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What to Do If You Need to Take Antibiotics


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what to take with antibiotics
Taking antibiotics is never ideal, but sometimes it's necessary. iStock.com/amphotora

Note: The Prescript-Assist supplements discussed in this article are no longer available. Please click here to learn more about a substitute, the Daily Synbiotic from Seed.

I wrote this a while back when I had more time, thinking it might come in handy during the book tour. I was right!

A few years ago, I wrote an article about the often devastating effects that antibiotics can have on the gut flora. While it’s extremely important to avoid unnecessary antibiotic use, what about those who have carefully considered their options and decided that antibiotics are necessary in their situation? Is there no hope for recovering a healthy microbiome?

Need to take antibiotics? You need to read this article.

While having to take antibiotics is never ideal, there are many cases where it is absolutely necessary, and don’t worry – the situation is far from hopeless. It will take some time and effort, but there are many things you can do both during and after a course of antibiotics to minimize the damage and encourage regrowth and diversification of your gut flora.


To some, taking probiotics during a course of antibiotics might seem contraindicated. After all, won’t the antibiotics just kill all of the probiotics anyways? First, keep in mind that probiotics don’t need to actually colonize the gut to be beneficial; even transient strains can have powerful therapeutic effects.

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. (1, 2, 3, 4, 5, 6, 7)

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.

One interesting study tracked changes in gut bacteria in three different groups of people receiving antibiotics, with one group receiving placebo, one group receiving probiotics beginning after the antibiotic treatment ended, and the third group receiving probiotics both during and after antibiotic use. (9) The group receiving placebo had significantly higher levels of facultative anaerobes (their chosen marker for gut dysbiosis) 20 days after finishing antibiotics compared with baseline, while the two groups receiving probiotics had no significant difference. But even though both of the probiotic groups ended up back at baseline levels, only the group taking probiotics during as well as after antibiotic treatment maintained stable levels of facultative anaerobes throughout the experiment. In the group receiving probiotics only after completion of antibiotic treatment, facultative anaerobes increased significantly during antibiotic treatment, and decreased only after beginning probiotic supplementation. This clearly demonstrates the importance of taking probiotics during antibiotic treatment, as well as after.

Most of these trials used different strains of Lactobacilli, Bifidobacteria, or Saccharomyces boulardii. Lactobacillus and Bifidobacterium are two of the most common genera used as probiotics, so these supplements are readily available in most health food stores or vitamin shops. S. boulardii is actually a beneficial yeast rather than a bacteria, so it’s particularly useful during antibiotic treatment because the antibiotics can’t kill it. 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 for probiotics is a blend of soil-based organisms, such as Prescript Assist. I haven’t located any studies on their effectiveness in conjunction with antibiotics, but based on my clinical experience, I believe they’re a great choice.

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 are S. boulardii and Prescript Assist. If you don’t do well on either of those supplements or just wish to add more variety, feel free to add in a supplement with strains of Lactobacillus and Bifidobacterium. Do your best to take any probiotic supplement as far away from your antibiotic dose as possible.


As I’ve mentioned before, 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. It might be best to avoid too much insoluble fiber while your gut is in a compromised state, since it can be irritating to the gut lining.

However, one type of insoluble fiber that can be extremely helpful for supporting healthy gut flora is resistant starch. (11) I’ve talked about resistant starch before here and here, and the easiest way to get a concentrated dose of RS is 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. If you find that RS doesn’t work well for you, you might consider trying an inulin-based prebiotic.

If possible, introduce any prebiotic supplements before beginning the course of antibiotics so your body can get used to them. That way, you won’t have to deal with possible side effects from introducing the prebiotic on top of possible side effects from the antibiotics.

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Supporting diversity

As I mentioned in my article about the impact antibiotics have on gut flora, the main difficulty after a course of antibiotics isn’t recovering the number of flora present; it’s recovering the diversity. As we’ve seen, 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 a period of time after finishing your treatment. 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, so I highly encourage you to experiment with a variety of different ferments.

These can include kefir, beet kvass, sauerkraut, kombucha, kimchi, and other fermented vegetables or fruits. Keep in mind that foods like yogurt and kefir will probably only have a handful of bacterial strains if you buy them from the store, so homemade is best.

Another way to diversify the bacteria you’re exposed to is by gardening or otherwise getting your hands dirty, although I haven’t seen any research on whether that exposure translates to a more diverse set of gut bacteria.

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, turnips, rutabagas, parsnips, beets, plantains, taro, and yuca. Green bananas and unripe plantains (which you can dehydrate to make chips) are good whole-food sources of resistant starch.

Support for the Gut and the Liver

When antibiotics throw your gut flora into turmoil, the gut lining and digestive function as a whole take a hit too. To soothe your digestive system, it’s a good idea to ramp up your consumption of bone broth and other glycine-rich foods while you’re on antibiotics, and continue to consume these foods after the treatment is finished to promote healing.

If you experience nausea or other digestive upset from the antibiotics, ginger can be extremely helpful for reducing inflammation and calming the digestive system. (12, 13) 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.

Antibiotics can also take a toll on your liver, particularly if you’re on them for an extended period of time. Not only is the liver is responsible for processing and detoxifying medications, it also has to deal with extra circulating lipopolysaccharides 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 (like this one) or as a tea. (14, 15) Glycine is also important for liver detox, so be sure to drink that bone broth!

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Join the conversation

  1. I often get the question if one can overdo it on pro adn pre biotics…. could you give me any clarity on this? is there a time you know you have taken too many or does that never happen. If yes How do you know?

  2. Hi, I have got a infection in my teeth. Then dentist told me to take amoxicillin. I am using it since 3 days. All the time I am feeling like something is crawling in my mouth. Specially on my tongue. And sometimes they are twisting my tongue. I think that is bacteria. Can any one please suggest me something. I don’t know what to do now.

    • I would find an oral surgeon as opposed to a dentist. They are more familiar with such things that are out of the ordinary. Something some people do not know, is that the health of your teeth is directly related your heart. I would consult your dr about that…a cardiologist if possible. The General Practitioners don’t seem to know much of anything these days.

  3. Having to take antibiotics its scary for me. Approximately one hour after taking them, I get severe lower back pain and period kind of pains. The pains go on for two or three weeks after finishing the antibiotic treatment. I also get weakness, tiredness and body aches. Has anyone experienced something similar? Any advice? Thank you

    • Sounds like you kill the good bacteria, leaving yeast to over multiply. This will result in feeling tired because of chemicals released by the yeast

    • Pl. don’t go by the overdose of misinformation. Most antibiotics work by reducing K & Mg in the body, which for more sensitive bodies could result in tiredness, fatigue, even feeling faint. The most logical thing would be to take a multivitamin while taking antibiotics.

  4. If a breastfeeding mother nurses her baby while she is on antibiotics, can the antibiotics affect the baby’s gut in a big way? I have read that breastfeeding is safe while taking antibiotics, but I have also read that some antibiotics can pass through into the breastmilk.

  5. Anyone have any tips for moms receiving antibiotics while in labor due to screening positive for group b strep??

  6. *Bottom line question: when using probiotics and exclusively breastfeeding, approximately how long does it take to restore a newborn’s gut bacteria after 2 (unfortunate) rounds of antibiotics?*

    Details: I gave birth to a healthy baby girl at the end of Dec. 2015. We had a natural birth, and for years I’ve eaten a “clean” diet with mostly veggies, lean proteins, fruit, nuts, some dairy and whole grains. I take probiotics regularly, am increasing fermented foods in my diet, and have only had antibiotics about 3x in my life.

    One week after birth, our baby experienced severe heavy/rapid breathing. Multiple doctors were concerned for the “worst” (sepsis/bacterial infection), so they started her on antibiotics immediately. Due to her age/the potential for severe illness, we reluctantly agreed. After a couple misdiagnoses, an ENT diagnosed her with laryngomalacia (a floppy epiglottis, which she should grow out of in 6-24 mo). She did not have any infection.

    So, unfortunately, my daughter’s gut flora was wiped out one week after birth. We started her on a probiotic the second evening of treatment and have since begun her on a high quality infant probiotic recommended on this site.

    I very concerned, however, about the potential damage that was done. She is almost 1 month old now and appears to be thriving. She has not received any vaccinations to date and we do a revised schedule. However, I am hesitant to start any vaccines at 2 months if her gut is not yet restored/healed, and therefore, am considering delaying this. She does have an older brother and is around other kids at play dates/church, however, so I don’t want to unnecessarily withhold basic vaccines.

    I’m not seeking to begin a debate about vaccines. My question focuses on restoring her gut health (see bottom line question at the top).

    Thank you!

    • I don’t have a reply, but I am interested in the advice because my baby also had to have a round of antibiotics at birth, and I am looking for the best way to restore his gut! I’m wondering how much good bacteria and probiotics pass through the breast milk, and how to get him the best pre & pro biotics since he can’t eat food yet.

    • My daughter was born 1 month early and after the doctors found a bacteria she was born after a cesarian. She received a lot of antibiotics afterwards.

      The result was severe eczema all over her body. None of the treatments and dietary advices of the paediatrician helped. We went to a doctor that did laser acupuncture and with muscle tests tested what she should and shouldnt eat. We adapted the diet and gave hrr the supplements prescribed such as zinc.

      After intense research we decided not vaccinate.

      She is now 4.5 yrs old and has always been extremely healthy. I am convinced that a combination of the right supplements, organic fruits and vegetables, no milk and limited wheat since she does not take breast milk and formula and not taking vaccines gives her this extraordinary health even after the antibiotics she had as a baby. So it is not hopeless. All the best…

  7. Always research your medications, including antibiotics, to understand how they are metabolized in your body and particularly in the liver. Many drugs are contraindicated with other drugs because of how they effect the enzyme system of the liver. Check out for yourself a comprehensive drug interaction chart that can give you information on your particular medications. There are only a few herbs that have been included, since not very many natural medicinal agents have been tested in this respect. Two that commonly show up on some lists are St. Johns Wort and Milk Thistle. Although there have been inconsistent studies concerning Milk Thistle, the University of Pittsburgh researchers published findings in 2000, that silymarin, one if not the most powerful medicinal agent in Milk Thistle, inhibits cytochrome P-450. What this means is that many drugs metabolized by these enzymes in the liver remain in the bloodstream longer with Milk Thistle than they would otherwise. Depending on the half-life (how long it takes a drug in your body to stay active before finally breaking down) of your medication and how often you dose, it would be likely to build up more of the drug in your system than desired or expected. If it remains in your system too long there could be a possibility of an overdose. If the benefits of milk thistle are substantial in your situation, at least ask your health care provider to do periodic blood tests to determine if the blood levels of the drug are escalating and getting out of hand.

  8. Hi everyone! I am on Doxycycline for skin rashes– experience has taught me that this is the only treatment (to include natural things and diet, I am sad to report) that has a strong impact. However, I am cautious about killing all the good bacteria along with the bad stuff. I have not had any adverse reactions from the Doxy and never have had in my experience. Can anyone recommend an appropriate probiotic?
    Thank you in advance!

  9. I have been recently diagnosed with SIBO. I’m taking an antibiotic and also started taking interfase plus. Does anyone have any information about whether or not to add a probiotic into the mix. For two days I’ve taken a probiotic that is primarily lactobacillus plantarum, which I’ve read work with SIBO. Any info is much appreciated.

  10. Great article,
    I was bit by a spider a few days ago. Before going to the doctor I rubbed a clove of garlic on the bite, the bite went away but my foot continued to swell up and turn red. I did not want to take any antibiotics as I know they are not necessarily good for your gut lining but unfortunately the infection from the bite was traveling up my leg. I decided to go ahead and take the antibiotics to be on the safe side. The doctor prescribed 4 daily for 7 days. So far I have only taken a few and I am not sure if I should continue taking them as I have ready so much negative things about the use of antibiotics.

    • You must ALWAYS finish a course of antibiotics even if you are already better as there will still be a few bacterium left in your body and if ever you got another serious infection like MRSA the antibiotics wont work as there will be an army of resistant bacteria in your body from that one time you didn’t finish the course. You did well to try to let your body do the healing and you were aware when it was getting too much for your body and it needed some help in the form of antibiotics. I also hate taking them for many reasons but when i do i make sure i finish the course especially as i had MRSA…

  11. I recently was prescribed metronidazole and for the first time my liver enzymes are elevated. I am concerned but I’m hoping this will be temporary. I was initially misdiagnosed in the ER, but when I followed up with my GP I actually had a bladder infection, and now I’m on Bactrim. By then I had finished a high dose regimen of Flagyl, 1500 mg a day. After two weeks on two different rough antibiotics I’m concerned. I’ve never been told I had elevated liver enzymes, and I’m hoping I can do something about it. I finish up my Bactrim regimen tomorrow morning.

    • Hi I’m in the same situation that you were and found this on a Google search. What protocol did you follow for elevated liver enzymes? Also I’m on 10 days bactrim and wonder about detoxing after (besides probiotics which I’m taking)

  12. I have been trying to find out if intravenous antibiotics kill gut biota. When I had ankle surgery for a fracture I had them only give me one intravenous shot of antibiotics. Is this a possible alternative for other courses of antibiotics?

    • Yes, they do kill gut biota as the antibiotic administered either way reaches the same level in your blood serum. Hence why it can be administered by either method to get rid of infections in random places like the gut, kidneys etc. Sometimes it’s just quicker, more convenient and easier to do the injection if you are doing surgery and they don’t want to wait. Or maybe they were worried you’d get nauseous from the anesthesia and wouldn’t keep the oral antibiotic down. One injection won’t ruin your system though…just follow a gut healthy diet.

  13. THANK YOU. I am currently 31 wks pregnant and have to resort to antibiotics to cure up a bladder infection. I have been trying five days using other natural routes to kick it, but the symptoms are still there and the irritation is also causing early contractions. I felt so terribly guilty about having to take the antibiotics (messing with my microbiome and baby’s likewise), but your article has left me much more at peace with the situation. I have some Garden of Life Raw Probiotics and will be taking those simultaneously with the meds. Thanks again; your website has been most helpful (baby thanks you, too)!!

  14. my 83 yo mother has had chronic bladder infections for years…meds, clear for 10 days or less, backs on meds, clear for about 20 days…anybody else deal with this issue? any ideas to naturally work with?

    • She could have a prolapse in the bladder so it does not empty completely, and a yeast overgrowth which perpetuates a compromised wall and makes it easier for opportunistic bacteria to get an advantage.

      A yeast cleanse program, herbs and homeopathics for the bladder would be good and general immune support herbals as well. Then have the bladder checked for prolapse. At her age they probably won’t do a surgery to tack it up, but at least you know.

      Uva Ursi, Buchu, couch Grass, Corn silk, Propolis, Echinacea, Goldenseal, are good herbs,

      Apis, Cantharis, Causticum at 6x, 12x would be helpful or a homeopathic bladder formula would be helpful.

    • For recurrent bladder infections, D-mannose is a wonderful natural preventative. It can sometimes stop an infection in its tracks. Google it!
      It has helped many of my friends and worked wonders on my bulldog.

    • Ruth Ann – same bladder problem wirh my mom. We finally discovered that activated charcoal is of great benefit. CharcoalRemedies.com is an excellent book and website.

    • Uva Ursi works wonders. Take in liquid form ( drops are easier and gets into system faster than pill form) it doesn’t taste very good, but she can avoid the vicious cycle with antibiotics! Natural and fast. Good luck! I can’t understand why doctors would not recommend.

  15. Dr. Kresser, could you please tell us if intravenous or intramuscular antibiotics also have such a pernicious effect on gut flora? Would it be preferable to oral antibiotics?

  16. If you are taking antiboitics, probiotics could also be beneficial to you. Antibiotics wipe out the bacteria in your body, both bad and good, which results to having different infections or diarrhea. Taking probiotics with strains like Saccharomyces boulardii and Lactobacillus rhamnosus GG will help prevent this from happening. It is recommended that you take probiotics six hours after each dose of antobiotics taken. Once the antibiotics are stopped, it is adviced to continue taking probiotics for one to two weeks.

    • I rarely ever comment However I was just diagnosed with h pylori. I will be taking a course of Antibiotics and I am not thrilled. I’m on a blood thinner and I just don’t want to take antibiotics and cause another issue to arise. Sigh…I have more to say but for now I’ll pray.

      • Hi Danielle,

        I’m facing the same treatment for H. Pylori too and like you I’m feeling very anxious about taking a variety of antibiotics and undoing all the work I’ve been putting into strengthening my gut – also worried about potential side effects, I’ll be taking Amoxicillin / Clarithromycin / Metronidazole.

        Just wondering how it all went for you since you posted this?

        Thanks so much

      • I also just received that diagnosis. I was a little overwhelmed when I saw the packets of 8 pills…every day for 14 days.
        I think I am in this mess BECAUSE of antibiotics and pain meds, as I had 3 major surgeries in 20 mos.
        I take live cultures of probiotics a few times a week on a normal day. Now I am taking every day and may add more. I have my follow up visit today, so will talk to My doctor (who is a soecialis) about it.
        I also will be praying. I am a born again Christian who has experienced the faithfulness of God. I have seen people healed through prayer many times, and have also been the recipient!! So you should keep on praying…get to know Jesus…He is your healer and Savior. He will give you peace beyond understanding as He died to save you. He is your best comfort! I will be praying with you…

  17. Hi! Thank you for the helpful article! I have a question concerning the introduction of solid foods to a 7 month old after a round of antibiotics. She had only had egg yolk a couple of times before we had to administer an antibiotic for a ruptured eardrum. I tried one more time, but she vomited big time(projectile) so I haven’t tried again. Do we run the risk of making her intolerant to any of the foods to be introduced, since her gut flora is destroyed by the antibiotics(has her gut possibly become leaky??) she’s currently only breastfeeding- till I figure out what to do next- and getting some probiotics and S. boulardii. Any suggestions as to how to go about the introduction of solids( my intention was to start with egg yolk and then introduce liver before anything else, but that might not be the best now) and any additional infant- appropriate supplements ?

    • I would think to keep her on breast milk to her bowel movements return to normal for her. If you don’t already have a chiropractor who does kiniesiology I would find one. Each person is so different and they could recommend the best supplements for your baby. Also, our chiropractors helped my babies beat ear infections without antibiotics.

      Good luck!
      p.s. I an not a doctor. I am a mom to five kiddos.

    • If you are still in the position of worrying about solids, I wouldn’t do so. I believe my first son would have been better without solids for much longer than the recommended time. Everything solid was difficult, we got through but I wish now I had waited until he was indicating he was ready for solids. Just a note, I breast-fed my first son to 9 months then became pregnant and stopped (due to sickness) the second until he was 16 months when he just fell asleep (without) one day and I took that as my cue to wean him fully. All the best to you and your baby.

  18. WHEN, in relation to when I take the antibiotics, should I take the probiotic? Same time? Before? After? Does it matter?

    Someone who knows, please answer. THANK YOU.

    • I am taking antibiotics for an infection after I got my big toe nail removed and I feel unwell since taking them. I have felt really sick and have had diarreah too. I also have a sore leg, the same leg as the sore toe. What should I do.?

  19. WHEN, in relation to the time of ingestion of the antibiotic, should I take the probiotic? Same time? Before? After? Does it matter?

    Someone who knows, please answer. Thank you.

  20. Prioris, thank you for such helpful and informative comments.

    I have been recently diagnosed with bronchitis and pneumonia and put on clarithromycin. Having a very sensitive stomach and colon/digestive system brings fears of side effects. My immune system is also drastically down due to recently endured stress.
    What probiotics do you recommend taking along and after the treatment? Thank you in advance