Probiotics and Allergies 101

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Probiotics are becoming an increasingly important part of health. Learn how having allergies and autoimmune disorders can be affected through probiotics. 

Probiotics are becoming a more common part of everyday supplement routines to help keep the immune system strong and the gut microbiota balanced. For people with food allergies, there are new studies showing how having a probiotic supplementation routine can have a positive and significant effect on your overall health.

If you have allergies, you need to be aware that some prebiotics may be causing more harm than good. Especially if you are allergic to milk, dairy, casein, or yeast, you need to be aware so you can make the best choice for you. 

This article breaks down what probiotics are, how they work for allergies and autoimmune disorders, the 4 main types, and benefits of regular use. It also shares my picks for the best probiotics for dairy allergies, yeast allergies, and overall the best probiotics.

illustration of a healthy GI system with a text box that reads probiotics

What are probiotics? 

Probiotics are natural dietary supplements that people take to help the gut bacteria. There are tiny good bacteria that live all over and inside your body that, when balanced, provide a health benefit to people who take them. Fermented foods naturally contain probiotics. For hundreds of years, people have been eating these natural probiotic rich foods.

Probiotic supplements are a mix of these good bacteria, yeast, and organisms that naturally are found in our gut. We normally think of bacteria as bad, but these are good! All healthy people need these beneficial bacteria in their bodies to have optimal health.

Probiotics have been studied for years with clinical research and we know they are very safe to use. They promote good health and improve the different systems all over the whole body.

What is the gut microbiome?

Before we get too far, let’s define the gut microbiome.

When talking about the gut microbiome, that refers to the trillions of microorganisms and good bacteria that live in the gastrointestinal tract. However, that is not the only place they live! You can also find microbiomes in your mouth, vagina, urinary tract, on your skin, and in your lungs. 

The gut contains anywhere between 400 and 600 different bacterial strains and species. The goal of taking a probiotic is to add more of the good bacteria into the gut so that the bad bacteria don’t overtake the good. These good bacteria improve the overall health of your gut, and you as a whole. 

What are CFUs? 

CFUs are Colony Forming Units. That is a measurement for how many units of probiotics are in each pill. These are typically measured per gram or per mililiter. 

The average CFU count in probiotics is typically between 1 and 10 billion CFUs per serving. 

Some companies would have you believe that the higher the CFU number, the more powerful (and expensive) the probiotic pill will be. However, this is not always true. 

If you take a probiotic that is too high in one specific strain, there may be a negative effect on the gut. That can happen as experiencing GI upset, nausea, stomach cramping, and diarrhea. This is because the good bacteria have overwhelmed the natural 400 to 600 strains that live in the gut. We need balance to be at our best.


Every person on Earth has a unique gut microbiome, shaped by our diet, environment, and lifestyle. We have a symbiotic relationship with probiotics. We need them to be our best selves. They help us digest food, absorb optimum nutrition, and strengthen our immune systems. 

The balance of good and bad gut flora can change from things such as travel, stress, taking antibiotics, diet, and many other things.

That is when the “bad” bacteria take over and cause the symptoms you may be familiar with: nausea, upset stomach, inconsistent bowels, etc. 

This is why some people are choosing to take probiotics. They help to support overall gut health, restore balance to an unbalanced gut, and make your overall health better! 

In both human and animal trials, probiotics have been studied to determine if there is a benefit to taking them in regards to autoimmune disorders. The overall consensus is YES! 

There are proven studies shown that probiotics help in inflammatory and autoimmune diseases such as rheumatoid arthritis, ulcerative colitis, multiple sclerosis, and hepatic encephalopathy. Additionally, they have discovered that pregnant and breast-feeding peoples who take probiotics can result in a lowered risk of eczema in their children.

While studies have said that no conclusions can be made about the prevention of allergies overall, they are starting to correlate leaky gut with allergies. 

illustration of the 4 main types of probiotics in  circles similar to Petri dishes

The 4 main types 

Out of the hundreds of different strains of bacteria, fungi, and yeast that reside in the gut naturally, there are 4 main probiotic strains that are the most common. 

Bifido bacterium is the first bacteria to enter your body as a baby. They have a main role of helping people digest food. 

Lactobacillus is a super common probiotic that is found in the mouth, GI tract, and female reproductive tract. It helps to promote the growth of good bacteria. However, if you have a dairy allergy, you need to use caution when taking this type of probiotic, more on this below. 

Soil based organisms such as Bacillus coagulans, Bacillus clausii, and Bacillus subtilis are super hardy organisms that help you with optimum nutrition absorption. 

Yeast, Saccahromyces boulardii and Candida albicans, helps with the digestion of food and also prevents the growth of Helicobacter pylori bacteria, the thing that causes ulcers. If you have a yeast allergy, you need to avoid these types of probiotics, more on that below. 

How do probiotics work? 

Probiotics work by essentially overtaking any bad bacteria in your gut and making it so that only the good kind wants to grow and live in your gut. The good bacteria make it undesirable for bad bacteria to survive. 

Probiotics also produce certain acids that prevent bad bacteria from growing. 

When your gut is in balance, you will notice a lot of benefits, especially an improvement in your digestion. This is because the bad bacteria produce acids that negatively affect our health as opposed to the probiotics which produce many beneficial things. There are 4 main ways in which probiotics help us:

  1. Probiotics produce beneficial short-chain fatty acids
  2. They metabolize tryptophan, helping you feel calmer and boosts the first responder of the GI tract to help you battle bacteria before it even spreads to the body to make you sick.
  3.  Decreases inflammation and keeps the gut in a healthy state so that it can self-modulate the immune response and cell proliferation. 
  4. Activation of the intestinal histamine-2 receptor. This is super beneficial to those of us with allergies as it is a natural antihistamine! 

Probiotics cause an immune response in the body that are first line response cells in the gut to keep you healthy by killing off bad bacteria before you get sick. 

The role of probiotics is to bring the gut flora to balance and then maintain that balance. 

To sum up: Taking probiotics help you to digest your food, prevent the bad bacteria from overwhelming your gut and makingyou sick, create vitamins for your body to digest, breakdown and absorb medications and nutrients, and support the other good bacteria in your gut (and other places) so that the bad bacteria have no chance of establishing.

When to take probiotics? 

Since you want the probiotics to survive their trip through the stomach acid, you should take your probiotics in the morning with your breakfast. The acid in the stomach is at the lowest level in the morning, plus, you just ate a meal. This should help the probiotics pass through the stomach and into the gut where they can begin to work! 

Probiotics and Allergies

For people with allergies and autoimmune diseases, taking probiotics can be super beneficial. Clinical trials are finding that many times, a person with allergies has excessive intestinal permeability, aka, Leaky Gut.

This is when there are large gaps in the gut that allow for large particles to get through. When the digestion and gut flora are off, the body has larger inflammatory responses, causing for the immune cells to go into overdrive, and creating a perfect environment for more autoimmune conditions.

Taking probiotics helps to combat the development of leaky gut.

This is, of course, in addition to the already mentioned benefits of taking probiotics. The 4th reason is especially important.

Taking a probiotic helps your body to naturally produce H2, a type of histamine blocker, causing your IgEs to not spike as much, and causing your mast cells to not produce as much histamine.

This results in lessened allergy symptoms.

For people with environmental allergies, this is especially true.

cute illustration of probiotics and bad bacteria in a gut

Taking Probiotics with Milk Allergies 

As said above, if you have a milk allergy, you need to use caution when taking probiotics with the lactobacillus probiotics. 

There are a few names and types of this probiotic. They are called:

  • Lactobacillus
  • Lactobacillus casei 
  • Lactobacillus brevis 
  • Lactobacillus acidophilus 
  • There is another type you need to be aware of called streptococcus thermophilus 

These are dairy based, gram positive anaerobic bacteria that will reside in your GI system. They are often found in milk based products. 

You need these bacteria to help you digest milk products like milk, yogurt, cheese, kefir, etc. They are very beneficial for the body. 

However. These bacteria are grown in a milk medium. So if you are super allergic to dairy, or very sensitive to milk, you may want to avoid any probiotics that have any type of lactobacillus in them. 

These bacteria themselves don’t contain any dairy, which is how many get labeled dairy free. In my experience, those with severe milk allergies can still react to them as they are grown in that milk medium. 

This is my favorite probiotic for those with a milk/dairy allergy as it does not contain any dairy.

Taking Probiotics with Yeast Allergies 

As mentioned above, if you have a yeast allergy, you may need to use caution when taking a probiotic with a yeast probiotic. 

There are a few types of yeast you need to watch out for, and they are called:

  • Saccahromyces boulardii
  • Candida albicans

Normally, this type of yeast resides in our bodies at small levels and helps in the digestion of all foods. They are also good at preventing GI issues that stem from an overgrowth of the helicobacter pylori bacteria. 

However. This is a yeast probiotic and if you are allergic to yeast, I would suggest avoiding these in your probiotics. The probiotics themselves are a type of yeast, so you have the potential of triggering an allergic reaction when you take them.

This is my favorite probiotic for those with a yeast allergy as it does not contain any yeast.

Probiotic FAQs

If I’m allergic to dairy/wheat/gluten, can I take a probiotic and eat dairy/wheat and be fine? 

No. The allergy response is an IgE response in the body and no matter what probiotic or enzyme you take, the food will always cause an allergic reaction. 

If I’m lactose intolerant, can I take a probiotic and be okay?

Taking the lactase enzyme, which is separate from a probiotic, can help digest the dairy you have eaten. 

Lactase enzymes are filled with enzymes to help you digest the dairy if you are lactose intolerant. 

A probiotic gives you the extra bacteria to help you digest but it doesn’t work quickly. A true lactose pill will work quicker. 

Do I need to refrigerate probiotics?

That depends on your probiotic type. typically , most need to be refrigerated. Soil based probiotics generally do not need to be refrigerated. However, always follow the instructions on your unique probiotic. 

Will taking probiotics interfere with my medication? 

Probably not. There are no medical prescriptions dosages on probiotics and there is no daily requirement. Most medications will not have an adverse effect on probiotics. In fact, if you are on antibiotics, some doctors recommend that you take probiotics to help reseed your gut! As always, if you have any questions, make sure to ask your doctor. 

Recommendations for Probiotics 

Keeping these things in mind, here are the things I look for when choosing a probiotic that is free from any and all forms of dairy and yeast. 

Make sure that you are looking for companies that talk about each individual strains specifically. What exactly is inside each probiotic pill? By knowing exactly what is there, you will be able to choose one that will be safe. 

Remember, more is not always better. More strains and more CFUs are not always better. It depends on how sensitive you are. Start with a smaller dose and see how you do. 

My Top Picks 

bottle of Amy Myers probiotics

Best Allergy Friendly Probiotic – Amy Myers MD – Primal Earth Probiotic for Adults 

Non-GMO, non-dairy, egg free, gluten free, soy free, corn free, yeast, no artificial sweeteners, keto and paleo friendly 

This probiotic is a great choice for allergies. They are soil-based probiotics that are not based in any dairy or wheat and are safe for most people with allergies.  

It also can be helpful in the cases of SIBO (Small Intestine Bacterial Overgrowth) and will not make SIBO worse. 

Learn more about Amy Myers MD Probiotics.

bottle of Ancient Nutrition probiotics

Best Dairy Free Probiotic – Ancient Nutrition Soil Based Organism Ultimate 

Dairy free, nut free, soy free, grain free 

This is a great option for those very sensitive and very allergic to dairy as it contains no lactobacilli strains. 

A combination of different soil based organisms, including yeast, this blend helps to support healthy gut function. What is great about this one is that it is a blend of prebiotics, probiotics, and postbiotics. That makes them more potent and balanced for the gut. 

These probiotics are not technically labeled free from allergy ingredients as they are made in facilities that may carry these allergens. 

Learn more about Ancient Nutrition Probiotics.

box of Culturelle probiotics

Best Grocery Store Probiotic – Culturelle 

Wheat free, egg free, tree nut free, peanut free 

This probiotic has been clinically studied for over 30 years. I love that it is one pill a day, comes in a blister card (no refrigeration required) and is vegetarian. 

This probiotic does contain lactobacillus so use caution if you are extremely sensitive to dairy. However, if you do not have an issue with dairy, this is a great option.

Learn more about Culturelle.

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