO-probiotics study found probiotics to be more effective than Metronidazole, an antibiotic treatment [36].
Functional dyspepsiaThree trials found modest evidence that probiotics, especially soil-based probiotic strains, in combination with proton pump inhibitors (acidity-lowering drugs) or prokinetics, may improve the symptoms of functional dyspepsia [4, 37].

The Best Probiotics for Stomach Problems

Many different types of bacteria have been shown to benefit gut issues. For example, the types used successfully in the stomach conditions detailed in the table above included:

  • Lactobacillus acidophilus
  • Saccharomyces boulardii 
  • Lactobacillus rhamnosus
  • Lactobacillus reuteri
  • Lactobacillus gasseri
  • Bifidobacteria lactis
  • Lactobacillus paracasei 
  • Lactobacillus plantarum
  • Bifidobacterium longum 
  • Bifidobacterium breve
  • Streptococcus thermophilus

That’s such a wide spectrum of probiotics that it’s not easy to say precisely which ones work best. Future research may unearth more on which healthy microbes seem to work best for what conditions. But we already know that many probiotic strains, species, and categories work across a wide range of conditions, so it’s not helpful to get hung up on specifics.

Probiotics for Stomach

Instead it is better to focus on getting a regular therapeutic dose of high-quality probiotics for stomach issues, rather than worrying about exactly what types.

Dosage and Timing 

The potency of probiotics is measured in CFU (coliform forming units) and is somewhat, but not critically, important. Of higher relevance is knowing that the product actually contains what it says on the label (it should be validated by third-party testing), and contains viable live bacteria that will thrive in your gut.

Probiotics for Stomach

Nevertheless, consuming a minimum of 5 to 10 billion CFU per daily dose is a good rule of thumb if you want to be assured of an efficacious probiotic product  [38, 39].

Think about when you take your probiotic too. Taking probiotics on an empty stomach first thing in the morning may help ensure lower stomach acidity and a better chance for probiotics to survive and thrive [40].

Benefits of Multi-Category Probiotics

One meta-analysis of 38 randomized controlled trials found that taking multiple species and/or strains of bacteria was more effective for inflammatory bowel disease (IBD), such as ulcerative colitis, than taking single strains [41, 42].

On the other hand, another literature review that looked at the efficacy of single-strain versus multi-strain probiotics did not find a significant difference in efficacy across eight different diseases [43].

As a general principle though it’s likely that the wider the variety of “good” bacteria you introduce to your gut the more robust your microbiota, and consequently gut health, will be. 

This is certainly what we have found at the Ruscio Clinic for Functional Health, working with many patients experiencing stomach and gut symptoms.

The difference in our approach is that we go further than just different strains and species.

Our triple-therapy approach employs the three main categories of probiotics, which are 

  • Lactobacillus /Bifidobacteria
  • Saccharomyces boulardii (a beneficial yeast)
  • Soil-based probiotics

When patients take all three of these categories together (including one or more strain/species within each category) they often see significantly improved results. Often, a patient will have had only partial success with a single-category probiotic product but much better results when they swap to this triple-therapy regimen.

What Diet Best Works with Probiotics?

Probiotics for Stomach

Alongside the use of probiotics, it’s important to try to eat in a way that will support the growth and establishment of healthy bacteria and not continue to feed gut microbial imbalances and gut inflammation.

Reducing gut inflammation and giving your gut microbiota an environment in which to thrive is as much about reducing the ultra-processed, low nutritional quality foods in your diet as it is eating a specific type of “healthy diet”.

Research shows that a high consumption of ultra-processed food can change the gut microbiota and lead to inflammation. That said, much of this evidence comes from animal studies, so more research is needed in humans, especially long-term clinical trials [44, 45].

Apart from eating to dampen inflammation, three other key components of a gut-healthy diet are:

  • Eating to keep your blood sugar levels stable.
  • Finding your comfortable intake of carbohydrates and prebiotics (fermentable food fibers that can trigger gut discomfort in some people). Everyone has their own ideal intake of both of these.
  • Identifying any food allergies and intolerances (which could also manifest as stomach problems).

A Mediterranean or Paleo Diet 

If you’re not too sure where to start with these key pillars of healthy eating, I’d recommend starting with either a Mediterranean style diet or a Paleo-style diet (both have worked well for many of my patients). 

A Mediterranean diet is easy to stick to, tasty, and has been linked with reduced inflammation in the body [46]

One year-long study looked at how the Mediterranean diet affected the microbiome in elderly people. It found encouraging upticks in types of bacteria associated with reduced frailty and better cognitive function [47] 

However, people vary in their tolerance of carbs and other ingredients and can find the Paleo diet more suitable if they are a little more sensitive (Paleo also avoids gluten, dairy, and nightshade veggies and works by minimizing your exposure to foods that can provoke an inflammatory/immune system response). [48]   

You can basically experiment to find out what works best for you but it’s best to work with the minimum amount of food exclusions you can get away with.

The Low FODMAP Diet

For those who experience more entrenched stomach symptoms, and who don’t get sufficient enough success with the Paleo diet, a more comprehensive elimination diet such as a low FODMAP diet may be successful.

Studies have shown that a low FODMAP diet can be particularly successful for IBS and SIBO symptoms [49, 50].

Probiotic Foods

Probiotics for Stomach

Whichever diet you choose, you may be able to enhance its gut-friendly nature by including some fermented probiotic foods, such as kimchi, kombucha, natural yogurt, sauerkraut, and kefir. These naturally contain live beneficial microorganisms. Be aware, however, that fermented foods by themselves do not meet the effectiveness or evidence standard of supplemental probiotics [51] — i.e. they are a good adjunct to probiotic supplementation but not an effective replacement.

Probiotics Work For Stomach Problems

To recap, probiotics can be a really useful supplement for many types of stomach disorders. One of the key ways they work is by helping to balance the microbiome, which is often disrupted when you experience gut symptoms. 

It’s always best to try to prevent gut dysbiosis by eating a healthy balanced diet and avoiding too many overly processed foods. When you do pick a probiotic, look for a researched strain or combination of microbes and a potency of around 5–10 billion CFU (coliform forming units) per daily dose.

For a more in-depth guide to healing your gut, there’s an eight-step process you can follow in my book Healthy Gut, Healthy You. Or if you would prefer a personal consultation with one of our experienced practitioners, get in touch with us at the Ruscio Institute for Functional Health. 

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.
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