How to Protect Your Gut When Taking Antibiotics is the Right Choice

It should not come as a surprise that as a practitioner of Integrative and Functional medicine I feel that antibiotics are grossly over prescribed in the United States.  It may or may not be a surprise to hear that I think the overuse of antibiotics is a major contributor to the dramatic rise of autoimmune disease, allergy related disease,  and even the obesity epidemic that is plaguing our country. That being said, there are clearly instances where I feel antibiotics are necessary.  A true Integrative and Functional practitioner utilizes the best of both conventional and natural approaches based on what the situation calls for.  One of my mentors, Dr. Andrew Weil, who is considered to be the “father” of Integrative Medicine, describes this approach well when he said, “Integrative Medicine neither rejects conventional medicine nor accepts alternative therapies uncritically.”

While having to take antibiotics is never ideal, there are many cases where it is clearly the right choice. When I am working in the hospital I commonly rely on antibiotics for things like pneumonia, cellulitis, and more serious infections and they can be absolutely life saving in certain situations. However they do take their toll on our gut and there are many things you can (and should) do before, during, and after antibiotic use to minimize the damage and encourage regrowth and diversification of your gut flora. 

To help explain this in more detail, I have summarized an article originally written by Chris Kresser who is a well known thought leader in the world of functional and ancestral medicine. Click Here to view the original article written by Chris Kresser.

Things to consider to minimize the negative effects of antibiotics on your health




The biggest question I get is, “Should I take probiotics at the same time as antibiotics? Won’t the antibiotics kill off all of the probiotics?” It is important to understand that probiotics don’t need to actually colonize the gut to be beneficial; even transient strains can have powerful therapeutic effects.  Think of probiotic pills like tourists… they come in, stimulate the economy, and then leave. There are quite a few randomized, placebo-controlled trials that have demonstrated the effectiveness of probiotic use during a course of antibiotics for reducing side effects and preventing gut infection. (1234567) For example, a study on 135 hospital patients taking antibiotics found that only 12% of the probiotic-receiving group developed antibiotic-associated diarrhea, compared with 34% of the placebo group. (8) Additionally, while 17% of the placebo group developed diarrhea specifically from C. difficile, nobody in the probiotic group did. Most of these trials used different strains of Lactobacilli, Bifidobacteria, or Saccharomyces boulardii. Lactobacillus and Bifidobacterium are two of the most common strains used as probiotics and are readily found in most probiotic supplements. S. boulardii is actually a beneficial yeast rather than a bacteria, so it’s particularly useful during antibiotic treatment because it is not killed by the antibiotic. S. boulardii is also preferable under these circumstances because there’s no risk of it harboring genes for antibiotic resistance and later transferring those genes to pathogenic bacteria. (10) Another option would be to choose a soil-based organisms (SBO) probiotic such as Prescript Assist during the time you are on the antibiotic. There are no current studies (that I know of) that have looked at SBO probiotics and their ability to withstand antibiotics, however they are generally considered to be more robust organisms.

As with anything else, the best probiotic to take will depend on a person’s particular circumstances (such as the antibiotic they’re on and the state of their digestive system), but the two supplements I recommend most often when you have to take an antibiotic are Floramyces (saccharomyces boulardii) by Designs for Health and Prescript Assist Pro by Researched Nutritionals. The probiotic I tend to recommend for general use is Ortho Biotic by Ortho Molecular. This particular probiotic has 20 billion CFU which includes 7 strains of organisms including S. boulardii and is shelf stable with no need for refrigeration. 


An important thing to remember is that prebiotics are much more effective than probiotics at promoting the growth of beneficial bacteria in the gut. Thus, prebiotics are an incredibly important part of any regimen to protect or rebuild a healthy microbiome. During and after antibiotic use, focus on getting plenty of soluble fiber, which feeds beneficial bacteria and is found in starchy tubers, squash, and peeled fruits.  The fiber supplement I generally recommend is PureLean Fiber by Pure Encapsulations. It has a good balance of soluble and insoluble fiber, as well as several beneficial prebiotics. One type of insoluble fiber that can be extremely helpful for supporting healthy gut flora is resistant starch. A great way to get more resistant starch in your body would be to use Bob’s Red Mill unmodified potato starch. As with any supplemental prebiotic, it’s a good idea to start with a small amount and work your way up. In this case, you could start with 1 teaspoon and work your way up to 2-4 tablespoons per day.

Supporting diversity

One of the biggest challenges after a course of antibiotics isn’t recovering the number of flora present; it’s recovering the diversity.  As we’ve discussed, probiotic supplements can be incredibly helpful for preventing antibiotic-associated diarrhea and lowering the risk of a gut infection, and I recommend continuing with probiotic supplementation for at least 3 months after you complete your course of antibiotics. However, you can’t expect manufactured probiotic and prebiotic supplements to achieve the diversity of an ancestral microbiome on their own. One of the best ways to expose yourself to more diverse beneficial bacteria is by consuming fermented foods. These can include kefir, sauerkraut (not out of a can), kimchi, and other fermented vegetables or fruits. When it comes to Kefir and yogurt, homemade is best as the store bought brands usually have very minimal live strains. One of my favorite ways to get a diverse mix of bacteria in your diet is drinking kombucha.  I highly recommend you check out Tea Biotics , which is a local company here in Kansas City that makes delicious, artisanal, organic, locally sourced kombucha. You can find them in many stores across the metro as well as at the Saturday Overland Park farmers market. Another way to diversify the bacteria you’re exposed to is by gardening or otherwise getting your hands dirty, so go on a hike and lay off the hand sanitizer! As far as prebiotics go, just try to get as much variety in your plant foods as you can, in addition to supplementation with resistant starch or another prebiotic formula. Some of the best sources of soluble fiber include carrots, winter squash, summer squash (especially peeled), starchy tubers (including my favorite, jicama), turnips, rutabagas, parsnips, beets, plantains, taro, and yucca.

Support for the gut and the liver

In addition to the damage to your microbiome noted above, antibiotics can also take a toll on your liver. This is particularly true if you have to be on them for an extended period of time. Not only is the liver responsible for processing and detoxifying medications, it also has to deal with extra circulating lipopolysaccharides (inflammatory components of bacteria cell wall) from the increased bacterial death and intestinal permeability. Milk thistle is one of my favorite supplements for supporting liver health, and can be taken in a pill or as a tea. Glycine is also important for liver detox, so be sure to drink plenty of bone broth! If you experience nausea or other digestive upset from the antibiotics, ginger can be extremely helpful for reducing inflammation and calming the digestive system. (1213) It’s best to use fresh ginger, and you can easily make ginger tea by slicing it and simmering it in water until the tea reaches your desired strength.  I also am a fan of Ginger-Tussin by Designs for Health, and commonly use it for coughs and sore throat as well. In my practice my patients and I generally come to a decision together on whether taking an antibiotic is the right choice based on each individual scenario. For the general population I recommend people be somewhat critical regarding their decision to take an antibiotic but also not completely resistant when the time calls.  If you do end up taking an antibiotic, following the steps above can be extremely effective at minimizing any potential negative side effects you may experience.

In health,

Dr. Bradley Dyer, DO

Dr. Dyer is a board certified physician with training in internal medicine, psychiatry, integrative medicine and functional medicine. He is the owner of Premier Integrative Health in Kansas City Missouri