Probiotics for Gut Health

Choose the right probiotics for gut health problems.

Key Takeaways

  • Probiotics are powerful balancers for your digestive system and overall health.
  • Specific probiotics are not condition specific and don’t work like medications.
  • Choose one probiotic of each type from a reputable brand that stands behind its label claims.
  • Do your homework to make sure you are choosing reputable products.
  • Probiotic foods are healthy, but aren’t strong enough to treat digestive health problems.
  • Prebiotics are food for your beneficial bacteria.

Our digestive systems are home to a community of trillions of live bacteria that help keep us healthy. Your good bacteria work constantly to regulate your immune system, keep inflammation and symptoms in check, and keep your digestion working smoothly.

But imbalances in this community of gut bacteria can lead to uncomfortable consequences. Digestive symptoms like bloating, constipation, frequent diarrhea, food sensitivities, and heartburn can all be related to an overgrowth of bad bacteria or a lack of enough beneficial bacteria. An imbalance can even cause symptoms beyond the digestive tract, like brain fog, joint pain, or insomnia. Fortunately, rebalancing your gut microbiome isn’t that complicated, and can help you improve all these symptoms. Let’s take a look at how probiotics can help restore your gut health.

Why Probiotics?

Probiotics are powerful balancers for your digestive system and overall health.

The Journal of Clinical Gastroenterology [1] and the journal Trends in Microbiology [2] share that probiotics:

  • Increase the health of your bacterial community [3]
  • Fight pathogens (harmful bugs) and their toxins [4, 5, 6]
  • Promote a more rapid recovery from imbalances in your gut microbiome [7]
  • Promote a healthy immune response in your gut [8, 9, 10]
  • Reduce gut inflammation [11]
  • Encourage the growth of healthier microbes in your gut [12]
  • Reduce leaky gut [13] [14] [15]

Said simply, probiotics can help improve the balance of organisms in your gut, reduce overzealous immune system activity and reduce the inflammation that causes many of the symptoms you may be experiencing. There is even some evidence that probiotics reduce the incidence of viral illnesses, which means probiotics could be part of your COVID-19 (coronavirus) prevention strategy. [16

One general approach to taking probiotics provides these health benefits, regardless of the specific gut health condition you are trying to address. Also, probiotic supplements have very few side effects.

Probiotics for Gut Health Conditions

Millions of Americans suffer with digestive complaints, such as constipation, diarrhea, gas, and bloating, as well as digestive diagnoses like Irritable Bowel Syndrome (IBS) or Inflammatory Bowel Disease (IBD). Let’s take a look at some specific gut health problems that probiotics have been shown to be effective for.

Probiotics for IBS

The American College of Gastroenterologists estimates that 10-15% of American adults have irritable bowel syndrome, or IBS. Symptoms of IBS include gas and bloating, gut pain, and stool changes, including diarrhea, constipation, or mixed types.

Adopting an anti-inflammatory diet, like the low FODMAP diet, is always important to address IBS. But probiotics have also been shown to be important players.

  • Two meta-analyses have shown probiotics to be an effective treatment for IBS, with no side effects [17, 18]
  • In another meta-analysis, the results of twenty clinical trials were reviewed with a total of 1,404 subjects. In all studies, subjects were given either probiotics or placebo. The probiotic group showed improvement in global IBS symptoms when compared to the placebo group. [19]
  • The Canadian Association of Gastroenterology Clinical Practice Guideline for the Management of Irritable Bowel Syndrome (IBS) recommends a trial on probiotics for IBS. [20]

Meta-analyses are the highest quality scientific evidence. These three meta-analyses together give very strong evidence that probiotics are worth trying if you are struggling with IBS symptoms.

Probiotics for Inflammatory Bowel Syndrome (IBD)

Inflammatory Bowel Disease is a general category of digestive disorders including Crohn’s disease and ulcerative colitis. IBD patients experience regular inflammatory flares of the gut lining, and may experience diarrhea, abdominal pain, and other symptoms.

Probiotics have been widely researched as a complementary therapy for IBD and have shown important benefits.

  • One review found that probiotics worked as well as the anti-inflammatory drug, mesalamine, in maintaining remission for Crohn’s disease. [21] Best results were for a combination of probiotics and mesalamine.
  • Another review found the best approach for treating active ulcerative colitis was a probiotic supplement combined with an anti-inflammatory drug. [22]
  • Other reviews have found probiotics to be equally effective for ulcerative colitis as anti-inflammatory drugs like mesalamine. [23]
  • One systematic review has found probiotics do not help maintain remission, but overall the data suggest probiotics are helpful. [24]

If you have IBD, the evidence suggests that including probiotics in your treatment regimen may help you maintain your gut health, or minimize flares.

Probiotics for Gut Infections, Including SIBO

Many digestive symptoms are caused by overgrowth of bad bacteria or other types of pathogens, like parasites or fungus. There is evidence that probiotics help restore the gut environment to make it less hospitable to pathogens. They also enhance the effectiveness of conventional treatments to remove infections.

  • In a study of 181 infants, probiotics were as effective as Nystatin (a standard antifungal medication) in reducing fungal infection and improving food intolerances. [25]
  • Two studies show that probiotics can be more effective than standard antiparasitic drug treatment in Blastocystis hominis and Giardia infections. [26] [27]

Small Intestinal Bacterial Overgrowth (SIBO) is thought to be one of the common underlying causes of IBS. It causes many of the same symptoms, such as gas and bloating, stool changes, and abdominal pain.

Some claim you should not take probiotics for SIBO because you already have too much bacteria. However, probiotics have been CLEARLY shown to be effective in treating SIBO, both in improving symptoms and in improving lab values. [28]

  • One study found probiotics to be more effective than the antibiotic metronidazole (a standard treatment for SIBO). [29]
  • A meta-analysis summarizing 18 clinical trials concluded that probiotics are an effective treatment for SIBO. [30] Specifically probiotics reduce bacterial overgrowths and hydrogen concentrations, and improve symptoms including abdominal pain.
  • Another study found that probiotics work substantially better in patients with both IBS and SIBO, as compared to those who have IBS without SIBO. [31]

Probiotics has been shown to help resolve gut infections of various kinds. If you are trying to heal from gut infections, including SIBO, probiotics are likely to help and should be included.

Probiotics for Leaky Gut

Leaky gut is when intestinal inflammation causes small gaps to open up in your intestinal wall, which allows bacterial and food fragments to enter your bloodstream. This leakage can lead to uncomfortable symptoms, including food sensitivities, joint pain, brain fog, and digestive symptoms.

Because probiotics help repair the gut lining and restore the gut environment, they help repair leaky gut.

  • One small clinical trial found that probiotics helped to promote intestinal repair in humans. [32]
  • Another trial found positive effects of probiotics when used to treat intestinal impairment after a GI infection. [33]
  • Another small clinical trial showed that probiotic supplements reduced zonulin, a protein marker for intestinal permeability. [34]

Including probiotics may be worthwhile to help repair the intestinal lining damage that occurs with a gut infection or other inflammation you are experiencing.

Choosing the Right Probiotics

Probiotics are not condition specific and don’t work like medications.

There’s a lot of advice online about how to choose the right probiotic strains. Most of this advice recommends choosing probiotic species and strains that have been studied for your particular condition, like irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD).

These claims are often promoted by companies selling products, and would have you believe that you need a different probiotic for every different symptom or condition. But probiotics are not condition specific and don’t work like medications. Rather, they influence the gut environment generally.

There are really only three categories of probiotics:

  • Type 1: Lactobacillus and Bifidobacterium blends
  • Type 2: Saccharomyces boulardii
  • Type 3: Soil-based probiotics, often Bacillus blends

There is ample evidence from clinical trials and high-quality studies that probiotics can help with various digestive conditions, such as IBS [35], and IBD [36] (Crohn’s disease or ulcerative colitis), and SIBO [37]. Many of these studies tested particular probiotic strains. But as an example, various IBD studies show benefits from probiotics, with positive results from all three probiotic categories. [38, 39, 40] Ultimately, this means that probiotic strains are not condition-specific and that different probiotics can work for the same symptoms or condition.

With all that in mind, here is how you can think about choosing the right probiotics for you.

Choosing Probiotics for Your Gut Health

All you need to do is choose one probiotic from each type from a reputable brand that stands behind its label claims.

There are hundreds of probiotic species, and different strains within each species. But I’ve found the best results in the clinic from encouraging my patients to use one probiotic from each category.

Lactobacillus & Bifidobacterium species predominated blends Saccharomyces boulardii (a healthy fungus) Soil-Based Probiotics using various Bacillus species
These are the most well-researched, with over 500 trials assessing their validity. These live microorganisms are also known as lactic-acid producing probiotic bacteria. They typically do not colonize the host, but do improve the health of the host. The second most researched probiotic, with over 100 studies.  Saccharomyces boulardii (S. boulardii for short) is not a normal part of human microbiome, meaning it does not colonize us, but does improve the health of the host. The third most researched category of probiotics is soil-based probiotics. This group has roughly 14 clinical trials evaluating their effectiveness. This category is also known as spore-forming bacteria. This category of probiotic can colonize the host. [41]

Many people don’t seem to achieve balance in their gut microbiota with just one strain of probiotic. I have seen the best results with my patients following a protocol that includes all three probiotic categories. For many patients who have tried probiotics in the past, this approach makes all the difference.

Using Probiotics for Gut Health – Easy as 1, 2, 3

1 Try a Quality Probiotic from Each Category; take all three together. 
2 Monitor your Symptoms for 3-4 Weeks. If you’re improving, stay on the protocol until your improvements have plateaued.
3 Once You’ve Plateaued, Stay Here for About a Month to allow your system to calibrate to these new improvements. Then reduce your dose and find the minimal effective dose.  Stay on the minimal effective dose.

If you haven’t noticed any change in your symptoms after 3-4 weeks, you can stop taking probiotics and feel confident that you have fully explored probiotic therapy. There’s no need to go shopping for other probiotic strains.

Choosing Quality Probiotics

Do your homework to make sure you are choosing reputable products.

One thing for sure is that all probiotic products are not created equally. Probiotic supplements are not heavily regulated by the Food and Drug Administration, and labels may not accurately reflect what is actually in the product. Two common problems in probiotic supplements are:

  • a low concentration of viable probiotic cells (i.e. you’re getting ripped off)
  • the presence of undesired (potentially harmful) organisms. [42]

One study found only half of the probiotics examined had the specific strain listed on the label! [43]

With this in mind, it’s important to do your homework to make sure you are choosing reputable products so that you aren’t wasting your money or exposing your digestive system to risks.

What to Look for in a Probiotic Supplement

Independent Laboratory Analysis

All probiotic raw materials and final products should undergo independent laboratory analysis. Look for some kind of assurance or certification on the label or the company’s website that it has done this analysis. This ensures the probiotic meets its label claims.

Genetic Identification

Look for probiotic products that guarantee and label the strain(s) of probiotics, thus protecting you from exposure to frankenstein probiotics or harmful organisms.

Free of Major Allergens

Probiotics should be grown on media which are free of the common allergens: wheat, gluten, milk, casein, eggs, fish, shellfish, tree nuts, peanuts, and soybeans. A quality probiotic will also be free of artificial colors, flavors, or preservatives. 

Validated Potency

Probiotics should always clearly state the number of colony-forming units (CFUs) on the label, and meet their claims upon testing. Certain probiotics should be stored by the manufacturer and shipped in refrigerated conditions to retain the potency claimed on the label.  

Good Manufacturing Practices (GMP) Manufacturing

GMP are a set of best practices for dietary supplement manufacturing in the United States. This includes utilizing a state-of-the-art facility where temperature and air quality are tightly controlled. You don’t need to purchase the most expensive probiotic supplements, but you should be wary of probiotics that are substantially cheaper than the rest. This usually indicates quality assurance corners have been cut.

Probiotic Foods

Probiotic foods are generally healthy, but aren’t strong enough to treat digestive health problems.

Probiotic and fermented foods, like kimchi, kefir, sauerkraut, and kombucha, have active cultures in them and are healthy foods for your gut. However, probiotic foods usually don’t have sufficient colony-forming units of probiotics to provide you with a clinical benefit. Include them in your diet if you tolerate them, but if you have gut health problems, be sure to include probiotic supplements as well.


Prebiotics are food for your beneficial bacteria.

Just like your garden plants need fertilizer, your probiotics need prebiotics to keep them healthy.

Some probiotics have prebiotics in the product, but prebiotics are also sold as separate supplements. Prebiotics and fiber help your gut bacteria produce short-chain fatty acids, which provide energy for your intestinal cells.

Prebiotics are important, but use with caution because they can make digestive symptoms worse.

If you can’t tolerate prebiotic supplements, never fear. A diet rich in dietary fiber usually contains all the prebiotics you need to support your probiotics. Food sources of prebiotics include fruits and vegetables, legumes, and nuts and seeds that you tolerate. By regularly including these foods, you’ll keep your good bacteria happy and healthy.

Bottom Line 

No matter whether you have general digestive complaints or a specific diagnosis, probiotics are a powerful and easy-to-use part of your health care strategy. By calming inflammation, healing your gut lining, and balancing your bacteria, probiotics help you reduce symptoms and improve your overall health. Choose high-quality, well-made probiotics from reputable companies and use one of each type, and you’ll likely be feeling much better in no time.

References (click to expand)
  1.  2011 Nov;45 Suppl:S115-9. doi: 10.1097/MCG.0b013e318227414a.
  2.  2015 Jun;23(6):354-66. doi: 10.1016/j.tim.2015.03.002. Epub 2015 Apr 1.
  3.  2018;15(12):1106-1113. doi: 10.2174/1389200219666180813144834.
  4.  2017 Sep;41(4):466-475. doi: 10.1016/j.clinre.2017.04.004. Epub 2017 May 25.
  5.  2020 Apr;65(4):1134-1143. doi: 10.1007/s10620-019-05830-0. Epub 2019 Sep 23.
  6.  2015;50(11):1376-81. doi: 10.3109/00365521.2015.1050691. Epub 2015 May 19.
  7.  2011 Nov;45 Suppl:S115-9. doi: 10.1097/MCG.0b013e318227414a.
  8.  2018 Apr 25;6(2). pii: E35. doi: 10.3390/microorganisms6020035.
  9.  2016 Nov;13:190-200. doi: 10.1016/j.ebiom.2016.10.036. Epub 2016 Oct 26.
  10.  2015 Mar;31(2):153-8. doi: 10.1097/MOG.0000000000000151.
  11.  2018;15(12):1106-1113. doi: 10.2174/1389200219666180813144834.
  12.  2018 Apr 25;6(2). pii: E35. doi: 10.3390/microorganisms6020035.
  13.  2017 Jan 3;7:40128. doi: 10.1038/srep40128.
  14.  2014 Apr;58(8):1107-15. doi: 10.1093/cid/ciu065. Epub 2014 Feb 5.
  15.  2012 Sep 20;9(1):45. doi: 10.1186/1550-2783-9-45.
  16.  2015 Feb 3;(2):CD006895. doi: 10.1002/14651858.CD006895.pub3.
  17.  2017 Jul;33(7):1191-1197. doi: 10.1080/03007995.2017.1292230. Epub 2017 Mar 7.
  18.  2015;54(3):243-9. doi: 10.2169/internalmedicine.54.2710.
  19.  2008 May 7;14(17):2650-61.
  20.  2019 Apr;2(1):6-29. doi: 10.1093/jcag/gwy071. Epub 2019 Jan 17.
  21.  2007 Aug;66(3):307-15.
  22. Proceedings of the Nutrition Society (2007), 66, 307–315
  23.  2004 Nov;53(11):1617-23.
  24.  2011 Dec 7;(12):CD007443. doi: 10.1002/14651858.CD007443.pub2.
  25.  2013 Oct;172(10):1321-6. doi: 10.1007/s00431-013-2041-4. Epub 2013 May 24.
  26.  2011 Mar;108(3):541-5. doi: 10.1007/s00436-010-2095-4. Epub 2010 Oct 5.
  27.  2006;38(6-7):479-81.
  28.  2017 Apr;51(4):300-311. doi: 10.1097/MCG.0000000000000814.
  29.  2010 Dec;40(4):323-7.
  30.  2017 Apr;51(4):300-311. doi: 10.1097/MCG.0000000000000814.
  31.  2019 Jun;11(2):627-634. doi: 10.1007/s12602-018-9401-3.
  32.  2017 Aug 15;8(3):117-126. doi: 10.4291/wjgp.v8.i3.117.
  33.  2014 Apr;58(8):1107-15. doi: 10.1093/cid/ciu065. Epub 2014 Feb 5.
  34.  2012 Sep 20;9(1):45. doi: 10.1186/1550-2783-9-45.
  35.  2008 May 7;14(17):2650-61.
  36.  2007 Aug;66(3):307-15.
  37.  2017 Apr;51(4):300-311. doi: 10.1097/MCG.0000000000000814.
  38.  2019 Jan 30;11(2). pii: E293. doi: 10.3390/nu11020293.
  39.  2015 May 21;21(19):5985-94. doi: 10.3748/wjg.v21.i19.5985.
  40.  2010 Mar;1(1):93-106. doi: 10.3920/BM2008.1005.
  41.  2017 Sep 1;8:1666. doi: 10.3389/fmicb.2017.01666. eCollection 2017.
  42. Biotechnology & Biotechnological Equipment. Volume 33, 2019 – Issue 1
  43.  2019 Mar 22;14(3):e0213841. doi: 10.1371/journal.pone.0213841. eCollection 2019.

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