Probiotics: What side effects might I have?

Probiotics are living microorganisms that provide health benefits.

Eating foods that contain probiotics may benefit your gut microbiome — the collection of microbes in your gut. 

Probiotics’ influence over your gut bacteria might help promote regular bowel movements. It may also help reduce inflammation and improve your blood sugar control. 

But while probiotics show promise, scientists need to do more research to confirm the benefits.

Most people can consume probiotics without having side effects. But they may not be safe for everyone.

In this article, we dive into some possible side effects of adding probiotics to your diet.

At ZOE, we know how important your gut microbiome is for your overall health. 

Our scientists run the largest nutrition science study in the world. They’ve identified 15 “good” bugs linked with good health and 15 “bad” bugs associated with poorer health outcomes. 

With our at-home test, you’ll learn which bugs you currently have and which foods to eat to support your “good” bugs and your health in general.

Take our free quiz to get started.

Digestive discomfort

Evidence suggests that probiotics may help relieve bloating, gas, and other gastrointestinal problems in people with certain conditions, like irritable bowel syndrome (IBS).

But when you first start consuming probiotics, you may notice an increase in gas or bloating.

Not everyone has this. And those who do typically feel better within a few weeks.

If you’re concerned that the discomfort is lasting too long, contact a healthcare provider.


Certain strains of probiotics may lead to headaches for some people.

Fermented dairy products, such as kefir or yogurt, often contain the bacterial strains Lactobacillus helveticus, L. buchneri, L. hilgardii, and Streptococcus thermophilus.

These probiotics can produce histamine during the fermentation process. Histamine belongs to a group of chemical messengers in your brain called biogenic amines.

Amines can change how much blood flows to your central nervous system, triggering a headache if you’re sensitive to histamines and other amine substances.


Probiotics can cause allergic reactions in certain people, but this is rare.

One study found that a strain of bacteria called L. acidophilus LAVRI-A1 was linked with allergic reactions in infants younger than 12 months.

And multiple studies have noted allergic reactions to a bacterial strain called L. rhamnosus GG. 

In one study in children, some participants who took the probiotic experienced asthma and allergic rhinitis — also known as hay fever. 

Live yogurts, certain cheeses, and other probiotic foods can also trigger an allergic reaction in people who are allergic to dairy. 

Antibiotic resistance

Probiotic bacteria contain certain genes that make them resistant to various antibiotics. On their own, these bacteria aren’t harmful. 

There is a concern, however, that if you consume high amounts of these probiotics, their antibiotic-resistant genes might transfer to potentially harmful bacteria in your gut.

This is a relatively new topic, so scientists are still investigating what factors influence whether the antibiotic-resistant genes move into the “bad” bugs, when it happens, and why. 

Infection and sepsis

Evidence suggests that consuming probiotics could help treat certain health conditions. 

But some people should consult a doctor before including probiotics in their diets, including people who: 

  • are critically ill

  • have recently had surgery

  • are undergoing chemotherapy

  • have weakened immune systems

It's rare, but probiotics can pass from the gut to the bloodstream, leading to an infection in people in high-risk groups.

And while it’s uncommon, probiotics can increase the risk of sepsis if the bacteria enter your bloodstream.

Sepsis is an extreme reaction to a viral or bacterial infection, and it can be life-threatening.

It’s important to note that sepsis from probiotics is incredibly rare. And some scientists argue that individual factors may be more relevant to a person’s risk than the bacteria. 

Still, if you have a weakened immune system or a medical condition that gives you a higher risk of infection, talk with your doctor before you start taking probiotics.

Benefits of probiotics

People respond to probiotics in different ways, and research into their benefits is ongoing.

While there may be risks for certain people, studies show that probiotics are safe for most people. 

And for some, they may provide health benefits.

For instance, probiotics can help some people with digestion issues — like IBS — experience less pain, bloating, and gas. They may also help promote regular bowel movements.

Animal studies suggest that probiotics might even help lower stress, improve sleep, and lower the risk of developing a sleep disorder.

Probiotics may also benefit:

Sources of probiotics

Probiotics often occur in fermented foods — but not all contain helpful microbes.

Here are some of the best probiotic-containing fermented foods to include in your diet:

At ZOE, we recommend getting your probiotics from foods rather than supplements. 

Supplements contain the probiotic strains that are easiest to manufacture, not necessarily the ones that benefit your health the most. 

Also, it’s worth keeping in mind that the United States Food and Drug Administration (FDA) doesn’t test and regulate supplements like it does over-the-counter medicines. 

Instead, it’s up to manufacturers to provide safe supplements, but the strains they use aren’t necessarily the best for your needs. 

Who should avoid probiotics?

The majority of the evidence suggests that probiotics are safe for most people.

But probiotics may not be safe for certain high-risk groups, including:

  • people who are critically ill

  • extremely sick infants

  • people recovering from surgery or hospitalization

  • people with weakened immune systems


Probiotics can benefit your health and are generally safe for most people. But there are possible side effects.

Temporary digestive issues like gas and bloating are the most common side effects. If you have these, they tend to subside in a few weeks.

To avoid any discomfort, it’s a good idea to add probiotics to your diet gradually.

Other side effects, such as headaches, allergic reactions, antibacterial resistance, infections, and sepsis, are much rarer.

If you have a weakened immune system or a high risk of side effects for another reason, ask your doctor if probiotics are a good idea.

With the ZOE program, you can learn which bacteria you currently have in your gut, as well as how your body responds to the foods you eat. With our personalized nutrition program, you’ll learn how to eat for your gut and overall health. 

You can take our free quiz to find out more. 


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A systematic review of the safety of probiotics. Expert Opinion on Drug Safety. (2014).

Biogenic amines: Signals between commensal microbiota and gut physiology. Frontiers in Endocrinology. (2019).

Effect of probiotics on blood pressure: A systematic review and meta-analysis of randomized, controlled trials. Hypertension. (2014).

Microbiome and intestinal ischemia/reperfusion injury. Journal of Clinical Biochemistry and Nutrition. (2018).

Modest effects of dietary supplements during the COVID-19 pandemic: Insights from 445850 users of the COVID-19 symptom study app. BMJ Nutrition, Prevention, and Health. (2021).

Probiotic supplements might not be universally effective and safe: A review. Biomedicine and Pharmacotherapy. (2019).

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. Nature Microbiology. (2021).

Probiotics: What you need to know. (2019).

Should you take probiotics? (2022).

What is sepsis? (2022).