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Do Probiotics Cause Bloating, or Could it Be Something Else?

Written by Dr. Michael Ruscio, DC on August 27, 2024

Written by Dr. Michael Ruscio, DC on August 27, 2024 — Reviewed by Hilary Watts

The Real Reason You’re Bloated on Probiotics and What to Do About It

• Probiotic Bacteria Are Not Likely to Cause Bloating|
• Probiotic Foods May Cause Bloating|
• How to Improve Persistent Bloating|
• You Can Navigate Bloating While Taking Probiotics|

Have you noticed an increase in gas, bloating, cramping, or other gastrointestinal symptoms that started around the time you began adding probiotics to your daily routine? While probiotic supplements have a strong safety record (even at very high doses), you may be wondering if they’re to blame for your new symptoms.

Usually, that’s just a sign that the gut is adjusting to changing gut bacteria, and it goes away in less than a week. 

So, why do some people get bloated after starting probiotics? In general, some probiotics are derived from common allergens, like dairy and egg, which could be responsible for bloating. Also, many probiotic formulas contain prebiotics, which could irritate the gut, especially if small intestinal bacterial overgrowth (SIBO) is present.

To maximize the health benefits of probiotics and minimize potential side effects, it’s important to pay attention to the ingredients. Just as important is to buy a good-quality product from a reputable supplement company.

Now let’s look more closely at why bloating might show up after starting a new probiotic regimen.

Probiotic Bacteria Are Not Likely to Cause Bloating 

Though this might seem counterintuitive, it’s highly unlikely that the healthy bacteria in a probiotic formula are to blame for bloating or other digestive issues [1, 2]. In fact, a large body of quality research has found that probiotics relieve bloating better than placebos do, especially for people with irritable bowel syndrome (IBS) [3, 4, 5, 6, 7, 8]. 

That said, some people are very sensitive to probiotics and may have temporary discomfort as they adjust to them. And sometimes probiotic supplements contain more than just bacteria.

Probiotics are generally considered safe, but like any dietary supplement, quality assurance and the particular ingredients matter. If you experience flatulence, constipation, or changes in bowel movements when introducing a new probiotic formula, it’s possible that the one you’ve chosen isn’t right for you. There are a few ways I’d recommend proceeding if this is the case.

First, Check for Allergens

To make probiotics, manufacturers first create a substrate that provides the nourishment probiotic bacteria (and sometimes fungi) need to grow. Then, they add probiotic strains and wait for them to ferment and multiply. Once they have the desired number of colony-forming units (CFUs), they separate out the probiotic bacteria, use various methods to make them shelf-stable, blend them with other strains if needed, and bottle them up.

Sometimes the initial substrate contains potential gut irritants like egg or dairy. If you have an allergy or sensitivity to eggs or dairy, then you will want to make sure your probiotic formula is completely egg- and dairy-free [1, 2]. Most probiotics will also highlight that they’re gluten-free, but that’s pretty standard—I’ve never seen a probiotic formula that contains gluten.

Additionally, some supplement companies include excipients, such as fillers, preservatives, or colorants. Excipients should be inert, but some people may react to certain kinds. Some probiotics, especially gummies, also contain flavorings, so be aware of flavoring ingredients when choosing your formula. In general, make sure your product says it’s allergen-free.

Second, Look for Prebiotic Dose

Prebiotics are fibers often included in probiotic formulas that are technically called synbiotics, with the prefix “syn” meaning together. Many healthy foods we regularly eat contain prebiotic fibers, but some people have a hard time digesting them. You might be hard-pressed to find a formula that contains zero prebiotics, so shoot for one that has no more than 3–5 grams per daily serving [9, 10, 11]. 

Third, Ensure Good Quality

Admittedly, it’s hard to know who to trust when it comes to supplements because they aren’t regulated by the Food and Drug Administration (FDA). However, the most reputable supplement companies will have a GMP (Good Manufacturing Practice) stamp indicating their products are consistently of high quality. They will also engage in third-party testing to ensure unbiased quality control. 

When shopping for a probiotic, look for a GMP stamp and a seal from one of the following:

• National Sanitation Foundation (NSF)
• The US Pharmacopeia (USP)
• Consumer Labs (CL)

You can also subscribe to ConsumerLab.com to find out which products they list as safe.

Fourth, Eliminate All But One

For clients taking multiple categories of probiotics, like I recommend in my triple-therapy approach, sometimes one category won’t feel great at first. Taking out two categories to see how one at a time feels doesn’t have a lot of research behind it. However, the principles of elimination diets and my clinical experience support the idea of trying to isolate what is creating side effects. The idea is to start slowly with a low dose of one category and slowly add the others, one by one, to let the body acclimate.There are three categories of probiotics. Category 1 consists of a blend of Lactobacillus and Bifidobacterium species. Category 2 is a healthy yeast called Saccharomyces boulardii, and category 3 is a soil-based probiotic containing various species of Bacillus.

I have my sensitive clients start off with half a recommended dose of Category 1, the most widely available type of probiotic. Using their symptoms as their guide, I coach my clients to slowly work their way up to the full dose (10 billion CFU) and stay on that for 2–3 months. However, if they’ve chosen a high-quality, allergen-free, low-prebiotic formula and still have symptoms like bloating after 1 month, their body may not be able to handle one or both of those strains of bacteria right now. 

If bloating persists, we discontinue the Category 1 probiotic and move on to a half dose of a different probiotic, one from Category 2. Again, they work their way up and stay on the recommended dose (10–15 billion CFU) for 2–3 months.

If they still have bloating or other GI symptoms, we discontinue Category 2 and try Category 3, starting with a half dose and gradually increasing to 2–6 billion CFU.

In my many years of experience, I’ve never had a client who couldn’t tolerate at least one category. Ultimately, as people continue on their gut health journey and begin to heal, they may find that they can reintroduce one or both of the other categories with no side effects.

Die-Off Symptoms

It’s unlikely that die-off reactions would include bloating, but I want to mention them here for those who experience some of the more common die-off symptoms. 

Also called a Herxheimer reaction, a die-off reaction occurs when we take something (like antibiotics, herbal antimicrobials, or even probiotics) that kills lots of bacteria in the gut. When the bacteria die, they release toxins into the bloodstream, which can set off the immune system. This creates symptoms as the body works to protect us from and get rid of the toxins [1, 2].

When assessing your own symptoms, it’s important to differentiate between temporary and long-term discomfort. Die-off symptoms typically include flu-like fatigue, headache, and brain fog, but none of these should last more than a week. If they do last longer, you’re probably dealing with something complex enough to bring to your healthcare provider. 

Probiotic Foods May Cause Bloating

While it’s unlikely that a probiotic supplement will cause bloating, it’s very possible that probiotic foods, like sauerkraut, kimchi, kombucha, or kefir, could. Bloating is typically associated with probiotic foods rather than probiotic supplements because these foods contain a few potential irritants, such as histamines, FODMAPs, and lactose.

Histamines in Fermented Foods

Histamines are a byproduct of the fermentation process that turns fresh foods and juices into probiotic foods. In other words, there are more histamines in fermented foods than in other types of food.

Some people find extra histamines irritating, and some even have histamine intolerance. Histamine intolerance is when the digestive enzymes your body uses to break down histamine in foods aren’t working properly. As a result, histamine can build up and cause symptoms like bloating, nausea, rash, headache, and itching [12].

Since probiotics are made through a process of fermentation, it’s logical to think they contain histamines and could lead to reactions in sensitive people. It’s true that some probiotic strains do produce histamine, but these are not common in probiotic formulas, and so far it doesn’t look like probiotics contain enough histamine to incite a reaction. In fact, probiotics tend to have a net anti-histamine effect.

Although we need human studies to conclude with any certainty, taking certain probiotic strains could theoretically help improve histamine intolerance [13]. In other words, continually using probiotic supplements may eventually increase tolerance to fermented foods again in the future, after the digestive system has reset. This may be especially true when following a low-histamine diet, which I’ll explain soon.

FODMAPs in Fermented Foods

FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols, which are short-chain carbohydrates. The small intestine sometimes has a hard time digesting these types of sugars, leading to gas and bloating. This is especially problematic in people with SIBO, whose excessive bacteria in the small intestine make a lot of gas from FODMAPs. 

The most common high-FODMAP probiotic foods are coconut yogurt, dairy yogurt, sauerkraut, and kombucha. These foods (and drinks) contain indigestible carbohydrates that can lead to flatulence and bloating in some people. 

In particular, when dealing with IBS or SIBO, it’s helpful to stay away from high-FODMAP foods and lean into a low-FODMAP diet, which I’ll explain more in the next section. Not only can this relieve gas and bloating, it can also help kill off the excessive gut bacteria colonizing the small intestine, where they don’t belong.

Lactose in Fermented Foods

I mentioned dairy earlier in the context of supplements, but it’s worth repeating here as well. Dairy-based probiotic foods like yogurt and kefir may cause bloating in those with lactose intolerance.

How to Improve Persistent Bloating

Most people take probiotics to improve some sort of microbial imbalance in the gut that’s causing symptoms. Usually, I find it takes at least 1–2 months for the gut microbiome to shift and improve on probiotics. But if bloating continues after 1–2 months, the probiotics may need a helping hand. 

For example, probiotics alone may not be able to fully take care of bloating if the following are also present:

• Food intolerances [14, 15, 16] 
• IBS or SIBO [17, 18]
• Stress [19, 20, 21, 22]
• Dysfunctional abdominal [23] or pelvic floor [24, 25, 26] muscles 

The good news is that multiple treatments combined with probiotics can take a firm stand against bloating.

Diets for Bloating Related to Food Intolerances, IBS, or SIBO

• Low-FODMAP Diet [27, 28, 29, 30, 31] – This diet restricts certain carbohydrates, including those in foods like garlic, onions, certain fruits (like apples and pears), and most cruciferous veggies (like broccoli and cabbage) that would otherwise fall into the “healthy food” category. Temporarily avoiding these foods can give the digestive system a break and begin starving out any excessive bacteria in the small intestine that may be the source of bloating. Even if SIBO isn’t an issue, IBS patients often respond well to removing FODMAPs for a while. I like to have my clients with bloating start with this diet and move on to a low-histamine diet if the needle on their bloating doesn’t move.
• Low-histamine diet [15] – If the low-FODMAP diet doesn’t cut it and I suspect a client is sensitive to high-histamine foods, such as aged cheeses, cured meats, chocolate, and fermented foods, we try going low histamine for about three weeks. If they notice less bloating and other symptoms, such as sniffling, sneezing, headaches, rashes, diarrhea, abdominal pain, or itching, they may have discovered a histamine intolerance. On the bright side, supporting the gut with probiotics often helps them tolerate higher-histamine foods over time. But if neither the low-FODMAP nor low-histamine diet is quite enough for their bloating, we might also try combining them. 

Whichever dietary route my clients take, we always make sure to start reintroducing foods as they feel better to get a full spectrum of nutrients and support their improving gut microbiome [32].

Here are some dietary add-ons that may amplify bloating relief:

• Elemental Diet [33] – This may be used as a short-term temporary gut reset alongside any of these plans to help heal underlying issues (like SIBO) contributing to bloating.
• Low-gluten diet [34] – A low-FODMAP diet is typically low in wheat and therefore gluten, but combining a low-histamine diet with eating less gluten may reduce bloating even more.
• Intermittent Fasting [35] – Eating during an 8-hour window and giving the gut a rest for the other 16 hours a day (including the hours of sleep) can accentuate reductions in bloating.
• Reducing dietary fiber [36] – Fiber triggers bloating in some people. A low-FODMAP diet is typically low in fiber, but reducing fiber may be a good addition to a low-histamine diet.

Supplements, Medications, and Herbs for Bloating Related to Sluggish Digestion, IBS, or SIBO

• Peppermint oil [37, 38, 39, 40] – Peppermint can improve digestion in some people and may reduce bloating. But be careful: Peppermint can make reflux and heartburn worse [41].
• Antibiotics like rifaximin [42, 43, 44] – This prescription medication can help probiotics eliminate SIBO that may contribute to bloating.
• Herbal antimicrobials, like Iranian thyme [45] – These can help probiotics eliminate SIBO or other imbalances in gut microbes that could contribute to bloating. 

Stress-Reduction Techniques for Bloating

• Gut-directed hypnotherapy [46, 47, 48, 49, 50] – With the help of a trained therapist, this can effectively reduce IBS symptoms, including bloating.
• Cognitive-behavioral therapy [46, 47, 48, 51, 52] – A trained CBT therapist can increase relief from IBS symptoms like bloating.
• Meditation [53, 54, 55, 56, 57, 58] – Meditation practices like mindfulness-based stress reduction can calm stress and related bloating.
• Yoga [59] – Yoga may be good for reducing IBS symptoms such as bloating.
• Walking [60] – Walking after meals may be a good way to reduce stress and put a dent in abdominal bloating.

Biofeedback Options for Bloating Related to Muscular Dysfunction of the Abdomen or Pelvis 

• Abdominal biofeedback [54, 61, 62] – You’ll need a skilled practitioner to get started, but breathing-focused biofeedback can reduce bloating.
• Pelvic floor biofeedback [25, 63] – With help, learning to reduce the effort we put into pooping can help relieve bloating. 

To simplify this long list of action items to help with persistent bloating, I recommend that my clients start by adding to their probiotics a low-FODMAP diet and 10–15 minute walks after meals. The low-FODMAP diet can improve symptoms like bloating by reducing inflammation and starving out bad bacteria living in the small intestine [64]. And walking is a no-cost, no-equipment intervention that can improve bloating, belching, flatulence, feelings of over-fullness, and abdominal discomfort [60].

I coach my clients to start there and see how they feel. They keep track of changes in their bloating and other digestive symptoms to see what has changed after several weeks. The other science-based options are available to try if they need a boost. 

If you want to try these steps for your own bloating, make sure to check out anything new you try with your healthcare provider.

You Can Navigate Bloating While Taking Probiotics

The relationship between probiotics and bloating is nuanced. While probiotics offer a myriad of potential benefits for the gut microbiome, some people experience digestive symptoms, like bloating, while taking them.

Potential reasons for a digestive reaction may reside inside the bottle of probiotics or within the digestive tract. To deal with potential probiotic product issues, it’s best to avoid untested formulas with common allergens like dairy or egg, unnecessary fillers, flavors, or colorants, and more than 3–5 grams of prebiotics.

To address issues with your digestive system, you might try a low-FODMAP diet and short walks after meals, and experiment with other gut-supportive treatments if necessary.

Understanding the factors that may contribute to your bloating and implementing practical strategies can empower you to troubleshoot and improve your digestive health over time. And if you’re looking for extra guidance and support, we’re here to help. Feel free to reach out to our clinic to set up a consultation to get started.

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