5 Uncommon Uses for Probiotics | Chris Kresser
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5 Uncommon Uses for Probiotics


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Probiotics are versatile and can be used in many unconventional ways. istock.com/Buba1955

Soon after the advent of the ‘germ theory of disease’ in the nineteenth century, the idea of voluntarily swallowing a pill full of bacteria would’ve sounded a little crazy. But as we learned more about the importance of the community of bacteria and other microorganisms occupying our intestines, eating probiotics has become the acceptable way to help re-populate our guts after courses of antibiotics or other stressors.

As we’ve continued to learn, it appears that our gut bugs influence far more than our digestive function and our ability to stay ‘regular.’ In fact, probiotics often aren’t that effective at re-populating the gut flora anyway. (Prebiotics tend to work better.) Our understanding of how probiotics work is evolving, and this is broadening the scope of health issues that probiotics can help treat.

We’re learning that the mechanisms behind the effect of probiotics are far more complicated than simply ‘topping off’ our supply of intestinal flora. Our gut bugs (even the transient ones) actually help modulate our immune system, and a robust immune system is necessary for the proper function of every other part of the body. Through the effect on immune regulation, probiotics can influence a number of conditions that may seem completely unrelated to the gut. In this post, I’ll describe five different uses for probiotics that are a bit unconventional but may be quite effective.

The benefits of probiotics go way beyond gut health.Tweet This


If you’ve been following my blog for any length of time, using probiotics to treat depression probably seems reasonable. But for the average person whose only knowledge of probiotics was gleaned from an Activia commercial, taking probiotics to treat any sort of mental disorder could seem ridiculous. Unfortunately, the average psychiatrist likely feels the same way.

Despite a lack of accord from the medical community, there’s a lot of research to suggest that probiotics can be remarkably useful in treating depression. I’ve talked in the past about the ‘gut-brain axis,’ whereby the health of the brain and the health of the gut are inextricably linked. This relationship is important and can make a huge difference in the mental health of those with gut dysbiosis.

A basic explanation of the relationship is that imbalances in intestinal flora can lead to inflammation in the gut, causing inflammatory cytokines to be released into the blood. These cytokines can then cross the blood-brain barrier and cause inflammation in the brain, which can create symptoms of depression. Probiotics – even if they don’t colonize the intestinal lining – can reduce this gut inflammation and subsequently reduce the brain inflammation, improving symptoms of depression.

Preclinical and clinical studies have shown reductions in anxiety and depression from probiotic supplements, with a reduction in inflammatory cytokines as a likely mechanism. (1, 2) Another potential connection between the gut and brain is through neurotransmitters produced in the gut. This topic really deserves its own post, but for now, suffice it to say that probiotics are a promising treatment for depression and other mental disorders, especially when combined with other gut-healing therapies.

Nasal Congestion

A lesser-known use for probiotics could be in treating congestion and other sinus issues. Just like everywhere else in your body, your nasal passages are colonized by microorganisms that help maintain the health of their environment, and disrupting that balance of beneficial flora can cause problems. There’s not a whole lot of research on this topic yet, but one study showed that a probiotic supplement (in the form of a ‘fermented milk drink’) decreased the levels of pathogenic bacteria in the nasal passages. Other research indicates that probiotics could be helpful in reducing the congestion and other symptoms associated with seasonal allergies. (3, 4) This is especially interesting because in Chinese medicine, they believe sinus issues are almost always related to the gut. Now modern research is beginning to show a connection!

Oral Health

Probiotics can also play a role in maintaining oral health, which isn’t all that surprising once you consider that your mouth is part of your digestive tract. Although your dentist probably won’t be recommending sauerkraut as an adjunct therapy to basic oral hygiene anytime soon, the relationship between probiotics and oral health has been discussed somewhat extensively in the scientific literature.

The ‘good’ bacteria in the mouth help maintain oral health by producing substances (such as hydrogen peroxide and other antimicrobial substances) that inhibit the growth of pathogens, and by competing with these pathogens for space. (5) If those beneficial bacteria are disrupted, pathogenic bacteria can move in and cause a variety of oral and dental issues, including tooth decay, gingivitis, and halitosis (bad breath).

Numerous trials, both observational and clinical, have shown that supplementation with probiotics can reduce cavities and improve overall oral health by rebalancing the bacteria in the mouth. (678) Although probiotic pills taken internally may very well have a beneficial impact on oral health, the benefits shown by these studies are from probiotics that actually come into contact with and are able to colonize the mouth. This is another point in favor of getting probiotics from fermented foods, such as kimchi and kefir. Studies done with probiotic gum, mouthwash, and lozenges have also shown promise in treating oral conditions.


Acne is another common condition that can be influenced by probiotics, despite its seemingly distant relationship with the gut. In reality, the skin is very closely connected to the gut through the ‘gut-skin axis,’ which I’ve previously mentioned on the blog and podcast. (91011) Just as inflammation in the gut can cause inflammation in the brain, it can also lead to inflammation in the skin. This inflammation can manifest as acne, psoriasis, eczema, dermatitis, or other skin conditions. So in the same way probiotics ameliorate symptoms of depression by reducing inflammation, they also improve skin disorders through a similar mechanism. (12)

In addition to taking probiotics internally, there’s some research showing that topical probiotics can reduce acne. (131415) The skin is naturally home to beneficial flora that protect the skin from pathogens and regulate inflammation, but these friendly populations of bacteria can be disturbed through harsh soaps and other environmental toxins. Restoring beneficial bacteria through probiotic lotions or spot treatments appears to reduce skin inflammation from the outside, thus improving acne.

Household Cleaners

The last unconventional use for probiotics I’ll mention is in household cleaning products. Natural House is one company that produces these types of products, and they include probiotics in everything from toilet bowl cleaner to all-purpose cleaner. The theory is that while antimicrobial formulas might temporarily sterilize whatever surface you’re cleaning, the pathogenic bacteria will quickly return because there’s nothing to stop them. By using household cleaners containing probiotics, you’re inoculating your house with beneficial bacteria that should make the environment less hospitable to pathogens. It’s the same concept as following up a course of antibiotics with probiotics – antibiotics will likely wipe out a bacterial infection, but if we don’t encourage beneficial bacteria to grow in its place, there’s a strong likelihood that the pathogenic bacteria will return.

There really aren’t any studies proving the effectiveness of these products, but I’d say it’s worth a shot! At the very least, you’ll be avoiding the toxic chemicals that are found in most household cleaners, and that’s reason enough to seek out alternative cleaning solutions.


  • Consume fermented foods and beverages like sauerkraut, kim chi, beet kvaas, kefir (water and dairy), yogurt, cortido, etc. on a daily basis.
  • Consume prebiotic foods that selectively stimulate the growth of beneficial bacteria already inhabiting the gut. These include onions, jerusalem artichoke, and fruits and vegetables high in soluble fiber (sweet potatoes, brussels sprouts, asparagus, turnips, mango, avocados, strawberries, apricots).
  • If you’re suffering from a chronic health problem, consider adding a supplemental probiotic and prebiotic. There are many considerations that determine which probiotic is optimal for a given health condition, but soil-based organisms are almost always effective and well-tolerated. I suggest the Daily Synbiotic from Seed, which you can purchase here. For prebiotics, I suggest a mix of arabinogalactan, beta-glucan, inulin, and oligofructose. My favorite product is Prebiogen. (Note: prebiotics are FODMAPs, which may cause difficulty for those with digestive problems. Start with a very small amount and increase slowly.)


Join the conversation

  1. Hi Chris – Thanks for your helpful website! I ran across your site and suggestion of taking Prescript-Assist last week and started it a few days ago at 1/3 capsule/day. I was taking it alongside Xifaxan for a 7 month bout of chronic diarrhea. I stopped because all of the sudden, my symptoms seemed to multiply. I should also mention that I’m 5.5 months pregnant. I’m desperate to heal my gut. I looked back at your recommendation and decided I should maybe start with one whole pill/day and increase like you suggest. Would you agree for someone who is pregnant? Will the higher dose cause a “die off” which is maybe what was happening and is it safe for baby?

  2. Hi!

    My 15-year-old son has had gastritis due to unknown causes for over a year. It’s not h-pylori, crohn’s, or celiac–he’s been tested. He is now on a gluten free diet, which seems to have had the most effect, but it is not completely disappearing. At one point I also gave him 18-24 oz of cabbage juice/day, which helped but didn’t cure.

    He is also taking a probiotic, and I am trying to figure out, does a probiotic helps stomach-based gastritis at all?

    Also would a soil-based probiotic be of even greater assistance?

    If so, what are the soil-based probiotic strains, so I can compare ingredients in the probiotics?

    Any other ideas for gastritis assistance?

    Thanks for your help!

    • Has your son been checked for other food allergies? I also had that issue. Turns out I was far more allergic to Eggs, dairy, and legumes than gluten. I feel so much better!!!!

  3. Hello Chris,
    Can probiotic survive / live on skin, like armpit environment or skin flora?
    Which probiotic can kill bad bacteria?

    • Dear Josie,
      1. Probiotics don’t kill bacteria. If a bacteria kill another bacteria, then is an antibiotic. Probiotics are competitors.
      2. For those of you confused about the whole probiotics in yogurt and in water and the ones you eat/drink and what not, here’s the deal: probiotics is bacteria, and just like human cells, bacteria have the ability to produce energy in an aerobic and anaerobic manner. What does that mean? There are certain bacteria that thrive in places where oxygen is available, hence the term aerobic, whereas there are bacteria that thrive through fermentation rather than cellular respiration. I know there are a lot of biological terms here, but the point is that there are some probiotics that do not need oxygen to live, which are the ones found in the yogurt. Those probiotics will not do anything to your skin if applied as yogurt because they cannot survive in the presence of oxygen; they are anaerobes. However, there are certain bacteria, probiotics of course, that do need oxygen to survive, and those are the ones you want to put on your skin. The other forms will live inside your body where oxygen is not available (fyi oxygen travels through the bloodstream to the multiple cells of our bodies that encompass all of our bodily structures, such as our organs, tissues, etc, and is not found inside the stomach, intestine, or any part of the alimentary canal). So to recap, if you want to treat acne with probiotics, do it with ones that live with oxygen and not with ones that you eat and live inside of you. Hope this helps!!

  4. I recently began taking a probiotic (Keybiotics) 37.5 billion CFU and 14 strains of bacteria. It is dairy, soy and gluten free. I am breaking out like crazy. Expecially on the chin around my mouth. Hard, cystic acne. I usually don’t have a problem with breakouts and my skin just exploded overnight. I have been researching and from what I have gathered is that I am purging toxins from candida and possibly other “bad” bacteria. That was what I immediately thought of when I saw the acne lesions beginning. My question is, if this is the case and I am having a “die off” how long will the side effect of the acne continue? My immediate instinct is to stop because I am an esthetician and acne is really bad for business not to mention I just hate it. If this is something that will eventually calm down I want to try to stick it out. Should I maybe cut back from the recommended dose of 1 per day to every other day?

    Kelly T

    • Hi Kelly T,
      If you decide to keep taking the probiotic (or even if you stop), you should seriously consider what you are eating. Eliminate all gluten, dairy, sugar, bad oils (anything except coconut oil, butter and olive oil, basically), fried and processed foods. You can also take vitamin A and it will help reduce the oiliness of your skin. A nutritionist told me I could take 30,000 IUs per day for up to three months at a time. You should also look into things that support getting rid of candida if you think it is that. Candex works.
      I hope this helps!

  5. Hi everyone,

    I’ve been taking Molkosan as a prebiotic. It’s made from organic whey and is rich in L+ lactic acid which I guess acts as a prebiotic. I noticed Chris’s Prebiogen has very different things in it and now I’m wondering if I should add that in along with the Molkosan (I’ve been feeling great on this supplement) or substitute it.


  6. What are your recommendations for children? I have 3 kids – 6, 4 and 1.. the 1 year old (despite being the only one primal-from-birth) has been sick ALL winter – ear infections, whooping cough, congestion, etc. She eats 1-2 yogurts a day, but that is obviously not helping.
    Would you recommend a probiotic supplement? Is there a difference between adult and children’s probiotics (other than the added sugar)?
    What about for the other kids?

  7. HSHi Chris

    I’m 24 and developed food intolerance to wheat dairy and sugar it’s frustrating that everything i seem to eat even a little will give me a breakout mainly on cheeks and sides of chin,i have started to take digestive enzymes and probiotics hoping it will help but I’m also scared of a detox reaction..could i please have some advice should i stick with it how long before results?oh yes i was also diagnosed with multiple sclerosis at 18…thank you for any help

  8. Hello Chris, I was wondering if you could tell me if Florastor would work to help with Bacterial Vaginosis? I have battled with this for years and have tried all the normal antibiotics usually prescribed but they do nothing. I have also tried different probiotics which also have not helped. I recently was admitted to the hospital and was on Rocephin antibiotics via IV. The doctor also ordered Florastor as a precaution. While in hospital and when I came home my BV was actually cured for first time in years! My gyno does not believe Rocephin would cure BV so I am wondering if Florastor may have done it. Everything I read online only shows it cures GI issues. Thank you!

  9. Thank you so much Chris!
    I had just purchased FLORA, High Potency 8 probiotics, when I noticed that it had potato starch and silicon-whatever… is this even real? or safe? I assumed, having bought it at my local health food store, that it would be the best, as it was VERY expensive. I came online to look it up and found no discerning reviews. That’s when I found your article here.

    What do you think? Should I return it?
    Thanks so much,

  10. I feel sluggish and depressed after eating garlic, which is a prebiotic. Anyone know why? Does this indicate SIBO or something like that?

    I’m wondering if I’ll have the same kind of reaction to pro biotics.

      • There are five different FODMAP sugars. I believe only two of the five can be confirmed by a hydrogen breath test?

        I would go to dietician who specializes in FODMAP issues and get diagnosed. To cut out all five FODMAP sources when you might only have reactions to three of them (for example) would a lot of unnecessary hassle and would deny you nutritious foods.

      • Can you explain what the difference is between SIBO and gut dysbiosis? Is gut dysbiosis just a general umbrella term for all this – SIBO, leaky gut, etc.

    • It could certainly be an allergy. I had a major food allergy test done, and I’m off-the-charts allergic to garlic. Too bad, since it’s a great food, but it’s best to know and to avoid.

  11. Hai chris,can you give me some more indications on dental where probiotics can be used.I am doing studies on probiotics in oral health.

  12. I just started prebiotics and, at the same time, upped my probiotic as I recover from c-diff. I’m taking a tiny amount of Biotagen by Klaire. I seem to feel depressed immediately afterward. Is it possible for a prebiotic (or probiotic) to CAUSE moderate depression? Could this be some sort of herxing that I should work through? Or should I back off? (I haven’t had this feeling with probiotics in the past; it seems to be a result of the prebiotic.)

  13. I heard pro biotic is a best anti biotic that helps to increase the immunity as well as best one against acne skin problems. It is quite effective one for skin disorders like acne.

  14. Hi,

    I’m lactose intolerant and have Hashimoto’s. What do you recommend for a probiotic that is dairy free and gluten free if I should be taking any probiotic at all? Maybe a different strategy would work better for me? I have only tried probiotics once a few years ago and had discomfort so I’m a little worried trying it again. Should a person start out with a lower dose?

    Thanks for your help!

  15. Hi Chris, Thanks for your article. I have a question. My 10 year old was having digestive problems and the doctor has pretty much ruled everything out. During this time I started him on probiotics. I won’t go into details but over the past few weeks I’ve seen big improvements so I think it’s working. Here’s my question. I think that what I’m giving him is working.
    Integrative Therapeutics Pro-Flora Concentrate Probiotic Pearls
    However, once this clears up is this a good overall probiotic to keep him on or should I switch? Thank you!

  16. I tried the Prescript Assist and it is giving symptoms that no one at their company can explain. I’m desperate for an answer as the reaction is the same i’d get from lactose based probiotics, Knots in my back and neck. Also mood swings from tears to anger. I started out slow, 1/4 capsule once a day. I’m only on day three. I’m hoping you have some wisdom for me. Thank you Chris!

    • I would bet it’s pathogenic bacteria fighting back. They’ll create toxins as a defense to protect themselves. I’d keep working on increasing the good flora, as tolerated. I’d also explore the possibility of Lyme disease or other tick-borne infection.

  17. Do probiotics need to be taken between meals (on an empty stomache), or can they be taken together with other food?