4 Reasons Why Probiotics Make You Feel Sick

Written By

Rhea Dali

Expert Reviewed By

Dr. Lauryn Lax, OTD, MS

Dr. Lauryn, OTD, MS is a doctor of occupational therapy, clinical nutritionists and functional medicine expert with 25 years of clinical and personal experience in healing from complex chronic health issues and helping others do the same.

Sauerkraut, Cucumber Pickles And Yogurt - Popular Probiotics

Probiotics make you feel bloated, gassy or nauseas? Or maybe they make your skin breakout or bring on brain fog?

Why Probiotics Make You Feel Sick

Here is why and what to do about it…

Your Probiotic Needs Are Unique

Sauerkraut Probiotics

The type of probiotic that is best for your microbiome is unique to every individual.

Any probiotic that cause bloating, gas or digestive upset are not friendly for your gut.

Ideally, if your probiotic is a good fit for you, it should promote digestive ease and regular, well-formed bowel movements that are easy to pass.

Although a “healing reaction” may occur during the first 3-7 days while starting a new probiotic as microbial composition may shift, typically if digestive distress continues, it’s a sign that something else may be going on under the hood.

Here are 4 Reasons Why Probiotics Make You Feel Sick:

1. Not all formulas are created equal.

Probiotics and gut bacteria belong in the colon, not the stomach or small intestine. Unfortunately, digestive distress may occur if the majority of these bacteria get stuck up top (1).

Upwards of 90% of probiotics in the form of lactobacilli and Bifidobacteria probiotic strains on shelves (even in the fridge) do not contain the probiotics they claim on their label. Why? Many of these formulas cannot withstand gastric acid, demonstrating a reduction of over 100 colony units within 5 minutes (2).

However, when probiotics are encapsulated for site-specific delivery into the distal parts of the gut (colon), up to 90% of the probiotics are still “alive” after two hours of stomach acid exposure, and remain in tact up to 75% by the time they make it to where they should be.

2. Digestive distress, brain fog & bloating can happen if you have SIBO, Dysbiosis or yeast overgrowth.

A news headline from a 2018 study tried to debunk the benefits of probiotics, stating: “Probiotic use can result in a significant accumulation of bacteria in the small intestine that can result in disorienting brain fogginess as well as rapid, significant belly bloating.” Why? The subjects who reported these symptoms also had SIBO and high D-Lactate levels—high amounts of lactic acid forming bacteria already—the most common strains in commercial probiotics (3).

3. There’s no one-size-fits-all approach.

A study on the probiotic byproducts in stool samples found the detection of the probiotic strains in the intestinal mucosa was highly person-specific. They use multiple analytic methods to examine samples from the study participants. In some people, the same strains from the probiotics were present. In others, the probiotic strains were undetectable in the intestinal samples even by the most sensitive methods, such as strain-specific PCR—revealing that the effectiveness of different probiotics is unique to each individual (4).

4. Probiotics are essential to pair with pre-biotics.

Prebiotic foods and supplements are perhaps more essential for a diverse, healthy microbiome since they are the food that feeds probiotics in the first place. Prebiotics also decrease in pathogenic bacteria populations, enhance gut barrier strength, boost the immune system, and promote increases of Bifidobacteria, lactobacilli and beneficial metabolites.

If you miss out on these guys, probiotics don’t “stick” and benefit your gut like intended. Prebiotics include various fiber rich foods in various categories (FOSs, inulin, GOSs, oligofructose, Beta-glucan, resistant starch, guar gum, Lactulose, Xylooligosaccharides). We will review the top food sources later on.

What to Do About It?

As a general rule of thumb, if you feel sick from your probiotic for longer than 3-7 days, it is best to discontinue its use and consider any underlying gut issues that may be at play.

Working with a functional medicine practitioner for proper gut testing and interpretation may help you figure out if you have an underlying gut condition, such as dysbiosis, SIBO or a yeast overgrowth.

In addition, choosing a quality probiotic supplement that is manufactured with proper gastrointestinal delivery in mind—making its way to your colon, rather than getting lost up in your stomach acid and small intestine before it gets to the colon—could also be a gamechanger.

Lastly, probiotics can do a body good…given you get the right formula and focus on “gut supportive” lifestyle, including a nutrient-dense diet, stress management, movement, quality sleep and plenty of clean water.


  1. Govender, M., Choonara, Y. E., Kumar, P., du Toit, L. C., van Vuuren, S., & Pillay, V. (2013). A review of the advancements in probiotic delivery: Conventional vs. non-conventional formulations for intestinal flora supplementation. AAPS PharmSciTech, 15(1), 29-43.
  2. Satish S. C. Rao, Abdul Rehman, Siegfried Yu, Nicole Martinez de Andino. Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis. Clinical and Translational Gastroenterology, 2018; 9 (6) DOI: 1038/s41424-018-0030-7
  3. Zmora, N. Et al. (2018). Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell. 174: 6; 1388-1405. DOI:https://doi.org/10.1016/j.cell.2018.08.041
  4. Guéniche A. G., Benyacoub J., Buetler T. M., Smola H., Blum S. (2006). Supplementation with oral probiotic bacteria maintains cutaneous immune homeostasis after UV exposure. J. Dermatol. 16 511–517. 10.1684/ejd.2006.0023

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