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What Are The Most Common Side Effects of Probiotics?

Common Side Effects of Probiotics

Most people who take a quality probiotic supplement only notice the positive effects, such as improved digestive functions, a stronger immune system, and a higher level of energy.

However, if the good and bad bacteria in your digestive tract are unbalanced, you may notice a few mild side effects of probiotics while your gut is transitioning to a healthier state. Thus, it is important that you learn how to select the right probiotic supplement.

Unfortunately, this aspect of taking a probiotic supplement is seldom discussed, which leads some people to conclude that their probiotic supplements are not working as they should. As a result, they stop taking the supplement before they’ve had a chance to reap the benefits.

Let’s take a closer look at some of the side effects of probiotics and what you can do to reduce or prevent them.

What are the Side Effects of Probiotics?

GI Discomfort

When you begin taking a probiotic supplement, the beneficial bacteria will establish themselves in your gut and start growing. Once their numbers are substantial enough they compete against and reduce the number of bad bacteria.

It is during this transition period that you may notice some minor side effects. How long they will last depends on the probiotics you are taking, and how long it takes your system to rebalance.

Side effects of starting probiotics, if they do occur, are usually very mild. When taking a powerful probiotic, you may experience: bloating, gas, and mild abdominal discomfort.1

The most commonly noted negative side effect is mild gas and bloating when you initially begin taking probiotics. If these side effects bother you, consider taking a digestive enzymes supplement along with your probiotics.

DrFormulas Digestive Enzymes for Bloating Relief, Gas

Digestive Enzymes for Bloating and Gas

After the initial period (within the first few days of taking probiotics), your body should gradually adapt to the new friendly bacteria, allowing for improved digestion. If you are still having discomfort try taking the probiotics on an empty stomach before bed. Probiotics can produce gas when provided with certain kinds of foods and taking probiotics before bed minimizes the chance of that happening.

probiotics side effects

Read on to learn how to to avoid probiotics side effects.

Can Probiotics Cause Diarrhea?

One other possible side effect is diarrhea or loose stools. That too should pass as your body gets fully adjusted to the new probiotics. In the long run, probiotics should not cause diarrhea.

Research shows that probiotics such as Lactobacillus and Saccharomyces boulardii are effective in reducing the duration of diarrhea, particularly cases of diarrhea caused by infections and antibiotics.

Can Probiotics Cause Constipation?

Does that mean that probiotics cause constipation? Sometimes. Constipation is generally more prevalent than diarrhea, affecting about 14 percent of adults in the United States and accounts for around 3.2 million medical visits every year.

If you are experiencing constipation with your probiotics, we recommend taking prebiotics with your probiotics. Be sure to select one that is organic and diverse so your probiotics can have good food to thrive.


Prebiotics to Support Digestive Health


In some cases, probiotics may actually reduce constipation. According to several studies, probiotics were found to increase the average number of weekly bowel movements by 1.3, and generally supported softer stools that were easier to pass. These studies found Bifidobacterium to be the most effective probiotic for supporting regular digestive health.5

It’s also important to understand that not all probiotics are created equal, meaning that no two probiotic strains will necessarily have the same benefits or side effects. For instance, if one strain of Lactobacillus supports better digestive health, that does not inherently mean that a different strain of Lactobacillus (or a completely different probiotic, like Saccharomyces boulardii) will have the same effect.


Headaches are an uncommon side effect of probiotic supplements. They may be experienced when consuming probiotic-rich foods such as yogurt, kimchi, and sauerkraut, contain biogenic amines, which are substances that naturally form in any protein-based foods as they age or ferment.3 

Common amines found in probiotic rich foods include histamine, tyramine, and tryptamine.4 Studies suggest that some people may be sensitive to amines, which can stimualte the central nervous system and potentially cause headaches.5

Maintaining a food diary can help you determine if fermented foods are causing these headaches. Thankfully, even if you do get headaches, you can still take probiotics in the form of supplements instead of through probiotic-rich foods to decrease the amount biogenic amines and heavy seasoning, both of which can cause headaches.

Can You Take Too Many Probiotics?

Probiotic-rich foods and supplements are generally considered safe. Your body is already filled with trillions of diverse bacteria, so overdosing is rare assuming that your immune system is healthy and functioning as normal.8

That said, you can potentially have too much of a good thing. Taking too many probiotics can create an unstable intestinal environment, which may result in many of the gastrointestinal side effects mentioned above, including diarrhea, abdominal pain, gas, bloating, and nausea.12

Ways to Reduce the Side Effects of Probiotics

If you are taking a probiotic and are noticing any of the aforementioned side effects, don’t give up on your probiotic supplement. There are things you can do to reduce these minor side effects:

1. Decrease the dosage

If you’re having some discomfort, try reducing the dosage by half. Once the symptoms have disappeared, you can gradually increase the dosage to a higher level.

Probiotics are measured by CFUs, or colony forming units. Colony forming units are used to measure the amount of viable bacterial cells in a supplement per milliliter.9 Studies have found that in order to be therapeutic in children, a probiotic should have at least 10 billion CFUs to reduce the duration of diarrhea.10

The amount of colony forming units that you actually need will either be higher or lower depending on your body size and health. The amount of probiotics you consume every day often comes down to consulting your doctor and potentially going through a period of trial and error.

Is a Higher CFU Count Better?

Along with the potential for overdosing, there’s also not much reason to take more probiotics than recommended or prescribed. Studies are still unclear about the potential benefits or drawbacks to consuming more than 45 billion CFUs of probiotics.11

The more effective solution may be to focus on diversity of bacteria. Probiotic supplements may contain a single bacterium or a combination of several types of bacteria.

While both can be effective, it’s often better to go with a supplement that offers a more diverse range of helpful bacteria. Different bacteria offer different potential benefits, so the more different kinds of probiotics in a supplement, the more potential benefits. Taking too much of a single strain can result in a monoculture, which may lead to imbalances and digestive problems.12

2. Take on an empty stomach

We recommend taking probiotics 30 minutes before you eat to maximize survival and effectiveness of your probiotic. If you’re still having issues taking probiotics 30 minutes before meals try taking it on an empty stomach before bed.

3. Stay hydrated

The side effects, such as bloating, gas, and mild abdominal cramps, are all happening as your body is detoxifying. Drinking plenty of water will help with the process while preventing you from becoming dehydrated.

4. Be patient

You should give your body at least a week or two to adjust to the beneficial bacteria regaining control of your digestive system. It will be worth it in the end.

      Contraindications for Probiotics

       Side Effects of Probioitcs

      Although probiotics benefit the immune system, they can potentially pose a danger to people with compromised immune systems who would be unable to respond properly if probiotics ended up somewhere other than the gastrointestinal tract.6  

      According to physicians who examined cases of probiotic infections, the people most at risk are immunosuppressed or are premature infants. Minor risks include having a central venous catheter, having an impaired intestinal barrier, cardiac valvular disease (if taking a probiotic with Lactobacillus), and simultaneously taking a broad spectrum antibiotic to which the probiotic is resistant (unlikely as most probiotics are susceptible to antibiotics), and taking probiotics via a jejestomy tube (a feeding tube that bypasses the stomach and goes straight into the small intestine). The authors of the review recommended that probiotics be used with caution if there is one major risk and one minor risk.13

      Immunocompromised people include those with untreated HIV, people with weakened immune systems (cancer patients, patients who have had recent bowel surgery, or those that are taking immunosuppressant drugs such as corticosteroids.)7

      If you have a weakened immune system you should consult your physician before taking a probiotic supplement.

      Allergic Reactions to Probiotics

      Another rare issue is allergic reactions. Humans can be allergic to just about anything, including milk which is often used in the probiotic production process.

      In conclusion, probiotic side effects may be not noticeable at all if you are taking a low-quality probiotic without live cultures. Others taking higher doses of more effective probiotics may cause mild stomach upset, gas, bloating, and in rare cases, diarrhea. When choosing a probiotic supplement, remember to look for the “three D’s” to make sure you are getting the best and highest-quality probiotic.




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