Side effects of probiotics on IBS symptoms (2023)

For those with IBS or other digestive symptoms, taking a probiotic supplement or eating fermented, probiotic-rich foods sounds like a great idea. After all, we know how important having a healthy and diverse microbiome is to our gut, and overall health. But probiotics don’t initially work for a number of our clients and can often make symptoms worse in the short-term for those with significant gut dysfunction or bacterial dysbiosis. So, what are the side effects of probiotics and what should you do if probiotics are making your IBS symptoms worse?!

Here’s what we’re going to cover:
> The proven health benefits of probiotics.
> List of common probiotic rich foods.
> The most common side effects of probiotics.
> Why probiotics can make you feel worse.
> How to choose a probiotic supplement.
> The importance of titration to minimize IBS symptom flairs from probiotics.
> When to get Functional GI lab testing completed.

What are probiotics and probiotic-rich foods?

According to the World Health Organisation’s technical definition, Probiotics are live microorganisms, typically bacteria or yeast, that give us health benefits when ingested in sufficient amounts. The most common species that we see in our supplement probiotics are strains of bifidobacterium and lactobacillus. They typically help maintain or restore a healthy balance of bacteria to our digestive tract and have many proven health benefits, including:
> boosting our immune system
> fighting pathogenic infections
> improving digestive function
> increasing absorption of nutrients
> preventing and treating UTIs
> reducing symptoms of IBS and IBD

And while most people look to a supplement to boost their probiotic intake, there are also food-based sources available. Some of the more common probiotic-rich foods include:
> Kefir
> Sauerkraut
> Kimchi
> Kvass
> Kombucha
> Miso

Most common side effects of probiotics

Despite their proven health benefits (for those who tolerate them really well), for those who don’t tolerate them, the most common side effects of probiotics we see in our clients are:
> Gas
> Bloating
> Looser stools
> Abdominal pain

(Video) Probiotic Side Effects

I really want to emphasize that the vast majority of these side effects of probiotics are experienced only temporarily and/or by those with a chronic gut infection or severe dysbiosis, and here’s why...

If the side effects of probiotics you are experiencing are actually the result of die-off during a protocol, we’ve written an entire blog post HERE explaining the mechanism and ways to manage these detox reactions.

Why probiotics can make you feel worse

The harmony (or otherwise) that exists within our GI tract is down to the number and variety of microorganisms that colonise it - a.k.a. our microbiome. Given that these bacteria, yeast and other species total in the trillions, with countless different strains represented, it’s an extremely complex interplay that exists within us.

Our gut bacteria have now been shown to play a crucial role in almost every process of the body. This is why introducing different species into the mix can temporarily have an impact on the environment and the symptoms we experience. This is particularly true of IBS-type symptoms like bloating, gas, abdominal pain and loose stools , which are the most common side effects of probiotics we see in our clinical practice.

There is a balance that exists within the GI tract and when we use supplement forms of probiotics or fermented foods we are temporarily changing that balance. This is not to say that the previous balance wasn’t doing us harm, it’s just that a level of equilibrium existed and that we have now potentially thrown it into chaos. It isn’t until a new, hopefully more beneficial, balance establishes itself that symptoms will stop.

It’s also important to point out that probiotics will not likely colonise, or take up residence, in our GI tract. They do however, have beneficial (or symptomatic) effects on the way through and help existing colonies of beneficial bacteria to grow and proliferate. It’s also worth noting that just because we experience symptoms as a result of probiotics, this doesn’t mean they’re not still doing us good. It is often the rebalancing of the gut microbiome that is resulting in symptoms but these teething problems may still lead to improved gut health in the long term. A little pain (or gas or bloating), for a lot of gain?!?

(Video) Probiotics Benefits + Myths | Improve Gut Health | Doctor Mike

When to persist and when to consider taking action

If a client only has a mild dysbiosis or imbalance of bacteria, without any significant pathogens or overgrowths, pushing through the initial mild reaction to probiotics may be advisable and sufficient to correct the gut dysfunction. Remember to start with small amounts of probiotics or probiotic-rich foods and build slowly. However, for clients who have diagnosable levels of bacterial or yeast pathogens or overgrowths, in my experience, probiotics alone will not likely fix the problem.

For these clients, continuing with the same probiotic that causes an initial reaction or side-effect will often see symptoms get worse, not better. If this is the case, and your practitioner has not been able to find a strain and brand that works for you, identifying the exact pathogen or overgrowth at the root of your gut microbiome imbalance is essential to any proper gut healing. More on this below.

How to choose a probiotic supplement

A reaction to probiotics may be more to do with the specific product you are using and not so much with probiotics in general. Here are three things you need to consider when choosing a good quality probiotic:

> Effectiveness of strains - some strains are more well researched than others so confer with your practitioner on what’s right for your condition. Three of the most beneficial strains for IBS-type symptoms to look out for are bifidus infantis, bifidus lactis, and lactobacillus plantarum. These can be taken individually, or in combination.

> Number of strains - diversity is your friend when it comes to a healthy microbiome. For this reason, a probiotic with 10-30 different strains is generally a good place to start, so long er you tolerate them all.

> Higher CFU’s - CFU stands for “colony forming units” and is used as a measure of how many bacteria are in probiotics. I typically recommend products that have at least 15-50 billion CFU’s. However, failure to titrate this type of product in slowly may cause symptoms because of the sheer amount of microorganisms introduced.

(Video) 5 Possible Side Effects of Probiotics

> Reputable brand - with probiotics not being regulated in many markets, ensuring you’re getting what you pay for can be difficult. For this reason, I recommend sticking with reputable brands recommended by your practitioner.

> Avoid fillers - Many store-bought probiotics contain ingredients that can aggravate symptoms for some people, including; D-lactate-forming species like Lactobacillus acidophilus, or tapioca and potato starch, maltodextrin, lactose, inulin, pectin as well as other prebiotics that may cause issues.

Working out the right probiotic for you, if you have IBS or other gut health issues, can be a complex process. Working closely with your practitioner and considering functional lab results, health history and any previous side effects of probiotics or probiotic-rich foods is a great way to ensure you’re onto the right strains for your healing journey. I wish it was easier to recommend well tolerated strains of probiotics, but unfortunately it is not, and I am often tailoring probiotic needs specifically to my clients. Sadly for those with gut health issues, a one-size-fits-all approach doesn’t work when it comes to probiotics.

Titrate probiotics in slowly to minimize side effects

To avoid any potential side effects of probiotics, as with any natural supplement, I recommend introducing probiotics in slowly. Titrating in gradually is particularly relevant for higher strength products. This often means breaking open a capsule and sprinkling out a small amount before building up to a more standard dosage. By titrating slowly, you’ll typically avoid any major reactions and will be able to reduce the dosage to the last tolerated amount. Once your body is comfortable, you can slowly increase the dosage.

The same goes for the probiotic-rich foods mentioned above like sauerkraut and kimchi. We like to start clients on small amounts of coconut kefir, before building up to fermented vegetables like sauerkraut, and so on.

Get Functional GI Lab Testing

If you find that you experience side effects of probiotics or eating probiotic-rich foods, even after using a high quality product recommended by your practitioner, titrating them in slowly and persisting for a few weeks, then functional GI testing is definitely recommended.

(Video) Probiotics treatment for Irritable Bowel Syndrome

The inability to tolerate probiotics is a common sign of gut pathogens like parasite and bacterial infections, as well as bacterial and yeast overgrowths like SIBO and Candida. For this reason, and because each condition requires separate treatment approaches, functional GI lab testing is key to working out exactly what is going on in your gut.

If you would like to learn more about four tests that cover-off the five most common root causes of IBS, check out this blog post for the full details. For those who don’t tolerate probiotics, I’d definitely recommend a comprehensive stool test and a SIBO breath best as a good place to start.

If you want to learn more about the testing process, or how we can help,please head to the Work With Us pageto learn more about how we work online at The Functional Gut Health Clinic with clients in many countries to test for and treat the many root causes of IBS symptoms and other GI conditions.


Can probiotics make IBS symptoms worse? ›

Can probiotics make IBS worse? Probiotics can make IBS worse if your IBS is triggered by SIBO. If you have SIBO, probiotics can get trapped in your small intestine and worsen your symptoms. Take a breath test to test for SIBO before treating IBS with probiotics.

What are the negative side effects of taking probiotics? ›

The most common side effects are a temporary increase in gas, bloating, constipation and thirst. Some people can also react poorly to ingredients used in probiotic supplements or to naturally occurring amines in probiotic foods. If this occurs, stop using probiotics.

Does probiotics help with IBS symptoms? ›

Probiotics may relieve symptoms of IBS

The American College of Gastroenterology conducted a meta-analysis of more than 30 studies, which found that probiotics may improve overall symptoms, as well as bloating and flatulence, in people with IBS.

Can probiotics make symptoms worse? ›

After all, we know how important having a healthy and diverse microbiome is to our gut, and overall health. But probiotics don't initially work for a number of our clients and can often make symptoms worse in the short-term for those with significant gut dysfunction or bacterial dysbiosis.

Can probiotics make you feel worse before better? ›

However, some patients take probiotics and feel even worse. Symptoms can include cramping, gassiness, diarrhea, fatigue, and even brain fog or memory problems. Often these symptoms intensify just after a meal.

Why do I feel sick after probiotics? ›

Because microbes used as probiotics already exist naturally in your body, probiotic foods and supplements are generally considered safe. They may trigger allergic reactions, and may also cause mild stomach upset, diarrhea, or flatulence (passing gas) and bloating for the first few days after starting to take them.

Who should not take probiotics? ›

Although probiotics are generally safe to use, findings of a review from 2017 suggest that children and adults with severe illnesses or compromised immune systems should avoid using probiotics. Some people with these conditions have experienced bacterial or fungal infections as a result of probiotic use.

What are the symptoms of too much probiotics? ›

Signs You May be Taking Too Many Probiotics
  • Diarrhea, Gas, Bloating, and other Digestive Symptoms. ...
  • Headaches from Amines in Probiotic Foods. ...
  • Certain Strains May Increase Histamine Levels. ...
  • Certain Ingredients Can Cause Adverse Reactions. ...
  • Probiotics May Increase the Risk of Infection for Some People.

How long do probiotic side effects last? ›

Most people do not experience side effects with probiotics -- but if they do, the side effects usually wear off after a few weeks of consistent use (12).

How long do probiotics take to work IBS? ›

For example, a review in Nutrients notes that people with irritable bowel syndrome (IBS) may notice the most benefit when taking probiotics for 8 weeks or more.

What is the best probiotic to take for irritable bowel syndrome? ›

According to one study, taking Lactobacillus acidophilus for 8 weeks significantly improved gas and overall symptoms of IBS in 80 people ( 14 ). It's also vegetarian, non-GMO, and free of artificial ingredients and gluten.

How do I get my IBS to calm down? ›

How to Calm an IBS Flare Up
  1. Apply Gentle Heat. ...
  2. Get Moving. ...
  3. Stay Away From Trigger Foods. ...
  4. Have a Soothing, Non-Caffeinated Tea. ...
  5. Dial Down Your Stress Levels. ...
  6. Try a Relaxation Technique.

Can probiotics cause more harm than good? ›

“When the gut barrier is healthy, probiotics are beneficial. When it is compromised, however, they can cause more harm than good.

How should I feel after taking probiotics? ›

If your gut microbiome is out of balance, you might be experiencing digestive discomfort such as gas, bloating and stomach aches, especially after eating. One of the first positive effects of a high-quality probiotic is improved digestion and a reduction in symptoms such as bloating, gas and stomach aches.

Can probiotics be damaging? ›

Possible harmful effects of probiotics include infections, production of harmful substances by the probiotic microorganisms, and transfer of antibiotic resistance genes from probiotic microorganisms to other microorganisms in the digestive tract.

How long does it take for gut bacteria to adjust? ›

How quickly does our diet affect the gut microbiome? What we eat impacts the microbes that call our guts home. But you might be surprised to hear that our microbial communities can respond drastically to dietary changes in as little as three days. This is exactly what a landmark study published in 2013 determined.

Do you feel sick when starting probiotics? ›

(7) However, when you start taking probiotics, you may experience mild increase in gas, bloating, thirst, and some digestive problems including diarrhea. Diarrhea can be uncomfortable, however, rest assured that your body's digestive system will regain balance within 14 days.

Should you take a break from probiotics? ›

If you experience ongoing side effects from probiotics such as bloating and gas, it may be a good idea to take a break from probiotics and ensure you are taking the correct strain and dose.

Why do doctors not recommend probiotics? ›

You might have stomach upset, gas, diarrhea, or bloating. Those symptoms usually go away after your body gets used to them. If you have an immune system problem or another serious health condition, you may have a greater chance of issues. Some reports have linked probiotics to serious infections and other side effects.

What foods to avoid while taking probiotics? ›

Foods That Interfere with Probiotics
  • Carbonated Drinks. Whether you are binging on regular or diet sodas, neither are good for your gut health. ...
  • Processed Foods and Probiotics. ...
  • GMO Products. ...
  • Red Meat. ...
  • Gluten-Rich Foods and Probiotics. ...
  • Refined Oils. ...
  • Dairy Foods and Probiotics. ...
  • Tap Water.
4 Feb 2020

What happens when you start taking probiotics everyday? ›

Your immune system will likely get stronger.

Studies have shown that several probiotic strains can enhance immune function, possibly resulting in a reduced risk of upper respiratory infections—including those that cause the common cold. "Up to 80% of the immune system is housed in the gut," explains Dr. Axe.

What happens if you take probiotics for too long? ›

Overdosing – can you take too many probiotics? There is absolutely no harm in taking probiotics in the long term, and there is generally no harm in increasing one's dose of a probiotic supplement if you feel the need.

Is it harmful to take probiotics every day? ›

A common question about probiotics is whether it is ok to take probiotic supplements every day. Whilst there may be a few exceptions to this rule, the general answer is yes, it's safe, and usually recommended, to take them daily. It's important to understand that probiotics are a natural supplement and not a medicine.

How long should you be on probiotics? ›

Bottom Line: For most conditions, take probiotics for at least 3-4 weeks to see if they work for you. Acute diarrhea and food intolerances are exceptions to these guidelines.

What helps IBS symptoms go away faster? ›

General tips to relieve irritable bowel syndrome (IBS) symptoms
  1. cook homemade meals using fresh ingredients when you can.
  2. keep a diary of what you eat and any symptoms you get – try to avoid things that trigger your IBS.
  3. try to find ways to relax.
  4. get plenty of exercise.
  5. try probiotics for a month to see if they help.

How long does it take for irritable bowel to heal? ›

How To Calm IBS Flare Ups. A typical flare up usually lasts between 2-4 days but can be much longer. However, taking action to calm a flare up can shorten the time you experience symptoms.

How long does it take for irritable bowel to settle down? ›

IBS flare up duration is different for everyone. Most people's IBS symptoms will flare-up for 2-4 days, after which your symptoms may lower in severity or disappear completely. Many people experience IBS in waves, in which symptoms may come and go over several days or weeks.

What heals IBS naturally? ›

7 Natural Remedies for IBS
  • A Specialized Diet Might Be Enough. ...
  • Psyllium Powder for Added Fiber. ...
  • L-Glutamine to Aid in the Function of Intestinal Tissue. ...
  • Acupuncture to Treat Chronic Pain. ...
  • Mindfulness for Stress Relief. ...
  • Yoga Brings IBS Symptom Relief. ...
  • Try Peppermint Oil to Help With Gas and Bloating.
28 Apr 2021

What medication calms IBS? ›

Drugs that relax muscles, called antispasmodics, such as dicyclomine (Bentyl) and hyoscyamine (Levsin). Muscle spasms in your digestive tract can cause belly pain. Many doctors prescribe these drugs to calm them. But some studies have found there's no clear evidence that they help everyone with IBS.

What foods are healing for IBS? ›

Some of the best foods for IBS include:
  • Eggs. Eggs are easy to digest and don't upset the colon. ...
  • Lean meats. Lean meats are another great source of protein and give you a lot of food options for meal planning. ...
  • Salmon and other fish high in omega-3s. ...
  • Low-FODMAP foods.
16 Mar 2022

What causes irritable bowel syndrome to flare up? ›

While we don't know what causes IBS, we do know that flare-ups are often triggered by food, caffeine, stress, carbonated drinks, artificial sugars, or infectious diarrhea. The more IBS episodes you have, the more sensitive your gut becomes to triggers.

Can probiotic cause inflammation? ›

Probiotic Lactobacillus Strains Stimulate the Inflammatory Response and Activate Human Macrophages.

Can probiotics increase inflammation? ›

Probiotics and Your Arthritis

The beneficial bacteria appear to have an impact on inflammation, reducing common biomarkers of inflammation, including C-reactive protein (CRP).

How do I know if I'm taking the right probiotic? ›

A general recommendation is to choose probiotic products with at least 1 billion colony-forming units and containing the genus Lactobacillus, Bifidobacterium, Bacillus or Saccharomyces boulardii, some of the most researched probiotics.

What triggers a flare up of your IBS symptoms? ›

While we don't know what causes IBS, we do know that flare-ups are often triggered by food, caffeine, stress, carbonated drinks, artificial sugars, or infectious diarrhea. The more IBS episodes you have, the more sensitive your gut becomes to triggers.

Why are my IBS symptoms getting worse? ›

The things most likely to worsen symptoms of IBS are diet and emotional stress. Treatment may include changing your diet and taking medicines.

Can probiotics cause intestinal distress? ›

They can trigger an allergic reaction. They might cause mild stomach problems, especially the first few days you start taking them. You might have stomach upset, gas, diarrhea, or bloating. Those symptoms usually go away after your body gets used to them.

What can calm a IBS flare up? ›

How to Calm an IBS Flare Up
  • Apply Gentle Heat. ...
  • Get Moving. ...
  • Stay Away From Trigger Foods. ...
  • Have a Soothing, Non-Caffeinated Tea. ...
  • Dial Down Your Stress Levels. ...
  • Try a Relaxation Technique.

What are the worst symptoms of IBS? ›

Main symptoms
  • abdominal (stomach) pain and cramping, which may be relieved by moving your bowels.
  • a change in your bowel habits – such as diarrhoea, constipation or sometimes both.
  • bloating and swelling of your stomach.
  • excessive wind (flatulence)
  • occasionally experiencing an urgent need to move your bowels.

What foods irritate IBS the most? ›

Foods that can make IBS-related diarrhea worse for some people include:
  • Too much fiber, especially the insoluble kind you get in the skin of fruits and vegetables.
  • Food and drinks with chocolate, alcohol, caffeine, fructose, or sorbitol.
  • Carbonated drinks.
  • Large meals.
  • Fried and fatty foods.
19 Aug 2021

Does IBS show on colonoscopy? ›

Can a colonoscopy detect IBS? No, a colonoscopy can't detect IBS, a condition also known as irritable bowel syndrome. You may wonder why a colonoscopy can't detect IBS when it can diagnose the IBD conditions we outlined earlier. IBS is different from IBD.

What painkiller is best for IBS? ›

Alosetron, granisetron and ondansetron can generally treat pain in IBS-D patients, of which alosetron needs to be used with caution due to cardiovascular toxicity. The optimal drugs for managing pain in IBS-D and IBS-C appear to be eluxadoline and linaclotide, respectively, both of which target peripheral GI tract.

Does sitting make IBS worse? ›

Since sitting compresses the organs and blood flow is decreased, it is common for bowel function to suffer. In fact, a sedentary lifestyle has been positively linked with inflammatory bowel disease and other digestive problems.

What time of day is IBS worse? ›

IBS tends to be worse in the morning. When you wake up, the motility of your large intestines increases. This can lead to IBS. Stress, which affects your gut motility, might also play a factor.

Do probiotics affect the colon? ›

Probiotics lower the pH level in the colon, which might help stool move faster through it. They may relieve antibiotic-related diarrhea. Probiotics may be especially helpful in relieving diarrhea associated with antibiotics and Clostridium difficile.

Is oatmeal good for IBS? ›

Certain grains: Gluten-free oatmeal and brown rice are usually well-received by people with IBS and provide soluble fiber, which helps regulate bowel movements. Low-fat yogurt: Some people with IBS have worse symptoms after eating dairy foods.

Where is IBS pain located? ›

The chronic pain (pain lasting 6 months or longer) in IBS can be felt anywhere in the abdomen (belly), though is most often reported in the lower abdomen. It may be worsened soon after eating, and relieved or at times worsened after a bowel movement. It is not always predictable and may change over time.

Does water help IBS? ›

Water intake might be associated with improvement of IBS through affecting GI function. Water intake might improve constipation among IBS-C patients. In addition, drinking water is a common suggestion for IBS-D patients to prevent diarrhea-induced dehydration.


1. Irritable Bowel Syndrome: Pathophysiology, Symptoms, Causes, Diagnosis and Treatment, Animation
(Alila Medical Media)
2. IBS - Can Probiotics Help?
3. Why Probiotics May Make You Feel Worse
(Just In Health)
4. Probiotics effect on IBS Symptoms
(MSAN Degree)
5. If You Take Probiotics For IBS, Watch This First Before You Spend More $$
(Diet vs Disease - FODMAP Dietitians Joe & Taylor)
6. Are Probiotics Causing Your SIBO IBS Symptoms? Why does my belly hurt when I take Probiotics?
(Dr. Richard Hagmeyer D.C, CFMP)
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